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Determinants of Vibrio cholerae transmission are incompletely understood. Here, the authors use an infant mouse model to show that events in the intestine govern inter-animal transmission and that bacterial motility along with cholera toxin-driven diarrhea are critical for pathogen spread.

Vibrio cholerae O1 outbreak strains are classified as Ogawa or Inaba serotypes, but the impact of serotype on pathogenicity is understudied. Here, the authors show that O1 antigen methylation in Ogawa strains promotes colonization and infectivity.

Here, using Citrobacter rodentium colonization of mice as a model, the authors characterize the impact of pathogen dose on the number of bacteria that initiate infection in the mouse gut, providing a framework for quantifying the host bottlenecks that eliminate pathogens to protect from infection.

Streptococcus equi subsp. zooepidemicus imports glucose via the bacterial mannose phosphotransferase system (PTS_man), which inhibits stringent response, supports growth in cerebrospinal fluid and promotes brain damage during meningitis.

Transposon insertion sequencing (TIS) enables genome-wide definition of loci that are required for growth in diverse conditions. In this article, Waldor and colleagues discuss the benefits and limitations of different experimental approaches to TIS analyses.

The Citrobacter rodentium CRISPR–Cas system is activated by the oxygen-responsive transcriptional regulator Fnr in the anoxic environment of the mouse gut.

InducTn-seq, a method for inducible mutagenesis followed by transposon insertion site sequencing, enables temporal control of transposition to bypass population bottlenecks and enable the quantification of gene fitness during in vivo Citrobacter rodentium infection.

Roles of serotonergic neurons in immune homeostasis and host defense are largely unexplored. Here the authors show that in mice enteric serotonergic neurons regulate immune homeostasis and host defense against Salmonella infection by orchestrating gut homing and activation of plasmacytoid dendritic cell, ultimately promoting the differentiation of protective IgA⁺ B cells.

Tracing barcoded clones of Klebsiella pneumoniae during pneumonia with bacteremia, Holmes and colleagues identify two modes of dissemination, with high or low bacterial burdens, and define the host and bacterial factors that influence this process.

Metabolic variation via a single substitution in the β-carbonic anhydrase CanB determines CO₂ dependence and influences fluoroquinolone resistance in Neisseria gonorrhoeae.

The pathogen Salmonella Typhimurium increases production of outer membrane vesicles (OMVs) inside acidic vacuoles of host cells, but the mechanisms are unclear. Here, Dehinwal et al. show that acidic pH induces conformational changes in an outer membrane protein that affect its interaction with membrane lipids, thus modulating OMV formation.

Integrative and conjugative elements are self-transmissible genetic elements that encode a core set of genes for their propagation and transfer and can also carry various other genes, including drug resistance markers. Here, Wozniak and Waldor describe the transmission of these elements and how this is regulated.

Oral vaccines against Vibrio cholera have been critical for cholera management, but the production of more efficacious and cost-effective approaches is still needed. Here the authors deliver a bivalent V_HH construct that binds to cholera toxin and show protection in a murine cholera model.

The ‘Pf’ bacteriophages of Pseudomonas aeruginosa play roles in biofilm formation and virulence. Here, the authors identify a prophage regulatory module, KKP (kinase-kinase-phosphatase), that controls virion production of co-resident Pf prophages and mediates host defense against diverse lytic phages.

C-to-Ψ conversion is a previously uncharacterized form of base editing. Here, the authors describe how the TrcP enzyme catalyzes this process in a stepwise fashion and how this editing process is controlled by a network of modifications and nutrient availability to optimize translation efficiency.

A combination of tRNA sequencing and mass spectrometry was developed to profile tRNA modification enabling identification of a new modification acacp³U and the presence of cytosine-to-pseudouracil RNA editing in Vibrio cholerae.

Members of the DUF368-containing and DedA transmembrane protein families have conditional roles in undecaprenyl phosphate translocation in Gram-negative and Gram-positive bacteria and may have a widely conserved function in the biogenesis of microbial cell surface glycopolymers.

An outbreak of diarrhoea and haemolytic uraemic syndrome in Germany in 2011 was caused by a Shiga toxin-producing enteroaggregative E. coli, which carried the aggregative adherence plasmid pAA. Here, the authors show that autotransporters, but not pAA, are required for intestinal colonization in an infant rabbit model.

