Fig. 2: Gut microbiome is rapidly and persistently modulated by diet with age-dependent differences in beta-diversity.

a Young (5 weeks) and old (≥73 weeks) mice received dietary interventions (DI) with either normal (ND), palmitic acid (PA) enriched diets (ED) or oleic acid (OA) ED for a total of 16 weeks. Animals received antibiotics for 5 d in week 9. Starting in week 10, they were either inoculated with Porphyromonas gingivalis (P.g.) or PBS as control three times a week for a total of 5 weeks. Animals were sacrificed in week 16. Microbiome samples were collected at four time points: after 1 week of dietary intervention (DI) (1wk), after 8 weeks of DI/before antibiosis (8wk/B), after antibiosis (At₁), after infection (uninfected also At₂). b–e Microbiome analyses of stool samples after 1 and 8 weeks of DI. b Taxonomic summary of bacterial compositional changes across age (‘young’, ‘old’) and nutrition (ND, PA-ED, OA-ED)-groups. c Samples from both investigated time points were combined to calculate Shannon indexes for alpha diversity in each nutrition group (ND – green, PA – blue, OA – pink) stratified by age (young–left, light colors; old – right – dark colors) (mean ± SEM). d Principal coordinates analysis of beta-diversity based on Bray-Curtis distances shows microbiome diversity in animal samples after 1 and 8 wk DI, grouped by age and nutrition. Shown ND – green, PA – blue, OA – pink; young light, old dark colors. The grey dots represent the data points of the two non-analyzed diets. e Relative abundance (%) at phylum level dependent on age and nutrition after 1 and 8 weeks of DI. Data derived from 3 to 7 mice per condition. DI dietary intervention, ND normal diet, PA-ED palmitic acid enriched diet, OA-ED oleic acid enriched diet, P.g. Porphyromonas gingivalis infection. Statistical analysis in (c): Mann–Whitney U-test, d: Permanova statistical test; ***p ≤ 0.001. a created with BioRender.