Karthik Anantharaman

ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 53

Top Venues

bioRxiv : the preprint server for biology

Nature methods

The ISME journal

Nature microbiology

University of Wisconsin Madison

University of Michigan (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Wisconsin Madison

United States

Assistant Professor :: Bacteriology

University of California Berkeley

United States

Postdoc :: Earth and Planetary Science

Education History

University of Michigan

United States

PHD :: Earth and Environmental Sciences

Publications

Nikhil A George, Zhichao Zhou, Karthik Anantharaman, Barbara A Katzenback
Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills. bioRxiv : the preprint server for biology (2024)
Etan Dieppa-Colón, Cody Martin, Karthik Anantharaman
Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages. bioRxiv : the preprint server for biology (2024)
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli
Massively parallel single-cell sequencing of diverse microbial populations. Nature methods 21 (2) (2024)
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli
Massively parallel single-cell sequencing of diverse microbial populations. Nature methods (2024)
Nikhil A George, Zhichao Zhou, Karthik Anantharaman, Barbara A Katzenback
Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills. bioRxiv : the preprint server for biology (2024)
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli
Massively parallel single-cell sequencing of diverse microbial populations. Nature methods (2024)
Nikhil A George, Zhichao Zhou, Karthik Anantharaman, Barbara A Katzenback
Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills. bioRxiv : the preprint server for biology (2024)
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli
Massively parallel single-cell sequencing of diverse microbial populations. Nature methods 21 (2) (2024)
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli
Massively parallel single-cell sequencing of diverse microbial populations. Nature methods 21 (2) (2024)
Chutikarn Chitboonthavisuk, Cody Martin, Phil Huss, Jason M Peters, Karthik Anantharaman, Srivatsan Raman
Systematic genome-wide discovery of host factors governing bacteriophage infectivity. bioRxiv : the preprint server for biology (2024)
Etan Dieppa-Colón, Cody Martin, Karthik Anantharaman
Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages. bioRxiv : the preprint server for biology (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, Christopher Daum, Alex Copeland, I-Min A Chen, Natalia N Ivanova, Nikos C Kyrpides, Nigel J Mouncey, Tijana Glavina Del Rio, Igor V Grigoriev, Steven Hofmeyr, Leonid Oliker, Katherine Yelick, Karthik Anantharaman, Katherine D McMahon, Tanja Woyke, Emiley A Eloe-Fadrosh
Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota. Scientific data 11 (1) (2024)
Kelly Y Olivos-Caicedo, Francelys V Fernandez-Materan, Steven L Daniel, Karthik Anantharaman, Jason M Ridlon, João Marcelo P Alves
Pangenome analysis of Clostridium scindens : a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains. bioRxiv : the preprint server for biology (2024)
Chutikarn Chitboonthavisuk, Cody Martin, Phil Huss, Jason M Peters, Karthik Anantharaman, Srivatsan Raman
Systematic genome-wide discovery of host factors governing bacteriophage infectivity. bioRxiv : the preprint server for biology (2024)
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli
Massively parallel single-cell sequencing of diverse microbial populations. Nature methods 21 (2) (2024)
Cody Martin, Anthony Gitter, Karthik Anantharaman
Protein Set Transformer: A protein-based genome language model to power high diversity viromics. bioRxiv : the preprint server for biology (2024)
Cody Martin, Anthony Gitter, Karthik Anantharaman
Protein Set Transformer: A protein-based genome language model to power high diversity viromics. bioRxiv : the preprint server for biology (2024)
Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli
Massively parallel single-cell sequencing of diverse microbial populations. Nature methods 21 (2) (2024)
