Long-read shotgun metagenomics identifies distinct urogenital microbial community states associated with functional potential and urinary tract infection during pregnancy

Long-read shotgun metagenomics in pregnant females identifies three urogenital microbial community states, with a Gardnerella-predominated state linked to a higher UTI frequency during pregnancy.

• Why it matters: UTIs are common in pregnancy and tied to adverse maternal and neonatal outcomes, yet the urogenital microbiome during pregnancy is still poorly characterized.
• What they did: Oxford Nanopore long-read shotgun metagenomic sequencing was used to profile urogenital microbial composition, functional potential, metagenome-assembled genomes, and the virome, recovering 415 MAGs including 29 high-quality genomes.
• The result: Functional profiles strongly track the community states, and viral sequences—mostly bacteriophages—are present in most samples, supporting state-specific taxonomic and functional differences during pregnancy.

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