Analyses

A systematic phylogenomic survey finds that growth temperature is a good quantitative predictor of nucleoid-associated protein abundance.

The COVID-19 pandemic in Brazil is assessed using phylogenetic and phylogeographic analysis.

Computational analyses reveal widespread recoding in gut phages, which is hypothesized to control timing of lysis.

A comprehensive survey of secondary metabolites encoded in bacteria identifies large differences in biosynthetic diversity among genera and pinpoints those that can be targeted for novel chemistries provisionally suitable as antimicrobials.

Large-scale gut microbiome analysis of a widely use mouse model of inflammatory bowel disease reveals that the gut microbiome is a driver of variability across genetically identical mice, in particular two species that are associated with variable treatment endpoints.

Phylogeography and phylogenomic analyses of E. coli isolates collected from humans and domesticated and wild animals across 99 households in Nairobi reveal strong intra-household, and lower but detectable inter-household and inter-host, strain-sharing patterns.

A systematic screen across hundreds of eukaryotes and thousands of viral taxa provides insights into the directionality and functionality of horizontal gene transfer in these organisms.

Quantification of gut bacterial strains after fecal microbiome transplantation using the Strainer algorithm delineates long-term stable engraftment that explains patient outcomes.

An analysis of more than 5,000 CBASS systems from 38,000 bacterial and archaeal genomes enabled a classification and nomenclature scheme to be devised for this growing field.

This is a comparative analysis of the performance of the primer–probe sets from four open-source molecular diagnostic assays for SARS-CoV-2 recommended by the World Health Organization.

A literature-based review evaluates host and bacterial biomarkers as well as biosignatures that may be leveraged for the diagnosis of tuberculosis.

Significant gaps in our characterization of microbial diversity remain; this meta-analysis of amplicon-based rRNA studies shows that they miss approximately 10% of environmental microbial sequences, most belonging to the candidate phyla radiation.