Below is a list of publications from our laboratory. For a more comprehensive list, please visit Karthik’s Google Scholar page


Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, Landick R, Venturelli OS (2023). Massively parallel single-cell sequencing of genetic loci in diverse microbial populations. Nature Methods (in press).

Huang X, Zhou Z, Liu H, Li Y, Ge T, Tang X, He Y, Ma B, Xu J, Anantharaman K, Li Y. Soil nutrient conditions alter viral lifestyle strategy and potential function in phosphorous and nitrogen metabolisms. Soil Biology and Biochemistry, 189, 109279.

Ji M, Xu X, Xu Q, Hsiao Y-C, Martin C, Ukraintseva S, Popov V, Arbeev KG, Randall TA, Wu X, Garcia-Peterson LM, Liu J, Xu X, Azcarate-Peril MA, Wan Y, Yashin AI, Anantharaman K, Lu K, Li J-L, Shats I, Xiaoling Li (2023). Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota. Nature Metabolism 5, 1526–1543.

Rahlff J, Wietz M, Giebel H-A, Bayfield O, Nilsson E, Bergström K, Kieft K, Anantharaman K, Ribas-Ribas M, Schweitzer HD, Wurl O, Hoetzinger M, Antson A, Holmfeldt K (2023). Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick. The ISME Journal, 3, 97.

Elsayed NS, Valenzuela RK, Kitchner T, Le T, Mayer J, Tang Z-Z, Bayanagari VR, Lu Q, Aston P, Anantharaman K, Shukla SK (2023). Genetic risk score in multiple sclerosis is associated with unique gut microbiome. Scientific Reports, 13, 1, 16269.

Zhou K, Wong TY, Long L, Anantharaman K, Weipeng Zhang, Wong WC, Zhang R, Qian P-Y (2023). Genomic and transcriptomic insights into complex virus–prokaryote interactions in marine biofilms. The ISME Journal (in press).

Diao M, Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, Pester M (2023). Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiology Reviews, 47, 5, fuad058.

Zhou Z, Tran PQ, Adams AM, Kieft K, Breier JA, Fortunato CS, Sheik CS, Huber JA, Li M, Dick GJ, Anantharaman K** (2023). Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes. The ISME Journal, 17, 1194-1207.

Baskaran DKK, 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.

Zhou Z, Martin C, Kosmopoulos JC, Anantharaman K** (2023). ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes. iMeta, e118.

Tran PQ ^, Bachand SC ^, Hotvedt JC ^, Kieft K, McDaniel EA, McMahon KD, and Anantharaman K** (2023). Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes. mSystems, e00201-23.

Cheng Y-Y, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM, and Venturelli OS (2023). Efficient plasmid transfer via natural competence in a synthetic microbial community. Molecular Systems Biology,




Lee JW, Cowley ES, Wolf PG, Doden HL, Murai T, Caicedo KYO, Ly LK, Sun F, Nittono H, Daniel SL, Cann I, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM (2022). Novel Firmicutes enzymes involved in allo-secondary bile acid production. Gut Microbes, 14 (1), 2132903.

Zhou Z ^, St. John E ^, Anantharaman K**, Anna-Louise Reysenbach**. Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits (2022). Microbiome, 10, 241.

Chelluboina B, Kieft K, Breister A, Anantharaman K, Vemuganti R (2022). Gut virome dysbiosis following focal cerebral ischemia in mice. Journal of Cerebral Blood Flow & Metabolism, 42 (9), 1597-1602.

Kieft K, Adams A, Salamzade R, Kalan L, and Anantharaman K** (2022). VRhyme enables binning of viral genomes from metagenomes. Nucleic Acids Research, 50 (14), e83.

Kieft K, Anantharaman K** (2022). Deciphering active prophages from metagenomes. mSystems, 7 (2), e00084-22.

Wolf PG^, Cowley ES^, Breister A, Matatov S, Lucio L, Polak P, Ridlon JM, Gaskins HR**, Anantharaman K** (2022). Diversity and distribution of sulfur metabolism in the human gut microbiome and its association with colorectal cancer. Microbiome, 10: 64. (+ co-first authors).

Zhou Z, Tran PQ, Breister A, Liu Y, Kieft K, Cowley E, Karaoz U, Anantharaman K** (2022). METABOLIC: A scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes. Microbiome, 10: 33.

Kieft K, Anantharaman K** (2022). Virus Genomics: What is being overlooked?. Current Opinion in Virology, 53 (April): 101200.

Feng J, Qian Y, Zhou Z, Ertmer S, Vivas E, Lan F, Rey FE, Anantharaman K, Venturelli OS (2022). Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell, Host and Microbe, 30 (2), 200-215.



Tran PQ, Anantharaman K** (2021). Biogeochemistry goes viral: towards a multifaceted approach to study viruses and biogeochemical cycling. mSystems, 6 (5), e01138-21.

Kieft K ^, Zhou Z ^, Anderson RE, Buchan A, Campbell BJ, Hallam SJ, Hess M, Sullivan MB, Walsh DA, Roux S, Anantharaman K** (2021). Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications, 12 (1), 1-16.

Tran PQ, McIntyre PB, Kraemer BM, Vadeboncoeur Y, Kimirei IA, Tamatamah R, McMahon KD, Anantharaman K** (2021) Depth-discrete ecogenomics of Lake Tanganyika reveals roles of diverse microbes, including candidate phyla, in tropical freshwater nutrient cycling. The ISME Journal, 15, 1971–1986.

Kieft K, Huss, P, Linz AM, Zanetakos E, Breister AM, Zhou Z, Roux S, Raman S, Anantharaman K** (2021). Virus-driven production of hydrogen sulfide in human and environmental systems. Cell Reports, 36(5): 109471.

Mangalea MR, Paez-Espino D, Kieft K ga, Chatterjee A, Seifert JA, Feser ML, Demoruelle MK, Chriswell ME, Sakatos A, Anantharaman K, Deane KD, Kuhn KA, Holers VM, Duerkop BA (2021). Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell, Host and Microbe, 29(5), 726-739.

Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JP, Ridlon JM (2021). Completion of the gut microbial epi-bile acid Gut Microbes, 13(1): 1–20.

Stewart BD, Sorensen J V., Wendt K, Sylvan JB, German CR, Anantharaman K, Dick GJ, Breier JA, Toner BM (2021). A multi-modal approach to measuring particulate iron speciation in buoyant hydrothermal plumes. Chemical Geology, 560:120018.


Zhou Z, Liu Y, Pan J, Cron BR, Toner BM, Anantharaman K, Breier JA, Dick GJ, Li M (2020) Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. The ISME Journal, :1–13.

Breister A, Imam MA, Zhou Z, Ahsan MA, Noveron JC, Anantharaman K*, Prabhakar P* (2020) Soil microbiomes mediate degradation of vinyl ester-based polymer composites. Communications Materials. 1, 101.

McDaniel EA, Peterson BD, Stevens SLR, Tran PQ, Anantharaman K, McMahon KD (2020) Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms. mSystems, 5(4).

Kieft K, Zhou Z, Anantharaman K (2020) VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome, 8(1):90.

Zhou Z, Tran PQ, Kieft K, Anantharaman K (2020) Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. The ISME Journal, 14(8):2060–2077.

Murray AE et al. (2020) Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5(8):987–994.


McDaniel EA, Anantharaman K, McMahon KD (2019) metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways. bioRxiv, 884627.