Karthik Anantharaman

• vClassifier: a toolkit for high-resolution phylogenetic classification of prokaryotic viruses
  June 29, 2026
  Kun Zhou, James C Kosmopoulos, Karthik Anantharaman Bioinformatics advances
• Computational Microbial and Viral Ecology Analysis
  May 19, 2026
  James C Kosmopoulos, Karthik Anantharaman Methods in molecular biology (Clifton, N.J.)
• V- and VL-scores unveil viral signatures and origins of protein families
  April 28, 2026
  Kun Zhou, James C Kosmopoulos, Etan Dieppa Colón, Peter John Badciong, Karthik Anantharaman Nature communications
• Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function
  March 19, 2026
  Qiyao Yang, Rosa Aghdam, Patricia Q Tran, Karthik Anantharaman, Claudia Solís-Lemus Environmental microbiology reports
• A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination
  February 27, 2026
  Ling Yuan, Yiting Qin, Jacob West-Roberts, Karthik Anantharaman, Haoyu Wang, Yuanqiang Zou, Yi Duan, Antonio Pedro Camargo, Eugene V Koonin, LinXing Chen bioRxiv : the preprint server for biology
• Phage-microbe interactions may contribute to the population structure and dynamics of hydrothermal vent symbionts
  February 25, 2026
  Michelle A Hauer, Katherine M Klier, Marguerite V Langwig, Karthik Anantharaman, Roxanne A Beinart ISME communications
• Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments
  December 11, 2025
  Marguerite V Langwig, Sunny Lyn Sneed, Anna Rasmussen, Kiley W Seitz, Jessica A Lee, Karthik Anantharaman, Valerie De Anda, Christopher A Francis, Brett J Baker ISME communications
• Ecosystem health shapes viral ecology in peatland soils
  December 10, 2025
  James C Kosmopoulos, William Pallier, Ashish A Malik, Karthik Anantharaman Nature microbiology
• STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies
  December 1, 2025
  Julia M Kelliher, Chloe Mirzayi, Sarah R Bordenstein, Aaron Oliver, Christina A Kellogg, Eneida L Hatcher, Maureen Berg, Petr Baldrian, Mashael Aljumaah, Cassandra Maria Luz Miller, Christopher Mungall, Vlastimil Novak, Alexis Palucki, Ethan Smith, Nazifa Tabassum, Gregory Bonito, J Rodney Brister, Patrick S G Chain, Mingfei Chen, Samuel Degregori, Jose Pablo Dundore-Arias, Joanne B Emerson, […]
• Mapping Structural Constraints and Adaptive Potential in a Capsule-Degrading Phage Tailspike Protein
  November 24, 2025
  Sarah Evert, Phill Huss, Dinesh Kumar Kuppa Baskaran, Karthik Anantharaman, Srivatsan Raman bioRxiv : the preprint server for biology
• Protein Set Transformer: a protein-based genome language model to power high-diversity viromics
  November 23, 2025
  Cody Martin, Anthony Gitter, Karthik Anantharaman Nature communications
• Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
  November 20, 2025
  James C Kosmopoulos, Karthik Anantharaman Biochemistry
• Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills
  November 11, 2025
  Nikhil A George, Zhichao Zhou, Karthik Anantharaman, Laura A Hug Virology journal
• Systematic genome-wide mapping of host determinants of bacteriophage infectivity
  October 16, 2025
  Chutikarn Chitboonthavisuk, Cody Martin, Phil Huss, Jason M Peters, Karthik Anantharaman, Srivatsan Raman Cell systems
• Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
  September 22, 2025
  James C Kosmopoulos, Karthik Anantharaman ArXiv
• An updated view of metabolic handoffs in microbiomes
  August 30, 2025
  Katherine M Klier, Karthik Anantharaman Trends in microbiology
• A call for caution in the biological interpretation of viral auxiliary metabolic genes
  August 27, 2025
  Cody Martin, Joanne B Emerson, Simon Roux, Karthik Anantharaman Nature microbiology
• Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms
  August 21, 2025
  Tao Wang, Peiyu Zhang, Karthik Anantharaman, Huan Wang, Huan Zhang, Min Zhang, Jun Xu Nature communications
• Author Correction: Elevated heterotrophic activity in Guaymas Basin hydrothermal plumes influences deep-sea carbon cycling
  July 14, 2025
