Metagenomics articles from across Nature Portfolio

Mangroves are increasingly exposed to plastic pollution. In this study, the authors performed microcosm experiments to show that mangrove soil microbial communities are reshaped by lignocellulose inputs yielding potential halophilic PET-degrading enzymes as promising candidates for plastic degradation.

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

Large DNA viruses (LDVs) are unique members of the Earth’s biosphere but remain poorly understood in many ecosystems. In this study, the authors uncovered the diversity, ecological patterns and drivers of intertidal LDVs in intertidal mudflats through large-scale sampling and sequencing efforts.

Zhao et al. investigate the effects of rectal douching on the gut ecosystem in men who have sex with men. They show that rectal douching is associated with gut microbiota dysbiosis, disrupted microbial metabolite homeostasis, and compromised intestinal barrier integrity.

There is an increasing interest in studying antibiotic resistance genes in microbial communities, however, there is no unified way to identify them in metagenomics datasets or to interpret the risks associated with them. In this Comment, the authors discuss current technical challenges and how to mitigate them.

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.