Faculty & Staff

  • Image of Garret Suen

    Garret Suen

    Associate Professor of Bacteriology
    Alfred Toepfer Faculty Fellow

    5159 Microbial Sciences Building
    Office: (608) 890-3971
    Lab: (608) 890-3972
    gsuen@wisc.edu
    Twitter feedGoogle ScholarORCID

Start and Promotion Dates

  • Assistant Professor: 2011
  • Associate Professor: 2017

Education

B.Sc., Biological Sciences, University of Calgary 2000
B.Sc., Computer Sciences, University of Calgary 2002
M.Sc., Computer Sciences, University of Calgary 2004
Ph.D., Biology, Syracuse University 2008
Postdoctoral Research: University of Wisconsin-Madison

Areas of Study

Herbivore-associated Microbial Ecology
Rumen Microbiology
Metagenomics
Biofuels

Research Overview

Microbial communities associated with herbivores are fundamental to ecosystem functioning in almost all environments on Earth. Specifically, these communities facilitate the conversion of plant biomass into nutrients usable by their host, thereby bridging primary producers and secondary consumers. My research is focused on understanding the evolution and ecology of herbivore-associated microbial communities on three different scales. At the broadest scale, I am interested in how these communities evolve across host type, host diet, and geographical distribution. At an intermediate level, I am interested in how members of these communities interact with each other to coordinate the breakdown of plant biomass and produce nutrients for their host. At the finest scale, I am interested in understanding how microbes fundamentally degrade polysaccharides (cellulose and hemicelluloses) in plant cell walls. My work can be applied to two specific fields as described below.

Biofuels. A major global challenge is to reduce our reliance on fossil fuels. Biofuels have been proposed as an alternative fuel source because of their cleanliness and sustainability. One proposed biofuel is cellulosic ethanol, which can supplement gasoline and integrate with our current transportation infrastructure. The generation of cellulosic ethanol requires the conversion of cellulose into simple sugars followed by fermentation into ethanol. My work directly impacts the first bottleneck of cellulose degradation. I use as a model system, ruminants, which are arguably one of the most efficient natural cellulose-degrading systems. Ruminants such as domesticated cattle harbor a specialized community of plant-degrading bacteria that ferment cellulose and other polysaccharides into small chain fatty acids. We are attempting to understand this process at a base level by characterizing the mechanisms through which ruminal bacteria like Fibrobacter succinogenes S85 and Ruminococcus albus 7 degrade cellulose. In particular, Ruminococcus albus 7 is capable of fermenting ethanol using cellulose in vitro. This work incorporates whole-genome sequencing, transcript sequencing using RNA-seq, prediction of protein-protein interactions using functional genomics, and in vitro cell-free expression of cellulolytic enzymes. Finally, these bacteria are known to work with other hemicellulolytic ruminal bacteria to synergistically enhance their overall cellulolytic and fermentative abilities. We are also investigating these interactions to gain an understanding of this process.

Animal Health and Production. Ruminants are major agricultural resources, particularly for the production of products like beef and milk. Milk production is linked to the ruminal microbial community, as the small chain fatty acids produced by these microbes directly impacts the quality of milk produced by cows. We are interested in understanding the ecology and evolution of these ruminal communities and their impact on milk production. Specifically, we are working to understand the confluence of diet, host genotype, and ruminal microbiota on milk quality. We use a combination of metagenomics, metatranscriptomics, milk production metrics, and cow health to assess these factors. We are also interested in understanding how rumen microbiota become established in developing calves, and in particular, how diet influences microbial composition. Finally, these studies have direct impact on human health and disease, particularly in development, lactation, and the influence of diet on host microbiota. Ruminants are excellent models for understanding these factors in humans as they share a large number of genes, can be directly manipulated at the ruminal level, and can be reared on controlled diets.

Teaching

Microbiology 526: Physiology of Microorganisms

Affiliations

Trainer, Molecular Biosciences Training Grant Program
Trainer, Microbes in Health and Disease Training Program
Trainer, Computational and Informatics in Biology and Medicine

Lab Personnel

Picture of Boschee
Claire Boschee
Research Intern
boschee@wisc.edu
Picture of Deblois
Courtney Deblois
Grad Student
cdeblois@wisc.edu
Picture of Rufino
Willian Rufino
Honorary Associate
rufinoandrad@wisc.edu
Picture of Scheftgen
Andrew Scheftgen
Grad Student
scheftgen@wisc.edu
Picture of Skarlupka
Joseph Skarlupka
Grad Student
jhskarlupka@wisc.edu
Picture of Steinberger
Andrew Steinberger
Grad Student
asteinberger@wisc.edu
Picture of Young
Juliana Young
Postdoc
jdias2@wisc.edu
Picture of Zuniga Chaves
Ibrahim Zuniga Chaves
Grad Student
zunigachaves@wisc.edu

Research Papers

  • Gonçalves JL, de Campos JL, Steinberger AJ, Safdar N, Kates A, Sethi A, Shutske J, Suen G, Goldberg T, Cue RI, Ruegg PL (2022) Incidence and Treatments of Bovine Mastitis and Other Diseases on 37 Dairy Farms in Wisconsin. Pathogens (Basel, Switzerland) 11((11)): PMC3995961 · Pubmed · DOI

    The aim of this research was to describe the incidence and treatments of mastitis and other common bovine diseases using one year of retrospective observational data (n = 50,329 cow-lactations) obtained from herd management software of 37 large dairy farms in Wisconsin. Incidence rate (IR) was defined as the number of first cases of each disease divided by the number of lactations per farm. Clinical mastitis (CM) remains the most diagnosed disease of dairy cows. Across all herds, the mean IR (cases per 100 cow-lactations) was 24.4 for clinical mastitis, 14.5 for foot disorders (FD), 11.2 for metritis (ME), 8.6 for ketosis (KE), 7.4 for retained fetal membranes (RFM), 4.5 for diarrhea (DI), 3.1 for displaced abomasum (DA), 2.9 for pneumonia (PN) and 1.9 for milk fever (MF). More than 30% of cows that had first cases of CM, DA, RFM, DI, and FD did not receive antibiotics. Of those treated, more than 50% of cows diagnosed with PN, ME and CM received ceftiofur as a treatment. The IR of mastitis and most other diseases was greater in older cows (parity ≥ 3) during the first 100 days of lactation and these cows were more likely to receive antibiotic treatments (as compared to younger cows diagnosed in later lactation). Cows of first and second parities in early lactation were more likely to remain in the herd after diagnosis of disease, as compared to older cows and cows in later stages of lactation. Most older cows diagnosed with CM in later lactation were culled before completion of the lactation. These results provide baseline data for disease incidence in dairy cows on modern U.S. dairy farms and reinforce the role of mastitis as an important cause of dairy cow morbidity.

  • Holzhausen EA, Malecki KC, Sethi AK, Gangnon R, Cadmus-Bertram L, Deblois CL, Suen G, Safdar N, Peppard PE (2022) Assessing the relationship between physical activity and the gut microbiome in a large, population-based sample of Wisconsin adults. PloS one 17((10)):e0276684 PMC7151736 · Pubmed · DOI

    The gut microbiome is an important factor in human health and disease. While preliminary studies have found some evidence that physical activity is associated with gut microbiome richness, diversity, and composition, this relationship is not fully understood and has not been previously characterized in a large, population-based cohort. In this study, we estimated the association between several measures of physical activity and the gut microbiota in a cohort of 720 Wisconsin residents. Our sample had a mean age of 55 years (range: 18, 94), was 42% male, and 83% of participants self-identified as White. Gut microbial composition was assessed using gene sequencing of the V3-V4 region of 16S rRNA extracted from stool. We found that an increase of one standard deviation in weekly minutes spent in active transportation was associated with an increase in alpha diversity, particularly in Chao1's richness (7.57, 95% CI: 2.55, 12.59) and Shannon's diversity (0.04, 95% CI: 0.0008, 0.09). We identified interactions in the association between Inverse Simpson's diversity and physical activity, wherein active transportation for individuals living in a rural environment was associated with additional increases in diversity (4.69, 95% CI: 1.64, 7.73). We also conducted several permutational ANOVAs (PERMANOVA) and negative binomial regression analyses to estimate the relationship between physical activity and microbiome composition. We found that being physically active and increased physical activity time were associated with increased abundance of bacteria in the family Erysipelotrichaceae. Active transportation was associated with increased abundance of bacteria in the genus Phascolarctobacterium, and decreased abundance of Clostridium. Minutes in active transportation was associated with a decreased abundance of the family Clostridiaceae.

  • Kates A, Keating J, Baubie K, Putman-Buehler N, Watson L, Godfrey J, Deblois CL, Suen G, Cook DB, Rabago D, Gangnon R, Safdar N (2022) Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study. PloS one 17((7)):e0268479 PMC5482335 · Pubmed · DOI

    Gulf War Illness (GWI) affects 25-35% of the 1991 Gulf War Veteran (GWV) population. Patients with GWI experience pain, fatigue, cognitive impairments, gastrointestinal dysfunction, skin disorders, and respiratory issues. In longitudinal studies, many patients with GWI have shown little to no improvement in symptoms since diagnosis. The gut microbiome and diet play an important role in human health and disease, and preliminary studies suggest it may play a role in GWI. To examine the relationship between the gut microbiota, diet, and GWI, we conducted an eight-week prospective cohort study collecting stool samples, medications, health history, and dietary data. Sixty-nine participants were enrolled into the study, 36 of which met the case definition for GWI. The gut microbiota of participants, determined by 16S rRNA sequencing of stool samples, was stable over the duration of the study and showed no within person (alpha diversity) differences. Between group analyses (beta diversity) identified statistically significant different between those with and without GWI. Several taxonomic lineages were identified as differentially abundant between those with and without GWI (n = 9) including a greater abundance of Lachnospiraceae and Ruminococcaceae in those without GWI. Additionally, there were taxonomic differences between those with high and low healthy eating index (HEI) scores including a greater abundance of Ruminococcaceae in those with higher HEI scores. This longitudinal cohort study of GWVs found that participants with GWI had significantly different microbiomes from those without GWI. Further studies are needed to determine the role these differences may play in the development and treatment of GWI.

  • Raabis SM, Holschbach CL, Skarlupka JH, Suen G, Ollivett TL (2022) Assessing the effects of experimental bacterial challenge with Pasteurella multocida and ampicillin on the respiratory microbiota of pre-weaned Holstein calves. Veterinary microbiology 269:109428 · Pubmed · DOI

    The association between changes in the respiratory microbiota and Bovine Respiratory Disease (BRD) in dairy calves is not well understood. We investigated characteristics of the nasopharyngeal (NP) microbiota associated with BRD following Pasteurella multocida infection. We also evaluated the effect of ampicillin on the respiratory microbiota. Calves (n = 30) were inoculated with P. multocida and randomly allocated into an antibiotic group (AMP; n = 17) or placebo group (PLAC; n = 11) when lung lesions developed. Deep NP swabs (DNPS) were collected before and after challenge. Monitoring was performed daily until euthanasia at day 14. Swabs and tissue samples were collected for analysis. The V4 hypervariable region of the 16 S rRNA gene was amplified and sequenced on an Illumina MiSeq. Increased species abundance in the pre-challenge DNPS was associated with a decrease in cumulative respiratory disease over 14 days post-infection. While NP beta diversity was affected by infection, antibiotic therapy showed no effect on the alpha and beta diversity nor the relative abundance (RA) of genera in the NP tonsil, lymph node and lung microbiota. Antibiotic therapy was associated with an increased RA of NP Pasteurella spp. and a decreased RA of NP Prevotella spp. Common taxa among all samples included GIT-associated bacteria, which suggests a possible link between the GIT microbiota and respiratory microbiota in dairy calves.

  • Silvestre AM, Pinto ACJ, Schleifer WF, Miranda LS, Silva LAF, Casali DM, Souza KLR, Gasparini VGL, Cruz GD, Suen G, Millen DD (2022) Relationships of the Microbial Communities with Rumen Epithelium Development of Nellore Cattle Finished in Feedlot Differing in Phenotypic Residual Feed Intake. Animals : an open access journal from MDPI 12((7)): PMC8996980 · Pubmed · DOI

    The objective of this study was to examine the relationships among ruminal microbial community, rumen morphometrics, feeding behavior, feedlot performance, and carcass characteristics of Nellore cattle, classified by residual feed intake (RFI). Twenty-seven Nellore yearling bulls with an initial body weight (BW) of 423.84 ± 21.81 kg were fed in feedlot for 107 d in individual pens to determine the RFI phenotype. Bulls were categorized as high RFI (>0.5 SD above the mean, n = 8), medium RFI (±0.5 SD from the mean, n = 9), and low RFI (<0.5 SD below the mean, n = 10). At harvest, whole rumen content samples were collected from each bull to evaluate ruminal microbial community, including bacteria and protozoa. The carcass characteristics were determined by ultrasonography at the beginning and at the end of the experimental period, and behavior data were collected on d 88. As a result of ranking Nellore bulls by RFI, cattle from low-RFI group presented lesser daily dry matter intake (DMI), either in kilograms ( p < 0.01) or as percentage of BW ( p < 0.01) than high-RFI yearling bulls, resulting in improved gain:feed (G:F). However, variables, such as average daily gain (ADG), final BW, hot carcass weight (HCW) and other carcass characteristics did not differ ( p > 0.05) across RFI groups. The eating rate of either dry matter (DM )( p = 0.04) or neutral detergent fiber (NDF) ( p < 0.01) was slower in medium-RFI yearling bulls. For ruminal morphometrics an RFI effect was observed only on keratinized layer thickness, in which a thinner layer ( p = 0.04) was observed in low-RFI Nellore yearling bulls. Likewise, Nellore yearling bulls classified by the RFI did not differ in terms of Shannon's diversity ( p = 0.57) and Chao richness ( p = 0.98). Our results suggest that the differences in feed efficiency of Nellore bulls differing in phenotypic RFI should be attributed to metabolic variables other than ruminal microorganisms and epithelium, and deserves further investigation.

  • Mote RS, Hill NS, Skarlupka JH, Carpenter JM, Lourenco JM, Callaway TR, Tran VT, Liu K, Smith MR, Jones DP, Suen G, Filipov NM (2022) Integrative interactomics applied to bovine fescue toxicosis. Scientific reports 12((1)):4899 PMC8941056 · Pubmed · DOI

    Bovine fescue toxicosis (FT) is caused by grazing ergot alkaloid-producing endophyte (Epichloë coenophiala)-infected tall fescue. Endophyte's effects on the animal's microbiota and metabolism were investigated recently, but its effects in planta or on the plant-animal interactions have not been considered. We examined multi-compartment microbiota-metabolome perturbations using multi-'omics (16S and ITS2 sequencing, plus untargeted metabolomics) in Angus steers grazing non-toxic (Max-Q) or toxic (E+) tall fescue for 28 days and in E+ plants. E+ altered the plant/animal microbiota, decreasing most ruminal fungi, with mixed effects on rumen bacteria and fecal microbiota. Metabolic perturbations occurred in all matrices, with some plant-animal overlap (e.g., Vitamin B6 metabolism). Integrative interactomics revealed unique E+ network constituents. Only E+ had ruminal solids OTUs within the network and fecal fungal OTUs in E+ had unique taxa (e.g., Anaeromyces). Three E+-unique urinary metabolites that could be potential biomarkers of FT and targeted therapeutically were identified.

