Growth trajectories in cases and controls: Mean height, weight, HAZ and WHZ scores and corresponding 95% confidence intervals (CI) were plotted over time from birth to 24 months of age.

<p>HAZ, Height for Age, WHZ, Weight for Height, UCI, Upper Confidence Interval, LCI, Lower Confidence Interval.</p

Longitudinal Analysis of the Intestinal Microbiota in Persistently Stunted Young Children in South India

<div><p>Stunting or reduced linear growth is very prevalent in low-income countries. Recent studies have demonstrated a causal relationship between alterations in the gut microbiome and moderate or severe acute malnutrition in children in these countries. However, there have been no primary longitudinal studies comparing the intestinal microbiota of persistently stunted children to that of non-stunted children in the same community. In this pilot study, we characterized gut microbial community composition and diversity of the fecal microbiota of 10 children with low birth weight and persistent stunting (cases) and 10 children with normal birth weight and no stunting (controls) from a birth cohort every 3 months up to 2 years of age in a slum community in south India. There was an increase in diversity indices (P <0.0001) with increasing age in all children. However, there were no differences in diversity indices or in the rates of their increase with increasing age between cases and controls. The percent relative abundance of the Bacteroidetes phylum was higher in stunted compared to control children at 12 months of age (P = 0.043). There was an increase in the relative abundance of this phylum with increasing age in all children (P = 0.0380) with no difference in the rate of increase between cases and controls. There was a decrease in the relative abundance of Proteobacteria (P = 0.0004) and Actinobacteria (P = 0.0489) with increasing age in cases. The microbiota of control children was enriched in probiotic species <i>Bifidobacterium longum</i> and <i>Lactobacillus mucosae</i>, whereas that of stunted children was enriched in inflammogenic taxa including those in the Desulfovibrio genus and Campylobacterales order. Larger, longitudinal studies on the compositional and functional maturation of the microbiome in children are needed.</p></div

Relative abundance of major phyla in cases and controls.

<p><b>a:</b> Average relative abundance of major phyla at each 3 monthly time point. <b>b:</b> inear regression model showing the change in relative abundance of each major phylum over time from 3 to 24 months of age.</p

Age-related effect on the relative abundance of major phyla^*.

<p>Age-related effect on the relative abundance of major phyla^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155405#t003fn001" target="_blank">*</a>}.</p

Differentially abundant taxa between cases and controls.

<p><b>a:</b> Linear Discriminant Analysis Effect Size (LEfSe) cladogram of differentially abundant taxa in cases and controls [phylum (p), class (c), order (o), family (f), genera (g), species (s)]. <b>b:</b> Linear Discriminant Analysis (LDA) scores of differentially abundant taxa in cases and controls. The LDA score indicates the effect size and ranking of each differentially abundant taxon.</p

Alpha diversity indices in cases and controls: Alpha diversity indices (Chao, Equitability, observed OTUs, Shannon and Phylogenetic Diversity (PD) were computed in QIIME.

<p>regression model showing the increase in individual diversity indices over time from 3 to 24 months of age.</p

Age related effect on alpha diversity indices^*.

<p>Age related effect on alpha diversity indices^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155405#t002fn001" target="_blank">*</a>}.</p

Baseline socio-demographic and clinical data in cases and controls.

<p>Baseline socio-demographic and clinical data in cases and controls.</p