ORIGINAL ARTICLE Microbial community analysis of rectal methanogens and sulfate reducing bacteria in two non-human primate species Noriko Nakamura 1,2 , Steven R. Leigh 1,3 , Roderick I. Mackie 1,2,5 & H. Rex Gaskins 1,2,4,5 1 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA 2 Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA 3 Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA 4 Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA 5 Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA Introduction Molecular hydrogen (H 2 ) is primarily formed in the digestive tract of human and animals as part of the fermentative breakdown of organic matter from the reoxidation of the reduced pyridine nucleotides NADH and NADPH [59]. Hydrogen is maintained at very low partial pressures to meet the thermodynamic requirements for anaerobic fermenta- tion processes in the colon. Methanogenesis and sulfate reduction are the major hydrogen oxidizing pathways in the human colon [18]. It has been suggested that these metabolic pathways occur in a mutually exclusive manner in the colon [18–20]. A variety of factors including intestinal transit rate [32], colonic pH [18], sulfate availability [4, 15, 16, 18, 32], host genetic background [25] and environmental factors [2, 12] are considered to influence which of the hydrogenotrophic pathways predominate in the colon. The symbiosis of animals and intestinal methano- gens has been observed in a wide range of animal spe- cies. While all ruminants have significant numbers of methanogens, animals with hindgut fermentation vary in the extent to which they harbor intestinal methano- gens [23]. Extended screening of methane emissions from arthropods and vertebrate species indicates that there are evolutionary rather than dietary constraints for the symbiosis between animals and methanogens Keywords Cercocebus atys – DGGE – intestinal hydrogenotrophs – Papio hamadryas – quantitative PCR Correspondence H. R. Gaskins, PhD, University of Illinois, 1207 W. Gregory Drive, Urbana, IL 61801, USA. Tel.: (217) 244-3165; fax: (217) 333-8286; e-mail: hgaskins@illinois.edu Accepted May 14, 2009. Abstract Background Methanogenesis by methanogenic Archaea and sulfate reduc- tion by sulfate reducing bacteria (SRB) are the major hydrogenotrophic pathways in the human colon. Methanogenic status of mammals is sug- gested to be under evolutionary rather than dietary control. However, information is lacking regarding the dynamics of hydrogenotrophic micro- bial communities among different primate species. Methods Rectal swabs were collected from 10 sooty mangabeys (Cercocebus atys) and 10 baboons (Papio hamadryas). The diversity and abundance of methanogens and SRB were examined using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR). Results The DGGE results revealed that intestinal Archaea and SRB com- munities differ between mangabeys and baboons. Phylogenetic analyses of Archaea DGGE bands revealed two distinct clusters with one representing a putative novel order of methanogenic Archaea. The qPCR detected a similar abundance of methanogens and SRB. Conclusions Intestinal Archaea and SRB coexist in these primates, and the community patterns are host species-specific. J Med Primatol doi:10.1111/j.1600-0684.2009.00361.x J Med Primatol (2009) 1–11 ª 2009 John Wiley & Sons A / S 1