  • Regan MD, Chiang E, Liu Y, Tonelli M, Verdoorn KM, Gugel SR, Suen G, Carey HV, Assadi-Porter FM (2022) Nitrogen recycling via gut symbionts increases in ground squirrels over the hibernation season. Science (New York, N.Y.) 375((6579)):460-463 PMC8936132 · Pubmed · DOI

    Hibernation is a mammalian strategy that uses metabolic plasticity to reduce energy demands and enable long-term fasting. Fasting mitigates winter food scarcity but eliminates dietary nitrogen, jeopardizing body protein balance. Here, we reveal gut microbiome-mediated urea nitrogen recycling in hibernating thirteen-lined ground squirrels ( Ictidomys tridecemlineatus ). Ureolytic gut microbes incorporate urea nitrogen into metabolites that are absorbed by the host, with the nitrogen reincorporated into the squirrel's protein pool. Urea nitrogen recycling is greatest after prolonged fasting in late winter, when urea transporter abundance in gut tissue and urease gene abundance in the microbiome are highest. These results reveal a functional role for the gut microbiome during hibernation and suggest mechanisms by which urea nitrogen recycling may contribute to protein balance in other monogastric animals.

  • Chiang E, Deblois CL, Carey HV, Suen G (2022) Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Animal microbiome 4((1)):1 PMC8722175 · Pubmed · DOI

    Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring.

  • Sapountzis P, Teseo S, Otani S, Aarestrup FM, Forano E, Suen G, Tsiamis G, Haley B, Van Kessel JA, Huws SA (2021) FI: The Fecobiome Initiative. Foodborne pathogens and disease 19((7)):441-447 PMC5897366 · Pubmed · DOI

    Animal husbandry has been key to the sustainability of human societies for millennia. Livestock animals, such as cattle, convert plants to protein biomass due to a compartmentalized gastrointestinal tract (GIT) and the complementary contributions of a diverse GIT microbiota, thereby providing humans with meat and dairy products. Research on cattle gut microbial symbionts has mainly focused on the rumen (which is the primary fermentation compartment) and there is a paucity of functional insight on the intestinal (distal end) microbiota, where most foodborne zoonotic bacteria reside. Here, we present the Fecobiome Initiative (or FI), an international effort that aims at facilitating collaboration on research projects related to the intestinal microbiota, disseminating research results, and increasing public availability of resources. By doing so, the FI can help mitigate foodborne and animal pathogens that threaten livestock and human health, reduce the emergence and spread of antimicrobial resistance in cattle and their proximate environment, and potentially improve the welfare and nutrition of animals. We invite all researchers interested in this type of research to join the FI through our website: www.fecobiome.com.

  • Holzhausen EA, Nikodemova M, Deblois CL, Barnet JH, Peppard PE, Suen G, Malecki KM (2021) Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition. Gut pathogens 13((1)):75 PMC8686582 · Pubmed · DOI

    New technologies like next-generation sequencing have led to a proliferation of studies investigating the role of the gut microbiome in human health, particularly population-based studies that rely upon participant self-collection of samples. However, the impact of methodological differences in sample shipping, storage, and processing are not well-characterized for these types of studies, especially when transit times may exceed 24 h. The aim of this study was to experimentally assess microbiota stability in stool samples stored at 4 °C for durations of 6, 24, 48, 72, and 96 h with no additives to better understand effects of variable shipping times in population-based studies. These data were compared to a baseline sample that was immediately stored at - 80 °C after stool production.

  • Kates AE, Knobloch MJ, Konkel A, Young A, Steinberger A, Shutske J, Ruegg PL, Sethi AK, Goldberg T, Leite de Campos J, Suen G, Safdar N (2021) Wisconsin dairy farm worker perceptions and practices related to antibiotic use, resistance, and infection prevention using a systems engineering framework. PloS one 16((12)):e0258290 PMC8675684 · Pubmed · DOI

    We studied farmworker practices and beliefs potentially contributing to transmission of bacteria and their associated antibiotic resistance genes (ARGs) among animals and farm workers to identify potential behavioral interventions to reduce the risk of bacterial transmission. Ten focus groups were conducted on eight Wisconsin dairy farms to assess potentially high-risk practices and farmworker knowledge and experiences with antibiotic use and resistance using the Systems Engineering in Patient Safety (SEIPS) framework. Farmworkers were asked to describe common on-farm tasks and the policies guiding these practices. We found workers demonstrated knowledge of the role of antibiotic stewardship in preventing the spread of ARGs. Worker knowledge of various forms of personal protective equipment was higher for workers who commonly reported glove-use. Additionally, workers knowledge regarding the importance of reducing ARG transmission varied but was higher than we had hypothesized. Programs to reduce ARG spread on dairy farms should focus on proper hand hygiene and personal protective equipment use at the level of knowledge, beliefs, and practices.

  • Pilch HE, Steinberger AJ, Sockett DC, Aulik N, Suen G, Czuprynski CJ (2021) Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm. Journal of animal science and biotechnology 12((1)):114 PMC8582206 · Pubmed · DOI

    Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing.

  • McKenzie SK, Winston ME, Grewe F, Vargas Asensio G, Rodríguez-Hernández N, Rubin BER, Murillo-Cruz C, von Beeren C, Moreau CS, Suen G, Pinto-Tomás AA, Kronauer DJC (2021) The genomic basis of army ant chemosensory adaptations. Molecular ecology 30((24)):6627-6641 PMC9292994 · Pubmed · DOI

    The evolution of mass raiding has allowed army ants to become dominant arthropod predators in the tropics. Although a century of research has led to many discoveries about behavioural, morphological and physiological adaptations in army ants, almost nothing is known about the molecular basis of army ant biology. Here we report the genome of the iconic New World army ant Eciton burchellii, and show that it is unusually compact, with a reduced gene complement relative to other ants. In contrast to this overall reduction, a particular gene subfamily (9-exon ORs) expressed predominantly in female antennae is expanded. This subfamily has previously been linked to the recognition of hydrocarbons, key olfactory cues used in insect communication and prey discrimination. Confocal microscopy of the brain showed a corresponding expansion in a putative hydrocarbon response centre within the antennal lobe, while scanning electron microscopy of the antenna revealed a particularly high density of hydrocarbon-sensitive sensory hairs. E. burchellii shares these features with its predatory and more cryptic relative, the clonal raider ant. By integrating genomic, transcriptomic and anatomical analyses in a comparative context, our work thus provides evidence that army ants and their relatives possess a suite of modifications in the chemosensory system that may be involved in behavioural coordination and prey selection during social predation. It also lays the groundwork for future studies of army ant biology at the molecular level.

  • Lopes DRG, de Souza Duarte M, La Reau AJ, Chaves IZ, de Oliveira Mendes TA, Detmann E, Bento CBP, Mercadante MEZ, Bonilha SFM, Suen G, Mantovani HC (2021) Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers. Journal of animal science and biotechnology 12((1)):79 PMC8281616 · Pubmed · DOI

    Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI).

  • Cox MS, Deblois CL, Suen G (2021) Assessing the Response of Ruminal Bacterial and Fungal Microbiota to Whole-Rumen Contents Exchange in Dairy Cows. Frontiers in microbiology 12:665776 PMC8203821 · Pubmed · DOI

    A major goal for the dairy industry is to improve overall milk production efficiency (MPE). With the advent of next-generation sequencing and advanced methods for characterizing microbial communities, efforts are underway to improve MPE by manipulating the rumen microbiome. Our previous work demonstrated that a near-total exchange of whole rumen contents between pairs of lactating Holstein dairy cows of disparate MPE resulted in a reversal of MPE status for ∼10 days: historically high-efficiency cows decreased in MPE, and historically low-efficiency cows increased in MPE. Importantly, this switch in MPE status was concomitant with a reversal in the ruminal bacterial microbiota, with the newly exchanged bacterial communities reverting to their pre-exchange state. However, this work did not include an in-depth analysis of the microbial community response or an interrogation of specific taxa correlating to production metrics. Here, we sought to better understand the response of rumen communities to this exchange protocol, including consideration of the rumen fungi. Rumen samples were collected from 8 days prior to, and 56 days following the exchange and were subjected to 16S rRNA and ITS amplicon sequencing to assess bacterial and fungal community composition, respectively. Our results show that the ruminal fungal community did not differ significantly between hosts of disparate efficiency prior to the exchange, and no change in community structure was observed over the time course. Correlation of microbial taxa to production metrics identified one fungal operational taxonomic unit (OTU) in the genus Neocallimastix that correlated positively to MPE, and several bacterial OTUs classified to the genus Prevotella . Within the Prevotella , Prevotella_1 was found to be more abundant in high-efficiency cows whereas Prevotella_7 was more abundant in low-efficiency cows. Overall, our results suggest that the rumen bacterial community is a primary microbial driver of host efficiency, that the ruminal fungi may not have as significant a role in MPE as previously thought, and that more work is needed to better understand the functional roles of specific ruminal microbial community members in modulating MPE.

  • Owens LA, Colitti B, Hirji I, Pizarro A, Jaffe JE, Moittié S, Bishop-Lilly KA, Estrella LA, Voegtly LJ, Kuhn JH, Suen G, Deblois CL, Dunn CD, Juan-Sallés C, Goldberg TL (2021) Publisher Correction: A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone. Nature communications 12((1)):2035 PMC7997875 · Pubmed · DOI

    No abstract available.

  • Huang S, Ji S, Suen G, Wang F, Li S (2021) The Rumen Bacterial Community in Dairy Cows Is Correlated to Production Traits During Freshening Period. Frontiers in microbiology 12:630605 PMC7969525 · Pubmed · DOI

    The rumen microbiome plays a vital role in providing nutrition to the host animal, thereby influencing ruminant production. Despite its importance, it is not fully understood how variation in the ruminal bacteria community composition influences dry matter intake (DMI), milk yield and ruminal fermentative parameters in dairy cows, especially during freshening period. Here, we hypothesized that during early lactation, high DMI cows having a different ruminal microbiota than low DMI cows, and that this difference persists over time. To test this, we enrolled 65 fresh and determinzed their DMI using an auto-feed intake recording system. Fourteen days after calving, the 10 animals with the lowest (LFI) and the 10 animals with the highest (HFI)-average DMI were selected for further analysis. Rumen fluid was collected from these two cohorts at 1 (Fresh1d) and 14 days (Fresh14d) after calving and their ruminal microbiota were assessed using 16S rRNA sequencing. Volatile fatty acid (VFA) concentrations were also quantified. Comparison of the ruminal microbiotas between Fresh1d and Fresh14d showed that Fresh14d cows had a significantly higher relative abundance of VFA-producing microbes ( P < 0.05), such as Prevotella_7 and Succinivibrionaceae_UCG-001 . This was commensurate with the concentrations of acetate, propionate, butyrate, valerate and total VFAs, were also significantly ( P < 0.05) increased in Fresh14d cows. We also found that the differences in the ruminal microbiota between LFI and HFI cows was limited, but DMI significantly altered ( P < 0.05) the relative proportion of bacteria in the families Coriobacteriaceae , and Succinivibrionaceae . Furthermore, specific operational taxonomic units belonging to the Anaeroplasma was significantly ( P < 0.05) correlated with DMI and milk yield. Taking together, our findings provide a framework for future studies of freshening period cow that seek to better understand the role of the ruminal microbiota during this critical period in the lactation cycle.

  • Bi Y, Tu Y, Zhang N, Wang S, Zhang F, Suen G, Shao D, Li S, Diao Q (2021) Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs. Gut 70((5)):853-864 PMC8040156 · Pubmed · DOI

    Microbial exposure is critical to neonatal and infant development, growth and immunity. However, whether a microbiome is present in the fetal gut prior to birth remains debated. In this study, lambs delivered by aseptic hysterectomy at full term were used as an animal model to investigate the presence of a microbiome in the prenatal gut using a multiomics approach.

  • de Campos JL, Kates A, Steinberger A, Sethi A, Suen G, Shutske J, Safdar N, Goldberg T, Ruegg PL (2021) Quantification of antimicrobial usage in adult cows and preweaned calves on 40 large Wisconsin dairy farms using dose-based and mass-based metrics. Journal of dairy science 104((4)):4727-4745 · Pubmed · DOI

    Use of antimicrobials in animal agriculture is under increasing scrutiny, but the quantity of antimicrobials used on large US dairy farms has not been evaluated using data from large farms and different metrics. This study investigated total antimicrobial usage (AMU) in adult dairy cows and preweaned calves (PWC) and contrasted 2 metrics used for measurement of AMU. Wisconsin dairy farms were eligible if they had >250 lactating cows, maintained computerized animal health records, and were willing to allow researchers access to treatment records. Animal health data for a 1-yr period was retrospectively collected from computerized records, and a farm visit was performed to verify case definitions and recording accuracy. Both dose-based (animal daily doses; ADD) and mass-based (total mg of antimicrobials per kg of body weight; BW) metrics were calculated at the herd, cow, and PWC levels. Descriptive statistics for AMU were examined for both age groups. Mean AMU was compared among active ingredients and route of usage using ANOVA models that included farm as a random variable. At enrollment, farms (n = 40) contained approximately 52,639 cows (mean: 1,316 ± 169; 95% CI: 975, 1657) and 6,281 PWC (mean: 180 ± 33; 95% CI: 112, 247). When estimated using ADD, total herd AMU was 17.2 ADD per 1,000 animal-days (95% CI: 14.9, 19.5), with 83% of total herd-level AMU in adult cows. When estimated using the mass-based metric, total herd AMU was 13.6 mg of antimicrobial per kilogram of animal BW (95% CI: 10.3, 17.0), with 86% of total AMU used in adult cows. For cows, 78% of total ADD (15.8 ADD per 1,000 cow-d) was administered as intramammary (IMM) preparations. In contrast, when AMU was estimated using a mass-based metric, IMM preparations represented only 24% of total AMU (12.1 mg of antimicrobial/kg of cow BW). For cows, ceftiofur was the primary antimicrobial used and accounted for 53% of total ADD, with 80% attributed to IMM and 20% attributed to injectable treatments. When estimated using a mass-based metric, ampicillin was the predominant antimicrobial used in cows and accounted for 33% of total antimicrobial mass per kilogram of BW. When AMU was estimated for PWC using ADD, injectable antimicrobials represented 79% of total usage (28.3 ADD per 1,000 PWC-d). In contrast, when AMU was estimated for PWC using a mass-based metric, injectable products represented 42% of total AMU, even though more farms administered antimicrobials using this route. When AMU in PWC was summarized using ADD, penicillin represented 32% of AMU, and there were no significant differences in ADD among ampicillin, oxytetracycline or enrofloxacin. When a mass-based metric was used to estimate AMU in PWC, oral products (sulfadimethoxine and trimethoprim-sulfa) represented more than half of the total AMU given to this group. Overall, these results showed that choice of metric and inclusion of different age groups can substantially influence interpretation of AMU on dairy farms.

