A sparse unit of covarying gut bacterial species that develops during the first 21 months of postnatal life reveals an underlying organization of the gut microbiota.. A sparse co-varying unit of gut microbiota structure that describes healthy and impaired community development

Interaction measurements at the scale of ecosystems are generally lacking. Using an approach inspired by statistical methods applied to financial markets and proteins, we conducted an analysis of covariance among bacterial taxa in the gut microbiota of healthy members of a Bangladeshi birth cohort sampled monthly from 1 to 60 months. Their microbiota can be decomposed into a sparse unit of 15 covarying bacterial taxa (an 'ecogroup'). A single ecogroup configuration is evident by the second postnatal month, and evolves in distinct phases to a mature form by 21 months, as defined by relative species abundance and architecture of microbial coupling. 'Ecogroup' provides a concise description of the organization of the gut microbiota in healthy versus undernourished children, a parameter for defining the extent of community repair achieved in the latter group by microbiota-directed foods and a framework for studying emergent characteristics of microbial communities.