Systems genetics reveals interactions between host and microbial phenotypes in the murine gut, including a role for Akkermansia muciniphila in the production of immunomodulatory ornithine lipids.

Eighty-nine percent of the Trypanosoma brucei proteome is mapped using fluorescence microscopy and cell lines expressing endogenously tagged proteins, and presented in a resource for the community named TrypTag.org.

Temporal single-cell RNA sequencing analysis of viral and host transcriptional responses during human cytomegalovirus infection of macrophages and monocytes reveals molecular features influencing distinct infection courses and suggests additional latency reservoirs.

Tracking labelled nitrogen atoms from multiple substrates into individual peptides within complex microbial communities shows which cellular functions constitute the bulk of proteomic N demand and the metabolic basis of N limitation.

Hi-C 3.0 and ChIP-seq show that SARS-CoV-2 infection alters the host cell 3D genome structure and epigenome.

Autophagy proteins differentially control Mycobacterium tuberculosis replication in human macrophages.

A compendium of Omnitrophota genomes is coupled with cell size and qSIP analyses to predict the physiology and lifestyle of this enigmatic phylum.

Bile salt hydrolases encoded by the gut microbiome shape the bile acid pool, including microbial conjugated bile acids, which impact Clostridioides difficile infection in the murine gut.

Enterovirus-infected cells are extruded from the apical surface of differentiated human colon organoids by a mechanical-force-dependent mechanism that preserves the uninfected host epithelium.

An uncultivated, aerobic chemolithotrophic Sulfurimonas species with a reduced genome is abundant across diverse, hydrogen-rich hydrothermal plumes in the deep ocean.

The extent and diversity of exposures to microbial stimuli have a crucial role in regulating the capacity of a host to mount an immune response to a challenge, such as vaccination, making exposure history an important factor to optimize in rodent models.

The SARS-CoV-2 Africa dashboard is an interactive tool that enables visualization of SARS-CoV-2 genomic information in African countries. The customizable app allows users to visualize the number of sequences deposited in each country, and the variants circulating over time. Our dashboard enables near real-time exploration of public data that can inform policymakers, healthcare professionals and the public about the ongoing pandemic.

Reports of diphtheria cases in asylum seekers in the UK remind us that understanding and mitigating the risks posed by infectious diseases to disadvantaged peoples remain important.

We present a series of commissioned articles authored by people from groups that are under-represented in research, to highlight past and present scientific contributions in microbiology and to increase the diversity of Nature Microbiology authors.