Healthy microbiota is very important for its host although defining it can be challenging because the composition of the microbiota is very diverse and highly variable depending on, for example, environment, genetics, and host health status. Drastic changes in environment or lifestyle can lead to the imbalance of microbiota. This can be problematic as healthy microbiota have myriad positive functions, including protection of a host from invasion of pathogenic bacteria and modulation of the immune system. We studied the effects of environmental conditions (water temperature and oxygen concentration) on zebrafish skin microbiota. We found that genotype did not have an effect on skin microbiota composition and extreme changes in water temperature only had a relatively minor effect. We further demonstrated that zebrafish skin microbiota composition changed when water temperature and oxygen concentration were altered but these perturbations did not permanently shift skin microbiota composition. Finally, we compared gut microbiota composition of healthy horses and horses suffering from inflammatory bowel disease (IBD). We show that IBD did not cause a dysbiosis in the entire gut microbiota but only approximately 200 OTUs (less than 1% of all analyzed OTUs) showed a significant increase or decrease in response to IBD. However, a metabolomic analysis revealed that the functioning of microbiota differed between healthy and IBD-horses. Overall, our results show that while zebrafish skin and horse gut microbiota appear robust and resilient to perturbations. However, a closer look revealed that the abundance of certain pathogenic bacteria was increased and microbiota metabolic were functions altered.