ArticleNature microbiology2026
Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.
Article in Nature microbiology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- Why probiotics fail: gut niche tension as the missing variable?Gut microbes · 2026Review
- From Gut Microbiota to Hepatic Pre-Metastatic Niches: Mechanism and Translational Prospects of the Gut-Liver Axis in Regulating Colorectal Cancer Liver Metastasis.Microorganisms · 2026Review
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- Spatial Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Tissue by spRandom-seq.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Metabolic strategies of Enterobacteriaceae gut colonization.Nature reviews. Microbiology · 2026Review
- Micro-scale spatial metagenomics opens a new era in microbiome ecology.Trends in microbiology · 2026Review
- Microbial single-cell transcriptomics links gut microbiota functional states to metabolic changes in male mice.Nature communications · 2026Article
- Review
- Gnotobiotic mouse models as tools for dissecting the role of the microbiota in allergy: contributions from the laboratory of gnotobiology in Nový Hrádek.Folia microbiologica · 2026Review
- The mycobiome, virome and archaeome in gastrointestinal cancers: molecular pathogenesis and therapeutic intervention.Molecular cancer · 2026Review
- Endozoicomonas acroporae enhances coral thermal resilience through host-microbe coordination.The ISME journal · 2026Article
- Grand challenge in microbiome data science: recovering the microbiome as a system.Frontiers in microbiology · 2026Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intermicrobial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong intermicrobial interactions at short length scales and tumour-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.
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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.