  Andrew Montgomery, Guang-Chao Zhuang, Zhichao Zhou, Marguerite V Langwig, María Del Carmen Millán-Motolinía, Hannah Y L Choi, Kimberley S Hunter, Carlos A Mortera-Gutiérrez, Christelle Hyacinthe, Zachary Marinelli, Karthik Anantharaman, Andreas Teske, Samantha B Joye Nature communications
• Elevated heterotrophic activity in Guaymas Basin hydrothermal plumes influences deep-sea carbon cycling
  May 28, 2025
  Andrew Montgomery, Guang-Chao Zhuang, Zhichao Zhou, Marguerite V Langwig, María Del Carmen Millán-Motolinía, Hannah Y L Choi, Kimberley S Hunter, Carlos A Mortera-Gutiérrez, Christelle Hyacinthe, Zachary Marinelli, Karthik Anantharaman, Andreas Teske, Samantha B Joye Nature communications
• Genetic keys to microbial gut colonization
  May 15, 2025
  Karthik Anantharaman, Cody Martin Cell host & microbe
• Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites
  May 8, 2025
  Yiyi Liu, Yu-Yu Cheng, Jaron Thompson, Zhichao Zhou, Eugenio I Vivas, Matthew F Warren, Julie M DuClos, Karthik Anantharaman, Federico E Rey, Ophelia S Venturelli Cell systems
• Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems
  April 30, 2025
  Marguerite V Langwig, Faith Koester, Cody Martin, Zhichao Zhou, Samantha B Joye, Anna-Louise Reysenbach, Karthik Anantharaman Nature communications
• Pangenome Analysis of Clostridium scindens: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains
  April 26, 2025
  Kelly Y Olivos-Caicedo, Francelys V Fernandez-Materan, Steven L Daniel, Karthik Anantharaman, Jason M Ridlon, João M P Alves Microorganisms
• An expanded metabolic pathway for androgen production by commensal bacteria
  April 21, 2025
  Taojun Wang, Saeed Ahmad, Angélica Cruz-Lebrón, Sarah E Ernst, Kelly Yovani Olivos Caicedo, Yoon Jeong, Briawna Binion, Pauline Mbuvi, Debapriya Dutta, Francelys V Fernandez-Materan, Adam M Breister, Elizabeth Tang, Jae Won Lee, Jason D Kang, Spencer C Harris, Shigeo Ikegawa, H Rex Gaskins, John W Erdman, Glen Yang, Isaac Cann, Steven L Daniel, Phillip B […]
• Engineering bacteriophages through deep mining of metagenomic motifs
  April 18, 2025
  Phil Huss, Kristopher Kieft, Anthony Meger, Kyle Nishikawa, Karthik Anantharaman, Srivatsan Raman Science advances
• zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters
  February 5, 2025
  Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Ashlee M Earl, Karthik Anantharaman, Lindsay R Kalan Nucleic acids research
• Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages
  January 13, 2025
  Etan Dieppa-Colón, Cody Martin, James C Kosmopoulos, Karthik Anantharaman Environmental microbiome
• Unravelling viral ecology and evolution over 20 years in a freshwater lake
  January 3, 2025
  Zhichao Zhou, Patricia Q Tran, Cody Martin, Robin R Rohwer, Brett J Baker, Katherine D McMahon, Karthik Anantharaman Nature microbiology
• Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories
  December 19, 2024
  Yuki Amano, Rohan Sachdeva, Daniel Gittins, Karthik Anantharaman, Shufei Lei, Luis E Valentin-Alvarado, Spencer Diamond, Hikari Beppu, Teruki Iwatsuki, Akihito Mochizuki, Kazuya Miyakawa, Eiichi Ishii, Hiroaki Murakami, Alexander L Jaffe, Cindy Castelle, Adi Lavy, Yohey Suzuki, Jillian F Banfield Environmental microbiome
• Publisher Correction: Massively parallel single-cell sequencing of diverse microbial populations
  November 29, 2024
  Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli Nature methods
• V- and VL-Scores Uncover Viral Signatures and Origins of Protein Families
  November 18, 2024
  Kun Zhou, James C Kosmopoulos, Etan Dieppa Colón, Peter John Badciong, Karthik Anantharaman bioRxiv : the preprint server for biology
• Diversity and ecology of microbial sulfur metabolism
  October 17, 2024
  Zhichao Zhou, Patricia Q Tran, Elise S Cowley, Elizabeth Trembath-Reichert, Karthik Anantharaman Nature reviews. Microbiology
• Protein Set Transformer: A protein-based genome language model to power high diversity viromics
  October 14, 2024
  Cody Martin, Anthony Gitter, Karthik Anantharaman Research square
• Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology
