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Differences in methanogenesis pathways and microbial diversity in the rumen of low- and high-methane-yield phenotype dairy cows.

D. Pitta




Differences in methanogenesis pathways and microbial diversity in the rumen of low- and high-methane-yield phenotype dairy cows.
D. Pitta*1, H. Stefenoni2, N. Indugu1, M. Hennessy1, B. Vecchiarelli1, V. Shabtai1, C. Welchez2, S. R�is�nen2, D. Wasson2, A. Melgar2, M. Fetter2, A. Hristov2. 1University of Pennsylvania School of Veterinary Medicine Kennett Square, PA, 2The Pennsylvania State University University Park, PA.

The objective of this experiment was to identify differences in microbiota and methanogenesis pathways in the rumen of phenotypically low and high methane-yield cows. Following an initial screening period, 5 phenotypically low (LOW) and 5 phenotypically high (HIGH) methane-emitting cows, blocked by parity, days in milk, and milk yield, were used to investigate the functional role of rumen microbiota. All cows were adapted to a standard diet for 3 weeks and sampled for rumen contents at 0, 2, 4, 8, 12, 14, 16, and 20 h post-feeding using the ororuminal technique. The solid fraction of the ruminal samples was extracted for DNA, PCR-amplified for the bacteria and archaea 16S rDNA gene, sequenced and analyzed for bacteria and archaeal diversity. Additionally, the genomic DNA from 2h post-fed rumen samples was prepared for metagenomic analysis and genes were annotated against the KEGG database. Methane emissions (346 vs 439 � 28.6 g/d) were lower (P = 0.03) for LOW vs. HIGH cows. At the community level, both unweighted and weighted UniFrac analysis revealed differences (P < 0.05) in bacteria and archaea communities between groups. Among methanogens, Methanobrevibacter was lower and Methanosphaera was higher (P < 0.05 for both) in LOW vs. HIGH groups. In bacterial DNA and cDNA, genera such as Prevotellaceae and Succinovibrionaceae were higher in the LOW group, while genera such as Ruminococcaceae were higher in the HIGH group. Among the methanogenesis pathways, across both groups, the CO2/formate-reducing pathway was predominant followed by the methanol-reducing pathway. Methanobrevibacter and Methanosphaera, respectively, played significant roles in these pathways. The number of gene copies encoding the α, β, and γ chains of methyl co-enzyme reductase (MCR), an enzyme present in all methanogens that facilitates the formation of methane, was lower (P < 0.05) in LOW vs. HIGH cows (336 vs. 452 copies per million, respectively). It can be concluded that the 22% difference in methane emissions is accompanied by a 25% difference in gene copies coding for MCR enzyme between HIGH and LOW cows.

Keywords: metagenomics, bacteria-archaea, methyl co-enzyme reductase (MCR).