Bacteroidetes to Firmicutes - how captivity changes the gut microbiome composition and diversity in a social subterranean rodent

Abstract Background: In mammals, the gut microbiome has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiome diversity and composition compared to wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the gut microbiome of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiome that occur within one generation in a long-lived, social rodent species. Results: We found a clear divergence in the composition of the gut microbiome of captive and wild Damaraland mole-rats. Although the dominating higher-rank taxa were the same in the two populations, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. Amplicon sequence variants (ASVs) within these two phyla were overrepresented among those ASVs that varied between the two populations. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes. Conclusion: We found that the gut microbiome of captive hosts differs substantially from the gut microbiome composition of wild hosts. The largest differences between the two populations were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.