  • Owens LA, Colitti B, Hirji I, Pizarro A, Jaffe JE, Moittié S, Bishop-Lilly KA, Estrella LA, Voegtly LJ, Kuhn JH, Suen G, Deblois CL, Dunn CD, Juan-Sallés C, Goldberg TL (2021) A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone. Nature communications 12((1)):763 PMC7859188 · Pubmed · DOI

    Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named "epizootic neurologic and gastroenteric syndrome" (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated with Sarcina infection. The microorganism is distinct from Sarcina ventriculi and other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named "Candidatus Sarcina troglodytae". Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of "Ca. S. troglodytae" in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.

  • Belanche A, Patra AK, Morgavi DP, Suen G, Newbold CJ, Yáñez-Ruiz DR (2021) Editorial: Gut Microbiome Modulation in Ruminants: Enhancing Advantages and Minimizing Drawbacks. Frontiers in microbiology 11:622002 PMC7829182 · Pubmed · DOI

    No abstract available.

  • Raabis SM, Quick AE, Skarlupka JH, Suen G, Ollivett TL (2021) The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung lesions. Journal of dairy science 104((3)):3386-3402 · Pubmed · DOI

    The primary objective of this cross-sectional study was to identify associations between the diversity and composition of the nasopharyngeal (NP) microbiota and pneumonia status, as diagnosed by ultrasonography (US), in preweaned dairy calves. Characteristics of the NP microbiota were compared between calves with and without pneumonia, as diagnosed by US. Secondary objectives were to compare the composition of the NP microbiota between calves by age, clinical respiratory score (CRS), and previous antibiotic therapy. Holstein heifer calves (n = 50) from a southern Wisconsin dairy were enrolled at either 3 or 6 wk of age; 4 calves were sampled at both time points. Antibiotic treatment history was also collected for the 30 d before enrollment. For the purpose of this study, pneumonia was defined as having lobar pneumonia, as diagnosed by US, in at least 1 lung lobe. Following examination by CRS and US, a deep nasopharyngeal swab was obtained for 16S rRNA amplicon sequencing. Alpha diversity was reduced in calves that were CRS positive, and beta diversity tended to be different in calves previously treated with antibiotics and in calves that were CRS positive. Microbial diversity was not different between calves with and without pneumonia. The most dominant genus identified was Mycoplasma spp.; however, there was no association between relative abundance (RA) and pneumonia status. The median RA of Mycoplasma spp. was increased by 25 (95% confidence interval, CI: 3, 40) in calves at 3 wk of age compared with 6 wk of age. The median RA of Pasteurella spp. was increased by 1.5 (95% CI: 0.1, 3) in calves with pneumonia, as diagnosed by US, compared with calves without pneumonia. Additionally, Pasteurella spp. was increased by 2.3 (95% CI: 0, 9) in CRS-positive calves compared with CRS-negative calves. The median RA of Psychrobacter spp. was increased by 2 (95% CI: 0, 12) and median RA of Chryseobacterium spp. was increased by 0.15 (95% CI: 0, 2) in calves that were not treated previously with antibiotics compared with calves previously treated with antibiotics.

  • Burgos HL, Burgos EF, Steinberger AJ, Suen G, Mandel MJ (2020) Multiplexed Competition in a Synthetic Squid Light Organ Microbiome Using Barcode-Tagged Gene Deletions. mSystems 5((6)): PMC7771539 · Pubmed · DOI

    Beneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and tfoX -based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio -squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces. IMPORTANCE Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes-both beneficial and pathogenic-colonize specific animal hosts.

  • Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernández SB, Heine V, Buhl EM, M D'Agostino P, Cumbo F, Fischöder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Spröer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T (2020) A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nature communications 11((1)):6389 PMC7738495 · Pubmed · DOI

    Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

  • Kates AE, Knobloch MJ, Konkel A, Young A, Steinberger A, Shutske J, Ruegg PL, Sethi AK, Goldberg T, de Campos JL, Suen G, Safdar N (2020) Use of a systems engineering framework to assess perceptions and practices about antimicrobial resistance of workers on large dairy farms in Wisconsin. medRxiv : the preprint server for health sciences : PMC7654902 · Pubmed · DOI

    We studied farmworker practices potentially contributing to transmission of bacteria and antimicrobial resistant genes (ARGs) among animals and farm workers to identify human behavioral interventions to reduce exposure risk. Ten focus groups were conducted on eight farms to explore potentially high-risk practices and farmworker knowledge and experiences with antimicrobial use and resistance using the Systems Engineering in Patient Safety (SEIPS) framework. Farmworkers were asked to describe common tasks and the policies guiding these practices. We found workers demonstrated knowledge of the role of antibiotic stewardship in preventing the spread of ARGs. Knowledge of various forms of personal protective equipment was higher for workers who commonly reported glove-use. Knowledge regarding the importance of reducing ARG transmission varied but was greater than previously reported. Programs to reduce ARG spread on dairy farms should focus on proper hand hygiene and personal protective equipment use but at the level of knowledge, beliefs, and practices.

  • Mote RS, Carpenter JM, Dockman RL, Steinberger AJ, Suen G, Norberg T, Harn DA, Wagner JJ, Filipov NM (2020) Assessing the Beneficial Effects of the Immunomodulatory Glycan LNFPIII on Gut Microbiota and Health in a Mouse Model of Gulf War Illness. International journal of environmental research and public health 17((19)): PMC7579323 · Pubmed · DOI

    The microbiota's influence on host (patho) physiology has gained interest in the context of Gulf War Illness (GWI), a chronic disorder featuring dysregulation of the gut-brain-immune axis. This study examined short- and long-term effects of GWI-related chemicals on gut health and fecal microbiota and the potential benefits of Lacto-N-fucopentaose-III (LNFPIII) treatment in a GWI model. Male C57BL/6J mice were administered pyridostigmine bromide (PB; 0.7 mg/kg) and permethrin (PM; 200 mg/kg) for 10 days with concurrent LNFPIII treatment (35 μg/mouse) in a short-term study (12 days total) and delayed LNFPIII treatment (2×/week) beginning 4 months after 10 days of PB/PM exposure in a long-term study (9 months total). Fecal 16S rRNA sequencing was performed on all samples post-LNFPIII treatment to assess microbiota effects of GWI chemicals and acute/delayed LNFPIII administration. Although PB/PM did not affect species composition on a global scale, it affected specific taxa in both short- and long-term settings. PB/PM elicited more prominent long-term effects, notably, on the abundances of bacteria belonging to Lachnospiraceae and Ruminococcaceae families and the genus Allobaculum . LNFPIII improved a marker of gut health (i.e., decreased lipocalin-2) independent of GWI and, importantly, increased butyrate producers (e.g., Butyricoccus , Ruminococcous ) in PB/PM-treated mice, indicating a positive selection pressure for these bacteria. Multiple operational taxonomic units correlated with aberrant behavior and lipocalin-2 in PB/PM samples; LNFPIII was modulatory. Overall, significant and lasting GWI effects occurred on specific microbiota and LNFPIII treatment was beneficial.

  • Pinto ACJ, Bertoldi GP, Felizari LD, Dias EFF, Demartini BL, Nunes ABCP, Squizatti MM, Silvestre AM, Oliveira LFR, Skarlupka JH, Rodrigues PHM, Cruz GD, Suen G, Millen DD (2020) Ruminal Fermentation Pattern, Bacterial Community Composition, and Nutrient Digestibility of Nellore Cattle Submitted to Either Nutritional Restriction or Intake of Concentrate Feedstuffs Prior to Adaptation Period. Frontiers in microbiology 11:1865 PMC7412545 · Pubmed · DOI

    Beef cattle are key contributors to meat production and represent critical drivers of the global agricultural economy. In Brazil, beef cattle are reared in tropical pastures and finished in feedlot systems. The introduction of cattle into a feedlot includes a period where they adapt to high-concentrate diets. This adaptation period is critical to the success of incoming cattle, as they must adjust to both a new diet and environment. Incoming animals are typically reared on a variety of diets, ranging from poor quality grasses to grazing systems supplemented with concentrate feedstuffs. These disparate pre-adaptation diets present a challenge, and here, we sought to understand this process by evaluating the adaptation of Nellore calves raised on either grazing on poor quality grasses (restriction diet) or grazing systems supplemented with concentrate (concentrate diet). Given that nutrient provisioning from the diet is the sole responsibility of the ruminal microbial community, we measured the impact of this dietary shift on feeding behavior, ruminal fermentation pattern, ruminal bacterial community composition (BCC), and total tract digestibility. Six cannulated Nellore bulls were randomly assigned to two 3 × 3 Latin squares, and received a control, restriction, or concentrate diet. All cohorts were then fed the same adaptation diet to mimic a standard feedlot. Ruminal BCC was determined using Illumina-based 16S rRNA amplicon community sequencing. We found that concentrate-fed cattle had greater dry matter intake ( P < 0.01) than restricted animals. Likewise, cattle fed concentrate had greater ( P = 0.02) propionate concentration during the adaptation phase than control animals and a lower Shannon's diversity ( P = 0.02), relative to the restricted animals. We also found that these animals had lower ( P = 0.04) relative abundances of Fibrobacter succinogenes when compared to control animals during the pre-adaptation phase and lower abundances of bacteria within the Succinivibrio during the finishing phase, when compared to the control animals ( P = 0.05). Finally, we found that animals previously exposed to concentrate were able to better adapt to high-concentrate diets when compared to restricted animals. Our study presents the first investigation of the impact of pre-adaptation diet on ruminal BCC and metabolism of bulls during the adaptation period. We suggest that these results may be useful for planning adaptation protocols of bulls entering the feedlot system and thereby improve animal production.

  • Young J, Skarlupka JH, Cox MS, Resende RT, Fischer A, Kalscheur KF, McClure JC, Cole JB, Suen G, Bickhart DM (2020) Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach. Applied and environmental microbiology 86((17)): PMC7440797 · Pubmed · DOI

    Analysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large scale are required. In this study, we further optimized the analysis of buccal swab samples as a proxy for direct bacterial samples of the rumen of dairy cows. To identify an optimal time for sampling, we collected buccal swab and rumen samples at six different time points relative to animal feeding. We then evaluated several biases in these samples using a machine learning classifier (random forest) to select taxa that discriminate between buccal swab and rumen samples. Differences in the inverse Simpson's diversity, Shannon's evenness, and Bray-Curtis dissimilarities between methods were significantly less apparent when sampling was performed prior to morning feeding ( P  60%) taxa in buccal and rumen samples had significant variance in relative abundances between sampling methods but could be qualitatively assessed via regular buccal swab sampling. This work not only provides new insights into the oral community of ruminants but also further validates and refines buccal swabbing as a method to assess the rumen bacterial in large herds. IMPORTANCE The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health, and performance. While the influence of environmental factors on rumen microbes is well documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of noninvasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.

  • Li W, Edwards A, Cox MS, Raabis SM, Skarlupka JH, Steinberger AJ, Murphy B, Larsen A, Suen G (2020) Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents. Physiological genomics 52((8)):333-346 · Pubmed · DOI

    Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk. Six calves were included in this study. At 8 wk of age, tissue from the ileum was collected and subjected to host transcriptome and microbial metatranscriptome analysis using RNA sequencing. A total of 333 genes showed significant differential expression (DE) (fold-change ≥2; adjusted P < 0.1, mean read-count ≥10) between the treated and control calves. Gene ontology analysis indicated that these DE genes are predominantly associated with processes related to the host immune response ( P < 0.0001). Association analysis between the host gene expression and the microbial genus abundance identified 57 genes as having significant correlation with the ileum microbial genera ( P < 0.0001). Of these, three genes showed significant association with six microbial genera: lysozyme 2 ( LYZ2 ), fatty acid binding protein 5 ( FABP5 ), and fucosyltransferase (FUT1 ). Specifically, the profound increase in expression of LYZ2 in treated calves suggests the initiation of antibacterial activity and innate response from the host. Despite the limitation of a relatively small sample size, this study sheds light on the potential impact of early introduction of microbes on the small intestine of calves.

  • Kates AE, Gaulke I, De Wolfe T, Zimbric M, Haight K, Watson L, Suen G, Kim K, Safdar N (2020) Fecal microbiota transplantation for patients on antibiotic treatment with C. difficile infection history (GRAFT): Study protocol for a phase II, randomized, double-blind, placebo-controlled trial to prevent recurrent C. difficile infections. Contemporary clinical trials communications 18:100576 PMC7270544 · Pubmed · DOI

    Recurrent Clostridiodes difficile infections (rCDIs) are a burdensome problem. Patients with a history of CDI that are prescribed antibiotics are at a high risk for recurrence. Fecal microbiota transplantation (FMT) has been shown to be an effective treatment for rCDI, though there is little information on the impact of FMT with antibiotics on the gut microbiome. We are conducting a clinical trial of FMT to prevent rCDI in patients with a history of CDI currently taking antibiotics. Our primary objective is to determine the effect of FMT on the gut microbiome during antibiotic exposure. Our secondary aim is to assess safety and feasibility of using FMT as a prophylaxis for CDI. We plan to enroll 30 patients into a phase II randomized, double-blind, placebo-controlled trial with three arms: (1) 5 FMT capsules per day during antibiotic treatment and for 7 days post antibiotic cessation, (2) a one-time dose of 30 FMT capsules 48-72 h post cessation of antibiotic treatment, or (3) 5 placebo capsules per day during antibiotic treatment and for 7 days post antibiotic treatment. Patients provide stool samples throughout the duration of the study and are cultured C. difficile. Sequencing of the V4 region of the 16S rRNA gene will be carried out to assess the gut microbiota. Results of this study will provide information on the impact of FMT on the gut microbiome as well as the necessary data to examine whether or not prophylactic FMT should be explored further as a way to prevent CDI recurrence.

  • Becker SL, Chiang E, Plantinga A, Carey HV, Suen G, Swoap SJ (2020) Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity. FEMS microbiology ecology 96((6)): PMC7233940 · Pubmed · DOI

    Artificial sweeteners have been shown to induce glucose intolerance by altering the gut microbiota; however, little is known about the effect of stevia. Here, we investigate whether stevia supplementation induces glucose intolerance by altering the gut microbiota in mice, hypothesizing that stevia would correct high fat diet-induced glucose intolerance and alter the gut microbiota. Mice were split into four treatment groups: low fat, high fat, high fat + saccharin and high fat + stevia. After 10 weeks of treatment, mice consuming a high fat diet (60% kcal from fat) developed glucose intolerance and gained more weight than mice consuming a low fat diet. Stevia supplementation did not impact body weight or glucose intolerance. Differences in species richness and relative abundances of several phyla were observed in low fat groups compared to high fat, stevia and saccharin. We identified two operational taxonomic groups that contributed to differences in beta-diversity between the stevia and saccharin groups: Lactococcus and Akkermansia in females and Lactococcus in males. Our results demonstrate that stevia does not rescue high fat diet-induced changes in glucose tolerance or the microbiota, and that stevia results in similar alterations to the gut microbiota as saccharin when administered in concordance with a high fat diet.

