Faculty & Staff

  • Image of Federico E. Rey

    Federico E. Rey

    Associate Professor of Bacteriology

    5157 Microbial Sciences Building
    Office: (608) 890-2046
    Lab: (608) 890-2366
    ferey@wisc.edu
    Google Scholar

Start and Promotion Dates

  • Assistant Professor: 2013
  • Associate Professor: 2019

Education

Licenciado en Bioquimica (equivalent to B.S. and M.S. in Clinical Chemistry). 1998 
Facultad de Ciencias Quimicas. Universidad Nacional de Cordoba, Cordoba, Argentina.
Ph.D. Microbiology. 2006 
University of Iowa Postdoctoral Research: Center for Genome Sciences and Systems Biology, Washington University

Areas of Study

Microbiome, Microbe-diet interactions, Cardiovascular disease

Research Overview

Humans studies have revealed consistent alterations in the gut microbiomes of patients with cardiometabolic and aging-associated diseases. A major focus of my group is to understand how variations in the gut microbiome modulate the effects of diet and host’s susceptibility to cardiometabolic disease. To address these questions we use a combination of hypothesis-generating, sequencing-centered analyses of microbiomes from humans and mice, followed by proof-of-principle/proof-of-mechanism studies in gnotobiotic mouse models of disease and classic bacteriology experiments.

Dissecting the impact of microbe-diet interactions on host health:

1. Bacterial choline metabolism: Choline is a water-soluble nutrient essential for human life. Gut microbial metabolism of choline results in the production of trimethylamine (TMA), which upon absorption by the host is converted in the liver to trimethylamine N-oxide (TMAO). TMAO exacerbates thrombosis and atherosclerosis in mice, and its abundance correlates with the severity of these diseases in humans. We have recently discovered that subjects with Alzheimer’s Disease (AD) have alterations in their microbiome and higher levels of TMAO in cerebrospinal fluid (CSF), and we have identified associations between this molecule and markers of AD (Vogt et al., 2017, Vogt et al., 2018). Given the importance of choline and vascular disease to AD development we are exploring the impact of choline-consuming/TMA(O)-producing bacteria on AD development using a gnotobiotic mouse model of AD (collaboration with Dr. Barbara Bendlin and Dr. Luigi Puglielli). Additionally, we are working with Dr. John Denu to explore the role of bacterial choline depletion, TMAO and bacterial metabolism on epigenetic regulation.

2. Diet-microbiota interactions that impact atherosclerosis: (a) variation in butyrate-producing bacteria: Consumption of dietary fiber decreases the risk of cardiometabolic disease. Recent studies suggest that some of the benefits associated with consumption of dietary fiber are mediated in part by gut microbes, with increased representation of butyrate-producing microbes proposed as one of the potential mediators. Moreover, gut butyrate-producing bacteria have been found at higher levels in healthy populations relative to patients suffering various inflammatory diseases such as atherosclerosis. We recently showed that the butyrate-producing bacterium Roseburia intestinalis interacts with dietary plant polysaccharides to generate large amounts of butyrate, modify epigenetic programming, impact gene expression in the intestine, and improve intestinal barrier function. These changes were associated with lower levels of pro-inflammatory molecules in systemic circulation, reduced inflammation in the aorta and smaller atherosclerotic lesions. By administering tributyrin in the diet, which delivers butyrate in the distal gut, we demonstrated that butyrate mimics the effects of R. intestinalis (Kasahara et al. 2018). We plan to identify fiber types and dietary sources that promote the growth of R. intestinalis and test whether these results can be extended to other butyrate-producing bacteria. Additionally, we are testing causal relationships of other associations that we have identified between gut microbes and atherosclerosis. (b) Interactions between gut bacteria and flavonoids: some of the health benefits associated with the consumption of fruits and vegetables are derived from flavonoids. However, our bodies do not absorb most flavonoids as they exist in food, and there is a large degree of interpersonal variation in the reported benefits. These observations in part reflect individual differences in gut microbiota, which metabolize ingested flavonoids to a variety of products that are more readily absorbed by the host, although the nature and extent of these transformations remain poorly characterized. We recently found that colonized mice fed a diet supplemented with quercetin accumulate high levels of biologically active (e.g., anti-thrombotic) metabolites and develop smaller atherosclerotic lesions relative to mice consuming a control diet, whereas age-matched germ-free Apolipoprotein E-deficient mice do not benefit from flavonoid supplementation. These preliminary results suggest that bacterial metabolism of quercetin may be necessary for some of the beneficial effects associated with flavonoid consumption. We are currently examining whether specific routes of flavonoid metabolism are required for its beneficial effects.

Deciphering the impact of host genetics on gut microbiome composition: Host genetic variation modulates the composition of the gut microbiota. We found significant variation in diabetes-related phenotypes, atherosclerosis and gut microbiota composition among different mouse strains, and identified microbes associated with these traits. Microbiota transplant experiments showed that altering the composition of the gut microbiota modifies strain-specific susceptibility to diet-induced metabolic disease (Kreznar et al., 2017) and atherosclerosis (Kasahara and Rey, unpublished). By using a genetically-diverse mouse cohort and quantitative trait loci (QTL) mapping, we are identifying gut microbes, microbial functions, microbial-derived metabolites and clinical phenotypes that are modulated by host genetics (collaboration with Dr. Alan Attie).

