Duodenal microbiota in stunted undernourished children with enteropathy

Robert Y. Chen, Vanderlene L. Kung, Subhasish Das, M. Shabab Hossain, Matthew C. Hibberd, Janaki Guruge, Mustafa Mahfuz, Khodeza Nahar Begum, M. Masudur Rahman, Shah Mohammad Fahim, M. Amran Gazi, Rashidul Haque, Shafiqul A. Sarker, Ramendra N. Mazumder, Blanda Di Luccia, Kazi Ahsan, Elizabeth Kennedy, Jesus Santiago-Borges, Dmitry A. Rodionov, Semen A. LeynAndrei L. Osterman, Michael J. Barratt, Tahmeed Ahmed, Jeffrey I. Gordon

Research output: Contribution to journalArticlepeer-review

98 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)321-333
Number of pages13
JournalNew England Journal of Medicine
Issue number4
StatePublished - Jul 23 2020
Externally publishedYes

ASJC Scopus subject areas

  • General Medicine


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