Harmonization of microbiome data in the Environmental influences on Child Health Outcomes (ECHO) Cohort to analyze environmental influences on the child microbiome

ECHO harmonized 15,509 high-quality microbiome samples from 1,086 pregnancies and 5,701 children across 21 U.S. sites, showing microbial communities vary by body site, participant type, age, and processing.

• Why it matters: Early-life environmental exposures may be linked to later health through the developing microbiome, but multi-site data need consistent processing to study these connections.
• What they did: The consortium used a common annotation protocol on pre-formation sequencing from ECHO sites, then summarized how participant characteristics relate to microbiome features, including gut samples with geolocation and PFAS measures.
• The result: The extant ECHO dataset enables characterization of how environmental exposures are associated with the developing human microbiome and how those microbiome differences may relate to long-term health outcomes.

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