Teaching

Microbiology 450: Diversity, Ecology, and Evolution of Microorganisms

Lab Personnel

Picture of An
Ran An
Scientist I
ran23@wisc.edu
Picture of Aquino
Ruben Aquino
Postdoc
aquinomartin@wisc.edu
Picture of Bussan
Hailey Bussan
Grad Student
hbussan@wisc.edu
Picture of Cattaneo
Lea Cattaneo
Grad Student
lcattaneo@wisc.edu
Picture of Han
Jessica Han
Grad Student
jhhan3@wisc.edu
Picture of Hutchison
Evan Hutchison
Grad Student
ehutchison2@wisc.edu
Picture of Kasahara
Kazu Kasahara
Scientist I
kasahara2@wisc.edu
Picture of Kerby
Bob Kerby
Scientist III
rlkerby@wisc.edu
Picture of Vemuganti
VV (Vaibhav) Vemuganti
Grad Student
vvemuganti@wisc.edu
Picture of Vivas
Nacho Vivas
Researcher II
eivivas@wisc.edu
Picture of Warren
Matthew Warren
Postdoc
mwarren8@wisc.edu
Picture of Zarbock
Katie Zarbock
Grad Student
kzarbock@wisc.edu
Picture of Zhang
Qijun Zhang
Grad Student
qzhang333@wisc.edu

Research Papers

  • Özçam M, Oh JH, Tocmo R, Acharya D, Zhang S, Astmann TJ, Heggen M, Ruiz-Ramírez S, Li F, Cheng CC, Vivas E, Rey FE, Claesen J, Bugni TS, Walter J, van Pijkeren JP (2022) A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation. Cell host & microbe 30((6)):824-835.e6 · Pubmed · DOI

    No abstract available.

  • Debédat J, Le Roy T, Voland L, Belda E, Alili R, Adriouch S, Bel Lassen P, Kasahara K, Hutchison E, Genser L, Torres L, Gamblin C, Rouault C, Zucker JD, Kapel N, Poitou C, Marcelin G, Rey FE, Aron-Wisnewsky J, Clément K (2022) The human gut microbiota contributes to type-2 diabetes non-resolution 5-years after Roux-en-Y gastric bypass. Gut microbes 14((1)):2050635 PMC9037437 · Pubmed · DOI

    No abstract available.

  • An R, Robbins D, Rey FE, Thibeault SL (2022) Vocal fold mucus layer: Comparison of histological protocols for visualization in mice. Laryngoscope investigative otolaryngology 7((2)):444-453 PMC9008169 · Pubmed · DOI

    No abstract available.

  • Thorstenson JC, Heston MB, Zarbock KR, Carlsson CM, Engelman CD, Deming Y, Johnson SC, Ulland TK, Asthana S, Kollmorgen G, Suridjan I, Blennow K, Zetterberg H, Chin NA, Rey FE, Bendlin BB (2022) Diet and APOE as moderators of the relationship between trimethylamine N-oxide and biomarkers of Alzheimer's disease and glial activation. Alzheimer's & dementia : the journal of the Alzheimer's Association 17 Suppl 3:e051827 · Pubmed · DOI

    No abstract available.

  • Feng J, Qian Y, Zhou Z, Ertmer S, Vivas EI, Lan F, Hamilton JJ, Rey FE, Anantharaman K, Venturelli OS (2022) Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell host & microbe 30((2)):200-215.e12 PMC9060796 · Pubmed · DOI

    No abstract available.

  • Buffa JA, Romano KA, Copeland MF, Cody DB, Zhu W, Galvez R, Fu X, Ward K, Ferrell M, Dai HJ, Skye S, Hu P, Li L, Parlov M, McMillan A, Wei X, Nemet I, Koeth RA, Li XS, Wang Z, Sangwan N, Hajjar AM, Dwidar M, Weeks TL, Bergeron N, Krauss RM, Tang WHW, Rey FE, DiDonato JA, Gogonea V, Gerberick GF, Garcia-Garcia JC, Hazen SL (2021) The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism. Nature microbiology 7((1)):73-86 PMC8732312 · Pubmed · DOI

    No abstract available.

  • Lobo AK, Traeger LL, Keller MP, Attie AD, Rey FE, Broman KW (2021) Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice. G3 (Bethesda, Md.) 11((11)): PMC8527510 · Pubmed · DOI

    No abstract available.

  • Lucas LN, Barrett K, Kerby RL, Zhang Q, Cattaneo LE, Stevenson D, Rey FE, Amador-Noguez D (2021) Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids. mSystems :e0080521 · Pubmed · DOI

    No abstract available.

