Ami Siddharth Bhatt

This study shows that habituation in black bears alters their gut microbiome composition and function, leading to increased antimicrobial resistance and other health-related changes.

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

The paper identifies immunomodulatory bacterial microproteins from Leptotrichia using a microproteome screen and shows they influence macrophage polarization.

The paper shows that the K5 capsular polysaccharide of E. coli Nissle 1917 sensitizes it to thioridazine and related antipsychotics, revealing CPS as a vulnerability under non-antibiotic drug pressure.

This paper describes a study on participant engagement and feedback in microbiome projects in Africa, finding that culturally appropriate and timely feedback can improve trust and motivate health behaviors.

This study identifies ISL3 elements as drivers of rapid genomic evolution in E. faecium, enabling metabolic adaptation in clinical settings through structural variation and gene regulation.

This study compares the effects of two GVHD prophylaxis regimens on the gut microbiome in allo-HCT recipients and finds that while PTCy reduces microbiome diversity and bile acid metabolism, it is linked to better clinical outcomes.

The paper identifies gut microbiome microproteins that modulate host metabolism using a whole-organism screening platform in C. elegans.

This study identifies sRNA 84 as a conserved regulator in Enterococcaceae that enhances mucin adhesion and gut colonization by upregulating cell surface proteins.

The paper presents a global virome atlas, UHGV, and identifies genomic factors influencing phage-host interactions.

The paper identifies age-related microbiome metabolites that alter RNA splicing and chromatin accessibility in the mouse brain using metabolomics, transcriptomic, and multi-omic approaches.

This study characterizes the crAssphage lifestyle as a phage-plasmid, demonstrating its persistence in the gut microbiome without causing host lysis or chromosomal integration.

The paper evaluates the Illumina Complete Long Read (ICLR) assay for metagenomic assembly, finding it produces higher contiguity and completeness compared to short-read and nanopore long-read methods.

The paper uses long-read metagenomics to study prophage integration dynamics in gut microbiota, finding dynamic phage-host interactions and a new class of phages.

This study investigates how the gut microbiome interacts with aging and dietary restriction in mice, finding that host genetics significantly influence microbiome features and that dietary restriction does not rejuvenate the microbiome.

The paper develops a method to detect invertons in gut microbiome metagenomic data and finds associations between inverton dynamics and intestinal colonization and surface adhesion.

This study expands the human gut microbiome atlas of Africa by analyzing 1,803 women from four countries, revealing geographic and lifestyle-associated taxa and novel microbial genomes.

The paper identifies a new class of viroid-like elements, Obelisks, prevalent in human microbiomes and capable of persistent colonization.

This study identifies two quorum-sensing systems in E. faecalis that regulate purine biosynthesis, enhancing its pathogenicity in macrophages and murine infections.

This study presents contiguous and complete assemblies of Blastocystis strains, revealing genetic and metabolic diversity linked to host ecology and horizontal gene transfer.

Phanta profiles human gut metagenomes to include viruses directly from short reads, identifying more viral species than assembly-based methods and revealing higher interindividual variability in the virome.

The paper compiles shotgun metagenomic data from stool samples of hospitalized hematopoietic cell transplant patients to enhance microbiome analysis beyond taxonomic composition.

This study shows butyrate induces chromatin accessibility changes in colon cancer cells, linking these changes to GWAS loci and somatic mutations in colorectal cancer.

This study introduces SmORFinder, a tool that improves small protein prediction in microbial genomes by combining pHMMs and deep learning, and identifies many core smORFs of unknown function.

This study uses read cloud sequencing to identify mobile elements in Bacteroides caccae that contribute to antibiotic resistance in a patient's microbiome over time.

This study uses short- and long-read metagenomics to analyze gut microbiomes in South African populations, revealing intermediate composition and novel taxa not captured by existing reference databases.

The paper introduces a method to generate closed bacterial genomes from nanopore long-read sequencing of microbiomes, achieving nine finished genomes including a closed genome of Prevotella copri.

This paper introduces a read cloud metagenomic sequencing approach combined with a new assembler, Athena, to generate high-quality microbial genome drafts from human and marine microbiomes without culturing.

The paper develops StrainSifter to identify concordant bacterial strains between bloodstream isolates and gut microbiota using whole genome sequencing.

This study examines how bacterial composition and function change over a year after fecal microbiota transplantation in immunocompromised patients, finding limited long-term donor strain persistence and complex functional shifts.