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Karthik Anantharaman, Ph.D - Publications

Affiliations: 
2018- Bacteriology University of Wisconsin, Madison, Madison, WI 
Area:
Microbial and viral ecology, bioinformatics, sulfur metabolism, biogeochemistry
Website:
https://anantharamanlab.wisc.edu/
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66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, Landick R, Venturelli OS. Massively parallel single-cell sequencing of diverse microbial populations. Nature Methods. PMID 38233503 DOI: 10.1038/s41592-023-02157-7  0.578
2023 Zhou Z, Martin C, Kosmopoulos JC, Anantharaman K. ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes. Imeta. 2. PMID 38152703 DOI: 10.1002/imt2.118  0.641
2023 Liu Y, Cheng YY, Zhou Z, Vivas EI, Warren MF, Rey FE, Anantharaman K, Venturelli OS. Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway. Biorxiv : the Preprint Server For Biology. PMID 37986770 DOI: 10.1101/2023.01.10.523442  0.586
2023 Kosmopoulos JC, Klier KM, Langwig MV, Tran PQ, Anantharaman K. Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology. Biorxiv : the Preprint Server For Biology. PMID 37904928 DOI: 10.1101/2023.10.15.562385  0.794
2023 Zhou K, Wong TY, Long L, Anantharaman K, Zhang W, Wong WC, Zhang R, Qian PY. Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms. The Isme Journal. PMID 37875603 DOI: 10.1038/s41396-023-01546-2  0.352
2023 Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M. Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. Fems Microbiology Reviews. 47. PMID 37796897 DOI: 10.1093/femsre/fuad058  0.4
2023 Rahlff J, Wietz M, Giebel HA, Bayfield O, Nilsson E, Bergström K, Kieft K, Anantharaman K, Ribas-Ribas M, Schweitzer HD, Wurl O, Hoetzinger M, Antson A, Holmfeldt K. Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick. Isme Communications. 3: 97. PMID 37723220 DOI: 10.1038/s43705-023-00307-8  0.804
2023 Salamzade R, Tran P, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. Biorxiv : the Preprint Server For Biology. PMID 37333121 DOI: 10.1101/2023.06.07.544063  0.747
2023 Tran PQ, Bachand SC, Hotvedt JC, Kieft K, McDaniel EA, McMahon KD, Anantharaman K. Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria. Msystems. e0020123. PMID 37285121 DOI: 10.1128/msystems.00201-23  0.799
2023 Mangalea MR, Keift K, Duerkop BA, Anantharaman K. Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data. Methods in Molecular Biology (Clifton, N.J.). 2649: 317-337. PMID 37258871 DOI: 10.1007/978-1-0716-3072-3_17  0.36
2023 Zhou Z, Tran PQ, Adams AM, Kieft K, Breier JA, Fortunato CS, Sheik CS, Huber JA, Li M, Dick GJ, Anantharaman K. Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes. The Isme Journal. PMID 37179442 DOI: 10.1038/s41396-023-01421-0  0.793
2023 Kuppa Baskaran DK, Umale S, Zhou Z, Raman K, Anantharaman K. Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes. Isme Communications. 3: 42. PMID 37120693 DOI: 10.1038/s43705-023-00242-8  0.631
2023 Huss P, Kieft K, Meger A, Nishikawa K, Anantharaman K, Raman S. Deep metagenomic mining reveals bacteriophage sequence motifs driving host specificity. Biorxiv : the Preprint Server For Biology. PMID 36798209 DOI: 10.1101/2023.02.07.527309  0.763
2023 Zhou Z, Martin C, Kosmopoulos JC, Anantharaman K. ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes. Biorxiv : the Preprint Server For Biology. PMID 36778280 DOI: 10.1101/2023.01.30.526317  0.641
2023 Cheng YY, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM, Venturelli OS. Efficient plasmid transfer via natural competence in a microbial co-culture. Molecular Systems Biology. e11406. PMID 36714980 DOI: 10.15252/msb.202211406  0.524
2022 Zhou Z, St John E, Anantharaman K, Reysenbach AL. Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits. Microbiome. 10: 241. PMID 36572924 DOI: 10.1186/s40168-022-01424-7  0.651
2022 Chelluboina B, Kieft K, Breister A, Anantharaman K, Vemuganti R. Gut virome dysbiosis following focal cerebral ischemia in mice. Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism. 271678X221107702. PMID 35702025 DOI: 10.1177/0271678X221107702  0.755
2022 Kieft K, Adams A, Salamzade R, Kalan L, Anantharaman K. vRhyme enables binning of viral genomes from metagenomes. Nucleic Acids Research. PMID 35544285 DOI: 10.1093/nar/gkac341  0.808
2022 Kieft K, Anantharaman K. Deciphering Active Prophages from Metagenomes. Msystems. e0008422. PMID 35323045 DOI: 10.1128/msystems.00084-22  0.796
2022 Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, Cowley ES, Karaoz U, Anantharaman K. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome. 10: 33. PMID 35172890 DOI: 10.1186/s40168-021-01213-8  0.813
