Karthik Anantharaman

The paper shows RNA polymerase backtracking promotes type III-A CRISPR DNA targeting by inhibiting GreA anti-backtracking factors, which suppress Cas10-Csm activity.

CheckAMG identifies auxiliary viral genes by combining annotation-based prediction with a genome-language model, improving accuracy and uncovering novel genes with no sequence similarity to references.

This study uses deep mutational scanning to analyze a phage tailspike protein, revealing structural constraints and adaptive flexibility that influence its function and host range.

This study identifies amoC-encoding phages in freshwater lakes and shows their depth-structured infection patterns linked to ammonia-oxidizing bacteria.

The paper shows that phage-host predictions from MAGs are unreliable due to scaffold-level errors and proposes a validation framework to improve accuracy.

The paper identifies conjugative megaplasmids in the human gut microbiome that can disseminate prophage genomes across bacterial lineages, explaining their wide distribution.

vClassifier provides species-level taxonomic classification of prokaryotic viruses using phylogeny-informed methods, achieving high congruence with ICTV and NCBI Virus databases.

The paper introduces PST, a protein-based genome language model that outperforms existing methods in relating viral genomes through shared protein content and demonstrates structural and functional awareness.

The paper identifies novel viruses, auxiliary metabolic genes, and CRISPR-Cas systems in landfill viromes, highlighting unique virus-host interactions and genetic features.

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

This study identifies viruses from hydrothermal vents and shows that while many are endemic, some share proteins related to core functions, suggesting geology influences viral ecology and host coevolution.

This study identifies a bacterial pathway for androgen production, showing that gut and urinary bacteria can convert androstenedione to epitestosterone and testosterone, which promote prostate cancer growth.

This paper introduces Meta-SIFT, a method to discover functional sequence motifs in metagenomes to engineer bacteriophage activity, demonstrating its utility in creating variants with novel host specificity.

This study analyzes the pangenome of 34 C. scindens strains and 200 MAGs to understand genetic variability and functional roles in bile acid and steroid metabolism.

The paper examines phage interactions with chemosynthetic symbionts of hydrothermal vent snails and mussels, finding species-specific phages influence strain-level diversity and population dynamics.

The paper introduces fai and zol for large-scale comparative analysis of gene clusters and MGEs, enabling comprehensive orthology inference and evolutionary studies across thousands of genomes.

The paper introduces Prophage-DB, a database of over 350,000 prophages and 35,000 auxiliary metabolic genes, providing insights into prophage diversity, distribution, and ecological roles.

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

This study identifies keystone taxa in Lake Mendota's microbial networks and shows their role in nutrient cycling and adaptability to environmental changes.

The paper introduces V-score and VL-score metrics to identify viral signatures in protein families and genomes, finding 38-77% of families are linked to viruses, up to 17x more auxiliary viral genes.

The paper introduces PHAGEPACK, a CRISPR-based assay to systematically identify host genes affecting phage infectivity, revealing new pathways in both permissive and non-permissive E. coli.

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.

ViWrap provides a modular pipeline for analyzing viruses in metagenomes, enabling identification, classification, and host prediction through integration of multiple tools.

This study shows that controlling the arginine dihydrolase pathway in E. coli affects gut community assembly and butyrate production in vitro and in mice.

The paper investigates the association between polygenic risk score and gut microbiome in MS patients, finding distinct microbiota profiles in clusters with higher genetic risk.

vRhyme is a software tool that bins viral genomes from metagenomes, producing more complete and uncontaminated viral metagenome-assembled genomes (vMAGs) than existing methods.

PropagAtE identifies active prophages in metagenomes by analyzing read coverage ratios, revealing distinct activation patterns across environments.

METABOLIC is a software tool for analyzing microbial genomes to predict metabolic functions, interactions, and contributions to biogeochemical cycles, showing better performance than existing tools.

The paper identifies PULs in B. uniformis that influence fitness and community interactions through glycan degradation and butyrate production.

The paper quantifies HGT efficiency in a synthetic microbial community and identifies factors influencing plasmid transfer via natural competence.