  • Zhu W, Romano KA, Li L, Buffa JA, Sangwan N, Prakash P, Tittle AN, Li XS, Fu X, Androjna C, DiDonato AJ, Brinson K, Trapp BD, Fischbach MA, Rey FE, Hajjar AM, DiDonato JA, Hazen SL (2021) Gut microbes impact stroke severity via the trimethylamine N-oxide pathway. Cell host & microbe 29((7)):1199-1208.e5 PMC8288076 · Pubmed · DOI

    No abstract available.

  • Murga-Garrido SM, Hong Q, Cross TL, Hutchison ER, Han J, Thomas SP, Vivas EI, Denu J, Ceschin DG, Tang ZZ, Rey FE (2021) Gut microbiome variation modulates the effects of dietary fiber on host metabolism. Microbiome 9((1)):117 PMC8138933 · Pubmed · DOI

    No abstract available.

  • Rodriguez-Castaño GP, Rey FE, Caro-Quintero A, Acosta-González A (2020) Gut-derived Flavonifractor species variants are differentially enriched during in vitro incubation with quercetin. PloS one 15((12)):e0227724 PMC7710108 · Pubmed · DOI

    No abstract available.

  • An R, Gowda M, Rey FE, Thibeault SL (2020) Selective Bacterial Colonization of the Murine Larynx in a Gnotobiotic Model. Frontiers in microbiology 11:594617 PMC7676279 · Pubmed · DOI

    No abstract available.

  • Sublette MG, Cross TL, Korcarz CE, Hansen KM, Murga-Garrido SM, Hazen SL, Wang Z, Oguss MK, Rey FE, Stein JH (2020) Effects of Smoking and Smoking Cessation on the Intestinal Microbiota. Journal of clinical medicine 9((9)): PMC7564179 · Pubmed · DOI

    No abstract available.

  • Liu R, Wei P, Keller C, Orefice NS, Shi Y, Li Z, Huang J, Cui Y, Frost DC, Han S, Cross TL, Rey FE, Li L (2020) Integrated Label-Free and 10-Plex DiLeu Isobaric Tag Quantitative Methods for Profiling Changes in the Mouse Hypothalamic Neuropeptidome and Proteome: Assessment of the Impact of the Gut Microbiome. Analytical chemistry 92((20)):14021-14030 PMC7577927 · Pubmed · DOI

    No abstract available.

  • Keller C, Wei P, Wancewicz B, Cross TL, Rey FE, Li L (2020) Extraction optimization for combined metabolomics, peptidomics, and proteomics analysis of gut microbiota samples. Journal of mass spectrometry : JMS 56((4)):e4625 PMC7855350 · Pubmed · DOI

    No abstract available.

  • Nemet I, Saha PP, Gupta N, Zhu W, Romano KA, Skye SM, Cajka T, Mohan ML, Li L, Wu Y, Funabashi M, Ramer-Tait AE, Naga Prasad SV, Fiehn O, Rey FE, Tang WHW, Fischbach MA, DiDonato JA, Hazen SL (2020) A Cardiovascular Disease-Linked Gut Microbial Metabolite Acts via Adrenergic Receptors. Cell 180((5)):862-877.e22 PMC7402401 · Pubmed · DOI

    No abstract available.

  • Kasahara K, Rey FE (2019) The emerging role of gut microbial metabolism on cardiovascular disease. Current opinion in microbiology 50:64-70 · Pubmed · DOI

    No abstract available.

  • Chen S, Henderson A, Petriello MC, Romano KA, Gearing M, Miao J, Schell M, Sandoval-Espinola WJ, Tao J, Sha B, Graham M, Crooke R, Kleinridders A, Balskus EP, Rey FE, Morris AJ, Biddinger SB (2019) Trimethylamine N-Oxide Binds and Activates PERK to Promote Metabolic Dysfunction. Cell metabolism 30((6)):1141-1151.e5 · Pubmed · DOI

    No abstract available.

  • Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA, Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie AD, Rey FE (2019) Genetic determinants of gut microbiota composition and bile acid profiles in mice. PLoS genetics 15((8)):e1008073 PMC6715156 · Pubmed · DOI

    No abstract available.

  • Rodriguez-Castaño GP, Dorris MR, Liu X, Bolling BW, Acosta-Gonzalez A, Rey FE (2019) Bacteroides thetaiotaomicron Starch Utilization Promotes Quercetin Degradation and Butyrate Production by Eubacterium ramulus . Frontiers in microbiology 10:1145 PMC6548854 · Pubmed · DOI

    No abstract available.

  • Bresciani L, Angelino D, Vivas EI, Kerby RL, García-Viguera C, Del Rio D, Rey FE, Mena P (2019) Differential Catabolism of an Anthocyanin-Rich Elderberry Extract by Three Gut Microbiota Bacterial Species. Journal of agricultural and food chemistry 68((7)):1837-1843 · Pubmed · DOI

    No abstract available.

  • Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC (2019) Autometa: automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic acids research 47((10)):e57 PMC6547426 · Pubmed · DOI

    No abstract available.

