ABSTRACT. Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan. The Japanese rock ptarmigan (Lagopus muta japonica) is a typical endangered species, and recently, a national program for its conservation was approved [19]. Apart from the in situ conservation program, a number of ex situ conservation approaches are currently being implemented at zoos. However, several health problems, such as diarrhea and kidney failure, due to lithiasis are frequently detected in captive bred and reared Japanese rock ptarmigans ([20, 23] and N. Miyano, personal communication), and thus, treatment with antibiotics has been obligatory. Unbalanced intestinal microbiota in captive birds may cause these symptoms, because, in absence of the barrier function of normal gastrointestinal (GIT) microbiota, diarrhea is usually caused by opportunistic enteropathogens [10], and kidney calculus is caused by accumulation of oxalic acid which, under normal circumstances, is degraded by indigenous intestinal bacteria [1,15].Identification of indigenous, health-promoting GIT microorganisms in rock ptarmigans is important for the success of captive breeding of these birds. Therefore, in the present study, we employed next-generation sequencing, also known as ultra-deep sequencing, in order to reveal the distinctiveness and key components of GIT microbiota in healthy wild rock ptarmigans in the Tateyama Mountains, Toyama Prefecture, Japan, by comparing the results with those from captive bred Svalbard rock ptarmigans (L. m. hyperborea) in a captive facil...