2022 Kieft K, Anantharaman K. Virus genomics: what is being overlooked? Current Opinion in Virology. 53: 101200. PMID 35051682 DOI: 10.1016/j.coviro.2022.101200  0.796
2022 Feng J, Qian Y, Zhou Z, Ertmer S, Vivas EI, Lan F, Hamilton JJ, Rey FE, Anantharaman K, Venturelli OS. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Host & Microbe. PMID 34995484 DOI: 10.1016/j.chom.2021.12.006  0.608
2021 Tran PQ, Anantharaman K. Biogeochemistry Goes Viral: towards a Multifaceted Approach To Study Viruses and Biogeochemical Cycling. Msystems. 6: e0113821. PMID 34636672 DOI: 10.1128/mSystems.01138-21  0.756
2021 Kieft K, Breister AM, Huss P, Linz AM, Zanetakos E, Zhou Z, Rahlff J, Esser SP, Probst AJ, Raman S, Roux S, Anantharaman K. Virus-associated organosulfur metabolism in human and environmental systems. Cell Reports. 36: 109471. PMID 34348151 DOI: 10.1016/j.celrep.2021.109471  0.802
2021 Kieft K, Zhou Z, Anderson RE, Buchan A, Campbell BJ, Hallam SJ, Hess M, Sullivan MB, Walsh DA, Roux S, Anantharaman K. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications. 12: 3503. PMID 34108477 DOI: 10.1038/s41467-021-23698-5  0.815
2021 Mangalea MR, Paez-Espino D, Kieft K, Chatterjee A, Chriswell ME, Seifert JA, Feser ML, Demoruelle MK, Sakatos A, Anantharaman K, Deane KD, Kuhn KA, Holers VM, Duerkop BA. Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell Host & Microbe. PMID 33957082 DOI: 10.1016/j.chom.2021.03.020  0.748
2021 Tran PQ, Bachand SC, McIntyre PB, Kraemer BM, Vadeboncoeur Y, Kimirei IA, Tamatamah R, McMahon KD, Anantharaman K. Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. The Isme Journal. PMID 33564113 DOI: 10.1038/s41396-021-00898-x  0.793
2020 Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, ... ... Anantharaman K, et al. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology. PMID 33184503 DOI: 10.1038/s41564-020-00827-2  0.521
2020 Zhou Z, Liu Y, Pan J, Cron BR, Toner BM, Anantharaman K, Breier JA, Dick GJ, Li M. Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. The Isme Journal. PMID 32820229 DOI: 10.1038/S41396-020-00745-5  0.707
2020 McDaniel EA, Peterson BD, Stevens SLR, Tran PQ, Anantharaman K, McMahon KD. Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms. Msystems. 5. PMID 32817383 DOI: 10.1128/mSystems.00299-20  0.786
2020 Kieft K, Zhou Z, Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 8: 90. PMID 32522236 DOI: 10.1186/s40168-020-00867-0  0.833
2020 Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, ... ... Anantharaman K, et al. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology. PMID 32514073 DOI: 10.1038/S41564-020-0733-X  0.659
2020 Zhou Z, Tran PQ, Kieft K, Anantharaman K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. The Isme Journal. PMID 32393808 DOI: 10.1038/s41396-020-0669-4  0.81
2020 Chen LX, Anantharaman K, Shaiber A, Eren AM, Banfield JF. Accurate and complete genomes from metagenomes. Genome Research. PMID 32188701 DOI: 10.1101/Gr.258640.119  0.589
2020 Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, ... ... Anantharaman K, et al. Clades of huge phages from across Earth's ecosystems. Nature. PMID 32051592 DOI: 10.1038/S41586-020-2007-4  0.803
2019 Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF. Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature Microbiology. PMID 31110364 DOI: 10.1038/S41564-019-0449-Y  0.551
2019 Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, et al. Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nature Communications. 10: 1451. PMID 30914645 DOI: 10.1038/S41467-019-09423-3  0.379
2019 Bouma-Gregson K, Olm MR, Probst AJ, Anantharaman K, Power ME, Banfield JF. Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. The Isme Journal. PMID 30809011 DOI: 10.1038/S41396-019-0374-3  0.551
2019 Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nature Microbiology. PMID 30692672 DOI: 10.1038/S41564-018-0338-9  0.593
2019 Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, et al. Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nature Communications. 10: 463. PMID 30692531 DOI: 10.1038/S41467-018-08246-Y  0.561
2018 Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. Peerj. 6: e6075. PMID 30581671 DOI: 10.7717/Peerj.6075  0.426
2018 Castelle CJ, Brown CT, Anantharaman K, Probst AJ, Huang RH, Banfield JF. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nature Reviews. Microbiology. PMID 30181663 DOI: 10.1038/S41579-018-0076-2  0.59
2018 Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. The Isme Journal. PMID 29467397 DOI: 10.1038/S41396-018-0078-0  0.598
2018 Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, Anantharaman K, Thomas BC, Malmstrom RR, Stieglmeier M, Klingl A, Woyke T, Ryan MC, Banfield JF. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nature Microbiology. PMID 29379208 DOI: 10.1038/S41564-017-0098-Y  0.605