  October 7, 2024
  James C Kosmopoulos, Katherine M Klier, Marguerite V Langwig, Patricia Q Tran, Karthik Anantharaman Microbiome
• Pangenome analysis of Clostridium scindens : a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains
  September 16, 2024
  Kelly Y Olivos-Caicedo, Francelys Fernandez, Steven L Daniel, Karthik Anantharaman, Jason M Ridlon, João M P Alves bioRxiv : the preprint server for biology
• Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota
  September 4, 2024
  Tiffany Oliver, Neha Varghese, Simon Roux, Frederik Schulz, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Robert Riley, Kurt LaButti, Robert Egan, Patrick Hajek, Supratim Mukherjee, Galina Ovchinnikova, T B K Reddy, Sara Calhoun, Richard D Hayes, Robin R Rohwer, Zhichao Zhou, Chris Daum, Alex Copeland, I-Min A Chen, Natalia N Ivanova, Nikos C Kyrpides, […]
• Evolutionary history and origins of Dsr-mediated sulfur oxidation
  August 29, 2024
  Katherine M Klier, Cody Martin, Marguerite V Langwig, Karthik Anantharaman The ISME journal
• Protein Set Transformer: A protein-based genome language model to power high diversity viromics
  August 12, 2024
  Cody Martin, Anthony Gitter, Karthik Anantharaman bioRxiv : the preprint server for biology
• Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients
  August 8, 2024
  Xing Huang, Jianjun Wang, Kenneth Dumack, Karthik Anantharaman, Bin Ma, Yan He, Weiping Liu, Hongjie Di, Yong Li, Jianming Xu The ISME journal
• Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages
  July 29, 2024
  Etan Dieppa-Colón, Cody Martin, Karthik Anantharaman bioRxiv : the preprint server for biology
• Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills
  June 10, 2024
  Nikhil A George, Zhichao Zhou, Karthik Anantharaman, Laura A Hug bioRxiv : the preprint server for biology
• The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis
  May 31, 2024
  Zhichao Zhou, Yang Liu, Karthik Anantharaman, Meng Li mLife
• Systematic genome-wide discovery of host factors governing bacteriophage infectivity
  April 25, 2024
  Chutikarn Chitboonthavisuk, Cody Martin, Phil Huss, Jason M Peters, Karthik Anantharaman, Srivatsan Raman bioRxiv : the preprint server for biology
• Massively parallel single-cell sequencing of diverse microbial populations
  January 17, 2024
  Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli Nature methods
• ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes
  December 28, 2023
  Zhichao Zhou, Cody Martin, James C Kosmopoulos, Karthik Anantharaman iMeta
• Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway
  November 21, 2023
  Yiyi Liu, Yu-Yu Cheng, Jaron Thompson, Zhichao Zhou, Eugenio I Vivas, Matthew F Warren, Federico E Rey, Karthik Anantharaman, Ophelia S Venturelli bioRxiv : the preprint server for biology
• Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology
  October 31, 2023
  James C Kosmopoulos, Katherine M Klier, Marguerite V Langwig, Patricia Q Tran, Karthik Anantharaman bioRxiv : the preprint server for biology
• Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms
  October 24, 2023
  Kun Zhou, Tin Yan Wong, Lexin Long, Karthik Anantharaman, Weipeng Zhang, Wai Chuen Wong, Rui Zhang, Pei-Yuan Qian The ISME journal
• Editorial: Advances in viromics: new tools, challenges, and data towards characterizing human and environmental viromes
  October 12, 2023
  Mária Džunková, Cristina Moraru, Karthik Anantharaman Frontiers in microbiology
• Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction
  October 5, 2023
  Muhe Diao, Stefan Dyksma, Elif Koeksoy, David Kamanda Ngugi, Karthik Anantharaman, Alexander Loy, Michael Pester FEMS microbiology reviews
• To cull or kill
  September 28, 2023
  James C Kosmopoulos, Karthik Anantharaman Nature ecology & evolution
• Genetic risk score in multiple sclerosis is associated with unique gut microbiome
  September 27, 2023
  Noha S Elsayed, Robert K Valenzuela, Terrie Kitchner, Thao Le, John Mayer, Zheng-Zheng Tang, Vishnu R Bayanagari, Qiongshi Lu, Paula Aston, Karthik Anantharaman, Sanjay K Shukla Scientific reports
• Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick
  September 18, 2023
  Janina Rahlff, Matthias Wietz, Helge-Ansgar Giebel, Oliver Bayfield, Emelie Nilsson, Kristofer Bergström, Kristopher Kieft, Karthik Anantharaman, Mariana Ribas-Ribas, Hannah D Schweitzer, Oliver Wurl, Matthias Hoetzinger, Alfred Antson, Karin Holmfeldt ISME communications
• Determinants of Gastrointestinal Group B Streptococcus Carriage in Adults
  August 30, 2023
  Elise S Cowley, Ibrahim Zuniga Chaves, Fauzia Osman, Garret Suen, Karthik Anantharaman, Andrew J Hryckowian bioRxiv : the preprint server for biology
• Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota
  August 3, 2023
  Ming Ji, Xiaojiang Xu, Qing Xu, Yun-Chung Hsiao, Cody Martin, Svetlana Ukraintseva, Vladimir Popov, Konstantin G Arbeev, Tom A Randall, Xiaoyue Wu, Liz M Garcia-Peterson, Juan Liu, Xin Xu, M Andrea Azcarate-Peril, Yisong Wan, Anatoliy I Yashin, Karthik Anantharaman, Kun Lu, Jian-Liang Li, Igor Shats, Xiaoling Li Nature metabolism
• zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters
  June 19, 2023
  Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Ashlee M Earl, Karthik Anantharaman, Lindsay R Kalan bioRxiv : the preprint server for biology
• Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria
  June 7, 2023
  Patricia Q Tran, Samantha C Bachand, Jacob C Hotvedt, Kristopher Kieft, Elizabeth A McDaniel, Katherine D McMahon, Karthik Anantharaman mSystems
• Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data
  May 31, 2023
  Mihnea R Mangalea, Kristopher Keift, Breck A Duerkop, Karthik Anantharaman Methods in molecular biology (Clifton, N.J.)
• Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes
  May 13, 2023
  Zhichao Zhou, Patricia Q Tran, Alyssa M Adams, Kristopher Kieft, John A Breier, Caroline S Fortunato, Cody S Sheik, Julie A Huber, Meng Li, Gregory J Dick, Karthik Anantharaman The ISME journal
• Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes
  April 29, 2023
  Dinesh Kumar Kuppa Baskaran, Shreyansh Umale, Zhichao Zhou, Karthik Raman, Karthik Anantharaman ISME communications
• Engineering bacteriophages through deep mining of metagenomic motifs
  February 17, 2023
  Phil Huss, Kristopher Kieft, Anthony Meger, Kyle Nishikawa, Karthik Anantharaman, Srivatsan Raman bioRxiv : the preprint server for biology
• ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes
  February 13, 2023
  Zhichao Zhou, Cody Martin, James C Kosmopoulos, Karthik Anantharaman bioRxiv : the preprint server for biology
• Efficient plasmid transfer via natural competence in a microbial co-culture
  January 30, 2023
  Yu-Yu Cheng, Zhichao Zhou, James M Papadopoulos, Jason D Zuke, Tanya G Falbel, Karthik Anantharaman, Briana M Burton, Ophelia S Venturelli Molecular systems biology
• Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits
  December 26, 2022
  Zhichao Zhou, Emily St John, Karthik Anantharaman, Anna-Louise Reysenbach Microbiome
• Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes
  November 7, 2022
  Jae Won Lee, Elise S Cowley, Patricia G Wolf, Heidi L Doden, Tsuyoshi Murai, Kelly Yovani Olivos Caicedo, Lindsey K Ly, Furong Sun, Hajime Takei, Hiroshi Nittono, Steven L Daniel, Isaac Cann, H Rex Gaskins, Karthik Anantharaman, João M P Alves, Jason M Ridlon Gut microbes
• Gut virome dysbiosis following focal cerebral ischemia in mice
  June 15, 2022
  Bharath Chelluboina, Kristopher Kieft, Adam Breister, Karthik Anantharaman, Raghu Vemuganti Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism
• vRhyme enables binning of viral genomes from metagenomes
  May 11, 2022
  Kristopher Kieft, Alyssa Adams, Rauf Salamzade, Lindsay Kalan, Karthik Anantharaman Nucleic acids research
• Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer
  April 20, 2022
  Patricia G Wolf, Elise S Cowley, Adam Breister, Sarah Matatov, Luke Lucio, Paige Polak, Jason M Ridlon, H Rex Gaskins, Karthik Anantharaman Microbiome
