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Accession: PRJEB32184 ID: 699779

Duodenal Microbiota in Stunted Undernourished Children with Enteropathy

BACKGROUND Environmental enteric dysfunction (EED) is an enigmatic disorder of the small intestine that is postulated to play a role in childhood undernutrition, a pressing global health problem. Defining the incidence of this disorder, its pathophysiological features, and its contribution to impaired linear and ponderal growth has been hampered by the difficulty in directly sampling the small intestinal mucosa and microbial community (microbiota). METHODS In this study, among 110 young children (mean age, 18 months) with linear growth stunting who were living in an urban slum in Dhaka, Bangladesh, and had not benefited from a nutritional intervention, we performed endoscopy in 80 children who had biopsy-confirmed EED and available plasma and duodenal samples. We quantified the levels of 4077 plasma proteins and 2619 proteins in duodenal biopsy samples obtained from these children. The levels of bacterial strains in microbiota recovered from duodenal aspirate from each child were determined with the use of culture-independent methods. In addition, we obtained 21 plasma samples and 27 fecal samples from age-matched healthy children living in the same area. Young germ-free mice that had been fed a Bangladeshi diet were colonized with bacterial strains cultured from the duodenal aspirates. RESULTS Of the bacterial strains that were obtained from the children, the absolute levels of a shared group of 14 taxa (which are not typically classified as enteropathogens) were negatively correlated with linear growth (length-for-age z score, r=−0.49; P=0.003) and positively correlated with duodenal proteins involved in immunoinflammatory responses. The representation of these 14 duodenal taxa in fecal microbiota was significantly different from that in samples obtained from healthy children (P<0.001 by permutational multivariate analysis of variance). Enteropathy of the small intestine developed in gnotobiotic mice that had been colonized with cultured duodenal strains obtained from children with EED. CONCLUSIONS These results provide support for a causal relationship between growth stunting and components of the small intestinal microbiota and enteropathy and offer a rationale for developing therapies that target these microbial contributions to EED. (Funded by the Bill and Melinda Gates Foundation and others; ClinicalTrials.gov number, NCT02812615. opens in new tab.)
AccessionPRJEB32184
Data TypeGenome sequencing and assembly
ScopeMonoisolate
SubmissionRegistration date: 5-Feb-2021
WASHINGTON UNIVERSITY CENTER FOR GENOME SCIENCES
Project Data:
Resource NameNumber
of Links
Sequence data
Nucleotide (total)2374
WGS master39
SRA Experiments209
Protein Sequences88205
Other datasets
BioSample108
Assembly39
Assembly details:
Assembly levelNumber of Assemblies
39
39
AssemblyLevelWGSBioSampleTaxonomy
GCA_901873405.1ContigCABFLT000000000SAMEA5664346
GCA_901873655.1ContigCABFLQ000000000SAMEA5664347
GCA_901873715.1ContigCABFLV000000000SAMEA5664348
GCA_901873505.1ContigCABFLL000000000SAMEA5664351
GCA_901874975.1ContigCABFLX000000000SAMEA5664352
GCA_901873525.1ContigCABFLK000000000SAMEA5664353
GCA_901873475.1ContigCABFLS000000000SAMEA5664354
GCA_901873465.1ContigCABFLU000000000SAMEA5664355
GCA_901873415.1ContigCABFLE000000000SAMEA5664356
GCA_901873395.1ContigCABFLP000000000SAMEA5664357
GCA_901873445.1ContigCABFLN000000000SAMEA5664358
GCA_901873425.1ContigCABFLJ000000000SAMEA5664359
GCA_901873495.1ContigCABFLR000000000SAMEA5664360
GCA_901873435.1ContigCABFLD000000000SAMEA5664361
GCA_901873375.1ContigCABFLI000000000SAMEA5664362
GCA_901873565.1ContigCABFLO000000000SAMEA5664363
GCA_901873385.1ContigCABFLG000000000SAMEA5664365
GCA_901873995.1ContigCABFLW000000000SAMEA5664366
GCA_901875325.1ContigCABFLZ000000000SAMEA5664367
GCA_901875335.1ContigCABFMA000000000SAMEA5664368
GCA_901875315.1ContigCABFMC000000000SAMEA5664370
GCA_901875305.1ContigCABFLY000000000SAMEA5664371
GCA_901875495.1ContigCABFMG000000000SAMEA5664372
GCA_901875485.1ContigCABFMI000000000SAMEA5664373
GCA_901875545.1ContigCABFME000000000SAMEA5664374
GCA_901875505.1ContigCABFMH000000000SAMEA5664375
GCA_901875565.1ContigCABFML000000000SAMEA5664376
GCA_901875555.1ContigCABFMD000000000SAMEA5664377
GCA_901875515.1ContigCABFMK000000000SAMEA5664378
GCA_901875525.1ContigCABFMJ000000000SAMEA5664379
GCA_901875595.1ContigCABFMM000000000SAMEA5664381
GCA_901875535.1ContigCABFMO000000000SAMEA5664382
GCA_901876955.1ContigCABFMP000000000SAMEA5664383
GCA_901875635.1ContigCABFMN000000000SAMEA5664384
GCA_901873455.1ContigCABFLF000000000SAMEA5664349
GCA_901873365.1ContigCABFLM000000000SAMEA5664350
GCA_901873485.1ContigCABFLH000000000SAMEA5664364
GCA_901875295.1ContigCABFMB000000000SAMEA5664369
GCA_901875575.1ContigCABFMF000000000SAMEA5664380
SRA Data Details
ParameterValue
Data volume, Gbases229
Data volume, Mbytes92984

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