  • Moriano-Gutierrez S, Koch EJ, Bussan H, Romano K, Belcaid M, Rey FE, Ruby EG, McFall-Ngai MJ (2019) Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression. Proceedings of the National Academy of Sciences of the United States of America 116((16)):7990-7999 PMC6475425 · Pubmed · DOI

    No abstract available.

  • Dill-McFarland KA, Tang ZZ, Kemis JH, Kerby RL, Chen G, Palloni A, Sorenson T, Rey FE, Herd P (2019) Close social relationships correlate with human gut microbiota composition. Scientific reports 9((1)):703 PMC6345772 · Pubmed · DOI

    No abstract available.

  • Tang TWH, Chen HC, Chen CY, Yen CYT, Lin CJ, Prajnamitra RP, Chen LL, Ruan SC, Lin JH, Lin PJ, Lu HH, Kuo CW, Chang CM, Hall AD, Vivas EI, Shui JW, Chen P, Hacker TA, Rey FE, Kamp TJ, Hsieh PCH (2018) Loss of Gut Microbiota Alters Immune System Composition and Cripples Postinfarction Cardiac Repair. Circulation 139((5)):647-659 · Pubmed · DOI

    No abstract available.

  • Vogt NM, Romano KA, Darst BF, Engelman CD, Johnson SC, Carlsson CM, Asthana S, Blennow K, Zetterberg H, Bendlin BB, Rey FE (2018) The gut microbiota-derived metabolite trimethylamine N-oxide is elevated in Alzheimer's disease. Alzheimer's research & therapy 10((1)):124 PMC6303862 · Pubmed · DOI

    No abstract available.

  • Pei R, Martin DA, Valdez JC, Liu J, Kerby RL, Rey FE, Smyth JA, Liu Z, Bolling BW (2018) Dietary Prevention of Colitis by Aronia Berry is Mediated Through Increased Th17 and Treg. Molecular nutrition & food research 63((5)):e1800985 · Pubmed · DOI

    No abstract available.

  • Bratburd JR, Keller C, Vivas E, Gemperline E, Li L, Rey FE, Currie CR (2018) Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans. mBio 9((6)): PMC6222126 · Pubmed · DOI

    No abstract available.

  • Kasahara K, Krautkramer KA, Org E, Romano KA, Kerby RL, Vivas EI, Mehrabian M, Denu JM, Bäckhed F, Lusis AJ, Rey FE (2018) Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model. Nature microbiology 3((12)):1461-1471 PMC6280189 · Pubmed · DOI

    No abstract available.

  • Skye SM, Zhu W, Romano KA, Guo CJ, Wang Z, Jia X, Kirsop J, Haag B, Lang JM, DiDonato JA, Tang WHW, Lusis AJ, Rey FE, Fischbach MA, Hazen SL (2018) Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential. Circulation research 123((10)):1164-1176 PMC6223262 · Pubmed · DOI

    No abstract available.

  • Romano KA, Rey FE (2018) Is maternal microbial metabolism an early-life determinant of health? Lab animal 47((9)):239-243 · Pubmed · DOI

    No abstract available.

  • Cross TL, Kasahara K, Rey FE (2018) Sexual dimorphism of cardiometabolic dysfunction: Gut microbiome in the play? Molecular metabolism 15:70-81 PMC6066746 · Pubmed · DOI

    No abstract available.

  • Yang H, Wang W, Romano KA, Gu M, Sanidad KZ, Kim D, Yang J, Schmidt B, Panigrahy D, Pei R, Martin DA, Ozay EI, Wang Y, Song M, Bolling BW, Xiao H, Minter LM, Yang GY, Liu Z, Rey FE, Zhang G (2018) A common antimicrobial additive increases colonic inflammation and colitis-associated colon tumorigenesis in mice. Science translational medicine 10((443)): PMC6343133 · Pubmed · DOI

    No abstract available.

  • Romano KA, Dill-McFarland KA, Kasahara K, Kerby RL, Vivas EI, Amador-Noguez D, Herd P, Rey FE (2018) Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation. Microbiome 6((1)):91 PMC5960144 · Pubmed · DOI

    No abstract available.

  • Li XS, Wang Z, Cajka T, Buffa JA, Nemet I, Hurd AG, Gu X, Skye SM, Roberts AB, Wu Y, Li L, Shahen CJ, Wagner MA, Hartiala JA, Kerby RL, Romano KA, Han Y, Obeid S, Lüscher TF, Allayee H, Rey FE, DiDonato JA, Fiehn O, Tang WHW, Hazen SL (2018) Untargeted metabolomics identifies trimethyllysine, a TMAO-producing nutrient precursor, as a predictor of incident cardiovascular disease risk. JCI insight 3((6)): PMC5926943 · Pubmed · DOI

    No abstract available.

  • Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlin BB, Rey FE (2017) Gut microbiome alterations in Alzheimer's disease. Scientific reports 7((1)):13537 PMC5648830 · Pubmed · DOI

    No abstract available.

