ArticleNature microbiology2024
Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Animal gut microbes and microbiomes in the 21st century and beyond.Science China. Life sciences · 2026Review
- Single-cell detection and quantification of the microbiota by MicFLY.Cell host & microbe · 2026Article
- Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Microbial single-cell transcriptomics links gut microbiota functional states to metabolic changes in male mice.Nature communications · 2026Article
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Lactate in ruminant health: metabolic roles and the emerging significance of lactylation.Journal of animal science and biotechnology · 2026Review
- Nutritional Strategies for Methane, Nitrogen, and Phosphorus Mitigation in Ruminants: Mechanisms, Applications, and Regional Adaptations.Microorganisms · 2026Review
- Goat gut microbiome as a reservoir for microorganism-encoded short peptides: regulation by host development age and nematode challenge.NPJ biofilms and microbiomes · 2026Article
- Fermented feed-rumen microbiota axis mediates goat kid growth via microbial amino acid synthesis and ruminal epithelial energy metabolism.NPJ biofilms and microbiomes · 2026Article
- Effects of Different Feeding Regimes on Rumen Microbial Composition, Functional Potential, and Fermentation Characteristics of Longdong Goats (Animals : an open access journal from MDPI · 2026Article
- Unravelling bacterial complexity at high resolution with single-cell transcriptomics.Nature microbiology · 2026Review
- Microbial landscapes in dairy cow diseases: from localized dysbiosis to inter-organ axes.NPJ biofilms and microbiomes · 2026Review
- Microbial single-cell omics in situ.Cell genomics · 2026Article
- Investigating the potential role of propionylcarnitine in milk pentadecanoic acid synthesis in Chinese holstein dairy cows using multi-omics analysis.BMC genomics · 2026Article
- Integrative analysis of rumen microbiota and host multi-organ interactions underlying feed conversion efficiency in Hu sheep.Journal of animal science and biotechnology · 2026Article
- Single-cell assembled genomes predict enhanced bacterial metabolic cross-feeding potential in carbon-enriched soils.The ISME journal · 2026Article
- Article
- Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.Microbiome · 2026Article
- Accessible, robust ultrahigh-throughput microbiome analysis via integration of uniform droplet-templated emulsification and FACS.PloS one · 2026Article
- Understanding microbial ecology and evolution with single-cell genomics.Nature reviews. Genetics · 2026Article
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Authors and funding
13 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.
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