<i>Vibrio cholerae</i> and other <i>Vibrio</i> spp. isolates analysed in this study.

*<p>Genome strains 1587 (GenBank Accession No. AAUR00000000); 623-39 (Accession No. AAWG00000000); AM-19226 (Accession No. AATY00000000); BX330286 (Accession No. ACIA00000000); CMCP6 (Accession No. AE016795.3); CT5369-93 (Accession No. ADAL00000000); M66-2 (Accession No. CP001233); MB451 (Accession No. ADAF00000000); MZO-2 (Accession No. AAWF00000000); MZO-3 (Accession No. AAUU00000000); N16961 (Accession No. AE003852); M1616/O395 (Accession No. CP000626); RC341 (Accession No. ACZT00000000); RC385 (Accession No. AAKH00000000); RC586 (Accession No. ADBD00000000); SX-4 (Accession No. ADOO00000000); TM11079-80 (Accession No. ACHW00000000); TMA21 (Accession No. ACHY00000000); V51 (Accession No. AAKI00000000); V52 (Accession No. AAKJ00000000); VL426 (Accession No. ACHV00000000); VM223 (Accession No. ADAJ00000000); VM573 (Accession No. ACYV00000000); VM603 (Accession No. ACYU00000000); 12129 (Accession No. ACFQ00000000).</p>†<p>Two primer pairs were used as previously described in Tay <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065342#pone.0065342-Tay1" target="_blank">[44]</a> to amplify divergent <i>tcpA</i> genes.</p>§<p>Two primer pairs were used for typing the type III secretion system (T3SS), one for <i>vcsC2</i> and one for <i>vcsV2</i>.</p>‡<p>N/A: Data not available.</p>#<p>Clonal complex (CC) as defined by eBURST analysis.</p>¶<p>Subpopulations are derived from STRUCTURE analysis.</p

Gut Microbiomes of Indian Children of Varying Nutritional Status

<div><p>Background</p><p>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.</p><p>Methodology/Principal Findings</p><p>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.</p><p>Conclusions</p><p>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.</p></div

Estimates of mutation (θ) and recombination (ρ) rates.

<p>Estimates of mutation (θ) and recombination (ρ) rates.</p

Clinical symptoms of patients with sole infections caused by different pathogroups of DEC.

<p>Numbers in parentheses indicates %. Numerators are number of patients with sole (single DEC) pathogen.</p><p>and the denominators represent numbers of patients infected with DEC along with other pathogen(s).</p

STRUCTURE analysis of <i>Vibrio cholerae</i> isolates including genome strains.

<p>The four subpopulations are colour-coded with red, green, blue and yellow for subpopulation I, II, III and IV respectively. Each isolate has been allocated to a subpopulation. Isolates were identified by strain name with ST in brackets on the left. Mosaic colours for an isolate indicate mixed population origin from respective populations of matching colour. Y-axis represents percentage of population assignment. Non-O1/non-O139 <i>V. cholerae</i> strains from clinical sources are marked with a dot.</p

Relationships of M1086 and pandemic related strains based on minimum spanning tree (MST).

<p>MST was constructed using allelic difference of 26 housekeeping (hk) genes which are either resulted from recombination (r) or mutation (m). Events were marked on the branches with gene symbol (r or m) or for multiple genes as number of hk genes affected. M1086 and V52 were analysed in this study. See Salim <i>et al.. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065342#pone.0065342-Salim1" target="_blank">[43]</a> for details of others. Changes of <i>Vibrio</i> pathogenicity island (VPI) and cholera toxin (CTX) are also indicated. Sequence data were M1086 from this study, V52 from Chun <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065342#pone.0065342-Chun1" target="_blank">[62]</a> and others from Salim <i>et al.. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065342#pone.0065342-Salim1" target="_blank">[43]</a>. Strain names, year of isolation and place of isolation were shown except for the pandemic strains and Australian and US Gulf toxigenic isolates.</p

Primers used in this study.

<p>Primers used in this study.</p

Prevalence of DEC pathogroups among different age groups of diarrheal patients.

<p>Figures in parentheses indicate %.</p

Variation of the normalized abundances (expressed as percentages) of the 23 core genera across the 20 gut metagenomes.

<p>Variation of the normalized abundances (expressed as percentages) of the 23 core genera across the 20 gut metagenomes.</p

Neighbour-net network of <i>Vibrio cholerae</i> isolates analysed in this study.

<p>Four subpopulations (I to IV) as determined by STRUCTURE analysis are indicated with curly brackets. Isolates associated with 6^th, pre-7^th and 7^th pandemics are indicated with an arrow.</p