  • Romano KA, Martinez-Del Campo A, Kasahara K, Chittim CL, Vivas EI, Amador-Noguez D, Balskus EP, Rey FE (2017) Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption. Cell host & microbe 22((3)):279-290.e7 PMC5599363 · Pubmed · DOI

    No abstract available.

  • Krautkramer KA, Rey FE, Denu JM (2017) Chemical signaling between gut microbiota and host chromatin: What is your gut really saying? The Journal of biological chemistry 292((21)):8582-8593 PMC5448088 · Pubmed · DOI

    No abstract available.

  • Kreznar JH, Keller MP, Traeger LL, Rabaglia ME, Schueler KL, Stapleton DS, Zhao W, Vivas EI, Yandell BS, Broman AT, Hagenbuch B, Attie AD, Rey FE (2017) Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes. Cell reports 18((7)):1739-1750 PMC5325228 · Pubmed · DOI

    No abstract available.

  • Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, Keller MP, Attie AD, Rey FE, Denu JM (2016) Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Mol. Cell 64(5):982-992 (PMC5227652) · Pubmed

    Histone-modifying enzymes regulate transcription and are sensitive to availability of endogenous small-molecule metabolites, allowing chromatin to respond to changes in environment. The gut microbiota produces a myriad of metabolites that affect host physiology and susceptibility to disease; however, the underlying molecular events remain largely unknown. Here we demonstrate that microbial colonization regulates global histone acetylation and methylation in multiple host tissues in a diet-dependent manner: consumption of a "Western-type" diet prevents many of the microbiota-dependent chromatin changes that occur in a polysaccharide-rich diet. Finally, we demonstrate that supplementation of germ-free mice with short-chain fatty acids, major products of gut bacterial fermentation, is sufficient to recapitulate chromatin modification states and transcriptional responses associated with colonization. These findings have profound implications for understanding the complex functional interactions between diet, gut microbiota, and host health.

  • Martínez-Del Campo A, Romano KA, Rey FE, Balskus EP (2016) The Plot Thickens: Diet Microbe Interactions May Modulate Thrombosis Risk. Cell Metab. 23(4):573-5 · Pubmed

    Thrombosis plays an important role in cardiovascular disease (CVD). Platelet activation is an essential step in the genesis and propagation of atherothrombotic complications. In a recent publication, Zhu and colleagues report that gut microbe-derived TMAO enhances platelet responsiveness and thrombosis, providing a novel mechanistic connection between microbes and CVD (Zhu et al., 2016).

  • Romano KA, Vivas EI, Amador-Noguez D, Rey FE (2015) Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide. MBio 6(2):e02481 (PMC4453578) · Pubmed

    Choline is a water-soluble nutrient essential for human life. Gut microbial metabolism of choline results in the production of trimethylamine (TMA), which upon absorption by the host is converted in the liver to trimethylamine-N-oxide (TMAO). Recent studies revealed that TMAO exacerbates atherosclerosis in mice and positively correlates with the severity of this disease in humans. However, which microbes contribute to TMA production in the human gut, the extent to which host factors (e.g., genotype) and diet affect TMA production and colonization of these microbes, and the effects TMA-producing microbes have on the bioavailability of dietary choline remain largely unknown. We screened a collection of 79 sequenced human intestinal isolates encompassing the major phyla found in the human gut and identified nine strains capable of producing TMA from choline in vitro. Gnotobiotic mouse studies showed that TMAO accumulates in the serum of animals colonized with TMA-producing species, but not in the serum of animals colonized with intestinal isolates that do not generate TMA from choline in vitro. Remarkably, low levels of colonization by TMA-producing bacteria significantly reduced choline levels available to the host. This effect was more pronounced as the abundance of TMA-producing bacteria increased. Our findings provide a framework for designing strategies aimed at changing the representation or activity of TMA-producing bacteria in the human gut and suggest that the TMA-producing status of the gut microbiota should be considered when making recommendations about choline intake requirements for humans. Cardiovascular disease (CVD) is the leading cause of death and disability worldwide, and increased trimethylamine N-oxide (TMAO) levels have been causally linked with CVD development. This work identifies members of the human gut microbiota responsible for both the accumulation of trimethylamine (TMA), the precursor of the proatherogenic compound TMAO, and subsequent decreased choline bioavailability to the host. Understanding how to manipulate the representation and function of choline-consuming, TMA-producing species in the intestinal microbiota could potentially lead to novel means for preventing or treating atherosclerosis and choline deficiency-associated diseases.

  • Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J, Rey FE, Smith MI, Simon GM, Scheffrahn RH, Woebken D, Spormann AM, Van Treuren W, Ursell LK, Pirrung M, Robbins-Pianka A, Cantarel BL, Lombard V, Henrissat B, Knight R, Gordon JI (2014) Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159(2):253-66 (PMC4194163) · Pubmed

    To study how microbes establish themselves in a mammalian gut environment, we colonized germ-free mice with microbial communities from human, zebrafish, and termite guts, human skin and tongue, soil, and estuarine microbial mats. Bacteria from these foreign environments colonized and persisted in the mouse gut; their capacity to metabolize dietary and host carbohydrates and bile acids correlated with colonization success. Cohousing mice harboring these xenomicrobiota or a mouse cecal microbiota, along with germ-free "bystanders," revealed the success of particular bacterial taxa in invading guts with established communities and empty gut habitats. Unanticipated patterns of ecological succession were observed; for example, a soil-derived bacterium dominated even in the presence of bacteria from other gut communities (zebrafish and termite), and human-derived bacteria colonized germ-free bystander mice before mouse-derived organisms. This approach can be generalized to address a variety of mechanistic questions about succession, including succession in the context of microbiota-directed therapeutics.

  • Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341(6150):1241214 (PMC3829625) · Pubmed

    The role of specific gut microbes in shaping body composition remains unclear. We transplanted fecal microbiota from adult female twin pairs discordant for obesity into germ-free mice fed low-fat mouse chow, as well as diets representing different levels of saturated fat and fruit and vegetable consumption typical of the U.S. diet. Increased total body and fat mass, as well as obesity-associated metabolic phenotypes, were transmissible with uncultured fecal communities and with their corresponding fecal bacterial culture collections. Cohousing mice harboring an obese twin's microbiota (Ob) with mice containing the lean co-twin's microbiota (Ln) prevented the development of increased body mass and obesity-associated metabolic phenotypes in Ob cage mates. Rescue correlated with invasion of specific members of Bacteroidetes from the Ln microbiota into Ob microbiota and was diet-dependent. These findings reveal transmissible, rapid, and modifiable effects of diet-by-microbiota interactions.

  • Rey FE, Gonzalez MD, Cheng J, Wu M, Ahern PP, Gordon JI (2013) Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proc. Natl. Acad. Sci. U.S.A. 110(33):13582-7 (PMC3746858) · Pubmed

    Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial nine-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for using ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. Although genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary-free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage's substrate utilization preferences, allowing consumption of more reduced carbon sources and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it.

  • Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222-7 (PMC3376388) · Pubmed

    Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

  • Wei X, Yang Z, Rey FE, Ridaura VK, Davidson NO, Gordon JI, Semenkovich CF (2012) Fatty acid synthase modulates intestinal barrier function through palmitoylation of mucin 2. Cell Host Microbe 11(2):140-52 (PMC3285413) · Pubmed

    No abstract available.

  • Faith JJ, McNulty NP, Rey FE, Gordon JI (2011) Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333(6038):101-4 (PMC3303606) · Pubmed

    The interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.

  • Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI (2011) Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc. Natl. Acad. Sci. U.S.A. 108 Suppl :4599-606 (PMC3063581) · Pubmed

    The human gut microbiota harbors three main groups of H(2)-consuming microbes: methanogens including the dominant archaeon, Methanobrevibacter smithii, a polyphyletic group of acetogens, and sulfate-reducing bacteria. Defining their roles in the gut is important for understanding how hydrogen metabolism affects the efficiency of fermentation of dietary components. We quantified methanogens in fecal samples from 40 healthy adult female monozygotic (MZ) and 28 dizygotic (DZ) twin pairs, analyzed bacterial 16S rRNA datasets generated from their fecal samples to identify taxa that co-occur with methanogens, sequenced the genomes of 20 M. smithii strains isolated from families of MZ and DZ twins, and performed RNA-Seq of a subset of strains to identify their responses to varied formate concentrations. The concordance rate for methanogen carriage was significantly higher for MZ versus DZ twin pairs. Co-occurrence analysis revealed 22 bacterial species-level taxa positively correlated with methanogens: all but two were members of the Clostridiales, with several being, or related to, known hydrogen-producing and -consuming bacteria. The M. smithii pan-genome contains 987 genes conserved in all strains, and 1,860 variably represented genes. Strains from MZ and DZ twin pairs had a similar degree of shared genes and SNPs, and were significantly more similar than strains isolated from mothers or members of other families. The 101 adhesin-like proteins (ALPs) in the pan-genome (45 ± 6 per strain) exhibit strain-specific differences in expression and responsiveness to formate. We hypothesize that M. smithii strains use their different repertoires of ALPs to create diversity in their metabolic niches, by allowing them to establish syntrophic relationships with bacterial partners with differing metabolic capabilities and patterns of co-occurrence.

  • Faith JJ, Rey FE, O'Donnell D, Karlsson M, McNulty NP, Kallstrom G, Goodman AL, Gordon JI (2010) Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME J 4(9):1094-8 (PMC2927777) · Pubmed

    No abstract available.

  • Rey FE, Faith JJ, Bain J, Muehlbauer MJ, Stevens RD, Newgard CB, Gordon JI (2010) Dissecting the in vivo metabolic potential of two human gut acetogens. J. Biol. Chem. 285(29):22082-90 (PMC2903421) · Pubmed

    Fermenting microbial communities generate hydrogen; its removal through the production of acetate, methane, or hydrogen sulfide modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers than components for methanogenesis or sulfate reduction and subsequently analyzed the metabolic potential of two sequenced human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally applicable method for multiplex sequencing of expressed microbial mRNAs (microbial RNA-Seq) and, together with mass spectrometry of metabolites, showed that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents, thereby maintaining a high NAD(+)/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest.