Zhichao Zhou, Patricia Q Tran, Alyssa M Adams, Kristopher Kieft, John A Breier, Caroline S Fortunato, Cody S Sheik, Julie A Huber, Yuhan Huang, Gregory J Dick, Karthik Anantharaman
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes. The ISME journal (2023)
Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Ashlee M Earl, Karthik Anantharaman, Lindsay R Kalan
zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. bioRxiv : the preprint server for biology (2023)
Yiyi Liu, Yu-Yu Cheng, Zhichao Zhou, Eugenio I Vivas, Matthew F Warren, Federico E Rey, Karthik Anantharaman, Ophelia S Venturelli
Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway. bioRxiv : the preprint server for biology (2023)
Dinesh Kumar Kuppa Baskaran, Shreyansh Umale, Zhichao Zhou, Karthik Raman, Karthik Anantharaman
Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes. ISME communications 3 (1) (2023)
Dinesh Kumar Kuppa Baskaran, Shreyansh Umale, Zhichao Zhou, Karthik Raman, Karthik Anantharaman
Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes. ISME communications 3 (1) (2023)
Ming Ji, Xiaojiang Xu, Qing Xu, Yun-Chung Hsiao, Cody Martin, Svetlana Ukraintseva, Vladimir Popov, Konstantin G Arbeev, Thomas A Randall, Xiaoyue Wu, Liz M Garcia-Peterson, Juan Liu, Xin Xu, M Andrea Azcarate-Peril, Yisong Y Wan, Anatoliy I Yashin, Karthik Anantharaman, Kun Lu, Jian-Liang Li, Igor Shats, Xiaoling Li
Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota. Nature metabolism (2023)
Zhichao Zhou, Cody Martin, James C Kosmopoulos, Karthik Anantharaman
ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes. bioRxiv : the preprint server for biology (2023)
James C Kosmopoulos, Katherine M Klier, Marguerite V Langwig, Patricia Q Tran, Karthik Anantharaman
Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology. bioRxiv : the preprint server for biology (2023)
Zhichao Zhou, Cody Martin, James C Kosmopoulos, Karthik Anantharaman
ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes. bioRxiv : the preprint server for biology (2023)
Zhichao Zhou, Cody Martin, James C Kosmopoulos, Karthik Anantharaman
ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes. bioRxiv : the preprint server for biology (2023)
Elise S Cowley, Ibrahim Zuniga Chaves, Fauzia Osman, Garret Suen, Karthik Anantharaman, Andrew J Hryckowian
Determinants of Gastrointestinal Group B Streptococcus Carriage in Adults. bioRxiv : the preprint server for biology (2023)
Patricia Q Tran, Samantha C Bachand, Jacob C Hotvedt, Kristopher Kieft, Elizabeth A McDaniel, Katherine D McMahon, Karthik Anantharaman
Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria. mSystems (2023)
Janina Rahlff, Matthias Wietz, Helge-Ansgar Giebel, Oliver W Bayfield, Emelie Nilsson, Kristofer Bergström, Kristopher Kieft, Karthik Anantharaman, Mariana Ribas-Ribas, Hannah D Schweitzer, Oliver Wurl, Matthias Hoetzinger, Alfred Antson, Karin Holmfeldt
Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick. ISME communications 3 (1) (2023)
Muhe Diao, Stefan Dyksma, Elif Koeksoy, David Kamanda Ngugi, Karthik Anantharaman, Alexander Loy, Michael Pester
Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS microbiology reviews (2023)
Kun Zhou, Tin Yan Wong, Lexin Long, Karthik Anantharaman, Weipeng Zhang, Wai Chuen Wong, Rui Zhang, Pei-Yuan Qian
Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms. The ISME journal (2023)
Phil Huss, Kristopher Kieft, Anthony Meger, Kyle K Nishikawa, Karthik Anantharaman, Srivatsan Raman
Deep metagenomic mining reveals bacteriophage sequence motifs driving host specificity. bioRxiv : the preprint server for biology (2023)
James C Kosmopoulos, Karthik Anantharaman
To cull or kill. Nature ecology & evolution (2023)
Kristopher Kieft, Alyssa Adams, Rauf Salamzade, Lindsay Kalan, Karthik Anantharaman
vRhyme enables binning of viral genomes from metagenomes. Nucleic acids research 50 (14) (2022)
Patricia G Wolf, Elise S Cowley, Adam Breister, Sarah Matatov, Luke Lucio, Paige Polak, Jason M Ridlon, H Rex Gaskins, Karthik Anantharaman
Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer. Microbiome 10 (1) (2022)
Zhichao Zhou, Patricia Q Tran, Adam M Breister, Yang Liu, Kristopher Kieft, Elise S Cowley, Ulas Karaoz, Karthik Anantharaman
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 10 (1) (2022)
