Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing

Abstract

This study aimed to determine the taxonomic and functional characteristics of the Japanese Black (JB) steer rumen microbiome. The rumen microbiomes of six JB steers (age 14.7 ± 1.44 months) and six JB sires × Holstein dams crossbred (F1) steers (age 11.1 ± 0.39 months), fed the same diet, were evaluated. Based on 16S rRNA gene sequencing, the beta diversity revealed differences in microbial community structures between the JB and F1 rumen. Shotgun sequencing showed that Fibrobacter succinogenes and two Ruminococcus spp., which are related to cellulose degradation were relatively more abundant in the JB steer rumen than in the F1 rumen. Furthermore, the 16S rRNA gene copy number of F. succinogenes was significantly higher in the JB steer rumen than in the F1 rumen according to quantitative real-time polymerase chain reaction analysis. Genes encoding the enzymes that accelerate cellulose degradation and those associated with hemicellulose degradation were enriched in the JB steer rumen. Although Prevotella spp. were predominant both in the JB and F1 rumen, the genes encoding carbohydrate-active enzymes of Prevotella spp. may differ between JB and F1.

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan

“…Most of the animals tested were offered highconcentrate diets (Table S1), resulting in the reconstruction of Prevotella MAGs. In the present study, 14 Lachnospiraceae MAGs were reconstructed; however, we previously recovered only 3 Lachnospiraceae MAGs (Sato et al, 2021). Lachnospiraceae is associated with feed efficiency in ruminants (Li and Guan, 2017) and is crucial for shaping the characteristics of JB rumen microbiomes (Ogata et al, 2019;Sato et al, 2021).…”

“…In the present study, 14 Lachnospiraceae MAGs were reconstructed; however, we previously recovered only 3 Lachnospiraceae MAGs (Sato et al, 2021). Lachnospiraceae is associated with feed efficiency in ruminants (Li and Guan, 2017) and is crucial for shaping the characteristics of JB rumen microbiomes (Ogata et al, 2019;Sato et al, 2021). Therefore, the Lachnospiraceae MAGs obtained herein may be useful for metagenomic and metatranscriptomic research in ruminants, particularly JB cattle.…”

“…Despite this, we are the only group to have reconstructed rumen MAGs from cattle in Japan. We previously reconstructed 114 rumen MAGs from the shotgun metagenome data of Japanese Black (JB) and F1 crossbred (JB sire×Holstein dam) steers in Japan ( Sato et al , 2021 ). We herein further expanded the catalogs of rumen microbial genomes in Japan with 146 MAGs from the rumen of JB, Japanese Shorthorn (JS), and F1 steers.…”

Lipidomics and Transcriptome Reveal the Effects of Feeding Systems on Fatty Acids in Yak’s Meat

“…Compared with monogastric animals, the fat metabolism in ruminants is more complex. The rumen microorganisms in ruminants can translate fatty acids from forage or feed into new fatty acids [ 26 ], and finally these new fatty acids deposit in subcutaneous, muscle and the abdomen. It is difficult to explore the effect of the feeding system on fatty acids in yak’s meat using a single molecular biology technique.…”

Using Untargeted LC-MS Metabolomics to Identify the Association of Biomarkers in Cattle Feces with Marbling Standard Longissimus Lumborum

“…Non-invasive methods are the better choice. Nowadays, there are a variety of omics methods to explore the molecular mechanism that influences IMF, such as genomics [ 4 , 5 ], transcriptomics [ 6 , 7 , 8 ], and 16S rRNA gene sequencing [ 9 , 10 ]. However, metabolic profiles are hardly used to explore marbling beef phenotypes.…”