Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet

Abstract

A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18–20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.

Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet

“…A comparable distribution of Bacteroidetes and Firmicutes and a similar F/B ratio in the present study led to a non-significant difference in the nutrient digestibility and VFA production between the cattle and buffaloes fed on a mixed diet consisting of equal proportions of dry and green roughages and concentrate. These findings are in good agreement with the recent reports [ 12 , 71 ]. However, a few reports revealed that buffaloes have a greater abundance of Firmicutes and Bacteroidetes than cattle [ 9 , 14 ].…”

“…The identified rumen microbiota affiliated with 43 phyla, 86 classes, 200 orders, 458 families, and 1722 genera in this study were consistent with the previous reports in cattle [ 10 , 32 , 70 ] and buffaloes [ 56 , 71 ]. The dominance of Bacteroidetes and Firmicutes phyla in the rumen metagenome of cattle and buffaloes was in good agreement with the recent reports [ 12 , 56 , 63 , 72 ]. These two bacterial phyla are primarily involved in the degradation of complex polysaccharides and VFA production.…”

“…Bacteroidetes, one of the major utilizers of H 2 [ 73 ], hold strong capabilities for protein and polysaccharide degradation [ 74 , 75 ], whereas Firmicutes are efficient in breaking lignocellulosic complexes and producing H 2 [ 73 ]. The F/B ratio and a negative correlation between these two phyla in the rumen metagenome of cattle and buffaloes are consistent with the previous studies [ 11 , 12 , 76 , 77 ]. A comparable distribution of Bacteroidetes and Firmicutes and a similar F/B ratio in the present study led to a non-significant difference in the nutrient digestibility and VFA production between the cattle and buffaloes fed on a mixed diet consisting of equal proportions of dry and green roughages and concentrate.…”

“…Cattle have a greater abundance of Methanobrevibacter than buffaloes [ 9 ]. On the contrary, some of the recent studies comparing the methane yield and microbiota composition using 16S rRNA [ 10 ] or shotgun metagenome sequencing [ 11 , 12 ] did not reveal any measurable difference in archaeal communities between cattle and buffaloes. Previous reports suggest that buffaloes are better fibre digesters and possess a different microbial profile than cattle [ 9 , 13 , 14 ].…”

Analysis of differences in the rumen microbiome and metabolic function in prepartum dairy cows with different body condition scores

“…Euryarchaeota are a class of archaea that encompasses most species within archaea and often includes methanogens found in animal intestines. In the cladogram, the abundances of Methanobacteria , Methanobacteriales , and Methanobacteriaceae significantly increased in the HBCS group, all of which are associated with methane production [ 27 ]. The primary function of these archaea is to generate methane using substrates obtained during rumen fermentation, an interesting phenomenon as increased methane production signifies a reduction in energy utilization efficiency, which leads to decreased energy for fat accumulation.…”