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. 2014 Apr 24;9(4):e95547.
doi: 10.1371/journal.pone.0095547. eCollection 2014.

Gut Microbiomes of Indian Children of Varying Nutritional Status

Free PMC article

Gut Microbiomes of Indian Children of Varying Nutritional Status

Tarini Shankar Ghosh et al. PLoS One. .
Free PMC article


Background: Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition.

Methodology/principal findings: Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered.

Conclusions: The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition.

Conflict of interest statement

Competing Interests: Although some of the authors are employed by a commercial company (TCS Innovation Labs, Pune, India), this does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.


Figure 1
Figure 1. Distribution of taxonomic groups at various levels (including the core set of 23 genera) commonly present across at least 50% metagenomes with normalized abundance ratios of more than 0.01.
Figure 2
Figure 2. Variation of the normalized abundances (expressed as percentages) of the 23 core genera across the 20 gut metagenomes.
Figure 3
Figure 3. Variation of the rank normalized abundances of the 23 genera and 8 phyla (in italics) across the 20 gut metagenomes.
The metagenomes are arranged in the bottom panel (from left to right) in decreasing order of their cumulative nutritional scores. The groups of microbiomes belonging to Apparently Healthy (AH), Borderline (BL) and Severely Malnourished (SM) children are also indicated. The taxa are arranged vertically on the left panel as a hierarchical tree based on the similarities in their abundance patterns. The four groups of taxa (G1–G4) with similar abundance patterns across the metagenomes are also demarcated. The cumulative rank normalized abundances of groups G1 (showing progressive increase with nutritional scores) and G4 (showing a progressive decrease with nutritional scores) across the 20 samples are provided in the bottom most panel.
Figure 4
Figure 4. Box-plots showing the abundances of the taxonomic groups significantly differing across the three groups (AH, BL and SM) of gut microbiomes.
Figure 5
Figure 5. Percentage abundances of the different functional categories corresponding to the COGs identified either as positively correlated (shown in green) or as negatively correlated (shown in red) with nutritional indices.
Figure 6
Figure 6. Abundance patterns of different groups of CAZyme families across gut metagenomes with varying nutritional status.
The metagenomes are arranged in the bottom panelin decreasing order of their cumulative nutritional scores. The groups of microbiomes belonging to Apparently Healthy (AH), Borderline (BL) and Severely Malnourished (SM) children are also indicated. “**”indicates the variation of the cumulated abundances of members belonging to groups 3, 6 and 7.
Figure 7
Figure 7. Genera co-occurrence networks obtained for gut microbiomes from (A) Apparently Healthy, AH, (B) Borderline, BL and, (C) Severely Malnourished, SM children.
Figure 8
Figure 8. Variations of graph properties (of the genera co-occurrence networks obtained for the overlapping groups of metagenomes) namely, (A) Average number of neighbors and, (B) Shortest path with the average nutritional index.

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Grant support

This work was supported by the financial grant from the Department of Biotechnology, Govt. of India, for the establishment of Center for Human Microbial Ecology (Grant No. BT/MB/THSTI/HMC-SFC/2011). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.