Here, the authors develop a genome evolution model to investigate the origin of functional redundancy in the human microbiome by analyzing its genomic content network and illustrate potential ecological and evolutionary processes that may contribute to its resilience.

A tRNA modification, named 2-aminovaleramididine (ava²C), has been discovered in plant organelles and bacteria. Structural analysis shows specific codon recognition by this modification, highlighting the evolutionary diversity of the essential tRNA modifications.

Metabolomic analysis of bile after infection by enteric bacteria in mice reveals composition changes including increased itaconate levels that promote intestinal homeostasis and reduce Vibrio cholerae colonization.

Surface protein tagging and mass spectrometry-based proteomics applied in a rabbit cholera model system identifies proteins involved in Vibrio cholera-host cell interactions and defines a cholera toxin-dependent role for host surfactant protein D.

Understanding ecological interactions in microbial communities is limited by lack of informative longitudinal abundance data necessary for reliable inference. Here, Xiao et al. develop a method to infer the interactions between microbes based on their abundances in steady-state samples.

Adherent-invasive E. coli (AIEC) are frequently isolated from Crohn’s disease (CD) patients. Here, Elhenawy et al. conduct a genome-wide screen to identify AIEC genes required for in vivo intestinal colonization, and show that a type IV secretion system contributes to AIEC persistence in the gut and is enriched in CD patients’ isolates.

Invariant natural killer T (iNKT) cells populate barrier surfaces during an early-life window. Blumberg and colleagues demonstrate that such barrier surface iNKT cells develop via an extrathymic pathway dependent on a specialized population of embryo-derived macrophages.

The multikilobase reads that can be produced by single-molecule sequencing technologies may span complex, repetitive genomic regions but have high error rates. Bashir et al. use these reads to organize contigs assembled from accurate, short-read data, facilitating the analysis of clinically important regions of an outbreak strain of cholera.

Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods for examining methylated genomes lack single-cell resolution. Here Beaulaurier et al. present Single Molecule Modification Analysis of Long Reads, a new tool for de novodetection of epigenetic heterogeneity.

Fang et al. generate the first genome-wide, strand-specific, single base–pair resolution map of m6A modifications in Escherichia coli.

Four secreted bacterial serine hydrolases found by an ABPP approach in Vibrio cholerae–infected rabbits, and one in human infection, regulate the levels of intelectin, an intestinal lectin that binds V. cholerae during infection and may facilitate bacterial surveillance in the intestine.

During hypoxic growth in the gut, the levels of nitrate and nitrite affect V. cholerae in a pH-dependent manner. At high pH, the bacteria can reduce nitrate for growth, whereas at low pH, nitrite accumulates, limits proliferation and promotes cell viability.

The combination of molecularly tagging bacteria prior to infection and high-throughput sequencing of infected sites allows the quantitative assessment of the founding population size and analysis of bacterial migration patterns.

The rapidly dividing bacterium Vibrio natriegens holds promise for transforming traditional molecular biology and biotechnology processes. New work demonstrates that CRISPR interference technology is a robust tool for rapid, genome-wide screens in V. natriegens, facilitating future bioengineering efforts.

The mouse gut microbiota produce free d-amino acids and induce the production of d-amino acid oxidase by intestinal epithelial cells. Oxidative deamination of d-amino acids yields H₂O₂, which protects the mucosa from Vibrio cholerae.

The genome sequence of the bug that causes cholera,Vibrio cholerae , is now published. The sequence will form a basis for studies of the evolution and pathogenicity of this bacterium, and may also aid in the development of new vaccines and medicines.

FusKR, a fucose-sensing two-component system, has been identified in enterohaemorrhagic E. coli, linking fucose utilization and virulence factor gene expression and providing insight into how sensing of a host signal can facilitate bacterial colonization.

Several bacteria of the Vibrio genus cause human infections; among these, Vibrio cholerae is responsible for cholera (a severe gastroenteritis that can be quickly fatal if untreated) and Vibrio vulnificus wound infections have a high mortality. Vibrio spp. are common in the environment in warm, low-salinity water and in fresh water, and increasing sea surface temperatures can further promote their spread.

Microbiome science is fast advancing and its careful integration into public health is detailed in this Perspective.