• Deciphering Active Prophages from Metagenomes
  March 24, 2022
  Kristopher Kieft, Karthik Anantharaman mSystems
• METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks
  February 17, 2022
  Zhichao Zhou, Patricia Q Tran, Adam M Breister, Yang Liu, Kristopher Kieft, Elise S Cowley, Ulas Karaoz, Karthik Anantharaman Microbiome
• Virus genomics: what is being overlooked?
  January 20, 2022
  Kristopher Kieft, Karthik Anantharaman Current opinion in virology
• Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions
  January 7, 2022
  Jun Feng, Yili Qian, Zhichao Zhou, Sarah Ertmer, Eugenio I Vivas, Freeman Lan, Joshua J Hamilton, Federico E Rey, Karthik Anantharaman, Ophelia S Venturelli Cell host & microbe
• Editorial: The Uncultured Microorganisms: Novel Technologies and Applications
  December 13, 2021
  Bin-Bin Xie, Meng Li, Karthik Anantharaman, Nikolai V Ravin Frontiers in microbiology
• Biogeochemistry Goes Viral: towards a Multifaceted Approach To Study Viruses and Biogeochemical Cycling
  October 12, 2021
  Patricia Q Tran, Karthik Anantharaman mSystems
• Virus-associated organosulfur metabolism in human and environmental systems
  August 4, 2021
  Kristopher Kieft, Adam M Breister, Phil Huss, Alexandra M Linz, Elizabeth Zanetakos, Zhichao Zhou, Janina Rahlff, Sarah P Esser, Alexander J Probst, Srivatsan Raman, Simon Roux, Karthik Anantharaman Cell reports
• Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages
  June 10, 2021
  Kristopher Kieft, Zhichao Zhou, Rika E Anderson, Alison Buchan, Barbara J Campbell, Steven J Hallam, Matthias Hess, Matthew B Sullivan, David A Walsh, Simon Roux, Karthik Anantharaman Nature communications
• Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential
  May 6, 2021
  Mihnea R Mangalea, David Paez-Espino, Kristopher Kieft, Anushila Chatterjee, Meagan E Chriswell, Jennifer A Seifert, Marie L Feser, M Kristen Demoruelle, Alexandra Sakatos, Karthik Anantharaman, Kevin D Deane, Kristine A Kuhn, V Michael Holers, Breck A Duerkop Cell host & microbe
• Completion of the gut microbial epi-bile acid pathway
  May 3, 2021
  Heidi L Doden, Patricia G Wolf, H Rex Gaskins, Karthik Anantharaman, João M P Alves, Jason M Ridlon Gut microbes
• Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
  February 10, 2021
  Patricia Q Tran, Samantha C Bachand, Peter B McIntyre, Benjamin M Kraemer, Yvonne Vadeboncoeur, Ismael A Kimirei, Rashid Tamatamah, Katherine D McMahon, Karthik Anantharaman The ISME journal
• Author Correction: Roadmap for naming uncultivated Archaea and Bacteria
  November 13, 2020
  Alison E Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T Konstantinidis, Christopher E Lane, R Thane Papke, Donovan H Parks, Ramon Rossello-Mora, Matthew B Stott, Iain C Sutcliffe, J Cameron Thrash, Stephanus N Venter, William B Whitman, Silvia G Acinas, Rudolf I Amann, Karthik Anantharaman, Jean Armengaud, Brett J Baker, […]
• Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes
  August 22, 2020
  Zhichao Zhou, Yang Liu, Jie Pan, Brandi R Cron, Brandy M Toner, Karthik Anantharaman, John A Breier, Gregory J Dick, Meng Li The ISME journal
• Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
  August 21, 2020
  Elizabeth A McDaniel, Benjamin D Peterson, Sarah L R Stevens, Patricia Q Tran, Karthik Anantharaman, Katherine D McMahon mSystems
• VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
  June 12, 2020
  Kristopher Kieft, Zhichao Zhou, Karthik Anantharaman Microbiome
• Roadmap for naming uncultivated Archaea and Bacteria
  June 10, 2020
  Alison E Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T Konstantinidis, Christopher E Lane, R Thane Papke, Donovan H Parks, Ramon Rossello-Mora, Matthew B Stott, Iain C Sutcliffe, J Cameron Thrash, Stephanus N Venter, William B Whitman, Silvia G Acinas, Rudolf I Amann, Karthik Anantharaman, Jean Armengaud, Brett J Baker, […]
• Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation
  May 13, 2020
  Zhichao Zhou, Patricia Q Tran, Kristopher Kieft, Karthik Anantharaman The ISME journal
