Differences in the bacterial profiles of infant gut by birth process, milk diet, and choice of 16S rRNA gene target region

Abstract Perinatal factors such as birth process and milk diet have been known to greatly influence the development of gut microbiota, which are often studied using amplicon sequencing of the 16S rRNA gene. However, targeting different hypervariable region/s generates variable bacterial community profiles that are critical in the interpretation of results attributed to such influential factors. In this study, we first determined the influence of birth process and milk diet on the bacterial diversity and profiles in the gut of 60 healthy Filipino infants, aged 2 to 4 months old. Our results revealed the combined influence of birth process and infant milk diet in the establishment and/or shifts of microbial communities in the gut of infants during this age, which blurs out the distinction of microbial community profiles of the infant gut known to one factor alone. On the technical aspect, we elected 10 stool samples from cesarean-delivered exclusively breast-fed infants to be amplified with both V3-V4 and V4-V5 primers and noted differences in the abundance Firmicutes and Actinobacteria. Despite variations in the relative abundance of these taxa, we noted at least 4 of the 10 CD-BF samples share similar enriched taxa with both primer sets used. Hence, the gut microbiota of infants during the age of 2 to 4 months old is highly dynamic with individualistic bacterial communities that can be critical for dietary mediations.