ArticleNature chemical biology2023
Spatial transcriptome uncovers rich coordination of metabolism in E. coli K12 biofilm.
Article in Nature chemical biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 52 citations in OpenAlex.
- Pan-tumor spatial transcriptomics reveals conserved properties of tumor organization.Cell reports. Medicine · 2026Article
- The power of ten: report from the 10th American Society for Microbiology Conference on Biofilms.Journal of bacteriology · 2026Article
- Phenotypic and Genomic Divergence in Biofilm Formation in STEC and Non-STECPathogens (Basel, Switzerland) · 2026Article
- Mechanism of persister formation in response to nitrogen starvation.Nature communications · 2026Article
- Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.Science advances · 2026Article
- A branching cell-fate decision in biofilm dispersal enables long-term surface persistence.bioRxiv : the preprint server for biology · 2026Article
- Waterborne pathogen mitigation: Decoding techno-ecological synergies in multiscale transmission networks.Innovation (Cambridge (Mass.)) · 2026Review
- Biofilm spatial structure and superinfection immunity modulate inter-phage competition.PLoS biology · 2026Article
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- Understanding the development of bacterial colony: Physiology, new technology, and modeling.Quantitative biology (Beijing, China) · 2025Review
- Single-cell lysis patterns morphogenesis of eDNA in the matrix ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Spatial self-organization of confined bacterial suspensions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Microbial consortia for the conversion of biomass into fuels and chemicals.Nature communications · 2025Review
- L-Arabinose Alters theMicroorganisms · 2025Article
- Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients.Nature communications · 2025Article
- Colony pattern multistability emerges from a bistable switch.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- First-ever ASM Global Research Symposium on Microbes in Human Health in Tsinghua, Beijing, China.mSphere · 2025Article
- Mechanisms ofInternational journal of molecular sciences · 2025Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities often display region-specific properties, which give rise to complex interactions and emergent behaviors that are critical to the homeostasis and stress response of the communities. However, systems-level understanding of these properties still remains elusive. In this study, we established RAINBOW-seq and profiled the transcriptome of Escherichia coli biofilm communities with high spatial resolution and high gene coverage. We uncovered three modes of community-level coordination, including cross-regional resource allocation, local cycling and feedback signaling, which were mediated by strengthened transmembrane transport and spatially specific activation of metabolism. As a consequence of such coordination, the nutrient-limited region of the community maintained an unexpectedly high level of metabolism, enabling it to express many signaling genes and functionally unknown genes with potential sociality functions. Our work provides an extended understanding of the metabolic interplay in biofilms and presents a new approach of investigating complex interactions in bacterial communities on the systems level.
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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.