• Accurate and complete genomes from metagenomes
  March 20, 2020
  Lin-Xing Chen, Karthik Anantharaman, Alon Shaiber, A Murat Eren, Jillian F Banfield Genome research
• Clades of huge phages from across Earth's ecosystems
  February 14, 2020
  Basem Al-Shayeb, Rohan Sachdeva, Lin-Xing Chen, Fred Ward, Patrick Munk, Audra Devoto, Cindy J Castelle, Matthew R Olm, Keith Bouma-Gregson, Yuki Amano, Christine He, Raphaël Méheust, Brandon Brooks, Alex Thomas, Adi Lavy, Paula Matheus-Carnevali, Christine Sun, Daniela S A Goltsman, Mikayla A Borton, Allison Sharrar, Alexander L Jaffe, Tara C Nelson, Rose Kantor, Ray Keren, […]
• Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms
  May 22, 2019
  Spencer Diamond, Peter F Andeer, Zhou Li, Alexander Crits-Christoph, David Burstein, Karthik Anantharaman, Katherine R Lane, Brian C Thomas, Chongle Pan, Trent R Northen, Jillian F Banfield Nature microbiology
• Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
  March 28, 2019
  Paula B Matheus Carnevali, Frederik Schulz, Cindy J Castelle, Rose S Kantor, Patrick M Shih, Itai Sharon, Joanne M Santini, Matthew R Olm, Yuki Amano, Brian C Thomas, Karthik Anantharaman, David Burstein, Eric D Becraft, Ramunas Stepanauskas, Tanja Woyke, Jillian F Banfield Nature communications
• Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network
  February 28, 2019
  Keith Bouma-Gregson, Matthew R Olm, Alexander J Probst, Karthik Anantharaman, Mary E Power, Jillian F Banfield The ISME journal
• Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
  January 30, 2019
  Paula B Matheus Carnevali, Frederik Schulz, Cindy J Castelle, Rose S Kantor, Patrick M Shih, Itai Sharon, Joanne M Santini, Matthew R Olm, Yuki Amano, Brian C Thomas, Karthik Anantharaman, David Burstein, Eric D Becraft, Ramunas Stepanauskas, Tanja Woyke, Jillian F Banfield Nature communications
• Megaphages infect Prevotella and variants are widespread in gut microbiomes
  January 30, 2019
  Audra E Devoto, Joanne M Santini, Matthew R Olm, Karthik Anantharaman, Patrick Munk, Jenny Tung, Elizabeth A Archie, Peter J Turnbaugh, Kimberley D Seed, Ran Blekhman, Frank M Aarestrup, Brian C Thomas, Jillian F Banfield Nature microbiology
• Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
  December 25, 2018
  Alexandra M Linz, Shaomei He, Sarah L R Stevens, Karthik Anantharaman, Robin R Rohwer, Rex R Malmstrom, Stefan Bertilsson, Katherine D McMahon PeerJ
• Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
  September 6, 2018
  Cindy J Castelle, Christopher T Brown, Karthik Anantharaman, Alexander J Probst, Raven H Huang, Jillian F Banfield Nature reviews. Microbiology
• Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle
  February 23, 2018
  Karthik Anantharaman, Bela Hausmann, Sean P Jungbluth, Rose S Kantor, Adi Lavy, Lesley A Warren, Michael S Rappé, Michael Pester, Alexander Loy, Brian C Thomas, Jillian F Banfield The ISME journal
• Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface
  January 31, 2018
  Alexander J Probst, Bethany Ladd, Jessica K Jarett, David E Geller-McGrath, Christian M K Sieber, Joanne B Emerson, Karthik Anantharaman, Brian C Thomas, Rex R Malmstrom, Michaela Stieglmeier, Andreas Klingl, Tanja Woyke, M Cathryn Ryan, Jillian F Banfield Nature microbiology
• Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium"
  December 17, 2017
  Sarah Zecchin, Ralf C Mueller, Jana Seifert, Ulrich Stingl, Karthik Anantharaman, Martin von Bergen, Lucia Cavalca, Michael Pester Applied and environmental microbiology
• Complete 4.55-Megabase-Pair Genome of "Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences
  November 24, 2017
  Jillian F Banfield, Karthik Anantharaman, Kenneth H Williams, Brian C Thomas Genome announcements
• Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments
  March 29, 2017
  Alex W Hernsdorf, Yuki Amano, Kazuya Miyakawa, Kotaro Ise, Yohey Suzuki, Karthik Anantharaman, Alexander Probst, David Burstein, Brian C Thomas, Jillian F Banfield The ISME journal

