Methanogenic archaea in adult human faecal samples are inversely related to butyrate concentration

Abstract

Background: We have examined the relationship between the presence and numbers of methanogenic archaea in the faeces of humans and levels of the short chain fatty acids (SCFAs), especially butyrate, to gain insight into factors that may influence bowel health. In doing so, we have carried out the first cultivation-independent, molecular analysis of methanogen diversity and abundance in the human gastrointestinal tract. Materials and methods: The faeces of eight healthy individuals on their normal diets were collected weekly over a 12 week period. DNA was extracted from the faeces and PCR-based assays, using methanogen-specific 16S rRNA gene primer sets, were used in conjunction with denaturing gradient gel electrophoresis (DGGE) to identify and enumerate methanogens present. Results: Methanogens were detected in all faecal samples from five of the eight individuals tested. Three distinct methanogen phylotypes were found, with two or three phylotypes present in some individuals. DNA sequencing of DGGE bands indicated that all phylotypes were closely related to Methanobrevibacter smithii (99–100%). Real-time PCR analyses revealed that faecal methanogen numbers varied significantly between individuals and over time by up to two orders of magnitude. Concentrations of acetate, butyrate and propionate in faeces also varied significantly between individuals and with time. There was a negative correlation between mean faecal butyrate concentration and methanogen abundance (R = − 0.729, pn=8), but no significant relationship existed for acetate, propionate or total SCFAs, and no relationship was found between total bacterial abundance and pH, SCFA concentration or methanogen abundance. Conclusion: As butyrate appears to be an important mediator of colonic health, the inverse relationship with methanogens uncovered here suggests that methanogens may be useful biomarkers of bowel health.