Life-long microbiome rejuvenation improves intestinal metabolism and inflammaging in mice [bulk RNA-seq]

Alterations in composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Physiological responses were analyzed by rotarod and a grip strength test, intestinal barrier function by FITC gavage and LAL assay, transcriptional responses by single cell RNA sequencing and microbiome function by 16S profiling and metagenomics. Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB hinting at more stable microbiome communities. Single cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways in enterocytes and TA cells but reduced inflammatory signaling in macrophages. Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including motor coordination, intestinal permeability and immune cell phenotypes. 8-week-old male C57Bl6/J mice (n=60) were subjected to successive 8-week-long cycles consisting of (i) a microbiome depletion for 14 days via antibiotic treatment, (ii) immediate recolonization via fecal microbiota transfer and (iii) 6 weeks of an intermittent phase. Freshly collected fecal pellets of unrelated and untreated male C57Bl6/J mice of the same age (isochronic microbiome transfer, iMB) or 8 weeks of age (young microbiome transfer, yMB) were orally gavaged with suspension to restore the depleted microbiomes. Total RNA-seq samples were obtained from the colon of these mice, early in the treatment (40w) and at the end of the treatment (120w-Final).