  • Kates AE, Jarrett O, Skarlupka JH, Sethi A, Duster M, Watson L, Suen G, Poulsen K, Safdar N (2020) Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota. Frontiers in cellular and infection microbiology 10:73 PMC7058978 · Pubmed · DOI

    The human gut microbiome has a great deal of interpersonal variation due to both endogenous and exogenous factors, like household pet exposure. To examine the relationship between having a pet in the home and the composition and diversity of the adult gut microbiome, we conducted a case-control study nested in a larger, statewide study, the Survey of the Health of Wisconsin. Stool samples were collected from 332 participants from unique households and analyzed using 16S rRNA sequencing on the Illumina MiSeq. One hundred and seventy-eight participants had some type of pet in the home with dogs and cats being the most prevalent. We observed no difference in alpha and beta diversity between those with and without pets, though seven OTUs were significantly more abundant in those without pets compared to those with pets, and four were significantly more abundant in those with pets. When stratifying by age, seven of these remained significant. These results suggest that pet ownership is associated with differences in the human gut microbiota. Further research is needed to better characterize the effect of pet ownership on the human gut microbiome.

  • Sbardellati DL, Fischer A, Cox MS, Li W, Kalscheur KF, Suen G (2020) The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations. Journal of dairy science 103((4)):3636-3647 · Pubmed · DOI

    Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important for providing nutrition from otherwise host-inaccessible dietary components. The rumen environment is noted for its substantial spatial heterogeneity, as illustrated by the stratification into ruminal solid and liquid phases. A third microbiota found directly attached to the ruminal epithelium (the epimural microbiota) also exists but is less well understood because of challenges in sampling the ruminal epithelium. As a result, our understanding of the epimural microbiota is based on analyses of cannulated animals sampled at a single location-the ventral sac-and does not account for other ruminal locations, which may have importance for overall rumen function. To address this knowledge gap, we hypothesize that the epimural microbiota at different ruminal locations differs due to known morphological, physiological, and functional differences across the geographic spread of the rumen epithelium. Here, we characterized bacterial epimural communities at different sites within 8 lactating Holstein dairy cows using 16S rRNA gene sequencing. Four different sites were sampled via rumen tissue biopsy: cranial sac (CS), ventral sac (VS), caudodorsal blind sac (CDBS), and caudoventral blind sac (CVBS). We found that locations differed in both epimural bacterial community structure and composition, with the CDBS community displaying the greatest diversity. Across all sampling sites, epimural bacterial communities were dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. Bacteria within Prevotellaceae, Butyrivibrio, Campylobacter, Mogibacterium, and Desulfobulbus all showed high relative sequence abundance and differential distributions according to sample location. There appears to be a core epimural microbiota present across all locations in all cows, although relative abundance was highly variable. The difference in relative abundance in epimural microbial communities, perhaps influenced by host physiology and the diversity within rumen contents, likely has important consequences for nutrition acquisition and general health. To the best of our knowledge, this work represents the first characterization of the ruminal epimural microbiota across different epithelial locations for any bovine ruminant.

  • Mote RS, Hill NS, Skarlupka JH, Tran VT, Walker DI, Turner ZB, Sanders ZP, Jones DP, Suen G, Filipov NM (2020) Toxic tall fescue grazing increases susceptibility of the Angus steer fecal microbiota and plasma/urine metabolome to environmental effects. Scientific reports 10((1)):2497 PMC7016188 · Pubmed · DOI

    Impaired thermoregulation and lowered average daily gains (ADG) result when livestock graze toxic endophyte (Epichloë coenophialum)-infected tall fescue (E+) and are hallmark signs of fescue toxicosis (FT), a disease exacerbated by increased temperature and humidity (+temperature-humidity index; +THI). We previously reported FT is associated with metabolic and microbiota perturbations under thermoneutral conditions; here, we assessed the influence of E+ grazing and +THI on the microbiota:metabolome interactions. Using high-resolution metabolomics and 16S rRNA gene sequencing, plasma/urine metabolomes and the fecal microbiota of Angus steers grazing non-toxic or E+ tall fescue were evaluated in the context of +THI. E+ grazing affected the fecal microbiota profile; +THI conditions modulated the microbiota only in E+ steers. E+ also perturbed many metabolic pathways, namely amino acid and inflammation-related metabolism; +THI affected these pathways only in E+ steers. Integrative analyses revealed the E+ microbiota correlated and co-varied with the metabolomes in a THI-dependent manner. Operational taxonomic units in the families Peptococcaceae, Clostridiaceae, and Ruminococcaceae correlated with production parameters (e.g., ADG) and with multiple plasma/urine metabolic features, providing putative FT biomarkers and/or targets for the development of FT therapeutics. Overall, this study suggests that E+ grazing increases Angus steer susceptibility to +THI, and offers possible targets for FT interventions.

  • Firmino FC, Porcellato D, Cox M, Suen G, Broadbent JR, Steele JL (2019) Characterization of microbial communities in ethanol biorefineries. Journal of industrial microbiology & biotechnology 47((2)):183-195 · Pubmed · DOI

    Bacterial contamination of corn-based ethanol biorefineries can reduce their efficiency and hence increase their carbon footprint. To enhance our understanding of these bacterial contaminants, we temporally sampled four biorefineries in the Midwestern USA that suffered from chronic contamination and characterized their microbiomes using both 16S rRNA sequencing and shotgun metagenomics. These microbiotas were determined to be relatively simple, with 13 operational taxonomic units (OTUs) accounting for 90% of the bacterial population. They were dominated by Firmicutes (89%), with Lactobacillus comprising 80% of the OTUs from this phylum. Shotgun metagenomics confirmed our 16S rRNA data and allowed us to characterize bacterial succession at the species level, with the results of this analysis being that Lb. helveticus was the dominant contaminant in this fermentation. Taken together, these results provide insights into the microbiome of ethanol biorefineries and identifies a species likely to be commonly responsible for chronic contamination of these facilities.

  • Eggers S, Safdar N, Sethi AK, Suen G, Peppard PE, Kates AE, Skarlupka JH, Kanarek M, Malecki KMC (2019) Urinary lead concentration and composition of the adult gut microbiota in a cross-sectional population-based sample. Environment international 133((Pt A)):105122 PMC7230144 · Pubmed · DOI

    Lead (Pb) is a ubiquitous environmental contaminant with an array of detrimental health effects in children and adults, including neurological and immune dysfunction. Emerging evidence suggests that Pb exposure may alter the composition of the gut microbiota, however few studies have examined this association in human populations. The purpose of this study was to examine the association between urinary Pb concentration and the composition of the adult gut microbiota in a population-based sample of adults.

  • Skarlupka JH, Kamenetsky ME, Jewell KA, Suen G (2019) The ruminal bacterial community in lactating dairy cows has limited variation on a day-to-day basis. Journal of animal science and biotechnology 10:66 PMC6698983 · Pubmed · DOI

    Dairy cows rely on a complex ruminal microbiota to digest their host-indigestible feed. Our ability to characterize this microbiota has advanced significantly due to developments in next-generation sequencing. However, efforts to sample the rumen, which typically involves removing digesta directly from the rumen via a cannula, intubation, or rumenocentesis, is costly and labor intensive. As a result, the majority of studies characterizing the rumen microbiota are conducted on samples collected at a single time point. Currently, it is unknown whether there is significant day-to-day variation in the rumen microbiota, a factor that could strongly influence conclusion drawn from studies that sample at a single time point. To address this, we examined day-to-day changes in the ruminal microbiota of lactating dairy cows using next-generation sequencing to determine if single-day sampling is representative of sampling across 3 consecutive days. We sequenced single-day solid and liquid fractions of ruminal digesta collected over 3 consecutive days from 12 cannulated dairy cows during the early, middle, and late stages of a single lactation cycle using the V4 region of the bacterial 16S rRNA gene. We then generated 97% similarity operational taxonomic units (OTUs) from these sequences and showed that any of the individual samples from a given 3-day sampling period is equivalent to the mean OTUs determined from the combined 3-d data set. This finding was consistent for both solid and liquid fractions of the rumen, and we thus conclude that there is limited day-to-day variability in the rumen microbiota.

  • Keating JA, Shaughnessy C, Baubie K, Kates AE, Putman-Buehler N, Watson L, Dominguez N, Watson K, Cook DB, Rabago D, Suen G, Gangnon R, Safdar N (2019) Characterising the gut microbiome in veterans with Gulf War Illness: a protocol for a longitudinal, prospective cohort study. BMJ open 9((8)):e031114 PMC6707676 · Pubmed · DOI

    Approximately 25%-35% of the 1991 Gulf War Veteran population report symptoms consistent with Gulf War Illness (GWI), a chronic, multi-symptom illness characterised by fatigue, pain, irritable bowel syndrome and problems with cognitive function. GWI is a disabling problem for Gulf War Veterans, and there remains a critical need to identify innovative, novel therapies.Gut microbiota perturbation plays a key role in the symptomatology of other chronic multi-symptom illnesses, including myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Given similarities between ME/CFS and GWI and the presence of gastrointestinal disorders in GWI patients, Veterans with GWI may also have gut abnormalities like those seen with ME/CFS. In this longitudinal cohort study, we are comparing the diversity (structure) and the metagenomes (function) of the gut microbiome between Gulf War Veterans with and without GWI. If we find differences in Veterans with GWI, the microbiome could be a target for therapeutic intervention to alleviate GWI symptoms.

  • Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL (2019) Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome biology 20((1)):153 PMC6676630 · Pubmed · DOI

    We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

  • Lopes DRG, La Reau AJ, Duarte MS, Detmann E, Bento CBP, Mercadante MEZ, Bonilha SFM, Suen G, Mantovani HC (2019) The Bacterial and Fungal Microbiota of Nelore Steers Is Dynamic Across the Gastrointestinal Tract and Its Fecal-Associated Microbiota Is Correlated to Feed Efficiency. Frontiers in microbiology 10:1263 PMC6603086 · Pubmed · DOI

    The ruminant gastrointestinal tract (GIT) microbiome plays a major role in the health, physiology and production traits of the host. In this work, we characterized the bacterial and fungal microbiota of the rumen, small intestine (SI), cecum and feces of 27 Nelore steers using next-generation sequencing and evaluated biochemical parameters within the GIT segments. We found that only the bacterial microbiota clustered according to each GIT segment. Bacterial diversity and richness as well as volatile fatty acid concentration was lowest in the SI. Taxonomic grouping of bacterial operational taxonomic units (OTUs) revealed that Lachnospiraceae (24.61 ± SD 6.58%) and Ruminococcaceae (20.87 ± SD 4.22%) were the two most abundant taxa across the GIT. For the fungi, the family Neocallismastigaceae dominated in all GIT segments, with the genus Orpinomyces being the most abundant. Twenty-eight bacterial and six fungal OTUs were shared across all GIT segments in at least 50% of the steers. We also evaluated if the fecal-associated microbiota of steers showing negative and positive residual feed intake (n-RFI and p-RFI, respectively) was associated with their feed efficiency phenotype. Diversity indices for both bacterial and fungal fecal microbiota did not vary between the two feed efficiency groups. Differences in the fecal bacterial composition between high and low feed efficiency steers were primarily assigned to OTUs belonging to the families Lachnospiraceae and Ruminococcaceae and to the genus Prevotella . The fungal OTUs shared across the GIT did not vary between feed efficiency groups, but 7 and 3 OTUs were found only in steers with positive and negative RFI, respectively. These results provide further insights into the composition of the Nelore GIT microbiota, which could have implications for improving animal health and productivity. Our findings also reveal differences in fecal-associated bacterial OTUs between steers from different feed efficiency groups, suggesting that fecal sampling may represent a non-invasive strategy to link the bovine microbiota with productivity phenotypes.

  • Li W, Edwards A, Riehle C, Cox MS, Raabis S, Skarlupka JH, Steinberger AJ, Walling J, Bickhart D, Suen G (2019) Author Correction: Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow. Scientific reports 9((1)):8116 PMC6536682 · Pubmed · DOI

    A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

  • Mote RS, Hill NS, Skarlupka JH, Turner ZB, Sanders ZP, Jones DP, Suen G, Filipov NM (2019) Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue. Applied and environmental microbiology 85((15)): PMC6643230 · Pubmed · DOI

    Tall fescue, the predominant southeastern United States cool-season forage grass, frequently becomes infected with an ergot alkaloid-producing toxic endophyte, Epichloë coenophialum Consumption of endophyte-infected fescue results in fescue toxicosis (FT), a condition that lowers beef cow productivity. Limited data on the influence of ergot alkaloids on rumen fermentation profiles or ruminal bacteria that could degrade the ergot alkaloids are available, but how FT influences the grazing bovine fecal microbiota or what role fecal microbiota might play in FT etiology and associated production losses has yet to be investigated. Here, we used 16S rRNA gene sequencing of fecal samples from weaned Angus steers grazing toxic endophyte-infected (E+; n  = 6) or nontoxic (Max-Q; n  = 6) tall fescue before and 1, 2, 14, and 28 days after pasture assignment. Bacteria in the Firmicutes and Bacteroidetes phyla comprised 90% of the Max-Q and E+ steer fecal microbiota throughout the trial. Early decreases in the Erysipelotrichaceae family and delayed increases of the Ruminococcaceae and Lachnospiraceae families were among the major effects of E+ grazing. E+ also increased abundances within the Planctomycetes , Chloroflexi , and Proteobacteria phyla and the Clostridiaceae family. Multiple operational taxonomic units classified as Ruminococcaceae and Lachnospiraceae were correlated negatively with weight gains (lower in E+) and positively with respiration rates (increased by E+). These data provide insights into how E+ grazing alters the Angus steer microbiota and the relationship of fecal microbiota dynamics with FT. IMPORTANCE Consumption of E+ tall fescue has an estimated annual $1 billion negative impact on the U.S. beef industry, with one driver of these costs being lowered weight gains. As global agricultural demand continues to grow, mitigating production losses resulting from grazing the predominant southeastern United States forage grass is of great value. Our investigation of the effects of E+ grazing on the fecal microbiota furthers our understanding of bovine fescue toxicosis in a real-world grazing production setting and provides a starting point for identifying easy-to-access fecal bacteria that could serve as potential biomarkers of animal productivity and/or FT severity for tall fescue-grazing livestock.

  • Hillel AT, Tang SS, Carlos C, Skarlupka JH, Gowda M, Yin LX, Motz K, Currie CR, Suen G, Thibeault SL (2019) Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis. mSphere 4((3)): PMC6495342 · Pubmed · DOI

    Laryngotracheal stenosis is an obstructive respiratory disease that leads to voicing difficulties and dyspnea with potential life-threatening consequences. The majority of incidences are due to iatrogenic etiology from endotracheal tube intubation; however, airway scarring also has idiopathic causes. While recent evidence suggests a microbial contribution to mucosal inflammation, the microbiota associated with different types of stenosis has not been characterized. High-throughput sequencing of the V4 region of the16S rRNA gene was performed to characterize the microbial communities of 61 swab samples from 17 iatrogenic and 10 adult idiopathic stenosis patients. Nonscar swabs from stenosis patients were internal controls, and eight swabs from four patients without stenosis represented external controls. Significant differences in diversity were observed between scar and nonscar samples and among sample sites, with decreased diversity detected in scar samples and the glottis region. Permutational analysis of variance (PERMANOVA) results revealed significant differences in community composition for scar versus nonscar samples, etiology type, sample site, groups (iatrogenic, idiopathic, and internal and external controls), and individual patients. Pairwise Spearman's correlation revealed a strong inverse correlation between Prevotella and Streptococcus among all samples. Finally, bacteria in the family Moraxellaceae were found to be distinctly associated with idiopathic stenosis samples in comparison with external controls. Our findings suggest that specific microbiota and community shifts are present with laryngotracheal stenosis in adults, with members of the family Moraxellaceae , including the known pathogens Moraxella and Acinetobacter , identified in idiopathic scar. Further work is warranted to elucidate the contributing role of bacteria on the pathogenesis of laryngotracheal stenosis. IMPORTANCE The laryngotracheal region resides at the intersection between the heavily studied nasal cavity and lungs; however, examination of the microbiome in chronic inflammatory conditions of the subglottis and trachea remains scarce. To date, studies have focused on the microbiota of the vocal folds, or the glottis, for laryngeal carcinoma, as well as healthy larynges, benign vocal fold lesions, and larynges exposed to smoking and refluxate. In this study, we seek to examine the structure and composition of the microbial community in adult laryngotracheal stenosis of various etiologies. Due to the heterogeneity among the underlying pathogenesis mechanisms and clinical outcomes seen in laryngotracheal stenosis disease, we hypothesized that different microbial profiles will be detected among various stenosis etiology types. Understanding differences in the microbiota for subglottic stenosis subtypes may shed light upon etiology-specific biomarker identification and offer novel insights into management approaches for this debilitating disease.

