<b>Impact of animal socioecology on gut microbial communities: insights from wild meerkats in the Kalahari</b>

<p dir="ltr">Addressing a critical gap in our understanding of wildlife microbiomes, our study used data on meerkats to investigate the relative importance of aspects of animal sociality, compared to biological characteristics, environmental exposure, and microbe-specific factors, on the composition and structure of their microbiomes. The study has now been accepted for publication in the<i> Journal of Animal Ecology</i> (Manuscript ID: JAE-2025-00186). </p><p dir="ltr">The files included here constitute R code used, datasets inputted, and/or output generated from, Network Analyses and Joint Species Distributions Models (JSDMs) that were used to realise the aims of the study. File names and text content embedded within the R code contain explanations pertaining to each dataset. For more information please contact either Krishna Balasubramaniam (kb99@aru.ac.uk) or Simone Sommer (simone-sommer@uni-ulm.de) who are the first and last authors of the study.</p><p dir="ltr"><b>Abstract of the study:</b></p><p dir="ltr">The social organisation of animals likely shapes the composition, diversity, and stability of microbiomes, giving rise to the concept of the 'social microbiome'—microbial communities shared within and across social units, or 'islands', ranging from individuals to entire ecosystems. Understanding the connections and their underlying drivers is crucial for revealing how socioecology influences microbiomes and associated health outcomes. However, empirical assessments are still limited, and the relative influence of social organisation compared to intrinsic (biological) and extrinsic (environmental) factors in shaping microbiomes is particularly unclear. Here, we used a long-term, individual-based study of Kalahari meerkats (<i>Suricata suricatta</i>) to test predictions from the social microbiome concept. We assessed the relative influence of social factors, biological traits, and environmental variables on gut microbial communities, while also accounting for the effects of microbial phylogenetic relatedness and within-host associations or co-occurrence independent of phylogeny. Meerkat microbiomes exhibited highly 'nested' and weakly 'modular' structures: individuals with lower diversity hosted ASVs that were subsets of the overall community, though some bacterial taxa clustered distinctly among hosts. Microbiomes were more similar within social groups than between them. Group membership strongly influenced the co-occurrence of many beneficial ASVs, as well as a few potentially harmful ones. This effect was stronger than that of kinship, though closer relatives shared more similar microbiomes within some groups. While a range of social, biological, and environmental factors influenced bacterial abundance, group membership, individual age, and sampling time since sunrise had the most significant impact. ASV-ASV co-occurrence within hosts, independent of phylogeny, also played a major role. In contrast, individual-level social traits (e.g. dominance, immigration), other environmental (e.g. sampling temperature, rainfall, hours since foraging), demographic (sex), and health-related factors (body condition, disease status) had weaker effects on bacterial abundance. We show that gut microbiomes are shaped by a combination of factors, highlighting the importance of separating the effects of social organisation from individual social traits, biological factors, environmental influences, and microbe-microbe interactions. By identifying drivers of both beneficial and detrimental bacterial co-occurrence, we provide a foundation for assessing how the social microbiome affects animal health and fitness.</p>