Abstract
Stable microbe and host interactions are established during the development of the infant gut microbial community that provide essential functions for the efficient digestion of food, immune development, and resistance to colonization with pathogens. To further delineate the stability of the gut microbial community during this time, we have used microbial strain tracking analysis with published longitudinal metagenomic data sets to identify strains that persist in the developing infant gut ecosystem. In the first study, 17 infants were evaluated that had not received antibiotics for 3 years after birth. An infant specific pattern was seen for stable and unstable microbial strains during this time, with only one infant having no stable strains identified out of available strains during the first 3 years. Strain tracking was also applied to follow microbes in a separate set of 14 infants that had multiple doses of antibiotics over the 3 years. In 10 out of 14 infants given multiple antibiotics during the first 3 years, we identified a unique pattern of transient strains that appeared after multiple antibiotic treatments for a short time compared to that in infants not on antibiotics. In a second, independent study, we selected a subset of 9 infants from a previously published study consisting of high-density longitudinal fecal sampling to analyze the gut microbial strain stability of Bacteroides vulgatus and Bifidobacterium adolescentis for up to 6 years following birth. Individual specific patterns were found consisting of varying dominant microbial strains that were independent of antibiotic exposure and birth mode. Our analysis demonstrates an individual specific inherent variability of extinction and persistence of microbial strains in the infant gut community during a time of development that is critical for interactions necessary for establishing normal metabolism and the development of the host immune response.
Highlights
Previous studies have described the development of the gut microbial ecosystem [1,2,3]
We found that only one infant (E001958) had no related strain pairs appearing during 3 years, this infant still showed the presence of Bacteroides, Faecalibacterium, and Parabacteroides, similar to what were observed in the majority of the other infants’ microbial communities
We demonstrate an infant specific variation of strain stability consistent with a dynamic process of ongoing strain competition for dominance in the infant microbial community
Summary
Previous studies have described the development of the gut microbial ecosystem [1,2,3]. The transition to solid foods and physical growth results in changes in the spatial structure of the gut that contributes to the variation in the physical and chemical environment that provides new ecological niche opportunities for growth of microbial strains [8]. This ecosystem transition correlates with the appearance of Bacteroidetes (such as Bacteroides vulgatus) within the gut microbial community structure
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