  • Bi Y, Cox MS, Zhang F, Suen G, Zhang N, Tu Y, Diao Q (2019) Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs. Environmental microbiology 21((7)):2333-2346 PMC6849743 · Pubmed · DOI

    Early gut microbial colonization is important for postnatal metabolic and immune development. However, little is known about the effects of different feeding modes (suckling versus bottle-feeding) or microbial sources on this process in farm animals. We found that suckled and bottle-fed newborn lambs had their own distinct gut microbiota. Results from 16S rRNA gene sequencing and qPCR showed that, compared with suckling, bottle feeding significantly increased the abundances of Escherichia/Shigella, Butyricicoccus, and Clostridium XlVa, while significantly decreased the abundance of Clostridium XI. The higher levels of Escherichia/Shigella in bottle-fed lambs suggest that artificial feeding may increase the number of potential pathogens and delay the establishment of the anaerobic environment and anaerobic microbes. Feeding modes also affected the direct transmission of bacteria from the mother and the environment to newborns. The SourceTracker analysis estimated that the early gut microbes of suckled lambs were mainly derived from the mother's teats (43%) and ambient air (28%); whereas those of bottle-fed lambs were dominated by bacteria from the mother's vagina (46%), ambient air (31%), and the sheep pen floor (12%). These findings advance our understanding of gut microbiota in early life and may help design techniques to improve gut microbiota and health.

  • Kehoe SI, Dill-McFarland KA, Breaker JD, Suen G (2019) Effects of corn silage inclusion in preweaning calf diets. Journal of dairy science 102((5)):4131-4137 · Pubmed · DOI

    The objective of this research was to evaluate the effects of corn silage inclusion in starter feed provided to calves after birth through weaning at 7 wk of age. Thirty-six heifer calves and 9 bull calves were individually housed in hutches. Calves in treatment groups received pasteurized milk with all calf starter, 25% calf starter and 75% corn silage, or all corn silage. Values were recorded daily for feed intake and health, which included fecal, respiratory, and attitude scores; and at wk 2, 4, and 8 for concentrations of serum protein, hematocrit, and serum β-hydroxybutyrate. Body weight, withers height, and hip height were measured at wk 2, 4, 8, and 52. Nine bull calves (3/treatment) were killed at 8 wk of age for assessment of rumen and intestinal tissue morphology. Feed intake and average daily gain were not different among treatments. Least squares means of rumen papillae lengths were significantly different and decreased as corn silage inclusion increased. Crypt depths and total thickness of epithelium were reduced for the corn silage group. Least squares means of body weight, heart girth, hip height, withers height, serum protein, hematocrit, and β-hydroxybutyrate concentrations did not differ among treatments. These data indicated that the mixture of corn silage and starter did not affect growth, feed intake, or intestinal morphology but did affect rumen wall morphology. Feeding solely corn silage as starter feed stunted the growth of rumen papillae and tended to impair intestinal morphology, indicating that only calf starter or a mixture of calf starter and corn silage is more appropriate.

  • Carroll C, Olsen KD, Ricks NJ, Dill-McFarland KA, Suen G, Robinson TF, Chaston JM (2019) Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site. Frontiers in microbiology 9:3334 PMC6345687 · Pubmed · DOI

    Gut -associated microbes ('gut microbiota') impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant alpaca. To better understand how body site and diet influence the alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of alpacas with normal versus poor body condition. Samples from GH- and AH-fed alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in alpaca body condition with variation in microbiota relative abundance or identity.

  • Li W, Edwards A, Riehle C, Cox MS, Raabis S, Skarlupka JH, Steinberger AJ, Walling J, Bickhart D, Suen G (2019) Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow. Scientific reports 9((1)):790 PMC6349911 · Pubmed · DOI

    In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle. In this study, we dosed young calves with exogenous rumen fluid obtained from an adult donor cow, starting at birth, and repeated every other week until six weeks of age. Eight Holstein bull calves were included in this study and were separated into two groups of four: the first group was treated with rumen content freshly extracted from an adult cow, and the second group was treated with sterilized rumen content. Using whole-transcriptome RNA-sequencing, we investigated the transcriptional changes in the host liver, which is a major metabolic organ and vital to the calf's growth performance. Additionally, the comparison of rumen epimural microbial communities between the treatment groups was performed using the rRNA reads generated by sequencing. Liver transcriptome changes were enriched with genes involved in cell signaling and protein phosphorylation. Specifically, up-regulation of SGPL1 suggests a potential increase in the metabolism of sphingolipids, an essential molecular signal for bacterial survival in digestive tracts. Notably, eight genera, belonging to four phyla, had significant increases in abundance in treated calves. Our study provides insight into host liver transcriptome changes associated with early colonization of the microbial communities in neonatal calves. Such knowledge provides a foundation for future probiotics-based research in microbial organism mediated rumen development and nutrition in ruminants.

  • Neumann AP, Suen G (2018) The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential. mSphere 3((6)): PMC6291624 · Pubmed · DOI

    No abstract available.

  • Neumann AP, Weimer PJ, Suen G (2018) A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates. Biotechnology for biofuels 11:295 PMC6204037 · Pubmed · DOI

    No abstract available.

  • Dill-McFarland KA, Weimer PJ, Breaker JD, Suen G (2018) Diet Influences Early Microbiota Development in Dairy Calves without Long-Term Impacts on Milk Production. Applied and environmental microbiology 85((2)): PMC6328763 · Pubmed · DOI

    Gastrointestinal tract (GIT) microorganisms play important roles in the health of ruminant livestock and affect the production of agriculturally relevant products, including milk and meat. Despite this link, interventions to alter the adult microbiota to improve production have proven ineffective, as established microbial communities are resilient to change. In contrast, developing communities in young animals may be more easily altered but are less well studied. Here, we measured the GIT-associated microbiota of 45 Holstein dairy cows from 2 weeks to the first lactation cycle, using Illumina amplicon sequencing of bacterial (16S rRNA V4), archaeal (16S rRNA V6 to V8), and fungal (internal transcribed region 1 [ITS1]) communities. Fecal and ruminal microbiota of cows raised on calf starter grains and/or corn silage were correlated to lifetime growth as well as milk production during the first lactation cycle, in order to determine whether early-life diets have long-term impacts. Significant diet-associated differences in total microbial communities and specific taxa were observed by weaning (8 weeks), but all animals reached an adult-like composition between weaning and 1 year. While some calf-diet-driven differences were apparent in the microbiota of adult cows, these dissimilarities did not correlate with animal growth or milk production. This finding suggests that initial microbial community establishment is affected by early-life diet but postweaning factors have a greater influence on adult communities and production outcomes. IMPORTANCE The gut microbiota is essential for the survival of many organisms, including ruminants that rely on microorganisms for nutrient acquisition from dietary inputs for the production of products such as milk and meat. While alteration of the adult ruminant microbiota to improve production is possible, changes are often unstable and fail to persist. In contrast, the early-life microbiota may be more amenable to sustained modification. However, few studies have determined the impact of early-life interventions on downstream production. Here, we investigated the impact of agriculturally relevant calf diets, including calf starter and corn silage, on gut microbial communities, growth, and production through the first lactation cycle. Thus, this work serves to further our understanding of early-life microbiota acquisition, as well as informing future practices in livestock management.

  • Metzger SA, Hernandez LL, Skarlupka JH, Walker TM, Suen G, Ruegg PL (2018) A Cohort Study of the Milk Microbiota of Healthy and Inflamed Bovine Mammary Glands From Dryoff Through 150 Days in Milk. Frontiers in veterinary science 5:247 PMC6189514 · Pubmed · DOI

    No abstract available.

  • Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, Muñoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan SJ, Yáñez-Ruiz DR, Belanche A, Guan L, Gruninger RJ, McAllister TA, Newbold CJ, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart EH, Kingston-Smith AH, Scollan ND, do Prado RM, Pilau EJ, Mantovani HC, Attwood GT, Edwards JE, McEwan NR, Morrisson S, Mayorga OL, Elliott C, Morgavi DP (2018) Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. Frontiers in microbiology 9:2161 PMC6167468 · Pubmed · DOI

    No abstract available.

  • Metzger SA, Hernandez LL, Suen G, Ruegg PL (2018) Understanding the Milk Microbiota. The Veterinary clinics of North America. Food animal practice 34((3)):427-438 · Pubmed · DOI

    No abstract available.

  • De Wolfe TJ, Eggers S, Barker AK, Kates AE, Dill-McFarland KA, Suen G, Safdar N (2018) Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection. PloS one 13((9)):e0204253 PMC6161886 · Pubmed · DOI

    No abstract available.

  • Cunha CS, Marcondes MI, Veloso CM, Mantovani HC, Pereira LGR, Tomich TR, Dill-McFarland KA, Suen G (2018) Compositional and structural dynamics of the ruminal microbiota in dairy heifers and its relationship to methane production. Journal of the science of food and agriculture 99((1)):210-218 · Pubmed · DOI

    Heifers emit more enteric methane (CH ) than adult cows and these emissions tend to decrease per unit feed intake as they age. However, common mitigation strategies like expensive high-quality feeds are not economically feasible for these pre-production animals. Given its direct role in CH production, altering the rumen microbiota is another potential avenue for reducing CH production by ruminants. However, to identify effective microbial targets, a better understanding of the rumen microbiota and its relationship to CH production across heifer development is needed.

  • Metzger SA, Hernandez LL, Skarlupka JH, Suen G, Walker TM, Ruegg PL (2018) Influence of sampling technique and bedding type on the milk microbiota: Results of a pilot study. Journal of dairy science 101((7)):6346-6356 · Pubmed · DOI

    No abstract available.

  • Eggers S, Malecki KM, Peppard P, Mares J, Shirley D, Shukla SK, Poulsen K, Gangnon R, Duster M, Kates A, Suen G, Sethi AK, Safdar N (2018) Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods. BMJ open 8((3)):e019450 PMC5875638 · Pubmed · DOI

    No abstract available.

  • La Reau AJ, Suen G (2018) The Ruminococci: key symbionts of the gut ecosystem. Journal of microbiology (Seoul, Korea) 56((3)):199-208 · Pubmed · DOI

    No abstract available.

  • Dias J, Marcondes MI, Motta de Souza S, Cardoso da Mata E Silva B, Fontes Noronha M, Tassinari Resende R, Machado FS, Cuquetto Mantovani H, Dill-McFarland KA, Suen G (2018) Bacterial Community Dynamics across the Gastrointestinal Tracts of Dairy Calves during Preweaning Development. Applied and environmental microbiology 84((9)): PMC5930334 · Pubmed · DOI

    No abstract available.

  • Williams CL, Dill-McFarland KA, Sparks DL, Kouba AJ, Willard ST, Suen G, Brown AE (2018) Dietary changes during weaning shape the gut microbiota of red pandas ( Ailurus fulgens ). Conservation physiology 6((1)):cox075 PMC5772406 · Pubmed · DOI

    No abstract available.

  • Dai X, Weimer PJ, Dill-McFarland KA, Brandao VLN, Suen G, Faciola AP (2017) Camelina Seed Supplementation at Two Dietary Fat Levels Change Ruminal Bacterial Community Composition in a Dual-Flow Continuous Culture System. Frontiers in microbiology 8:2147 PMC5675879 · Pubmed · DOI

    No abstract available.

  • Cunha CS, Veloso CM, Marcondes MI, Mantovani HC, Tomich TR, Pereira LGR, Ferreira MFL, Dill-McFarland KA, Suen G (2017) Assessing the impact of rumen microbial communities on methane emissions and production traits in Holstein cows in a tropical climate. Systematic and applied microbiology 40((8)):492-499 · Pubmed · DOI

    No abstract available.

  • Dias J, Marcondes MI, Noronha MF, Resende RT, Machado FS, Mantovani HC, Dill-McFarland KA, Suen G (2017) Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves. Frontiers in microbiology 8:1553 PMC5559706 · Pubmed · DOI

    No abstract available.

  • Neumann AP, McCormick CA, Suen G (2017) Fibrobacter communities in the gastrointestinal tracts of diverse hindgut-fermenting herbivores are distinct from those of the rumen. Environmental microbiology 19((9)):3768-3783 PMC5599356 · Pubmed · DOI

    No abstract available.

  • Weimer PJ, Cox MS, Vieira de Paula T, Lin M, Hall MB, Suen G (2017) Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows. Journal of dairy science 100((9)):7165-7182 · Pubmed · DOI

    No abstract available.

  • La Reau AJ, Meier-Kolthoff JP, Suen G (2017) Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association. Microb Genom 2(12):e000099 (PMC5359413) · Pubmed

    It has become increasingly clear that the composition of mammalian gut microbial communities is substantially diet driven. These microbiota form intricate mutualisms with their hosts, which have profound implications on overall health. For example, many gut microbes are involved in the conversion of host-ingested dietary polysaccharides into host-usable nutrients. One group of important gut microbial symbionts are bacteria in the genus Ruminococcus. Originally isolated from the bovine rumen, ruminococci have been found in numerous mammalian hosts, including other ruminants, and non-ruminants such as horses, pigs and humans. All ruminococci require fermentable carbohydrates for growth, and their substrate preferences appear to be based on the diet of their particular host. Most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic non-ruminant-associated species, and even less is known about the environmental distribution of ruminococci as a whole. Here, we capitalized on the wealth of publicly available 16S rRNA gene sequences, genomes and large-scale microbiota studies to both resolve the phylogenetic placement of described species in the genus Ruminococcus, and further demonstrate that this genus has largely unexplored diversity and a staggering host distribution. We present evidence that ruminococci are predominantly associated with herbivores and omnivores, and our data supports the hypothesis that very few ruminococci are found consistently in non-host-associated environments. This study not only helps to resolve the phylogeny of this important genus, but also provides a framework for understanding its distribution in natural systems.

  • Dill-McFarland KA, Breaker JD, Suen G (2017) Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Scientific reports 7:40864 PMC5241668 · Pubmed · DOI

    No abstract available.

