Rumen microbiota and fermentation characteristics diverge in Hanwoo steers with different methane emissions

This study compared the rumen microbiota and fermentation characteristics between Hanwoo steers with low and high methane emissions. Eighteen steers (seven months old) were fed an identical diet for 60 days, and their methane emissions were measured using the GreenFeed system at nine months of age. Based on their methane emission data, steers in the top 25% (high-methane group, HM; n = 4) and bottom 25% (low-methane group, LM; n = 4) were selected for analysis of rumen microbiota and fermentation characteristics. Rumen samples were collected, and the microbial composition was analyzed using metataxonomics based on full-length bacterial 16S rRNA gene sequencing on the PacBio Sequel II platform and archaeal 16S rRNA gene sequencing on the Illumina MiSeq platform. The data were processed using the QIIME2 pipeline and the MicrobiomeAnalyst platform. Rumen fermentation characteristics were analyzed using gas chromatography. Compared with the HM group, steers in the LM group exhibited significantly lower methane production (g/day), yield (g/kg DMI), and intensity (g/kg metabolic body weight (MBW)), but similar body weight and dry-matter intake, while showing greater average daily gain. Moreover, higher propionate concentrations and greater abundances of Prevotella and Succinivibrio were found in the LM group. Methane yield was negatively correlated with the relative abundances of Prevotella and Succinivibrio, as well as with propionate concentration. However, no significant differences in alpha diversity metrics or overall microbiota composition were observed between the two groups. Similarly, no clear separation between the HM and LM groups was observed in beta-diversity analyses for either bacterial or archaeal communities. In the archaeal community, Methanobrevibacter was dominant, and no significant differences in archaeal taxonomic composition were observed between the two groups. The ciliate protozoal population was lower in the LM group than in the HM group, whereas the abundances of total bacteria, total archaea, and total fungi did not differ significantly. These findings suggest that the specific rumen microbial taxa and fermentation profiles, rather than overall microbial community diversity, were associated with the differences in methane emissions.