Gut microbiota individuality is contingent on temporal scale and age in wild meerkats

Abstract

Inter-individual differences in gut microbiota composition are hypothesized to generate variation in host fitness—a premise for the evolution of host–gut microbe symbioses. However, recent evidence suggests that gut microbial communities are highly dynamic, challenging the notion that individuals harbour unique gut microbial phenotypes. Leveraging a long-term dataset of wild meerkats, we reconcile these concepts by demonstrating that the relative importance of identity for shaping gut microbiota phenotypes depends on the temporal scale. Across meerkat lifespan, year-to-year variation overshadowed the effects of identity and social group in predicting gut microbiota composition, with identity explaining on average less than 2% of variation. However, identity was the strongest predictor of microbial phenotypes over short sampling intervals (less than two months), predicting on average 20% of variation. The effect of identity was also dependent on meerkat age, with the gut microbiota becoming more individualized and stable as meerkats aged. Nevertheless, while the predictive power of identity was negligible after two months, gut microbiota composition remained weakly individualized compared to that of other meerkats for up to 1 year. These findings illuminate the degree to which individualized gut microbial signatures can be expected, with important implications for the time frames over which gut microbial phenotypes may mediate host physiology, behaviour and fitness in natural populations.

Individual variation in the avian gut microbiota: The influence of host state and environmental heterogeneity

“…Mixed models also enable an examination of whether individual differences are independent of other factors that can be included as random or fixed effects. Despite its widespread use in animal personality and cognition literature (Bell et al, 2009; Cauchoix et al, 2018), to our knowledge this approach has only been applied once to identify the sources of individual level variation in the gut microbiota (Risely et al, 2022). Repeatability analysis represents a novel technique that will allow microbiome researchers a greater understanding of microbiome individuality than has been achieved to date (Mallott, 2022).…”

Individualized composition or community dynamics? A new statistical approach to assess the individuality of host-associated microbiomes

“…Risely et al [ 9 ] tackle this question of the individuality of the gut microbiome using a robust longitudinal dataset from wild meerkats and a sophisticated statistical approach not yet applied to microbiome studies. The authors leverage almost 1000 samples collected from 157 meerkats across two decades.…”

Circadian rhythms of hosts and their gut microbiomes: Implications for animal physiology and ecology

“…Although age‐dependent changes to gut microbial composition are known from a variety of wildlife species (Barbosa et al, 2016; Risely et al, 2022; Sadoughi et al, 2022), it remains unknown how changes in composition relate to changes in rhythms. Exploiting systems with high survival rates that have previously been used to model senescence and demography, such as seabirds (Fay et al, 2018; Patrick & Weimerskirch, 2015) or long‐lived mammals (Robinson et al, 2012), may help clarify this question.…”