  • Jetté ME, Dill-McFarland KA, Hanshew AS, Suen G, Thibeault SL (2016) The human laryngeal microbiome: effects of cigarette smoke and reflux. Sci Rep 6:35882 (PMC5075886) · Pubmed

    Prolonged diffuse laryngeal inflammation from smoking and/or reflux is commonly diagnosed as chronic laryngitis and treated empirically with expensive drugs that have not proven effective. Shifts in microbiota have been associated with many inflammatory diseases, though little is known about how resident microbes may contribute to chronic laryngitis. We sought to characterize the core microbiota of disease-free human laryngeal tissue and to investigate shifts in microbial community membership associated with exposure to cigarette smoke and reflux. Using 454 pyrosequencing of the 16S rRNA gene, we compared bacterial communities of laryngeal tissue biopsies collected from 97 non-treatment-seeking volunteers based on reflux and smoking status. The core community was characterized by a highly abundant OTU within the family Comamonadaceae found in all laryngeal tissues. Smokers demonstrated less microbial diversity than nonsmokers, with differences in relative abundances of OTUs classified as Streptococcus, unclassified Comamonadaceae, Cloacibacterium, and Helicobacter. Reflux status did not affect microbial diversity nor community structure nor composition. Comparison of healthy laryngeal microbial communities to benign vocal fold disease samples revealed greater abundance of Streptococcus in benign vocal fold disease suggesting that mucosal dominance by Streptococcus may be a factor in disease etiology.

  • Williams CL, Dill-McFarland KA, Vandewege MW, Sparks DL, Willard ST, Kouba AJ, Suen G, Brown AE (2016) Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca). Front Microbiol 7:661 (PMC4858621) · Pubmed

    Dietary shifts can result in changes to the gastrointestinal tract (GIT) microbiota, leading to negative outcomes for the host, including inflammation. Giant pandas (Ailuropoda melanoleuca) are physiologically classified as carnivores; however, they consume an herbivorous diet with dramatic seasonal dietary shifts and episodes of chronic GIT distress with symptoms including abdominal pain, loss of appetite and the excretion of mucous stools (mucoids). These episodes adversely affect the overall nutritional and health status of giant pandas. Here, we examined the fecal microbiota of two giant pandas' non-mucoid and mucoid stools and compared these to samples from a previous winter season that had historically few mucoid episodes. To identify the microbiota present, we isolated and sequenced the 16S rRNA using next-generation sequencing. Mucoids occurred following a seasonal feeding switch from predominately bamboo culm (stalk) to leaves. All fecal samples displayed low diversity and were dominated by bacteria in the phyla Firmicutes and to a lesser extent, Proteobacteria. Fecal samples immediately prior to mucoid episodes had lower microbial diversity as compared to mucoids. Mucoids were mostly comprised of common mucosal-associated taxa including Streptococcus and Leuconostoc species, and exhibited increased abundance for bacteria in the family Pasteurellaceae. Taken together, these findings indicate that mucoids may represent an expulsion of the mucosal lining that is driven by changes in diet. We suggest that these occurrences serve to reset their GIT microbiota following changes in bamboo part preference, as giant pandas have retained a carnivorous GIT anatomy while shifting to an herbivorous diet.

  • de Man TJ, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SS, Barribeau SM, Bozick BA, Suen G, Currie CR, Gerardo NM (2016) Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proc. Natl. Acad. Sci. U.S.A. 113(13):3567-72 (PMC4822581) · Pubmed

    Many microorganisms with specialized lifestyles have reduced genomes. This is best understood in beneficial bacterial symbioses, where partner fidelity facilitates loss of genes necessary for living independently. Specialized microbial pathogens may also exhibit gene loss relative to generalists. Here, we demonstrate that Escovopsis weberi, a fungal parasite of the crops of fungus-growing ants, has a reduced genome in terms of both size and gene content relative to closely related but less specialized fungi. Although primary metabolism genes have been retained, the E. weberi genome is depleted in carbohydrate active enzymes, which is consistent with reliance on a host with these functions. E. weberi has also lost genes considered necessary for sexual reproduction. Contrasting these losses, the genome encodes unique secondary metabolite biosynthesis clusters, some of which include genes that exhibit up-regulated expression during host attack. Thus, the specialized nature of the interaction between Escovopsis and ant agriculture is reflected in the parasite's genome.

  • Dill-McFarland KA, Suen G, Carey HV (2016) Bears Arouse Interest in Microbiota's Role in Health. Trends Microbiol. 24(4):245-6 · Pubmed

    The first report of the effect of hibernation on the gut microbiota of bears reveals trends both similar and distinct from those found in small hibernators. A model mouse system also suggested possible roles of the microbiota for healthy weight gain and insulin tolerance in bears during their active season.

  • Neumann AP, Suen G (2015) Differences in major bacterial populations in the intestines of mature broilers after feeding virginiamycin or bacitracin methylene disalicylate. J. Appl. Microbiol. 119(6):1515-26 · Pubmed

    The purpose of this study was to compare the effects of feeding virginiamycin or bacitracin methylene disalicylate (BMD), two in-feed antibiotics typically used by commercial poultry producers in the United States, on the chicken gastrointestinal microbiota. 454 pyrosequencing of the V6-V8 region of the 16S rRNA gene and quantitative PCR were employed to examine the bacterial microbiota and Clostridium perfringens, respectively, in the jejunum and caecum of market-age broiler chickens over four replicate grow-outs. Our results suggest that virginiamycin has a more pronounced impact on broiler gastrointestinal tract bacterial communities, relative to BMD, manifested primarily through significant enrichments in the genus Faecalibacterium in the caecum and a distinct population of Lactobacillus, OTU_02, in both the jejunum and caecum. No evidence for a difference among the diets in Cl. perfringens levels in the jejunum or caecum was observed. This work represents the highest resolution comparison to date of the jejunum and caecum microbiota in broilers fed either virginiamycin or BMD, and provides evidence for specific bacterial OTUs potentially involved in the health and performance benefits typically attributed to these in-feed antibiotics.

  • Burnet MC, Dohnalkova AC, Neumann AP, Lipton MS, Smith RD, Suen G, Callister SJ (2015) Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85. PLoS ONE 10(12):e0143809 (PMC4668043) · Pubmed

    Fibrobacter succinogenes S85 is an anaerobic non-cellulosome utilizing cellulolytic bacterium originally isolated from the cow rumen microbial community. Efforts to elucidate its cellulolytic machinery have resulted in the proposal of numerous models which involve cell-surface attachment via a combination of cellulose-binding fibro-slime proteins and pili, the production of cellulolytic vesicles, and the entry of cellulose fibers into the periplasmic space. Here, we used a combination of RNA-sequencing, proteomics, and transmission electron microscopy (TEM) to further clarify the cellulolytic mechanism of F. succinogenes. Our RNA-sequence analysis shows that genes encoding type II and III secretion systems, fibro-slime proteins, and pili are differentially expressed on cellulose, relative to glucose. A subcellular fractionation of cells grown on cellulose revealed that carbohydrate active enzymes associated with cellulose deconstruction and fibro-slime proteins were greater in the extracellular medium, as compared to the periplasm and outer membrane fractions. TEMs of samples harvested at mid-exponential and stationary phases of growth on cellulose and glucose showed the presence of grooves in the cellulose between the bacterial cells and substrate, suggesting enzymes work extracellularly for cellulose degradation. Membrane vesicles were only observed in stationary phase cultures grown on cellulose. These results provide evidence that F. succinogenes attaches to cellulose fibers using fibro-slime and pili, produces cellulases, such as endoglucanases, that are secreted extracellularly using type II and III secretion systems, and degrades the cellulose into cellodextrins that are then imported back into the periplasm for further digestion by β-glucanases and other cellulases.

  • Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, Suen G (2015) Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environ. Microbiol. 18(5):1391-402 · Pubmed

    Symbiotic microbial communities are critical to the function and survival of animals. This relationship is obligatory for herbivores that engage gut microorganisms for the conversion of dietary plant materials into nutrients such as short-chain organic acids (SCOAs). The constraint on body size imposed by their arboreal lifestyle is thought to make this symbiosis especially important for sloths. Here, we use next-generation sequencing to identify the bacteria present in the fore and distal guts of wild two- and three-toed sloths, and correlate these communities with both diet and SCOAs. We show that, unlike other mammalian herbivores, sloth gut communities are dominated by the bacterial phyla Proteobacteria and Firmicutes. Specifically, three-toed sloths possess a highly conserved, low-diversity foregut community with a highly abundant Neisseria species associated with foregut lactate. In contrast, two-toed sloths have a more variable and diverse foregut microbiota correlated with a variety of SCOAs. These differences support the hypothesis that feeding behaviour selects for specific gut bacterial communities, as three-toed sloths subsist primarily on Cecropia tree leaves while two-toed sloths have a more generalist diet. The less diverse diet and gut microbiota of three-toed sloths may render them more susceptible to habitat loss and other diet-altering conditions.

  • Stuecker TN, Bramhacharya S, Hodge-Hanson KM, Suen G, Escalante-Semerena JC (2015) Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain. BMC Res Notes 8:354 (PMC4537548) · Pubmed

    All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by L-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the active-site pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo. Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial L-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I L-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II L-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II L-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with L-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions. Experimental results indicate that S. enterica and C. glutamicum L-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and L-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of L-aspartate-α-decarboxylases.

  • Jewell KA, McCormick CA, Odt CL, Weimer PJ, Suen G (2015) Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency. Appl. Environ. Microbiol. 81(14):4697-710 (PMC4551193) · Pubmed

    Fourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows were Bacteroidetes (49.42%), Firmicutes (39.32%), Proteobacteria (5.67%), and Tenericutes (2.17%), and the most abundant genera included Prevotella (40.15%), Butyrivibrio (2.38%), Ruminococcus (2.35%), Coprococcus (2.29%), and Succiniclasticum (2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.

  • Christopherson MR, Dawson JA, Stevenson DM, Cunningham AC, Bramhacharya S, Weimer PJ, Kendziorski C, Suen G (2014) Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis. BMC Genomics 15:1066 (PMC4300822) · Pubmed

    Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. Moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a glycocalyx, and cellulosomes. Here, we used a combination of comparative genomics, fermentation analyses, and transcriptomics to further clarify the cellulolytic and fermentative potential of R. albus 7. A comparison of the R. albus 7 genome sequence against the genome sequences of related bacteria that either encode or do not encode cellulosomes revealed that R. albus 7 does not encode for most canonical cellulosomal components. Fermentation analysis of R. albus 7 revealed the ability to produce ethanol and acetate on a wide range of fibrous substrates in vitro. Global transcriptomic analysis of R. albus 7 grown at identical dilution rates on cellulose and cellobiose in a chemostat showed that this bacterium, when growing on cellulose, utilizes a carbohydrate-degrading strategy that involves increased transcription of the rare carbohydrate-binding module (CBM) family 37 domain and the tryptophan biosynthetic operon. Our data suggest that R. albus 7 does not use canonical cellulosomal components to degrade cellulose, but rather up-regulates the expression of CBM37-containing enzymes and tryptophan biosynthesis. This study contributes to a revised model of carbohydrate degradation by this key member of the rumen ecosystem.

  • Mohammed R, Brink GE, Stevenson DM, Neumann AP, Beauchemin KA, Suen G, Weimer PJ (2014) Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay. Front Microbiol 5:689 (PMC4260508) · Pubmed

    The rich and diverse microbiota of the rumen provides ruminant animals the capacity to utilize highly fibrous feedstuffs as their energy source, but there is surprisingly little information on the composition of the microbiome of ruminants fed all-forage diets, despite the importance of such agricultural production systems worldwide. In three 28-day periods, three ruminally-cannulated Holstein heifers sequentially grazed orchardgrass pasture (OP), then were fed orchardgrass hay (OH), then returned to OP. These heifers displayed greater shifts in ruminal bacterial community composition (determined by automated ribosomal intergenic spacer analysis and by pyrotag sequencing of 16S rRNA genes) than did two other heifers maintained 84 d on the same OP. Phyla Firmicutes and Bacteroidetes dominated all ruminal samples, and quantitative PCR indicated that members of the genus Prevotella averaged 23% of the 16S rRNA gene copies, well below levels previously reported with cows fed total mixed rations. Differences in bacterial community composition and ruminal volatile fatty acid (VFA) profiles were observed between the OP and OH despite similarities in gross chemical composition. Compared to OP, feeding OH increased the molar proportion of ruminal acetate (P = 0.02) and decreased the proportion of ruminal butyrate (P < 0.01), branched-chain VFA (P < 0.01) and the relative population size of the abundant genus Butyrivibrio (P < 0.001), as determined by pyrotag sequencing. Despite the low numbers of animals examined, the observed changes in VFA profile in the rumens of heifers on OP vs. OH are consistent with the shifts in Butyrivibrio abundance and its known physiology as a butyrate producer that ferments both carbohydrates and proteins.

  • Aylward FO, Suen G, Biedermann PH, Adams AS, Scott JJ, Malfatti SA, Glavina del Rio T, Tringe SG, Poulsen M, Raffa KF, Klepzig KD, Currie CR (2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio 5(6):e02077 (PMC4251994) · Pubmed

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes. The cultivation of fungi for food is a behavior that has evolved independently in ants, beetles, and termites and has enabled many species of these insects to become ecologically important and widely distributed herbivores and forest pests. Although the primary fungal cultivars of these insects have been studied for decades, comparatively little is known of their bacterial microbiota. In this study, we show that diverse fungus-growing insects are associated with a common bacterial community composed of the same dominant members. Furthermore, by demonstrating that many of these bacteria have high whole-genome similarity across distantly related insect hosts that reside thousands of miles apart, we show that these bacteria are an important and underappreciated feature of diverse fungus-growing insects. Because of the similarities in the agricultural lifestyles of these insects, this is an example of convergence between both the life histories of the host insects and their symbiotic microbiota.

  • Dill-McFarland KA, Neil KL, Zeng A, Sprenger RJ, Kurtz CC, Suen G, Carey HV (2014) Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels. Mol. Ecol. 23(18):4658-69 · Pubmed

    The gut microbiota plays important roles in animal nutrition and health. This relationship is particularly dynamic in hibernating mammals where fasting drives the gut community to rely on host-derived nutrients instead of exogenous substrates. We used 16S rRNA pyrosequencing and caecal tissue protein analysis to investigate the effects of hibernation on the mucosa-associated bacterial microbiota and host responses in 13-lined ground squirrels. The mucosal microbiota was less diverse in winter hibernators than in actively feeding spring and summer squirrels. UniFrac analysis revealed distinct summer and late winter microbiota clusters, while spring and early winter clusters overlapped slightly, consistent with their transitional structures. Communities in all seasons were dominated by Firmicutes and Bacteroidetes, with lesser contributions from Proteobacteria, Verrucomicrobia, Tenericutes and Actinobacteria. Hibernators had lower relative abundances of Firmicutes, which include genera that prefer plant polysaccharides, and higher abundances of Bacteroidetes and Verrucomicrobia, some of which can survive solely on host-derived mucins. A core mucosal assemblage of nine operational taxonomic units shared among all individuals was identified with an average total sequence abundance of 60.2%. This core community, together with moderate shifts in specific taxa, indicates that the mucosal microbiota remains relatively stable over the annual cycle yet responds to substrate changes while potentially serving as a pool for 'seeding' the microbiota once exogenous substrates return in spring. Relative to summer, hibernation reduced caecal crypt length and increased MUC2 expression in early winter and spring. Hibernation also decreased caecal TLR4 and increased TLR5 expression, suggesting a protective response that minimizes inflammation.

