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Background  Chronic malnutrition, termed stunting, is defined as suboptimal linear growth, affects one third of children in developing countries, and leads to increased mortality and poor developmental outcomes. The causes of childhood stunting are unknown, and strategies to improve growth and related outcomes in children have only had modest impacts. Recent studies have shown that the ecosystem of microbes in the human gut, termed the microbiota, can induce changes in weight. However, the specific changes in the gut microbiota that contribute to growth remain unknown, and no studies have investigated the gut microbiota as a determinant of chronic malnutrition.    Results  We performed secondary analyses of data from two well-characterized twin cohorts of children from Malawi and Bangladesh to identify bacterial genera associated with linear growth. In a case-control analysis, we used the graphical lasso to estimate covariance network models of gut microbial interactions from relative genus abundances and used network analysis methods to select genera associated with stunting severity. In longitudinal analyses, we determined associations between these selected microbes and linear growth using between-within twin regression models to adjust for confounding and introduce temporality. Reduced microbiota diversity and increased covariance network density were associated with stunting severity, while increased relative abundance of  Acidaminococcus  sp. was associated with future linear growth deficits.    Conclusions  We show that length growth in children is associated with community-wide changes in the gut microbiota and with the abundance of the bacterial genus,  Acidaminococcus . Larger cohorts are needed to confirm these findings and to clarify the mechanisms involved.    Electronic supplementary material  The online version of this article (doi:10.1186/s40168-015-0089-2) contains supplementary material, which is available to authorized users.

Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota