Taxon-in-context reveals ecological individuality in the human gut microbiome

Common gut microbial species occupy different taxon-in-contexts across people, with context flexibility peaking in early life and declining through adulthood across 7,700 metagenomes.

• Why it matters: Ecological roles depend on community context, but abundance profiles and fixed groupings leave each microbe’s individual context implicit.
• What they did: The study introduced taxon-in-context, a reproducible representation of each microbe’s context within an individual microbiome, and validated it across 7,700 metagenomes and a larger genus-level compendium.
• The result: For selected species, taxon-in-context revealed age associations beyond species abundance and enabled recurrence prediction where an abundance-based model performed near chance, and microbes switched contexts within individuals in an independent longitudinal urinary tract infection cohort.