Effect of Relocation, Social Housing Changes, and Diarrhea Status on Microbiome Composition of Juvenile Cynomolgus Macaques (Macaca fascicularis)

Social housing changes are likely stressful and can be associated with diarrhea, the most common health problem noted in captive macaque populations. Diarrhea may reflect a negative shift in the gut flora (“gut dysbiosis”). This study reported on changes in the gut microbiome composition of juvenile primates (Macaca fascicularis) that experienced a change in social housing and exhibited diarrhea. A matched-case–control design was utilized to compare fecal samples from gut-unhealthy animals to healthy counterparts (n = 61). Baseline samples from recently imported animals were collected during routine sedation events. When an animal experienced a housing change, the entire cohort was monitored for diarrhea. Post-relocation samples were collected from animals that exhibited diarrhea and from their matched controls. Samples were assessed via 16S rRNA next-generation sequencing for a microbiome analysis and by ELISA for cortisol levels. Fecal cortisol levels did not differ between groups or across time points. Alpha diversity increased after relocation and differed by sex with males demonstrating a greater change in alpha diversity (p < 0.01). Although exhibiting diarrhea did not affect alpha diversity levels, it was associated with increased beta diversity (p < 0.05). Understanding how the microbiome may be affected by relocation will help guide prevention strategies such as the use of specific probiotics to reduce the incidence of diarrhea.