Metagenomics articles from across Nature Portfolio

Acetylcholine levels are reduced in gut dysmotility conditions. We find that gut acetylcholine levels induce a compensatory increase in gut microbiota urease activity and ammonia production. By upregulating presynaptic Cav2.1 calcium channels in enteric neurons, ammonia enhances calcium influx and restores acetylcholine release neurotransmission, revealing a microbiota-driven mechanism that preserves gut motility.

Using individual-level data from the Swedish Prescribed Drug Register and fecal metagenomes of 14,979 individuals in Sweden, the authors examined the association between oral antibiotic use over 8 years and gut microbiome and found evidence that antibiotics can have long-lasting impacts on the gut microbiome.

Benoit et al. present nanoMDBG, a scalable metagenome assembler for the latest ONT long reads, developed by adding error correction to metaMDBG. They demonstrate superior performance to the state-of-the-art and equivalent results to PacBio HiFi reads.

The gut microbiome-kidney crosstalk has been previously linked with metabolic and kidney diseases. Here, the authors show that microbial amino acid metabolism interacts with host kidney function to influence cardiorenal physiology in the early stages, with potential implications for long-term risk of cardiovascular disease in human populations.

Segmented Filamentous Bacteria (SFB) in mice are important gut commensals in both health and disease. Here, Kiran et al. characterize a novel human SFB species that is widespread in Africa and show that humans worldwide harbor multiple SFB species and at least six SFB lineages.

Acetylcholine levels are reduced in gut dysmotility conditions. We find that gut acetylcholine levels induce a compensatory increase in gut microbiota urease activity and ammonia production. By upregulating presynaptic Cav2.1 calcium channels in enteric neurons, ammonia enhances calcium influx and restores acetylcholine release neurotransmission, revealing a microbiota-driven mechanism that preserves gut motility.

A study by Jin et al. shows that oral–gut translocation of prtC⁺ bacteria is implicated in the well-known link between gut microbiome dysbiosis and advanced liver disease in humans.

This study reports that the tree bark microbial community actively modulates fluxes of climate-active gases and volatile organic compounds, and may mediate global atmospheric gas cycling.

Microbial genomics has yielded transformative insights into the ecology and evolution of microorganisms. Nature Reviews Genetics presents a Focus issue that explores how genomic approaches reveal microbial dynamics across ecological and evolutionary contexts.

In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between two genomes, which helped to operationally define bacterial species.