Microbial community structure analysis

The differences in the rumen microbiota of sheep with naturally high (HM) and low methane (LM) emissions were evaluated using amplicon sequencing of bacterial and archaeal 16S rRNA, ciliate 18S rRNA and anaerobic fungal ITS1 marker genes. While total numbers of methanogenic archaea per gram freeze-dried rumen sample were not significantly different, archaeal community structure analysis revealed that sequences assigned to the genus Methanosphaera were significantly more abundant in LM-related rumen samples. Methanogen community structure differences were corroborated by volatile fatty acid data showing that the acetate:propionate ratio was lower in LM animals, conditions that potentially result in a higher hydrogen partial pressure. This was likely due to differences within the domain Bacteria and the different fermentation pathways employed by these: HM related samples harboured significantly more species belonging to the Prevotella, Bacteroidales, Ruminococcaceae, Catabacteriaceae, YS2 and Oscillospira. Interestingly, bacterial communities in samples related to LM showed one of two different community types (in humans previously named enterotypes). Low-methane enterotype 1 (LM1) was composed of significantly higher numbers of sequences closely related to the propionate producing Quinella ovalis (Quins oval). Species belonging to potentially lactate and propionate producing Lachnospiraceae, Fibrobacter succinogenes, Sharpea azabuensis, Prevotella bryantii, Kandleria vitulina, Olsenella, and Eubacterium were characteristic for LM2. Composition of ciliate or anaerobic fungal community structure did not appear to be important for expression of the methane phenotype. The specific host genetic or physiological factors that caused the differences in microbial community structure and ultimately methane phenotype remain to be elucidated.