Microbiota-host crosstalk in the newborn and adult rumen at single-cell resolution

Abstract

Background The rumen is the hallmark organ of ruminants, playing a vital role in their nutrition and providing products for humans. In newborn suckling ruminants milk bypasses the rumen, while in adults this first chamber of the forestomach has developed to become the principal site of microbial fermentation of plant fibers. With the advent of single-cell transcriptomics, it is now possible to study the underlying cell composition of rumen tissues and investigate how this relates the development of mutualistic symbiosis between the rumen and its epithelium-attached microbes. Results We constructed a comprehensive cell landscape of the rumen epithelium, based on single-cell RNA sequencing of 49,689 high-quality single cells from newborn and adult rumen tissues. Our single-cell analysis identified six immune cell subtypes and seventeen non-immune cell subtypes of the rumen. On performing cross-species analysis of orthologous genes expressed in epithelial cells of cattle rumen and the human stomach and skin, we observed that the species difference overrides any cross-species cell-type similarity. Comparing adult with newborn cattle samples, we found fewer epithelial cell subtypes and more abundant immune cells, dominated by T helper type 17 cells in the rumen tissue of adult cattle. In newborns, there were more fibroblasts and myofibroblasts, an IGFBP3+ epithelial cell subtype not seen in adults, while dendritic cells were the most prevalent immune cell subtype. Metabolism-related functions and the oxidation-reduction process were significantly upregulated in adult rumen epithelial cells. Using 16S rDNA sequencing, fluorescence in situ hybridization, and absolute quantitative real-time PCR, we found that epithelial Desulfovibrio was significantly enriched in the adult cattle. Integrating the microbiome and metabolome analysis of rumen tissues revealed a high co-occurrence probability of Desulfovibrio with pyridoxal in the adult cattle compared with newborn ones while the scRNA-seq data indicated a stronger ability of pyroxidal binding in the adult rumen epithelial cell subtypes. These findings indicate that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in the adult rumen. Conclusions Our integrated multi-omics analysis provides novel insights into rumen development and function and may facilitate the future precision improvement of rumen function and milk/meat production in cattle.

Age- and Microbiota-Dependent Cell Stemness Plasticity Revealed by Cattle Cell Landscape

“…Herein, to further unveil the molecular events associated with differentiation states within the MC, the differentially expressed genes (DEGs) were identified in NB and AD cattle. The upregulated DEGs of the MCs in the reticulum and omasum were enriched in the epithelial cell differentiation and cell proliferation, which is consistent with our previous findings in the rumen tissue [ 21 ]. Thus, the MC in forestomach tissue may possess different differentiation patterns in the early postnatal period compared with adulthood.…”

“…We further manually removed cell clusters (potential doublets) that had overlapping gene profiles of multiple different cell types and excluded the hemocytes. The rumen age-dependent cell atlas was collected from our previous study [ 21 ].…”

“…Six animals (3 per group) were selected to collect the mucosa. The mucosal bacterial profiles of the rumen in the NB and AD cattle were collected from our previous study [ 21 ]. Total DNA of the mucosal microbiota was extracted from each reticulum and omasum epithelial tissue using the E.Z.N.A.® DNA Kit (Omega Bio-Tek) according to the manufacturer’s instructions.…”

“…The same animals were selected to conduct metabolomics analysis. The mucosal metabolite profiles of the rumen in the NB and AD cattle were collected from our previous study [ 21 ]. The epithelial tissues of the reticulum and omasum were homogenized with 1,000 μl of 70% (v/v) ice-cold methanol/water and cold steel balls at 30 Hz for 3 min and then were whirled for 1 min without steel balls.…”

— Invited Review — Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality

“…However, the heritability and the roles of these microbes in affecting methane emission, meat quality are largely unknown, although there is evidence that they may have an impact on cattle feed efficiency. Future research using single-cell RNA-seq based transcriptomics may allow us to investigate the relevance of the development of mutualism between the rumen and its epithelial-attached microbes, in addition to it as a powerful tool to characterize the cell types and cellular functions in the rumen epithelial tissues [ 90 ]. Regardless, the information from this review has provided scientific bases for future novel microbiome-based solutions to enhance the production sustainability and improve the meat quality.…”