Ageing processes in the bonobo gut microbiome mirror human patterns

Ageing is associated with changes in the human gut bacterial microbiome: with age, it becomes more diverse, intra- and interindividual variability increases and it shows a decline in core bacterial genera and an expansion of rarer genera. While recent evidence in model organisms suggests these patterns may arise through stochastic processes rather than host-driven selection, the role of life-time exposures, or the exposome, remains poorly understood. Here, we characterise age-related gut microbiome dynamics in 165 bonobos (Pan paniscus) from wild and zoo-housed populations, aged 2 to 71 years, providing a comparative framework to disentangle conserved from context-dependent ageing trajectories in the gut microbiome in hominids. Across both environments, ageing was associated with increased microbial diversity and reduced core microbiome abundance, paralleled by a rise in low-abundance taxa, recapitulating patterns seen in humans. Notably, instability and uniqueness increased with age in zoo-housed, but not wild bonobos, mirroring patterns restricted to industrialised human populations. Moreover, cumulative exposure to distinct environments over an individual's lifetime substantially contributes to microbiome uniqueness. Our findings suggest that while gut microbiome ageing is broadly conserved across hominids, its expression is modulated by environmental context, offering insight into the evolutionary and ecological drivers of microbial ageing in humans.