Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa

Abstract

Linear growth delay (stunting) affects roughly 155 million children under the age of 5 years worldwide. Treatment has been limited by a lack of understanding of the underlying pathophysiological mechanisms. Stunting is most likely associated with changes in the microbial community of the small intestine, a compartment vital for digestion and nutrient absorption. Efforts to better understand the pathophysiology have been hampered by difficulty of access to small intestinal fluids. Here, we describe the microbial community found in the upper gastrointestinal tract of stunted children aged 2-5 y living in sub-Saharan Africa. We studied 46 duodenal and 57 gastric samples from stunted children, as well as 404 fecal samples from stunted and nonstunted children living in Bangui, Central African Republic, and in Antananarivo, Madagascar, using 16S Illumina Amplicon sequencing and semiquantitative culture methods. The vast majority of the stunted children showed small intestinal bacterial overgrowth dominated by bacteria that normally reside in the oropharyngeal cavity. There was an overrepresentation of oral bacteria in fecal samples of stunted children, opening the way for developing noninvasive diagnostic markers. In addition, sp. and sp. were found to be more prevalent in stunted children, while , well-known butyrate producers, were reduced. Our data suggest that stunting is associated with a microbiome "decompartmentalization" of the gastrointestinal tract characterized by an increased presence of oropharyngeal bacteria from the stomach to the colon, hence challenging the current view of stunting arising solely as a consequence of small intestine overstimulation through recurrent infections by enteric pathogens.

Systematic review: gastric microbiota in health and disease

“…However, although it is not frequently addressed, it appears that gastric and duodenal microbiota share many common features . Microbiota analysis of African children showed that the stomach and duodenum microbiota are alike but different from the faecal microbiota . Interestingly the level of inter‐individual variation of microbiota was present at much lower level in gastric and duodenal samples when compared to stool samples.…”

“…7 Several studies have also detected representatives of other uncultured bacteria designed as hypothetical phylum SR1. [8][9][10][11] Still, there was a significant overlap with previous cultivation findings, 6,12 mainly because gastric microbes are oxygen tolerant and therefore more readily cultured and described compared to the predominantly anaerobic colonic microbiota.…”

“…47 that the stomach and duodenum microbiota are alike but different from the faecal microbiota. 8 Interestingly the level of inter-individual variation of microbiota was present at much lower level in gastric and duodenal samples when compared to stool samples. Consequently, 50 core species that were present in the upper GI tract of 90% of African children were defined, while only three of these species were found in stool samples.…”

“…Among these, an uncultured species related to the extremophile Deinococcus was discovered as well as members of the hypothetical phylum of enigmatic uncultured bacteria—TM7—referred to as ‘microbial dark matter’ . Several studies have also detected representatives of other uncultured bacteria designed as hypothetical phylum SR1 . Still, there was a significant overlap with previous cultivation findings, mainly because gastric microbes are oxygen tolerant and therefore more readily cultured and described compared to the predominantly anaerobic colonic microbiota.…”

Microbiology and immunology: An ideal partnership for a tango at the gut surface—A tribute toPhilippe Sansonetti

“…Given the capacity of Shigella to acquire and accumulate multiple antibiotic resistances (Njamkepo et al, ), this vaccine remains more than ever indispensable. Over the past 15 years, Philippe and his collaborators have progressively extended their expertise to the field of host–microbiota interactions, with notably the goal to understand how the gut can aggravate or, on the contrary protect, against stunting and environmental enteropathy, a devastating condition that increases susceptibility to infections and impairs the development of young children in developing countries (Vonaesch et al, ; Vonaesch et al, ). The interest of Philippe into host–microbiota provided our team with the chance to set up the very rewarding collaboration that is discussed below to study an unusual symbiont, segmented filamentous bacteria (SFB).…”