2017 Zecchin S, Mueller RC, Seifert J, Stingl U, Anantharaman K, von Bergen M, Cavalca L, Pester M. Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium. Applied and Environmental Microbiology. PMID 29247059 DOI: 10.1128/Aem.02224-17  0.344
2017 Banfield JF, Anantharaman K, Williams KH, Thomas BC. Complete 4.55-Megabase-Pair Genome of "Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences. Genome Announcements. 5. PMID 29167246 DOI: 10.1128/Genomea.01299-17  0.516
2017 Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst A, Burstein D, Thomas BC, Banfield JF. Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. The Isme Journal. PMID 28350393 DOI: 10.1038/Ismej.2017.39  0.665
2017 Kantor RS, Huddy RJ, Iyer RM, Thomas BC, Brown CT, Anantharaman K, Tringe SG, Hettich RL, Harrison ST, Banfield JF. Genome-resolved meta-omics ties microbial dynamics to process performance in biotechnology for thiocyanate degradation. Environmental Science & Technology. PMID 28139919 DOI: 10.1021/Acs.Est.6B04477  0.534
2017 Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. PMID 28077874 DOI: 10.1038/Nature21031  0.682
2016 Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR-Cas systems from uncultivated microbes. Nature. PMID 28005056 DOI: 10.1038/Nature21059  0.476
2016 Marcus DN, Pinto A, Anantharaman K, Ruberg SA, Kramer EL, Raskin L, Dick GJ. Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems. Environmental Microbiology Reports. PMID 27935222 DOI: 10.1111/1758-2229.12508  0.536
2016 Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications. 7: 13219. PMID 27774985 DOI: 10.1038/Ncomms13219  0.622
2016 Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, et al. A new view of the tree of life. Nature Microbiology. 1: 16048. PMID 27572647 DOI: 10.1038/Nmicrobiol.2016.48  0.766
2016 Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, Hug LA, Burstein D, Emerson JB, Thomas BC, Banfield JF. Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Environmental Microbiology. PMID 27112493 DOI: 10.1111/1462-2920.13362  0.566
2016 Anantharaman K, Brown CT, Burstein D, Castelle CJ, Probst AJ, Thomas BC, Williams KH, Banfield JF. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. Peerj. 4: e1607. PMID 26844018 DOI: 10.7717/Peerj.1607  0.566
2016 Burstein D, Sun CL, Brown CT, Sharon I, Anantharaman K, Probst AJ, Thomas BC, Banfield JF. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. Nature Communications. 7: 10613. PMID 26837824 DOI: 10.1038/Ncomms10613  0.507
2016 Anantharaman K, Breier JA, Dick GJ. Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center. The Isme Journal. 10: 225-39. PMID 26046257 DOI: 10.1038/Ismej.2015.81  0.678
2015 Varaljay VA, Satagopan S, North JA, Witte B, Dourado MN, Anantharaman K, Arbing MA, Hoeft McCann S, Oremland RS, Banfield JF, Wrighton KC, Tabita FR. Functional metagenomic selection of RubisCO from uncultivated bacteria. Environmental Microbiology. PMID 26617072 DOI: 10.1111/1462-2920.13138  0.486
2015 Li M, Baker BJ, Anantharaman K, Jain S, Breier JA, Dick GJ. Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea. Nature Communications. 6: 8933. PMID 26573375 DOI: 10.1038/Ncomms9933  0.759
2015 Reed DC, Breier JA, Jiang H, Anantharaman K, Klausmeier CA, Toner BM, Hancock C, Speer K, Thurnherr AM, Dick GJ. Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents. The Isme Journal. PMID 25658053 DOI: 10.1038/Ismej.2015.4  0.611
2015 Sheik CS, Anantharaman K, Breier JA, Sylvan JB, Edwards KJ, Dick GJ. Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin. The Isme Journal. 9: 1434-45. PMID 25489728 DOI: 10.1038/Ismej.2014.228  0.59
2014 Anantharaman K, Duhaime MB, Breier JA, Wendt KA, Toner BM, Dick GJ. Sulfur oxidation genes in diverse deep-sea viruses. Science (New York, N.Y.). 344: 757-60. PMID 24789974 DOI: 10.1126/Science.1252229  0.663
2014 Vorobev A, Jagadevan S, Jain S, Anantharaman K, Dick GJ, Vuilleumier S, Semrau JD. Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. Applied and Environmental Microbiology. 80: 3044-52. PMID 24610846 DOI: 10.1128/Aem.00218-14  0.553
2013 Dick GJ, Anantharaman K, Baker BJ, Li M, Reed DC, Sheik CS. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology. 4: 124. PMID 23720658 DOI: 10.3389/Fmicb.2013.00124  0.748
2013 Anantharaman K, Breier JA, Sheik CS, Dick GJ. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proceedings of the National Academy of Sciences of the United States of America. 110: 330-5. PMID 23263870 DOI: 10.1073/Pnas.1215340110  0.598
2012 Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. The Isme Journal. 6: 2257-68. PMID 22695860 DOI: 10.1038/Ismej.2012.63  0.641
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