A. S. Bhatt

Viroid-like colonists of human microbiomes

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

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

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

Expanding the human gut microbiome atlas of Africa

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.

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales

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

Interactions between the gut microbiome, dietary restriction, and aging in genetically diverse mice

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.

Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology

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

Human gut metagenomic mining reveals an untapped source of peptide antibiotics

The paper identifies hundreds of novel peptide antibiotics from human gut metagenomes, showing antimicrobial activity and potential therapeutic applications.

Intragenic DNA inversions expand bacterial coding capacity

The paper identifies intragenic DNA inversions in prokaryotes using long-read sequencing, showing they allow genes to encode multiple protein versions without increasing genome size.

Tomato brown rugose fruit virus Mo gene is a novel microbial source tracking marker

The paper designs and tests novel viral microbial source tracking markers based on ToBRFV genomes, finding they are sensitive, specific, and more prevalent in human stool and wastewater than existing markers.

Achieving quantitative and accurate measurement of the human gut microbiome

This study evaluates how stool preservatives and storage conditions affect microbiome measurements, finding that OMNIgene GUT is more robust and recommends RNA-preserved kits for metatranscriptomics.

The TaxUMAP atlas: efficient display of large clinical microbiome data reveals ecological competition involved in protection against bacteremia

The paper introduces TaxUMAP, a visualization tool for microbiome data, revealing that Klebsiella species reduce bacteremia risk through competition with other pathogens.

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition

The paper identifies metabolic diversity in commensal protists and shows how it influences intestinal immunity and trans-kingdom competition with bacteria.

The circulating phageome reflects bacterial infections

The paper shows that circulating phageome in cfDNA reflects bacterial infections and can distinguish between pathogenic and contaminant bacteria.

Chemoproteomic identification of a dipeptidyl peptidase 4 (DPP4) homolog in Bacteroides thetaiotaomicron important for envelope integrity and fitness

The paper identifies a DPP4 homolog in Bacteroides thetaiotaomicron important for envelope integrity and fitness, showing it is inhibited by diabetes drugs.

Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults

This study identifies potential bacterial transmission between hospitalized HCT patients through metagenomic sequencing, finding shared strains in some pairs but not widespread colonization.

Large-scale discovery of recombinases for integrating DNA into the human genome

This paper identifies and validates new large serine recombinases (LSRs) for efficient DNA integration into human genomes, achieving higher efficiency than existing tools.

A screen of covalent inhibitors in Mycobacterium tuberculosis identifies serine hydrolases involved in lipid metabolism as potential therapeutic targets

Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition

This study compares gut microbiomes of rural and urban South African women to identify microbial biomarkers linked to lifestyle and obesity.

Repurposing Ribo-Seq to provide insights into structured RNAs

The paper shows that contaminant RNAs in bacterial Ribo-Seq data can reveal secondary structures of non-coding RNAs, enabling large-scale in vivo RNA structure analysis.

A combined RNA-Seq and comparative genomics approach identifies 1,085 candidate structured RNAs expressed in human microbiomes

The paper uses RNA-Seq and comparative genomics to identify 1,085 candidate structured RNAs transcribed in human fecal microbiomes.

Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

The paper analyzes gut metagenomic data to study the acquisition, transmission, and strain diversity of crAss-like phages in mother-infant pairs and fecal microbiota transplantation recipients.

Mobile genetic element insertions drive antibiotic resistance across pathogens

The paper develops a de novo method to identify mobile genetic elements and their insertion sites in bacterial genomes, revealing their role in antibiotic resistance across pathogens.

Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions

This study identifies thousands of novel small genes in human microbiomes and predicts their functions, highlighting their potential roles in host interactions and bacterial adaptation.

Metagenome-wide measurement of protein synthesis in the human fecal microbiota using MetaRibo-Seq

This study introduces MetaRibo-Seq, a method for ribosome profiling in complex bacterial communities, showing it correlates better with protein abundance than metatranscriptomics in low diversity samples.

Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome

This study examines the impact of triclosan and triclocarban exposure on the intestinal microbiome of adults and infants, finding no major disruption in infants but increased antibiotic-resistant species in mothers.