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.

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.

生态系统尺度的物种互作测量数据整体仍较为匮乏。本研究借鉴应用于金融市场与蛋白质组学的统计方法，对孟加拉国出生队列中健康个体的肠道菌群内细菌分类群间的协方差展开分析；该队列在1至60月龄期间每月接受采样。其肠道菌群可拆解为包含15个共变细菌分类群的稀疏单元，即“生态组（ecogroup）”。基于物种相对丰度与微生物互作耦合结构的定义，生态组的构型在出生后第二个月即可显现，并历经不同演化阶段，最终于21月龄时形成成熟结构。“生态组”可简洁描述健康儿童与营养不良儿童的肠道菌群组织模式，同时可作为量化菌群靶向食品修复营养不良儿童菌群群落修复程度的参数，亦为研究微生物群落涌现特性提供了分析框架。