  • Rey FE, Harwood CS (2010) FixK, a global regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas palustris. Mol. Microbiol. 75(4):1007-20 · Pubmed

    Purple non-sulphur phototrophic bacteria (PNSB) are excellent models for analysing the co-ordination of major metabolisms, including oxidative phosphorylation, photophosphorylation, carbon dioxide fixation and nitrogen fixation. In species studied to date, a two-component system called RegBA controls these functions and it has been thought that this redox sensing regulatory system is essential for co-ordinating electron flow and cannot be easily replaced. Here we show that this is not the case for all PNSB and that the oxygen-sensing FixLJ-K system, initially described in rhizobia, controls microaerobic respiration, photophosphorylation and other major metabolic traits in Rhodopseudomonas palustris. A R. palustris fixK mutant grew normally aerobically but was impaired in microaerobic growth. It was also severely impaired in photosynthetic growth. Transcriptome analyses indicated that FixK positively regulates haem and bacteriochlorophyll biosynthesis, cbb3 oxidase and NADH dehydrogenase genes, as well as genes for autotrophy and aromatic compound degradation. Purified FixK interacted with the promoters of a bacteriochlorophyll biosynthesis operon, a bacteriophytochrome-histidine kinase gene and the fnr-type regulatory gene, aadR. A FixK-AadR hierarchy mediates the transition from microaerobic to anaerobic growth. These results underscore that physiologically similar bacteria can use very different regulatory strategies to control common major metabolisms.

  • Rey FE, Harwood CS (2010) FixK, a global regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas palustris. Mol. Microbiol. : · Pubmed

    No abstract available.

  • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1(6):6ra14 (PMC2894525) · Pubmed

    Diet and nutritional status are among the most important modifiable determinants of human health. The nutritional value of food is influenced in part by a person's gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelations among diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology, and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent metagenomic analysis of the temporal, spatial, and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized and reproduced much of the bacterial diversity of the donor's microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a high-fat, high-sugar "Western" diet shifted the structure of the microbiota within a single day, changed the representation of metabolic pathways in the microbiome, and altered microbiome gene expression. Reciprocal transplants involving various combinations of donor and recipient diets revealed that colonization history influences the initial structure of the microbial community but that these effects can be rapidly altered by diet. Humanized mice fed the Western diet have increased adiposity; this trait is transmissible via microbiota transplantation. Humanized gnotobiotic mice will be useful for conducting proof-of-principle "clinical trials" that test the effects of environmental and genetic factors on the gut microbiota and host physiology. Nearly full-length 16S rRNA gene sequences are deposited in GenBank under the accession numbers GQ491120 to GQ493997.

  • Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI (2009) Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. U.S.A. 106(14):5859-64 (PMC2660063) · Pubmed

    The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial-microbial and microbial-host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

  • Samuel BS, Shaito A, Motoike T, Rey FE, Backhed F, Manchester JK, Hammer RE, Williams SC, Crowley J, Yanagisawa M, Gordon JI (2008) Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc. Natl. Acad. Sci. U.S.A. 105(43):16767-72 (PMC2569967) · Pubmed

    The distal human intestine harbors trillions of microbes that allow us to extract calories from otherwise indigestible dietary polysaccharides. The products of polysaccharide fermentation include short-chain fatty acids that are ligands for Gpr41, a G protein-coupled receptor expressed by a subset of enteroendocrine cells in the gut epithelium. To examine the contribution of Gpr41 to energy balance, we compared Gpr41-/- and Gpr41+/+ mice that were either conventionally-raised with a complete gut microbiota or were reared germ-free and then cocolonized as young adults with two prominent members of the human distal gut microbial community: the saccharolytic bacterium, Bacteroides thetaiotaomicron and the methanogenic archaeon, Methanobrevibacter smithii. Both conventionally-raised and gnotobiotic Gpr41-/- mice colonized with the model fermentative community are significantly leaner and weigh less than their WT (+/+) littermates, despite similar levels of chow consumption. These differences are not evident when germ-free WT and germ-free Gpr41 knockout animals are compared. Functional genomic, biochemical, and physiologic studies of germ-free and cocolonized Gpr41-/- and +/+ littermates disclosed that Gpr41-deficiency is associated with reduced expression of PYY, an enteroendocrine cell-derived hormone that normally inhibits gut motility, increased intestinal transit rate, and reduced harvest of energy (short-chain fatty acids) from the diet. These results reveal that Gpr41 is a regulator of host energy balance through effects that are dependent upon the gut microbiota.

  • Rey FE, Heiniger EK, Harwood CS (2007) Redirection of metabolism for biological hydrogen production. Appl. Environ. Microbiol. 73(5):1665-71 (PMC1828789) · Pubmed

    No abstract available.

  • Gosse JL, Engel BJ, Rey FE, Harwood CS, Scriven LE, Flickinger MC (2007) Hydrogen production by photoreactive nanoporous latex coatings of nongrowing Rhodopseudomonas palustris CGA009. Biotechnol. Prog. 23(1):124-30 · Pubmed

    No abstract available.

