ArticleGenome research2023
Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 20 citations in OpenAlex.
- Single-Cell Omics Advances in Understanding Tissue Development and Complex Trait Formation in Sheep and Goats.Animals : an open access journal from MDPI · 2026Review
- Rumen Mycobiome Thiamine Metabolism Contributes to Subacute Rumen Acidosis Tolerance in Goats Through Enhancing Epithelial Cell Proliferation via IGFBP2/IGF1 Axis Activation.Exploration (Beijing, China) · 2026Article
- Review
- Mechanisms and Applications of Gastrointestinal Microbiota-Metabolite Interactions in Ruminants: A Review.Microorganisms · 2025Review
- Unveiling the rumen-microbiome-brain circuit: a unique dimension of gut-brain axis in ruminants.Journal of animal science and biotechnology · 2025Review
- Revealing the adaptive metabolic differences of different sheep breeds in plateau areas based on the Gut-Cardiac axis.BMC genomics · 2025Article
- Transcriptomic profiling of rumen epithelium, liver, and muscle reveals tissue-specific gene expression patterns in Hu sheep.BMC genomics · 2025Article
- Early rumen development in calves: Biological processes and nutritional strategies-A mini-review.JDS communications · 2025Article
- Genetic and Epigenetic Adaptation Mechanisms of Sheep Under Multi-Environmental Stress Environment.International journal of molecular sciences · 2025Review
- Investigating the establishment of the rumen and oral bacterial communities in beef cattle and assessing the applicability of using the oral bacterial community composition as a proxy for rumen bacterial community structure in cattle.Frontiers in microbiology · 2025Article
- A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation.Molecular biology and evolution · 2024Article
- Application of Pan-Omics Technologies in Research on Important Economic Traits for Ruminants.International journal of molecular sciences · 2024Review
- Exploring the Effect of GastrointestinalAnimals : an open access journal from MDPI · 2024Review
- Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities.Current issues in molecular biology · 2024Review
- Inter-kingdom communication and the sympoietic way of life.Frontiers in cell and developmental biology · 2024Article
Corrections and comments
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Authors and funding
18 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.