Kristopher Kieft, Karthik Anantharaman
Deciphering Active Prophages from Metagenomes. mSystems 7 (2) (2022)
Patricia Q Tran, Samantha C Bachand, Peter B McIntyre, Benjamin M Kraemer, Yvonne Vadeboncoeur, Ismael Aaron Kimirei, Rashid Tamatamah, Katherine D McMahon, Karthik Anantharaman
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. The ISME journal 15 (7) (2021)
Kristopher Kieft, Zhichao Zhou, Rika E Anderson, Alison Buchan, Barbara J Campbell, Steven James Hallam, Matthias Hess, Matthew B Sullivan, David A Walsh, Simon Roux, Karthik Anantharaman
Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature communications 12 (1) (2021)
Kristopher Kieft, Zhichao Zhou, Karthik Anantharaman
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8 (1) (2020)
Zhichao Zhou, Patricia Q Tran, Kristopher Kieft, Karthik Anantharaman
Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. The ISME journal 14 (8) (2020)
Lin-Xing Chen, Karthik Anantharaman, Alon Shaiber, A Murat Eren, Jillian F Banfield
Accurate and complete genomes from metagenomes. Genome research 30 (3) (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, Roman A Barco, Helge B Bode, Eric S Boyd, Carrie L Brady, Paul Carini, Patrick S G Chain, Daniel R Colman, Kristen M DeAngelis, Maria Asuncion de Los Rios, Paulina Estrada-de Los Santos, Christopher A Dunlap, Jonathan A Eisen, David Emerson, Thijs J G Ettema, Damien Eveillard, Peter R Girguis, Ute Hentschel, James T Hollibaugh, Laura A Hug, William P Inskeep, Elena P Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G Lloyd, Frank E Löffler, Thulani Peter Makhalanyane, Duane P Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedrós-Alió, Alexander J Probst, Theo H M Smits, Andrew D Steen, Emma T Steenkamp, Anja Spang, Frank J Stewart, James M Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P Hedlund, Anna-Louise Reysenbach
Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology (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, Roman A Barco, Helge B Bode, Eric S Boyd, Carrie L Brady, Paul Carini, Patrick S G Chain, Daniel R Colman, Kristen M DeAngelis, Maria Asuncion de Los Rios, Paulina Estrada-de Los Santos, Christopher A Dunlap, Jonathan A Eisen, David Emerson, Thijs J G Ettema, Damien Eveillard, Peter R Girguis, Ute Hentschel, James T Hollibaugh, Laura A Hug, William P Inskeep, Elena P Ivanova, Hans-Peter Klenk, Wen-Jun Li, Karen G Lloyd, Frank E Löffler, Thulani Peter Makhalanyane, Duane P Moser, Takuro Nunoura, Marike Palmer, Victor Parro, Carlos Pedrós-Alió, Alexander J Probst, Theo H M Smits, Andrew D Steen, Emma T Steenkamp, Anja Spang, Frank J Stewart, James M Tiedje, Peter Vandamme, Michael Wagner, Feng-Ping Wang, Pablo Yarza, Brian P Hedlund, Anna-Louise Reysenbach
Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology 5 (8) (2020)
Zhichao Zhou, Yang Liu, Jie Pan, Brandi R Cron, Brandy M Toner, Karthik Anantharaman, John A Breier, Gregory J Dick, Yuhan Huang
Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. The ISME journal 14 (12) (2020)
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
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nature communications 10 (1) (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
Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature microbiology 4 (8) (2019)
Cindy J Castelle, Christopher T Brown, Karthik Anantharaman, Alexander J Probst, Raven H Huang, Jillian F Banfield
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nature reviews. Microbiology 16 (10) (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
Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nature communications 10 (1) (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 Møller Aarestrup, Brian C Thomas, Jillian F Banfield
Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nature microbiology 4 (4) (2019)
Keith Bouma-Gregson, Matthew R Olm, Alexander J Probst, Karthik Anantharaman, Mary E Power, Jillian F Banfield
Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. The ISME journal 13 (6) (2019)

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Publication Activity (10 Years)

Top Topics

Top Venues

Karthik Anantharaman