The fundamental focus of our interdisciplinary research program is to integrate microbial and viral ecology with data science to study human health, ecosystem change, and biogeochemistry. Towards this, we study the basic biology and ecology of phage and microbial metabolic interactions in human and environmental microbiomes, and integrate omics approaches with ecological data to enhance our ability to predict microbiome, ecosystem, and host health states.

There are three distinct facets of our research program:

1. Computational Biology (Microbial and Viral bioinformatics)

Our research program in computational biology is focused on microbial and viral bioinformatics with a concentration on developing algorithms, software, and databases to advance ecological interpretations from microbiome and genomic data. We have developed widely used scalable approaches and software to use metagenomic data and characterize viruses (VIBRANT, vRhyme, PropagAtE, ViWrap) and microbial metabolism and interactions from microbiomes (METABOLIC).

2. Viral and Microbial Ecology

Our research program in viral and microbial ecology spans both human and environmental systems with a focus on studying the ecological roles and contributions of individual organisms and viruses. Our research involves collaborations with clinicians to study human microbiomes, as well as fieldwork in freshwater and deep-sea systems to study environmental microbiomes.

3. Sulfur Metabolism and Biogeochemistry

Our research program in sulfur metabolism and biogeochemistry focuses on (i) unraveling the role of viruses in modulating sulfur metabolism and biogeochemistry, and (ii) characterizing the ecology and physiology of microorganisms and metabolic pathways in sulfur transformations.

Microbiology 450: Diversity, Ecology and Evolution of Microorganisms

• 2022, UW-Madison Vilas Faculty Early Career Investigator
• 2022, American Society for Microbiology (ASM) Early Career Award for Environmental Research
• 2022, Kavli Fellow – National Academy of Sciences
• 2021, NIH NIGMS Outstanding Investigator Award
• 2021, NSF CAREER Award

Start and Promotion Dates

• Assistant Professor: 2018
• Associate Professor: 2023

Education

B.Tech., Civil Engineering, National Institute of Technology, Karnataka, India
M.S.E., Civil and Environmental Engineering, University of Michigan
Ph.D., Earth and Environmental Sciences, University of Michigan
Postdoctoral Research: University of California-Berkeley

• Peter Badciong – Grad Student
• Mattie Carmody – Undergrad Student
• Mia Chen – Honorary Associate
• Etan Dieppa – Grad Student
• Amelia Harrison – Undergrad Student
• Xing Huang – Postdoc
• Neha Kashyap – Research Technician
• Katherine Klier – Grad Student
• James Kosmopoulos – Grad Student
• Dinesh Kumar Kuppa Baskaran – Grad Student
• Maggie Langwig – Grad Student
• Jaimie West – Honorary Associate