The FDA-approved antiviral baloxavir improves disease outcomes in mice compared with oseltamivir after ocular and intranasal challenge with A(H5N1)-contaminated cow milk.

Reduced dietary fibre together with mutations in the host mismatch repair machinery promote colon carcinogenesis by increasing inflammation, nitrate-fuelled growth of colibactin-producing Escherichia coli and colibactin-dependent genotoxic tissue damage.

Disrupting the prefoldin–chaperonin complex in various species of Anopheles mosquitoes results in a compromised intestinal barrier leading to an immune response that inhibits the malaria parasite.

An engineered one-carbon-fixation pathway increases biomass yields of Cupriavidus necator compared with the Calvin cycle and can support future, sustainable bio-based production.

Countering the effects of Bacillus anthracis lethal toxin proteolytic activity with a growth factor cocktail reactivates ERK, prevents cytotoxicity and promotes survival of B. anthracis-infected mice.

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.

DEBIAS-M corrects technical variability in microbiome data in a manner both interpretable and suitable for machine learning. In extensive benchmarks, DEBIAS-M facilitates robust analyses that generalize across datasets.

In vivo and in silico analyses suggest that bradyzoite-directed immunity contributes to control of cyst numbers, tissue damage and mortality in mice.

A sequential propagation strategy shows how the microbes initially on seeds are key to building complex, reproducible and heritable plant microbiomes.

A multi-omics approach reveals host–microbiome interactions in aging in mice.

Combining antibiotics remains a promising approach to treat patients and to prevent the emergence of antimicrobial resistance

It is increasingly clear that microplastic pollution can be detrimental to human, animal and environmental health. More research is needed to determine if and how our microbial partners are also negatively impacted, and what this means for host and ecosystem health.

Alison Criss discusses the features of Neisseria gonorrhoeae, its intricate interactions with innate immunity and how this challenges our understanding of what makes a pathogen pathogenic.

We provide guidance on the planning, execution and description of statistical analyses in microbiome studies.

Determining whether human organs house a resident microbiome is challenging and the findings can be controversial. However, forging collaborations and careful study design can help overcome these issues.