  • Omoniyi LA, Jewell KA, Isah OA, Neumann AP, Onwuka CF, Onagbesan OM, Suen G (2014) An analysis of the ruminal bacterial microbiota in West African Dwarf sheep fed grass- and tree-based diets. J. Appl. Microbiol. 116(5):1094-105 · Pubmed

    To measure the impact of supplementing a forage diet with tree-based browse on the ruminal bacterial communities of Nigerian West African Dwarf (WAD) sheep. Fifteen WAD sheep were fed a control diet of forage (Panicum maximum), with 12 animals shifted in groups of three to one of four browse-supplemented diets (Albizia saman, Bridelia micrantha, Ficus sur, or Gmelina arborea). These browse plants were shown in a concurrent but separate study to be reasonably nutritious (based on chemical composition and fibre constituents) and nontoxic (based on tannin, phytate, saponin, alkaloid and oxalate levels). Rumen liquids and solids for DNA extraction were collected via intubation from two animals in each group before and after dietary shift. Bacterial 16S rRNA gene regions V6-V8 were sequenced by 454 pyrosequencing. All communities were highly diverse and dominated by the phyla Firmicutes, Bacteroidetes, Tenericutes, Actinobacteria and Proteobacteria. All communities shared members of the genera Butryivibrio, Prevotella and Ruminococcus. Our analysis defined a core sets of bacteria shared by all animals, forage-fed animals and browse-fed animals. Community structure shifted dramatically in animals fed A. saman or G. arborea. The impact of tree-based browse on the ruminal bacterial community of Nigerian WAD sheep varies by browse species, likely due to differences in browse composition. Our study describes the first neotropical small ruminant bacterial microbiome and supports diet supplementation with specific tree-based browse for WAD sheep.

  • Jewell KA, Scott JJ, Adams SM, Suen G (2013) A phylogenetic analysis of the phylum Fibrobacteres. Syst. Appl. Microbiol. 36(6):376-82 · Pubmed

    Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.

  • Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, Wen J, Parker BJ, Cash E, Privman E, Childers CP, Muñoz-Torres MC, Boomsma JJ, Bornberg-Bauer E, Currie CR, Elsik CG, Suen G, Goodisman MA, Keller L, Liebig J, Rawls A, Reinberg D, Smith CD, Smith CR, Tsutsui N, Wurm Y, Zdobnov EM, Berger SL, Gadau J (2013) Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res. 23(8):1235-47 (PMC3730098) · Pubmed

    Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor-binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the "socio-genomes" of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.

  • de Oliveira MN, Jewell KA, Freitas FS, Benjamin LA, Tótola MR, Borges AC, Moraes CA, Suen G (2013) Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer. Vet. Microbiol. 164(3-4):307-14 · Pubmed

    The gastrointestinal tracts (GIT) of herbivores harbor dense and diverse microbiota that has beneficial interactions with the host, particularly for agriculturally relevant animals like ruminants such as cattle. When assessing ruminant health, microbiological indicators are often derived from the rumen or feces. However, it is probable that ruminal and fecal microbiota do not reflect the microbial communities within the GIT of ruminants. To test this, we investigated the compartments of the GIT from a Brazilian Nelore steer and performed a 16S rRNA pyrosequencing analysis on the collected samples. Our results showed high intra-individual variation, with samples clustering according to their location in the GIT including the forestomach, small intestine, and large intestine. Although sequences related to the phyla Firmicutes and Bacteroidetes predominated all samples, there was a remarkable variation at the family level. Comparisons between the microbiota in the rumen, feces, and other GIT components showed distinct differences in microbial community. This work is the first intensive non-culture based GIT microbiota analysis for any ruminant and provides a framework for understanding how host microbiota impact the health of bovines.

  • Adams AS, Aylward FO, Adams SM, Erbilgin N, Aukema BH, Currie CR, Suen G, Raffa KF (2013) Mountain pine beetles colonizing historical and naive host trees are associated with a bacterial community highly enriched in genes contributing to terpene metabolism. Appl. Environ. Microbiol. 79(11):3468-75 (PMC3648045) · Pubmed

    The mountain pine beetle, Dendroctonus ponderosae, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of D. ponderosae to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with D. ponderosae beetles and their galleries from their historical host, Pinus contorta, and their more recent host, hybrid P. contorta-Pinus banksiana. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera Pseudomonas, Rahnella, Serratia, and Burkholderia, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.

  • Aylward FO, McDonald BR, Adams SM, Valenzuela A, Schmidt RA, Goodwin LA, Woyke T, Currie CR, Suen G, Poulsen M (2013) Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl. Environ. Microbiol. 79(12):3724-33 (PMC3675938) · Pubmed

    Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.

  • Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD, Malfatti SA, Monroe ME, Purvine SO, Goodwin LA, Smith RD, Weinstock GM, Gerardo NM, Suen G, Lipton MS, Currie CR (2013) Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl. Environ. Microbiol. 79(12):3770-8 (PMC3675943) · Pubmed

    Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate gardens composed primarily of Leucoagaricus gongylophorus, a basidiomycetous fungus that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of L. gongylophorus, and, using genomic and metaproteomic tools, we investigate its role in lignocellulose degradation in the gardens of both Atta cephalotes and Acromyrmex echinatior leaf-cutter ants. We show that L. gongylophorus produces a diversity of lignocellulases in ant gardens and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that likely play an important role in lignocellulose degradation. Our study provides a detailed analysis of plant biomass degradation in leaf-cutter ant fungus gardens and insight into the enzymes underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.

  • Christopherson MR, Suen G, Bramhacharya S, Jewell KA, Aylward FO, Mead D, Brumm PJ (2013) The genome sequences of Cellulomonas fimi and "Cellvibrio gilvus" reveal the cellulolytic strategies of two facultative anaerobes, transfer of "Cellvibrio gilvus" to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov. PLoS ONE 8(1):e53954 (PMC3544764) · Pubmed

    Actinobacteria in the genus Cellulomonas are the only known and reported cellulolytic facultative anaerobes. To better understand the cellulolytic strategy employed by these bacteria, we sequenced the genome of the Cellulomonas fimi ATCC 484(T). For comparative purposes, we also sequenced the genome of the aerobic cellulolytic "Cellvibrio gilvus" ATCC 13127(T). An initial analysis of these genomes using phylogenetic and whole-genome comparison revealed that "Cellvibrio gilvus" belongs to the genus Cellulomonas. We thus propose to assign "Cellvibrio gilvus" to the genus Cellulomonas. A comparative genomics analysis between these two Cellulomonas genome sequences and the recently completed genome for Cellulomonas flavigena ATCC 482(T) showed that these cellulomonads do not encode cellulosomes but appear to degrade cellulose by secreting multi-domain glycoside hydrolases. Despite the minimal number of carbohydrate-active enzymes encoded by these genomes, as compared to other known cellulolytic organisms, these bacteria were found to be proficient at degrading and utilizing a diverse set of carbohydrates, including crystalline cellulose. Moreover, they also encode for proteins required for the fermentation of hexose and xylose sugars into products such as ethanol. Finally, we found relatively few significant differences between the predicted carbohydrate-active enzymes encoded by these Cellulomonas genomes, in contrast to previous studies reporting differences in physiological approaches for carbohydrate degradation. Our sequencing and analysis of these genomes sheds light onto the mechanism through which these facultative anaerobes degrade cellulose, suggesting that the sequenced cellulomonads use secreted, multidomain enzymes to degrade cellulose in a way that is distinct from known anaerobic cellulolytic strategies.

  • Aylward FO, Burnum KE, Scott JJ, Suen G, Tringe SG, Adams SM, Barry KW, Nicora CD, Piehowski PD, Purvine SO, Starrett GJ, Goodwin LA, Smith RD, Lipton MS, Currie CR (2012) Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J 6(9):1688-701 (PMC3498920) · Pubmed

    Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus-bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans.

  • Miller DA, Suen G, Clements KD, Angert ER (2012) The genomic basis for the evolution of a novel form of cellular reproduction in the bacterium Epulopiscium. BMC Genomics 13:265 (PMC3416734) · Pubmed

    Epulopiscium sp. type B, a large intestinal bacterial symbiont of the surgeonfish Naso tonganus, does not reproduce by binary fission. Instead, it forms multiple intracellular offspring using a process with morphological features similar to the survival strategy of endospore formation in other Firmicutes. We hypothesize that intracellular offspring formation in Epulopiscium evolved from endospore formation and these two developmental programs share molecular mechanisms that are responsible for the observed morphological similarities. To test this, we sequenced the genome of Epulopiscium sp. type B to draft quality. Comparative analysis with the complete genome of its close, endospore-forming relative, Cellulosilyticum lentocellum, identified homologs of well-known sporulation genes characterized in Bacillus subtilis. Of the 147 highly conserved B. subtilis sporulation genes used in this analysis, we found 57 homologs in the Epulopiscium genome and 87 homologs in the C. lentocellum genome. Genes coding for components of the central regulatory network which govern the expression of forespore and mother-cell-specific sporulation genes and the machinery used for engulfment appear best conserved. Low conservation of genes expressed late in endospore formation, particularly those that confer resistance properties and encode germinant receptors, suggest that Epulopiscium has lost the ability to form a mature spore. Our findings provide a framework for understanding the evolution of a novel form of cellular reproduction.

  • Gadau J, Helmkampf M, Nygaard S, Roux J, Simola DF, Smith CR, Suen G, Wurm Y, Smith CD (2012) The genomic impact of 100 million years of social evolution in seven ant species. Trends Genet. 28(1):14-21 (PMC3314025) · Pubmed

    Ants (Hymenoptera, Formicidae) represent one of the most successful eusocial taxa in terms of both their geographic distribution and species number. The publication of seven ant genomes within the past year was a quantum leap for socio- and ant genomics. The diversity of social organization in ants makes them excellent model organisms to study the evolution of social systems. Comparing the ant genomes with those of the honeybee, a lineage that evolved eusociality independently from ants, and solitary insects suggests that there are significant differences in key aspects of genome organization between social and solitary insects, as well as among ant species. Altogether, these seven ant genomes open exciting new research avenues and opportunities for understanding the genetic basis and regulation of social species, and adaptive complex systems in general.

  • Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Léon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Médigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H (2011) The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PLoS ONE 6(11):e27909 (PMC3220699) · Pubmed

    Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.

  • Suen G, Stevenson DM, Bruce DC, Chertkov O, Copeland A, Cheng JF, Detter C, Detter JC, Goodwin LA, Han CS, Hauser LJ, Ivanova NN, Kyrpides NC, Land ML, Lapidus A, Lucas S, Ovchinnikova G, Pitluck S, Tapia R, Woyke T, Boyum J, Mead D, Weimer PJ (2011) Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7. J. Bacteriol. 193(19):5574-5 (PMC3187470) · Pubmed

    Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.

  • Adams AS, Jordan MS, Adams SM, Suen G, Goodwin LA, Davenport KW, Currie CR, Raffa KF (2011) Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio. ISME J 5(8):1323-31 (PMC3146269) · Pubmed

    Sirex noctilio is an invasive wood-feeding wasp that threatens the world's commercial and natural pine forests. Successful tree colonization by this insect is contingent on the decline of host defenses and the ability to utilize the woody substrate as a source of energy. We explored its potential association with bacterial symbionts that may assist in nutrient acquisition via plant biomass deconstruction using growth assays, culture-dependent and -independent analysis of bacterial frequency of association and whole-genome analysis. We identified Streptomyces and γ-Proteobacteria that were each associated with 94% and 88% of wasps, respectively. Streptomyces isolates grew on all three cellulose substrates tested and across a range of pH 5.6 to 9. On the basis of whole-genome sequencing, three Streptomyces isolates have some of the highest proportions of genes predicted to encode for carbohydrate-active enzymes (CAZyme) of sequenced Actinobacteria. γ-Proteobacteria isolates grew on a cellulose derivative and a structurally diverse substrate, ammonia fiber explosion-treated corn stover, but not on microcrystalline cellulose. Analysis of the genome of a Pantoea isolate detected genes putatively encoding for CAZymes, the majority predicted to be active on hemicellulose and more simple sugars. We propose that a consortium of microorganisms, including the described bacteria and the fungal symbiont Amylostereum areolatum, has complementary functions for degrading woody substrates and that such degradation may assist in nutrient acquisition by S. noctilio, thus contributing to its ability to be established in forested habitats worldwide.

  • Giglio KM, Caberoy N, Suen G, Kaiser D, Garza AG (2011) A cascade of coregulating enhancer binding proteins initiates and propagates a multicellular developmental program. Proc. Natl. Acad. Sci. U.S.A. 108(32):E431-9 (PMC3156219) · Pubmed

    The signal transduction networks that initiate multicellular development in bacteria remain largely undefined. Here, we report that Myxococcus xanthus regulates entry into its multicellular developmental program using a novel strategy: a cascade of transcriptional activators known as enhancer binding proteins (EBPs). The EBPs in the cascade function in sequential stages of early development, and several lines of evidence indicate that the cascade is propagated when EBPs that function at one stage of development directly regulate transcription of an EBP gene important for the next developmental stage. We also show that the regulatory cascade is designed in a novel way that extensively expands on the typical use of EBPs: Instead of using only one EBP to regulate a particular gene or group of genes, which is the norm in other bacterial systems, the cascade uses multiple EBPs to regulate EBP genes that are positioned at key transition points in early development. Based on the locations of the putative EBP promoter binding sites, several different mechanisms of EBP coregulation are possible, including the formation of coregulating EBP transcriptional complexes. We propose that M. xanthus uses an EBP coregulation strategy to make expression of EBP genes that modulate stage-stage transitions responsive to multiple signal transduction pathways, which provide information that is important for a coordinated decision to advance the developmental process.

  • Grubbs KJ, Biedermann PH, Suen G, Adams SM, Moeller JA, Klassen JL, Goodwin LA, Woyke T, Munk AC, Bruce D, Detter C, Tapia R, Han CS, Currie CR (2011) Genome sequence of Streptomyces griseus strain XylebKG-1, an ambrosia beetle-associated actinomycete. J. Bacteriol. 193(11):2890-1 (PMC3133108) · Pubmed

    Streptomyces griseus strain XylebKG-1 is an insect-associated strain of the well-studied actinobacterial species S. griseus. Here, we present the genome of XylebKG-1 and discuss its similarity to the genome of S. griseus subsp. griseus NBRC13350. XylebKG-1 was isolated from the fungus-cultivating Xyleborinus saxesenii system. Given its similarity to free-living S. griseus subsp. griseus NBRC13350, comparative genomics will elucidate critical components of bacterial interactions with insects.

