Cross-tissue single-cell transcriptomic landscape reveals the key cell subtypes and their potential roles in the nutrient absorption and metabolism in dairy cattle

Wu, Jiajin; Zhu, Senlin; Gu, Fengfei; Valencak, Teresa G.; Liu, Jianxin; Sun, Hui-Zeng

doi:10.1016/j.jare.2021.11.009

Cited by 21 publications

(28 citation statements)

References 78 publications

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“…In our other paper [ 20 ], we also found the MC, BC, cg-like SC, SC, and GC cell types and all of them had more subtypes than that of this study (3 vs. 2, 4 vs. 3, 3 vs. 1, 3 vs. 2, and 5 vs. 3, respectively). This was in line with expectations because our other paper [ 20 ] carried out reclustering analysis on the epithelial cells collected from the same scRNA-seq data of AD rumen [ 19 ] with higher resolution (1.6 vs. 0.8), which can identify more cell subtype clusters. It should be noted that the TNFRSF6B + EC was observed in this study but not in our other study.…”

Section: Resultssupporting

confidence: 88%

“…A list of differentially expressed genes for each cluster was also available in Table S3. In our other paper [ 19 ], the myofibroblasts, PAM + fibroblast, and MFAP5 + fibroblast cell clusters were not identified. This is because they could not form the cell cluster and algorithmically grouped with a more populous cell cluster due to the small number (only 9, 2, and 0, for the myofibroblasts, PAM + fibroblast, and MFAP5 + fibroblast cell clusters, respectively; Additional file 2 : Table S1) when analyzing solely the scRNA-seq data of the AD rumen.…”

Section: Resultsmentioning

confidence: 85%

“…In this study, we have taken a multi-omic approach that includes scRNA-seq to explore the cell-type composition, associated microbiome, and metabolome of rumen epithelium in a comparative analysis of undeveloped rumen tissues from newborn calves and mature rumen tissues from adult lactating cattle. Our scRNA-seq data from the rumens of these adult cattle has also been reported and analyzed in two other studies (embarked upon after this one, but already published [ 19 , 20 ]).…”

Section: Introductionmentioning

confidence: 73%

“…2 B; Additional file 2 : Table S2). Our other paper, which analyzed the same scRNA-seq data form the AD rumen but without the NB rumen, also identified the Th17 cells, MKI67 + Th17 cells, γδ T cells, and DC, but no NKT cells and plasmacytoid DC [ 19 ]. However, we found the NKT cells and plasmacytoid DC by integrating scRNA-seq datasets of the NB and AD rumen in this study.…”

Section: Resultsmentioning

confidence: 99%

“…In one study [ 19 ], we compared scRNA-seq data and metabolites from multiple tissue types (rumen, reticulum, omasum, abomasum, ileum, rectum, liver, salivary gland, mammary gland, and peripheral blood), originating from the same lactating adult dairy cattle. In the other study [ 20 ], we investigated the contribution of interactions between adult rumen epithelial cell subtypes and rumen digesta microbiota to fiber utilization by integrating the data of meta-genome assembled microbial genomes and scRNA-seq [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

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

Zhu

Tang

et al. 2022

BMC Biol

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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.

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Section: Resultssupporting

confidence: 88%

Section: Resultsmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 73%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Zhu

Tang

et al. 2022

BMC Biol

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Mapping Cell Atlases at the Single‐Cell Level

Ye,

Wang,

et al. 2023

Advanced Science

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Recent advancements in single‐cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single‐cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.

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Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle

Liu

Tang

et al. 2022

Animal Nutrition

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Cross-tissue single-cell transcriptomic landscape reveals the key cell subtypes and their potential roles in the nutrient absorption and metabolism in dairy cattle

Cited by 21 publications

References 78 publications

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

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

Mapping Cell Atlases at the Single‐Cell Level

Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle

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