  • Rey FE, Oda Y, Harwood CS (2006) Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris. J. Bacteriol. 188(17):6143-52 (PMC1595397) · Pubmed

    Rhodopseudomonas palustris is a purple, facultatively phototrophic bacterium that uses hydrogen gas as an electron donor for carbon dioxide fixation during photoautotrophic growth or for ammonia synthesis during nitrogen fixation. It also uses hydrogen as an electron supplement to enable the complete assimilation of oxidized carbon compounds, such as malate, into cell material during photoheterotrophic growth. The R. palustris genome predicts a membrane-bound nickel-iron uptake hydrogenase and several regulatory proteins to control hydrogenase synthesis. There is also a novel sensor kinase gene (RPA0981) directly adjacent to the hydrogenase gene cluster. Here we show that the R. palustris regulatory sensor hydrogenase HupUV acts in conjunction with the sensor kinase-response regulator protein pair HoxJ-HoxA to activate hydrogenase expression in response to hydrogen gas. Transcriptome analysis indicated that the HupUV-HoxJA regulatory system also controls the expression of genes encoding a predicted dicarboxylic acid transport system, a putative formate transporter, and a glutamine synthetase. RPA0981 had a small effect in repressing hydrogenase synthesis. We also determined that the two-component system RegS-RegR repressed expression of the uptake hydrogenase, probably in response to changes in intracellular redox status. Transcriptome analysis indicated that about 30 genes were differentially expressed in R. palustris cells that utilized hydrogen when growing photoheterotrophically on malate under nitrogen-fixing conditions compared to a mutant strain that lacked uptake hydrogenase. From this it appears that the recycling of reductant in the form of hydrogen does not have extensive nonspecific effects on gene expression in R. palustris.

  • Oda Y, Samanta SK, Rey FE, Wu L, Liu X, Yan T, Zhou J, Harwood CS (2005) Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris. J. Bacteriol. 187(22):7784-94 (PMC1280311) · Pubmed

    The photosynthetic bacterium Rhodopseudomonas palustris is one of just a few prokaryotes described so far that has vnf and anf genes for alternative vanadium cofactor (V) and iron cofactor (Fe) nitrogenases in addition to nif genes for a molybdenum cofactor (Mo) nitrogenase. Transcriptome data indicated that the 32 genes in the nif gene cluster, but not the anf or vnf genes, were induced in wild-type and Mo nitrogenase-expressing strains grown under nitrogen-fixing conditions in Mo-containing medium. Strains that were unable to express a functional Mo nitrogenase due to mutations in Mo nitrogenase structural genes synthesized functional V and Fe nitrogenases and expressed vnf and anf genes in nitrogen-fixing growth media that contained Mo and V at concentrations far in excess of those that repress alternative nitrogenase gene expression in other bacteria. Thus, not only does R. palustris have multiple enzymatic options for nitrogen fixation, but in contrast to reports on other nitrogen-fixing bacteria, the expression of its alternative nitrogenases is not repressed by transition metals. Between 95 and 295 genes that are not directly associated with nitrogenase synthesis and assembly were induced under nitrogen-fixing conditions, depending on which nitrogenase was being used by R. palustris. Genes for nitrogen acquisition were expressed at particularly high levels during alternative nitrogenase-dependent growth. This suggests that alternative nitrogenase-expressing cells are relatively starved for nitrogen and raises the possibility that fixed nitrogen availability may be the primary signal that controls the synthesis of the V and Fe nitrogenases.

  • Rey FE, Pagano PJ (2002) The reactive adventitia: fibroblast oxidase in vascular function. Arterioscler. Thromb. Vasc. Biol. 22(12):1962-71 · Pubmed

    No abstract available.

  • Rey FE, Li XC, Carretero OA, Garvin JL, Pagano PJ (2002) Perivascular superoxide anion contributes to impairment of endothelium-dependent relaxation: role of gp91(phox). Circulation 106(19):2497-502 · Pubmed

    No abstract available.

  • Rey FE, Cifuentes ME, Kiarash A, Quinn MT, Pagano PJ (2001) Novel competitive inhibitor of NAD(P)H oxidase assembly attenuates vascular O(2)(-) and systolic blood pressure in mice. Circ. Res. 89(5):408-14 · Pubmed

    No abstract available.

  • Cifuentes ME, Rey FE, Carretero OA, Pagano PJ (2000) Upregulation of p67(phox) and gp91(phox) in aortas from angiotensin II-infused mice. Am. J. Physiol. Heart Circ. Physiol. 279(5):H2234-40 · Pubmed

    No abstract available.

  • Hsich E, Segal BH, Pagano PJ, Rey FE, Paigen B, Deleonardis J, Hoyt RF, Holland SM, Finkel T (2000) Vascular effects following homozygous disruption of p47(phox) : An essential component of NADPH oxidase. Circulation 101(11):1234-6 · Pubmed

    No abstract available.