Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people

Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by <i>Bacteroides</i> (ET-<i>Bacteroides</i>) and <i>Prevotella</i> (ET-<i>Prevotella</i>), we identified a novel enterotype dominated by <i>Escherichia</i> (ET-<i>Escherichia</i>), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-<i>Escherichia</i>, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of <i>Escherichia</i> members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by <i>Escherichia</i> enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.