Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort

While a proportion of the microbiota plays a beneficial role, there is no conclusive evidence that the entire microbiome is mutualistic. Here, we have studied the intestinal microbiota of three healthy age groups from the Valencian Region (Spain). We have periodically obtained stool samples to determine the 16S rRNA gene amplicons, metagenomes, and metatranscriptomes, and we have observed that the microbiota’s stability differs with age, being less stable in infants. Regarding analyses of the conserved microbiota across the three age groups throughout the study period, shared genera account for about 60%. In addition, we identified a core of microbial taxa present in all individuals, which could represent mutualistic symbionts. Finally, in a previous study, we detected that tryptophan and indole production by intestinal bacteria decreases substantially with host age. Metagenomics and metatranscriptomics analyses show that tryptophanase mRNA synthesis in the genus Akkermansia is approximately 10 times lower in adults and the elderly than in children, consistent with this enzyme’s low levels or absence in these groups. Consequently, this supports the hypothesis that an uncoupling might occur between some microbiota taxa and the human host at older ages.