Bacterial genomics articles from across Nature Portfolio

Kayama et al. present a blueprint for a national genomic surveillance study that conducts genome sequencing of thousands of strains, integrates standardized quantitative antimicrobial susceptibility testing, and characterizes antimicrobial resistance determinants.

Core genome multilocus sequence typing (cgMLST) is used to classify bacterial strains for epidemiological applications. Here, the authors describe a distributed cgMLST scheme that does not require a central database of allelic sequences, and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria.

Many microorganisms are auxotrophic, that is, unable to synthesize the compounds they require for growth. Here, Ramoneda et al. predict amino acid biosynthetic capabilities of over 26,000 bacterial genomes using a metabolic pathway model validated with empirical data, and identify ecological contexts in which auxotrophy can be a successful strategy.

Bacterial functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, Wang et al. investigate bacterial communities along a natural pH gradient in forest soils, and find that average genome size and functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral.

Genomic epidemiology of the Yemen cholera outbreak reveals the genetic basis for emergence of multidrug resistance with implications for Vibrio cholerae surveillance and control.

This study reports a bacterial antiphage protein that contains a NACHT domain, which is also found in metazoan proteins that mediate immunity and inflammation.

The Tibetan glacier genome and gene catalog includes 3,241 metagenome-assembled or cultured genomes spanning 30 phyla and over 25 million genes encoding non-redundant proteins. This catalog provides a wealth of resources for archiving glacier microbial diversity and bioprospecting for bioactive compounds, as well as a platform for global comparison of glacier microbiomes.

This study reports the discovery of two new DNA defence modules, termed DdmABC and DdmDE, in Vibrio cholerae.

This month’s Genome Watch highlights how genome and transcriptome sequencing of newly identified endosymbionts helps to connect genetic information to their protective functions.

A whole-genome sequencing study reveals a bottleneck in syphilis spread in the late 1990s followed by global spread.