ArticleiMeta2025
Single-microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut.
Article in iMeta, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- A Microcapsule-Integrated smRandom-seq Platform Enables Fixation-Free Single Microbe RNA Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 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
- Effects of Soybean- and Cottonseed-Based Diets on Growth Performance and Gut Microbiota of Black Soldier Fly Larvae.Insects · 2026Article
- Parabacteroides distasonis ameliorates ETEC-induced diarrhea in weaned piglets by regulating intestinal barrier function and intestinal inflammation.Porcine health management · 2026Article
- BACON: decoding the dynamic social networks of complex microbial communities at single-cell resolution.Briefings in bioinformatics · 2026Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Article
- Total alkaloids ofFrontiers in pharmacology · 2025Article
Corrections and comments
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Authors and funding
22 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human body is inhabited by trillions of microorganisms that play a crucial role in health and diseases. Our understanding of the species and functional composition of the human gut microbiome is rapidly expanding, but it is still mainly based on taxonomic profiles or gene abundance measurements. As such, little is known about the species-function heterogeneity and dynamic activities in human microecosystem niches. By applying a novel gut-specific single-microbe ribonucleic acid (RNA) sequencing and analytical framework on three healthy donors with distinct enterotypes, we created a comprehensive transcriptional landscape of the human gut microbiome and dissected functional specialization in 38,922 single microbes across 198 species. We investigated the functional redundancy and complementarity involved in short-chain fatty acids related central carbon metabolism and studied the heterogeneity and covariation of single-microbe metabolic capacity. Comparing the human gut microbiome at different times throughout the day, we were able to map diurnal dynamic activities of the gut microbiome and discovered its association with sub-population functional heterogeneous. Remarkably, using single-microbe RNA sequencing, we systematically dissected the metabolic function heterogeneity of
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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.