Potential role of the oropharyngeal microbiota in stunted childhood growth


Stunted growth is the consequence of chronic malnutrition, probably initiated or exacerbated by recurrent enteric infections and poor hygiene. Affected children seem to present a gut dysbiosis characterized by the unexpected presence of oral and pharyngeal microorganisms.


Stunted growth affects one quarter of children under 5 years old in the world. One possible cause is pediatric environmental enteropathy (PEE), a syndrome responsible for malnutrition that associates repeated bacterial gut infections (caused by poor hygiene) and chronic inflammation attributable to SIBO*. According to a French study on children with stunted growth (from Madagascar and Central African Republic), this syndrome is not the only factor.

Translocation of the oral microbiota

Despite genetic, environmental and nutritional differences between the two countries, researchers discovered that affected children from either community have a gut microbiota colonization by bacteria from the oropharyngeal microbiota. Species belonging to Haemophilus, Neisseria, Moraxella or even Porphyromonas genera (that usually colonize the oral flora) were observed in the 57 gastric samples and 46 duodenal samples collected. However, according to the scientific literature, some of these bacteria are associated with inflammatory diseases (including gastrointestinal cancers, type 2 diabetes, cardiovascular diseases).

A fecal marker with diagnostic value

These oropharyngeal bacteria were also found in the duodenal samples and overrepresented in the 404 perirectal samples collected from children with stunted growth, and not in children from the control group. Enteropathogenic bacteria belonging to the Escherichia coli/Shigella and Campylobacter genera were also more abundant. A decrease in Clostridiales was also found in affected children. These bacteria produce butyrate, a short-chain fatty acid (SCFA) that feeds epithelial cells and participates in the resistance of the host against opportunistic bacteria proliferation. The stool of affected children could thus contain a characteristic signature of stunted growth combining oropharyngeal bacteria, enteropathogens and low level of Clostridiales. This could pave the way to the development of non-invasive markers.

New hypothesis

The authors suggest that the presence of oropharyngeal bacteria in the fecal microbiota could be a contributing factor to PEE physiopathology. Proliferation of these oropharyngeal bacteria in the small intestine and colon could lead to inflammation. Associated to the presence of enteropathogens and decreased rates of butyrate, it could prompt chronic malnutrition in children, and thus result into stunted growth. This hypothesis could be confirmed by the cohort study of 1,000 children which is currently in progress.


*SIBO = small intestine bacterial overgrowth



Vonaesch P et al. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. PNAS September 4, 2018 115 (36) E8489-E8498