K. Anantharaman

Characterization of sediment and granite hosted deep underground research laboratories reveals diverse microbiome functions, limited temporal variation and substantial genomic conservation

The paper characterizes microbiomes in underground research labs, finding genomic conservation and similar functional profiles despite environmental differences.

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

The paper analyzes a 20-year viral time-series in a freshwater lake to uncover seasonal dynamics, environmental drivers, and evolutionary patterns of viral diversity and ecology.

SAR324 and related lineages are associated with the evolutionary history and origins of dsr-mediated sulfur oxidation

This study investigates the evolutionary history of sulfur oxidation by analyzing SAR324 and related bacterial phyla, finding that they are linked to the origins of the reverse dsr pathway.

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

This study compares viral communities from viromes and metagenomes across diverse environments, showing method choice affects ecological interpretation and recommending both approaches for comprehensive analysis.

Determinants of Gastrointestinal Group B Streptococcus Carriage in Adults

This study identifies risk factors for gastrointestinal Group B Streptococcus (GBS) carriage in adults by analyzing stool samples and survey data, finding associations with iron consumption and dental hygiene.

Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction

This study redefines the global diversity of sulfate/sulfite-reducing microorganisms using metagenomic data and identifies genetic markers for their ecophysiology.

Viral impacts on microbial activity and biogeochemical cycling in a seasonally anoxic freshwater lake

The paper examines how seasonal anoxia affects viral and microbial biogeochemical cycling in a freshwater lake using metagenomic and metatranscriptomic data.

Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick

The paper investigates viral and bacterial communities in slick and non-slick sea-surface microlayers, finding distinct viral communities and metabolic profiles in slicks.

Massively parallel single-cell sequencing of genetic loci in diverse microbial populations

This paper introduces DoTA-seq, a method for single-cell sequencing of genetic loci in microbial populations, and demonstrates its application in studying phase-variable operons and antibiotic resistance gene shifts.

Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes

The paper uses metagenome-based metabolic modeling to predict microbial interactions in deep-sea hydrothermal plume microbiomes, identifying key species and metabolic exchanges.

Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes

This paper identifies novel enzymes from gut Firmicutes that convert 'kinked' primary bile acids into 'flat' secondary bile acids, with increased abundance in colorectal cancer patients.

Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

This study analyzes microbial diversity and metabolism in deep-sea hydrothermal vent deposits, identifying novel taxa and metabolic pathways across multiple sites.

The sulfur cycle connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes

This study links sulfur metabolism in deep-sea hydrothermal plumes to microbial biogeography and biogeochemical cycling using genomic data from 37 plumes across 8 ocean basins.

Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes

This study identifies bacteria in oxic freshwater lakes that produce hydrogen sulfide through cysteine degradation, revealing a new pathway for sulfur cycling in oxygenated environments.

Diversity and distribution of sulfur metabolism in the human gut microbiome and its association with colorectal cancer

The paper examines sulfur metabolism in the human gut microbiome, finding it more diverse and associated with colorectal cancer.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

This study uses depth-discrete metagenomics to reveal microbial roles in biogeochemical cycling in Lake Tanganyika's anoxic waters.

Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

The paper identifies differential intestinal bacteriophage communities in individuals at risk for RA based on anti-CCP status, linking them to distinct metabolic potentials and potential roles in RA pathogenesis.

Virus-associated organosulfur metabolism in human and environmental systems

This study identifies 39 viral gene families involved in organosulfur metabolism across diverse ecosystems, showing their role in sulfide production and viral fitness.

Completion of the gut microbial epi-bile acid pathway

The paper identifies the gene encoding 12{beta}-HSDH, completes the epi-bile acid pathway, and shows its prevalence in the human gut microbiome.

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

The paper identifies 227 auxiliary metabolic genes in 191 phages from twelve environments, showing their role in sulfur and thiosulfate oxidation and ecological impact on biogeochemistry.

Microbial dark matter driven degradation of carbon fiber polymer composites

The paper investigates microbial degradation of carbon fiber polymer composites using multi-omics and materials characterization, identifying key microbial groups and pathways involved in composite breakdown.

Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation

This study identifies a broader phylogenetic and metabolic diversity of microbial mercury methylators using genome-resolved metagenomics and metatranscriptomics.

Accurate and Complete Genomes from Metagenomes

The paper improves metagenome-assembled genomes (MAGs) by curating them to achieve complete, circularized genomes (CMAGs) using cumulative GC skew and other metrics.

Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation

The paper characterizes novel marine Proteobacteria from hydrothermal vents using multi-omics, revealing their metabolic diversity and environmental adaptation strategies.

Clades of huge phage from across Earth’s ecosystems

The paper identifies major clades of large phage genomes across diverse ecosystems and highlights their expanded genetic repertoires and potential functional roles.

Connections between freshwater carbon and nutrient cycles revealed through reconstructed population genomes

The paper links freshwater carbon and nutrient cycles by analyzing microbial population genomes and marker genes from two aquatic environments, showing co-occurrence of metabolic pathways and taxonomic patterns.

Megaphage infect Prevotella and variants are widespread in gut microbiomes

The paper identifies large phage (Lak phage) in gut microbiomes that infect Prevotella and are widespread, especially in developing-world individuals.

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

This paper predicts the metabolisms of Margulisbacteria and Saganbacteria using genomic data and compares them to their phylogenetic neighbors, supporting the hypothesis that their ancestor used hydrogen metabolism and fermentation.

Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium

The paper identifies a novel Nitrospirae genus, Candidatus Sulfobium, in rice paddy soil that encodes and expresses genes for sulfate respiration and nitrate reduction, suggesting its role in sulfur cycling.

Dramatic expansion of microbial groups that shape the global sulfur cycle

This study identifies sulfate reduction capacity in twelve bacterial and archaeal phyla, doubling the known diversity of microbes involved in the sulfur cycle.