Long-read sequencing of rectal swabs in Rwandan children shows links between gut microbiota composition and malnutrition-associated variables

Abstract Gut microbiome composition has been suggested as a factor in the development of malnutrition, which affects one fifth of all children. The microbiome is dependent on environmental and dietary factors, therefore studies on the gut microbiota diversity and relative abundance of bacteria in children with and without malnutrition in different geographical regions are needed. In this study, rectal swabs were collected from 134 Rwandan children 1–36 months of age with (n = 66) or without (n = 68) malnutrition. DNA was extracted from rectal swabs and the full 16S rRNA gene deep sequenced using Nanopore sequencing for analysis of the gut microbiota. Gut microbiota alpha diversity correlated positively with age ( P < 0.0001). Neither alpha nor beta diversity differed between the study-defined malnourished and non-malnourished groups, however, participants with WAZ ≥ − 2 and < − 2 differed in beta diversity analysis ( P = 0.02). The most abundant species, Peptostreptococcaceae bacterium oral taxon 929, showed an association with WAZ, in mean 18% and 9% relative abundance among those with WAZ ≥ − 2 and < − 2, respectively ( p = 0.04). Results suggested that the gut microbiota might be associated with being underweight (WAZ < − 2), highlighting the need for future, larger studies of the gut microbiota in malnourished children.