<b>Impact of animal sociality on microbiome community ecology: insights from meerkats in the Kalahari</b>

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 is currently <i>under review</i>. The datasets included here constitute R code used, or data files input or generated from, Network Analyses and Joint Species Distributions Models that were used to realise the study objectives. File names and content embedded within the R code contain explanations pertaining to each dataset. For more information please contact either Krishna Balasubramaniam ([e-mail]) or Simone Sommer ([e-mail]) who are the first and last authors of the study.<b>Abstract of the study:</b>The social organisation of animals is likely to influence the composition, structure and stability of their microbiomes, but we currently know little about these effects. Addressing this gap is critical to advance knowledge of the impact of the ‘social microbiome’ on animal health and survival. Here we use a long-term, individual based study of Kalahari meerkats to assess the relative importance of multiple aspects of animal sociality, and social compared to biological, environmental, and microbe-specific factors, in influencing microbiome communities. Bacterial ASVs exhibited highly 'nested', weakly 'modular' structures: hosts with lower diversity harboured ASVs that were subsets of the overall diversity, but a few bacterial taxa were found in distinct host clusters. Many meerkats showed high diversity of ASVs, while only a minority exhibited lower bacterial diversity. Meerkats within the same group had greater bacterial similarity compared to those from different groups. Moreover group membership strongly influenced the co-occurrence of many beneficial ASVs, but also few ASVs that are detrimental to host health. This effect of group membership was stronger than kinship, although closer relatives showed greater bacterial similarity within some groups. While social, biological, and environmental factors all influenced bacterial abundance, meerkats' group membership, age, and sampling time after sunrise had the greatest impact. In comparison, individual-level social variables (dominance, immigration status), and other environmental (temperature, rainfall, hours since foraging), demographic (sex), and health-related (body condition, disease status) factors, all had weaker effects on bacterial abundance. Finally, within-host ASV-ASV co-occurrence irrespective of phylogenetic relatedness also had a strong impact on bacterial communities. Our study demonstrates that microbiome communities are shaped by multiple factors, thus emphasizing the need to effectively distinguish the influence of host social organisation from individual-specific aspects of sociality, biological characteristics, environmental exposure, and microbe-microbe associations. By evaluating the ecological and evolutionary drivers of beneficial and detrimental microbes and their co-occurrence, we also lay the foundation for exploring the links between the ‘social microbiome’ and animal health.