Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing

Abstract

Background Dairy cows utilize human-inedible, low-value plant biomass to produce milk, a low-cost product with rich nutrients and high proteins. This process largely relies on rumen microbes that ferment lignocellulose and cellulose to produce volatile fatty acids (VFAs). The VFAs are absorbed and partly metabolized by the stratified squamous rumen epithelium, which is mediated by diverse cell types. Here, we applied a metagenomic binning approach to explore the individual microbes involved in fiber digestion and performed single-cell RNA sequencing on rumen epithelial cells to investigate the cell subtypes contributing to VFA absorption and metabolism. Results The 52 mid-lactating dairy cows in our study (parity = 2.62 ± 0.91) had milk yield of 33.10 ± 6.72 kg. We determined the fiber digestion and fermentation capacities of 186 bacterial genomes using metagenomic binning and identified specific bacterial genomes with strong cellulose/xylan/pectin degradation capabilities that were highly associated with the biosynthesis of VFAs. Furthermore, we constructed a rumen epithelial single-cell map consisting of 18 rumen epithelial cell subtypes based on the transcriptome of 20,728 individual epithelial cells. A systematic survey of the expression profiles of genes encoding candidates for VFA transporters revealed that IGFBP5+ cg-like spinous cells uniquely highly expressed SLC16A1 and SLC4A9, suggesting that this cell type may play important roles in VFA absorption. Potential cross-talk between the microbiome and host cells and their roles in modulating the expression of key genes in the key rumen epithelial cell subtypes were also identified. Conclusions We discovered the key individual microbial genomes and epithelial cell subtypes involved in fiber digestion, VFA uptake and metabolism, respectively, in the rumen. The integration of these data enables us to link microbial genomes and epithelial single cells to the trophic system.

Heritable and Nonheritable Rumen Bacteria Are Associated with Different Characters of Lactation Performance of Dairy Cows

“…CCSER1 was reported to be involved in the cell division defect with a potential impact on microbiome components in human colorectal cancer ( 28 ). The expression of this gene has been found in rumen epithelial tissues of dairy and beef cattle based on their transcriptome profiles ( 29 , 30 ), suggesting that this SNP may potentially influence the rumen microbiota by affecting the cell functions of the rumen epithelial wall. Of the heritable bacteria-associated SNPs, five are also associated with the variation of lactation performance.…”

Regulation of Dietary Protein Solubility Improves Ruminal Nitrogen Metabolism In Vitro: Role of Bacteria–Protozoa Interactions

“…In addition, VFA, acetate, propionate and valerate were also elevated with S30 and S40, which may be attributed to the enrichment of Prevotella , which was the core genus of Bacteroidetes. The functions of this microbe include the fermentation of carbohydrates, the utilization of nitrogenous substances, and the biotransformation of bile acids and other steroids; the main by-products of anaerobic respiration are acetate, isovalerate, and succinate, which are closely related to VFA biosynthesis [ 39 , 40 ]. Moreover, propionate is a major substrate of gluconeogenesis, and a recent study also showed that it is closely related to ruminal N metabolism [ 41 ].…”

Residual feed intake in peripartal dairy cows is associated with differences in milk fat yield, ruminal bacteria, biopolymer hydrolyzing enzymes, and circulating biomarkers of immunometabolism

“…For example, our group has determined temporal changes in several nutrient transporters and metabolic genes in ruminal epithelium around parturition and, in some cases [e.g., HMGCS2 (rate-limiting ketogenic enzyme), SLC16A1 (VFA transporter)], mRNA abundance is stable from −14 through 10 DIM, after which upregulation occurs by d 28 (Minuti et al, 2015). Recent studies with lactating cows have underscored the complexity of the ruminal epithelium, highlighting the existence of cell subtypes that seem to be crucial for VFA uptake and metabolism (Xue et al, 2022). Among these findings, an IGFBP5+ cg-like spinous cell population is unique because of its high expression of SLC16A1 and the cation-HCO 3 − exchanger SLC4A9.…”