Microbiome changes are linked to health in many animals, but the exact mechanisms are not known particularly in non-model organisms, like ostriches. Farmed ostriches have high neonatal mortality, primarily driven by gastrointestinal disease. A new study explored the possible role of microbiome patterns in growing captive ostriches. To do this, researchers examined the gut flora of several intestinal regions and sampled environmental bacteria. Individuals that succumbed to gastroenteritis had dramatically lower microbial diversity than age-matched controls, particularly in the ileum. The cecal and colon microbiomes of healthy individuals were similar to each other across hosts and ages, but diseased individuals had major disruptions. There was no evidence the taxa associated with mortality infiltrated from the environment at the onset of disease. Instead, they were present in the gut shortly after hatching and proliferated in individuals with low microbial diversity. Future work is needed to determine the causes of this low diversity and to examine other life stages. For example, current husbandry practices separate chicks from adults, which might prevent the formation of healthy gut microbiota. Many of the bacterial taxa identified here have shown similar roles in other animals, suggesting shared host-microbe interactions across species.