B. Jesse Shapiro

This study screens Arctic bacteria to discover antibacterial compounds, identifying koreenceine A from a Pseudomonas isolate and confirming its antibiotic activity through genetic analysis.

This study investigates prophage induction in human gut metagenomes in response to ciprofloxacin, finding species-specific increases in prophage-to-bacterial host read depth ratios.

The paper identifies a microbiota-dependent type 3 immune response in mice during weaning that involves γδ T cells, which limit C. difficile growth and maintain intestinal barrier integrity.

The paper introduces DBCO-modified PCR primers for enzyme-free click chemistry ligation in nanopore amplicon sequencing, achieving higher pore occupation and reads than commercial solutions.

This study links cyanobacterial genome variations to toxin dynamics using metagenomic analysis of Microcystis in a lake over 10 months, showing genotype-level and single nucleotide variant associations with toxin production and release.

The paper identifies new phosphorothioate DNA modification systems in the human gut microbiome using genomic and mass spectrometric analysis.

This study shows nutrient enrichment reduces bacterioplankton taxonomic diversity but connectivity can restore functional diversity in highly stressed freshwater communities.

This study shows that glyphosate-based herbicide affects bacterial community diversity but not within-species genetic diversity, identifying gene targets of selection in freshwater bacterioplankton.

The paper investigates the relationship between co-occurrence and horizontal gene transfer (HGT) in marine bacteria, finding a significant association independent of phylogeny.

The paper investigates how industrialization affects microbial and physiological traits in the human gut across diverse populations, finding homogenized microbiomes, reduced diversity, and impaired disease prediction accuracy in less industrialized groups.

This study sequenced V. cholerae genomes from Bangladesh in 2018, revealing geographic variation in lineage dominance and pangenome diversity across regions.

The paper reports chromosome fusions in clinical V. cholerae O1 isolates, showing stable transmission between patients within a household.

This study investigates phage-cyanobacteria interactions in Lake Champlain over a decade, finding that phages share environmental niches with bacteria but exhibit distinct dynamics and co-variation patterns.

The paper shows that pre-exposure to stress increases community and genetic diversity resilience in bacterial communities under severe acidification.

The paper quantifies within-host SARS-CoV-2 genetic diversity across animal species and finds deer exhibit higher diversity, likely due to higher mutation rates, longer infections, and selective pressures.

The paper evaluates nine computational tools for identifying SARS-CoV-2 lineages in wastewater sequencing data using simulated samples, finding most tools reliably detect lineages above 5% frequency.

This study compares genetic diversity of Vibrio cholerae O1 in vomit and stool from cholera patients, finding reduced diversity in stool and some gene loss between samples.

This study uses phylogenetic analysis and genome-wide association studies to investigate SARS-CoV-2 transmission between humans and animals, identifying species-specific mutations.

The paper uses phylogenomic analysis of 189 Methylobacterium genomes to reveal four evolutionary groups and identify 45 candidate species, highlighting phyllosphere diversity and an ancient transition to plant association.

The paper identifies immune evasion mechanisms in SARS-CoV-2 by mapping epitopes and analyzing viral genome sequences to understand evolutionary pressures and immune responses.

The paper presents computational tools for analyzing SARS-CoV-2 genetic data, showing that haplotype networks and unsupervised learning can reveal lineage emergence and population dynamics.

This paper shows that classical GWAS methods fail to identify causal variants in strongly clonal microbial populations due to linkage disequilibrium, and introduces a new method called POUTINE to address this issue.

This paper benchmarks bacterial GWAS methods using simulated data, finding that elastic net models outperform others in detecting causal variants, especially in highly clonal genomes.