Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island
Fecal DNA-based 16S ribosomal RNA (rRNA) gene sequencing using next-generation sequencers allows us to understand the dynamic gut microbiome adaptation of animals to their specific habitats. Conventional techniques of fecal microbiome analysis have been developed within the broad contexts defined by human biology; hence, many of these techniques are not immediately applicable to wild nonhuman primates. In order to establish a standard experimental protocol for the analysis of the gut microbiomes of wild animals, we selected the Japanese macaques (Macaca fuscata yakui) on Yakushima Island. We tested different protocols for each stage of fecal sample processing: storage, DNA extraction, and choice of the sequencing region in the bacterial 16S rRNA gene. We also analyzed the gut microbiome of captive Japanese macaques as the control. The comparison of samples obtained from identical macaques but subjected to different protocols showed that the tested storage methods (RNAlater and lysis buffer) produced effectively the same composition of bacterial operational taxonomic units (OTUs) as the standard frozen storage method, although the relative abundance of each OTU was quantitatively affected. Taxonomic assignment of the detected bacterial groups was also significantly affected by the region being sequenced, indicating that sequencing regions and the corresponding polymerase chain reaction (PCR) primer pairs for the 16S rRNA gene should be carefully selected. This study improves the current standard methods for microbiome analysis in wild nonhuman primates. Japanese macaques were shown to be a suitable model for understanding microbiome adaptation to various environments.
KeywordsJapanese macaque Gut microbiome Field biology Fecal collection Next-generation sequencing 16S rRNA gene
We would like to thank our friends and colleagues in Yakushima. Experiment 3 of this study was performed in the Yakushima Field and Genome Science Courses of Kyoto University in spring 2014 and we thank the fellow students and lectures who joined in the courses and the administration staff for making these courses possible behind the scene. We are grateful to Dr. Hirohisa Hirai, Dr. Hiroo Imai, Dr. Nami Suzuki-Hashido, and other members of the Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University for valuable discussions. We also thank members of the Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, particularly Mr. Takayoshi Natsume for collecting samples from captive animals. The study was financed by the Leading Graduate Program of Primatology and Wildlife Science (PWS) of Kyoto University, MEXT/JSPS KAKENHI (#12J04270 and #16K18630 to TH, #17H01911 to TH and GH, #25840170 to AS, and #25291100 to GH) and Fund for the Promotion of Joint International Research (#15KK0256 to GH).
- Balvočiūtė M, Huson DH (2017) SILVA, RDP, greengenes, NCBI and OTT—how do these taxonomies compare? BMC Genom 18(Suppl 2):114Google Scholar
- Hanya G, Naito S, Namioka E, Ueda Y, Sato Y, Pastrana JA, He T, Yan X, Saito M, Costa RFP, Allanic M, Honda T, Kurihara Y, Yumoto T, Hayakawa T (2017) Morphometric and genetic determination of age class and sex for fecal pellets of Sika deer (Cervus nippon). Mammal Study 42:1–8CrossRefGoogle Scholar
- Hayaishi S, Kawamoto Y (2002) Fecal genotyping of mitochondrial DNA polymorphism and fecal age-class estimation of Macaca fuscata yakui: a preliminary report. Mammal Sci 42:161–166 (in Japanese) Google Scholar
- Hiergeist A, Reischl U, Gessner A, Priority Program 1656 Intestinal Microbiota Consortium/quality assessment participants (2016) Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. Int J Med Microbiol 306:334–342CrossRefPubMedGoogle Scholar
- Longmire JL, Maltbie M, Baker RJ (1997) Use of ‘lysis buffer’ in DNA isolation and its implication for museum collections. Occ Pap Mus Texas Tech Univ 163:1–3Google Scholar