  • Miller DA, Suen G, Bruce D, Copeland A, Cheng JF, Detter C, Goodwin LA, Han CS, Hauser LJ, Land ML, Lapidus A, Lucas S, Meincke L, Pitluck S, Tapia R, Teshima H, Woyke T, Fox BG, Angert ER, Currie CR (2011) Complete genome sequence of the cellulose-degrading bacterium Cellulosilyticum lentocellum. J. Bacteriol. 193(9):2357-8 (PMC3133088) · Pubmed

    Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium, which was originally isolated from estuarine sediment of a river that received both domestic and paper mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors that influence degradation rates.

  • Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Favé MJ, Fernandes V, Gibson JD, Graur D, Gronenberg W, Grubbs KJ, Hagen DE, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND, Viljakainen L, Wolschin F, Gadau J (2011) Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc. Natl. Acad. Sci. U.S.A. 108(14):5667-72 (PMC3078412) · Pubmed

    We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

  • Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley JA, Hu H, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA, Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van Wilgenburg E, Viljakainen L, Walden KK, Wild AL, Yandell M, Yorke JA, Tsutsui ND (2011) Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc. Natl. Acad. Sci. U.S.A. 108(14):5673-8 (PMC3078359) · Pubmed

    Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.

  • Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, Drinkwater C, Ivanova NN, Mikhailova N, Chertkov O, Goodwin LA, Currie CR, Mead D, Brumm PJ (2011) The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS ONE 6(4):e18814 (PMC3079729) · Pubmed

    Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.

  • Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Favé MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muñoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ, Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR (2011) The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet. 7(2):e1002007 (PMC3037820) · Pubmed

    Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.

  • Ogier JC, Calteau A, Forst S, Goodrich-Blair H, Roche D, Rouy Z, Suen G, Zumbihl R, Givaudan A, Tailliez P, Médigue C, Gaudriault S (2010) Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus. BMC Genomics 11:568 (PMC3091717) · Pubmed

    Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigated plasticity units in bacterial genomes, by exhaustive description of the RGPs in two Photorhabdus and two Xenorhabdus strains, belonging to the Enterobacteriaceae and interacting with invertebrates (insects and nematodes). RGPs account for about 60% of the genome in each of the four genomes studied. We classified RGPs into genomic islands (GIs), prophages and two new classes of RGP without the features of classical mobile genetic elements (MGEs) but harboring genes encoding enzymes catalyzing DNA recombination (RGPmob), or with no remarkable feature (RGPnone). These new classes accounted for most of the RGPs and are probably hypervariable regions, ancient MGEs with degraded mobilization machinery or non canonical MGEs for which the mobility mechanism has yet to be described. We provide evidence that not only the GIs and the prophages, but also RGPmob and RGPnone, have a mosaic structure consisting of modules. A module is a block of genes, 0.5 to 60 kb in length, displaying a conserved genomic organization among the different Enterobacteriaceae. Modules are functional units involved in host/environment interactions (22-31%), metabolism (22-27%), intracellular or intercellular DNA mobility (13-30%), drug resistance (4-5%) and antibiotic synthesis (3-6%). Finally, in silico comparisons and PCR multiplex analysis indicated that these modules served as plasticity units within the bacterial genome during genome speciation and as deletion units in clonal variants of Photorhabdus. This led us to consider the modules, rather than the entire RGP, as the true unit of plasticity in bacterial genomes, during both short-term and long-term genome evolution.

  • Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR (2010) An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet. 6(9):e1001129 (PMC2944797) · Pubmed

    Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiome's predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.

  • Gauthier GM, Sullivan TD, Gallardo SS, Brandhorst TT, Vanden Wymelenberg AJ, Cuomo CA, Suen G, Currie CR, Klein BS (2010) SREB, a GATA transcription factor that directs disparate fates in Blastomyces dermatitidis including morphogenesis and siderophore biosynthesis. PLoS Pathog. 6(4):e1000846 (PMC2848559) · Pubmed

    Blastomyces dermatitidis belongs to a group of human pathogenic fungi that exhibit thermal dimorphism. At 22 degrees C, these fungi grow as mold that produce conidia or infectious particles, whereas at 37 degrees C they convert to budding yeast. The ability to switch between these forms is essential for virulence in mammals and may enable these organisms to survive in the soil. To identify genes that regulate this phase transition, we used Agrobacterium tumefaciens to mutagenize B. dermatitidis conidia and screened transformants for defects in morphogenesis. We found that the GATA transcription factor SREB governs multiple fates in B. dermatitidis: phase transition from yeast to mold, cell growth at 22 degrees C, and biosynthesis of siderophores under iron-replete conditions. Insertional and null mutants fail to convert to mold, do not accumulate significant biomass at 22 degrees C, and are unable to suppress siderophore biosynthesis under iron-replete conditions. The defect in morphogenesis in the SREB mutant was independent of exogenous iron concentration, suggesting that SREB promotes the phase transition by altering the expression of genes that are unrelated to siderophore biosynthesis. Using bioinformatic and gene expression analyses, we identified candidate genes with upstream GATA sites whose expression is altered in the null mutant that may be direct or indirect targets of SREB and promote the phase transition. We conclude that SREB functions as a transcription factor that promotes morphogenesis and regulates siderophore biosynthesis. To our knowledge, this is the first gene identified that promotes the conversion from yeast to mold in the dimorphic fungi, and may shed light on environmental persistence of these pathogens.

  • Scott JJ, Budsberg KJ, Suen G, Wixon DL, Balser TC, Currie CR (2010) Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps. PLoS ONE 5(3):e9922 (PMC2847949) · Pubmed

    Leaf-cutter ants use fresh plant material to grow a mutualistic fungus that serves as the ants' primary food source. Within fungus gardens, various plant compounds are metabolized and transformed into nutrients suitable for ant consumption. This symbiotic association produces a large amount of refuse consisting primarily of partly degraded plant material. A leaf-cutter ant colony is thus divided into two spatially and chemically distinct environments that together represent a plant biomass degradation gradient. Little is known about the microbial community structure in gardens and dumps or variation between lab and field colonies. Using microbial membrane lipid analysis and a variety of community metrics, we assessed and compared the microbiota of fungus gardens and refuse dumps from both laboratory-maintained and field-collected colonies. We found that gardens contained a diverse and consistent community of microbes, dominated by Gram-negative bacteria, particularly gamma-Proteobacteria and Bacteroidetes. These findings were consistent across lab and field gardens, as well as host ant taxa. In contrast, dumps were enriched for Gram-positive and anaerobic bacteria. Broad-scale clustering analyses revealed that community relatedness between samples reflected system component (gardens/dumps) rather than colony source (lab/field). At finer scales samples clustered according to colony source. Here we report the first comparative analysis of the microbiota from leaf-cutter ant colonies. Our work reveals the presence of two distinct communities: one in the fungus garden and the other in the refuse dump. Though we find some effect of colony source on community structure, our data indicate the presence of consistently associated microbes within gardens and dumps. Substrate composition and system component appear to be the most important factor in structuring the microbial communities. These results thus suggest that resident communities are shaped by the plant degradation gradient created by ant behavior, specifically their fungiculture and waste management.

  • Pinto-Tomás AA, Anderson MA, Suen G, Stevenson DM, Chu FS, Cleland WW, Weimer PJ, Currie CR (2009) Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants. Science 326(5956):1120-3 · Pubmed

    Bacteria-mediated acquisition of atmospheric N2 serves as a critical source of nitrogen in terrestrial ecosystems. Here we reveal that symbiotic nitrogen fixation facilitates the cultivation of specialized fungal crops by leaf-cutter ants. By using acetylene reduction and stable isotope experiments, we demonstrated that N2 fixation occurred in the fungus gardens of eight leaf-cutter ant species and, further, that this fixed nitrogen was incorporated into ant biomass. Symbiotic N2-fixing bacteria were consistently isolated from the fungus gardens of 80 leaf-cutter ant colonies collected in Argentina, Costa Rica, and Panama. The discovery of N2 fixation within the leaf-cutter ant-microbe symbiosis reveals a previously unrecognized nitrogen source in neotropical ecosystems.

  • Richards GR, Vivas EI, Andersen AW, Rivera-Santos D, Gilmore S, Suen G, Goodrich-Blair H (2009) Isolation and characterization of Xenorhabdus nematophila transposon insertion mutants defective in lipase activity against Tween. J. Bacteriol. 191(16):5325-31 (PMC2725573) · Pubmed

    We identified Xenorhabdus nematophila transposon mutants with defects in lipase activity. One of the mutations, in yigL, a conserved gene of unknown function, resulted in attenuated virulence against Manduca sexta insects. We discuss possible connections between lipase production, YigL, and specific metabolic pathways.

  • Slater SC, Goldman BS, Goodner B, Setubal JC, Farrand SK, Nester EW, Burr TJ, Banta L, Dickerman AW, Paulsen I, Otten L, Suen G, Welch R, Almeida NF, Arnold F, Burton OT, Du Z, Ewing A, Godsy E, Heisel S, Houmiel KL, Jhaveri J, Lu J, Miller NM, Norton S, Chen Q, Phoolcharoen W, Ohlin V, Ondrusek D, Pride N, Stricklin SL, Sun J, Wheeler C, Wilson L, Zhu H, Wood DW (2009) Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J. Bacteriol. 191(8):2501-11 (PMC2668409) · Pubmed

    The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.

  • Caldera EJ, Poulsen M, Suen G, Currie CR (2009) Insect symbioses: a case study of past, present, and future fungus-growing ant research. Environ. Entomol. 38(1):78-92 · Pubmed

    Fungus-growing ants (Attini: Formicidae) engage in an obligate mutualism with fungi they cultivate for food. Although biologists have been fascinated with fungus-growing ants since the resurgence of natural history in the modern era, the early stages of research focused mainly on the foraging behavior of the leaf-cutters (the most derived attine lineage). Indeed, the discovery that the ants actually use leaf fragments to manure a fungus did not come until the 1800s. More recently, three additional microbial symbionts have been described, including specialized microfungal parasites of the ant's fungus garden, antibiotic-producing actinobacteria that help protect the fungus garden from the parasite, and a black yeast that parasitizes the ant-actinobacteria mutualism. The fungus-growing ant symbiosis serves as a particularly useful model system for studying insect-microbe symbioses, because, to date, it contains four well-characterized microbial symbionts, including mutualists and parasites that encompass micro-fungi, macro-fungi, yeasts, and bacteria. Here, we discuss approaches for studying insect-microbe symbioses, using the attine ant-microbial symbiosis as our framework. We draw attention to particular challenges in the field of symbiosis, including the establishment of symbiotic associations and symbiont function. Finally, we discuss future directions in insect-microbe research, with particular focus on applying recent advances in DNA sequencing technologies.

  • Suen G, Arshinoff BI, Taylor RG, Welch RD (2007) Practical applications of bacterial functional genomics. Biotechnol. Genet. Eng. Rev. 24:213-42 · Pubmed

    No abstract available.

  • Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat. Biotechnol. 25(11):1281-9 · Pubmed

    The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.

  • Suen G, Goldman BS, Welch RD (2007) Predicting prokaryotic ecological niches using genome sequence analysis. PLoS ONE 2(8):e743 (PMC1937020) · Pubmed

    Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as 'mountains' on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.

  • Arshinoff BI, Suen G, Just EM, Merchant SM, Kibbe WA, Chisholm RL, Welch RD (2007) Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. 35(Database i):D422-6 (PMC1669732) · Pubmed

    xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.

  • Suen G, Jakobsen JS, Goldman BS, Singer M, Garza AG, Welch RD (2006) Bacterial postgenomics: the promise and peril of systems biology. J. Bacteriol. 188(23):7999-8004 (PMC1698175) · Pubmed

    No abstract available.

  • Srinivasan BS, Caberoy NB, Suen G, Taylor RG, Shah R, Tengra F, Goldman BS, Garza AG, Welch RD (2005) Functional genome annotation through phylogenomic mapping. Nat. Biotechnol. 23(6):691-8 · Pubmed

    Accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. Here we introduce a genome-scale approach to functional protein annotation--phylogenomic mapping--that requires only sequence data, can be applied equally well to both finished and unfinished genomes, and can be extended beyond single genomes to annotate multiple genomes simultaneously. We have developed and applied it to more than 200 sequenced bacterial genomes. Proteins with similar evolutionary histories were grouped together, placed on a three dimensional map and visualized as a topographical landscape. The resulting phylogenomic maps display thousands of proteins clustered in mountains on the basis of coinheritance, a strong indicator of shared function. In addition to systematic computational validation, we have experimentally confirmed the ability of phylogenomic maps to predict both mutant phenotype and gene function in the delta proteobacterium Myxococcus xanthus.

  • You QS, Wang RZ, Suen GQ, Yan FC, Gao YJ, Cui SR, Zhao JH, Zhao TZ, Ding L (1993) Combination preoperative radiation and endocavitary hyperthermia for rectal cancer: long-term results of 44 patients. Int J Hyperthermia 9(1):19-24 · Pubmed

    Long-term results of 122 patients with advanced rectal cancer who were randomly treated with three different methods from July 1984 to July 1986. Of 122 patients, 44 were treated with endocavitary 915 MHz microwave applicators combined with 10 MeV X-ray or 60CO followed by surgery (group A), 38 with preoperative radiation (group B) and 40 with surgery (group C) as a control group. The temperature on the surface of the applicator touching the middle of the caudad to cephaladic extent of disease was 45-50 degrees C for 45 min twice a week for 6-8 sessions. Radiation dose was 30 Gy or 40 Gy/4 weeks. Of cases with stages 0 and A, 45.5% (20/44) were in group A, 23.7% (9/38) in group B and 12.5% (5/40) in group C (chi 2 test p < 0.05 and p < 0.01, respectively). Five-year survival rate was 66.7% (24/36) in group A, 50% (14/28) in group B and 40.5% (15/37) in group C. Percentage of survival at 5 years was 73.7% (14/19) for 40 Gy plus heat, 57.1% (8/14) for 40 Gy alone, 58.8% (10/17) for 30 Gy plus heat, and 42.9% (6/14) for 30 Gy alone. Data suggest a survival advantage for patients treated with preoperative radiation combined with endocavitary hyperthermia.

  • Shiau SY, Suen GS (1992) Estimation of the niacin requirements for tilapia fed diets containing glucose or dextrin. J. Nutr. 122(10):2030-6 · Pubmed

    Two 12-wk experiments were conducted to determine the adequate dietary niacin levels for juvenile hybrid tilapia, Oreochromis niloticus x O. aureus, when diets containing either 38% D(+)-glucose or 38% dextrin (type III, from corn) as the carbohydrate source were fed. In Experiment 1, we used 0, 40, 80, 120, 160 and 200 mg/kg of supplemental niacin in both the glucose- and dextrin-containing diets. In Experiment 2, 0, 10, 25, 40 and 55 mg/kg or 0, 10, 25, 40, 80, 120 and 160 mg/kg of supplemental niacin was incorporated in diets containing glucose or dextrin, respectively. In both experiments, fish fed niacin-deficient diets grew poorly. They developed skin, fin and mouth lesions and hemorrhages; the snout was deformed and there was gill edema. These pathologies began 6 wk after the experiments started. Plasma glucose concentrations were higher in fish fed glucose diets than those fed dextrin diets. Weight gain analyzed by broken-line regression indicated that the adequate dietary niacin level for maximal growth in rapidly growing tilapia fingerlings is 26 mg/kg in fish fed the glucose diet and 121 mg/kg in fish fed the dextrin diet.

  • (0) :

    No abstract available.