B. J. Shapiro

Diversity of Vibrio cholerae O1 through the human gastrointestinal tract during cholera

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.

Phage predation, disease severity and pathogen genetic diversity in cholera patients

A study of cholera patients in Bangladesh identifies phage predation as a biomarker of disease severity and driver of coevolution within patients.

Pseudogenes as a neutral reference for detecting selection in prokaryotic pangenomes

The paper uses pseudogenes as a neutral reference to assess the role of selection in prokaryotic pangenome divergence, finding evidence for adaptive rare accessory genes.

Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome

The paper shows that community diversity in the human gut microbiome is linked to intra-species genetic diversity and gene loss, supporting both Diversity Begets Diversity and Black Queen Hypothesis mechanisms.

A glyphosate-based herbicide cross-selects for antibiotic resistance genes in bacterioplankton communities

This study shows that glyphosate-based herbicides increase antibiotic resistance gene frequencies in freshwater bacterioplankton by selecting for multidrug efflux pumps.

A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients

The paper combines metagenomics and cultivation approaches to show V. cholerae hypermutator phenotypes in infected patients, with evidence of adaptive mutations and transversion mutations.

Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions

This study shows that antimicrobial resistance in Vibrio cholerae increases under anaerobic conditions and identifies distinct genetic factors associated with resistance in these conditions.

Fine-scale adaptations to environmental variation and growth strategies drive phyllosphere Methylobacterium diversity.

This study investigates how Methylobacterium diversity in the phyllosphere is shaped by environmental factors and growth strategies, revealing temperature adaptation and seasonal community shifts.

Genome evolution in bacteria isolated from million-year-old subseafloor sediments

This study examines genome evolution in Thalassospira bacteria from million-year-old subseafloor sediments, finding reduced recombination, increased pseudogenes, and genetic drift as dominant evolutionary forces.

Does diversity beget diversity in microbiomes?

The paper investigates how microbial diversity influences further diversity in different biomes, finding that positive feedback is strongest in low-diversity environments but plateaus in high-diversity ones.

Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacterium Microcystis and its microbiome

The paper analyzes genomic data from Microcystis colonies and their microbiomes to reveal phylosymbiosis, co-phylogeny, and horizontal gene transfer patterns.

Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota

The paper uses BONCAT and FACS-Seq to identify translationally active bacteria in the gut microbiota and finds they are not distinct from the whole community, while high nucleic acid content bacteria are distinct and correlate with damaged cells.

Pangenome sequence evolution within human gut microbiomes is explained by gene-specific rather than host-specific selective pressures

The paper investigates selective pressures on mobile genes in human gut microbiomes, finding gene-specific selection dominates over host-specific pressures on short time scales.

Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment

This study examines how freshwater bacterioplankton communities respond to agricultural stressors in mesocosms, finding that only high glyphosate doses alter community structure while functional redundancy persists.

Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study

This study uses metagenomic sequencing to predict cholera infection and disease severity in a cohort, identifying protective bacterial species and genes.

The evolution of realized niches within freshwater Synechococcus

This study investigates how closely-related Synechococcus taxa share similar ecological niches in freshwater environments, finding that co-occurrence patterns suggest phylogenetic conservation of realized niches over evolutionary time.

Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome

The paper shows that horizontal gene transfer in the human microbiome is more common within the same host and is linked to industrialization and lifestyle factors.

A large-scale assessment of lake bacterial communities reveals pervasive impacts of human activities

This study assesses the impact of human activities on bacterial communities in 220 lakes across Eastern Canada, finding widespread changes in richness, composition, and network structure.

Two cases of type-a Haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes

This paper reports two unrelated H. influenzae meningitis cases in the same hospital, showing they were not part of a local outbreak but instead involved horizontal gene transfer of capsule genes, enabling vaccine evasion.

Coherence of Microcystis species revealed through population genomics

This study uses population genomics to show Microcystis species are not coherent, with genomic clusters suggesting species boundaries and gene flow barriers, but also local adaptation through horizontal gene transfer.

Niche separation increases with genetic distance among bloom-forming cyanobacteria

The paper examines niche separation among bloom-forming cyanobacteria, finding that niche similarity declines with genetic distance, but some traits show complex relationships.

Vibrio cholerae genomic diversity within and between patients

This study examines V. cholerae genomic diversity within and between patients, finding limited point mutations but higher gene content variation, including phage and plasmid exchanges, which may impact disease outcomes.

Origins of pandemic clones from environmental gene pools

The paper identifies virulence adaptive polymorphisms (VAPs) in environmental bacterial populations that are required for the transition to pathogenicity in Vibrio cholerae.

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course

This study uses 16S amplicon sequencing to analyze cyanobacterial blooms in Lake Champlain over 8 years, finding that blooms can be predicted with high accuracy using sequence data.