Early-life mortality linked to gut dysbiosis in ostriches
The gut microbiome of vertebrates has a major effect on host health and fitness, and imbalances in the microbial community (dysbiosis) have been linked with several gut- and autoimmune diseases. However, whether gut dysbiosis is associated with the presence or absence of particular taxa, and how it relates to the development of gut microbiota during early life is unclear. Research to date has focused on a limited range of hosts, making it difficult to infer more general principles of gut dysbiosis across different species and contexts. Here, we first evaluate mortality patterns during the first three months of life in the ostrich (Struthio camelus), a species known to experience extreme juvenile mortality rates. Gut-associated diseases, such as enteritis, have been suggested as a potential cause, but microbial communities of healthy and diseased individuals have yet to be characterised. As a result, we also examined the microbiota of three regions of the ostrich gastrointestinal tract (ileum, caecum, and colon) of 68 individuals that died of suspected disease, and of 50 individuals that were euthanized as age-matched controls. Diseased individuals had drastically lower microbial diversity in all gut regions, and shared more microbiota similarities to each other in the ileum but not in the caecum and colon, compared to controls. The relationship between low diversity and disease was consistent across ages in the ileum, but decreased with age in the caecum and colon. Several taxa were associated with disease (e.g. Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium spp.) and some with health (e.g. S24-7, Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, and Turicibacter). Together, our results illustrate that early-life mortality is associated with extreme dysbiosis along the gastrointestinal tract of ostrich chicks. Furthermore, the highly reduced microbial diversity in diseased individuals shortly after hatching, suggests that the factors influencing the initial seeding of gut microbiota may be key to understanding dysbiosis and host development.