ArticleNature biotechnology2024
Spatial host-microbiome sequencing reveals niches in the mouse gut.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers, 1 of them a synthesis that pooled it.
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
92 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Opportunities and challenges of proximity labeling for microbe-host cell interactions in tumor microenvironment.Frontiers in cellular and infection microbiology · 2025Pooled it
- Dynamic feedback BacGuard anchors microbial metabolism to host symbiosis in real-time ulcerative colitis therapy.Bioactive materials · 2026Article
- 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
- An engineered bacterial symbiont maps micron-scale sugar gradients in the honeybee gut.PLoS biology · 2026Article
- Micro-scale spatial metagenomics opens a new era in microbiome ecology.Trends in microbiology · 2026Review
- Modeling cancer with bacteria-integrated tumor microenvironments using biomaterials: Emerging concepts and opportunities.Materials today. Bio · 2026Review
- The Gut-Lung Microbiome Axis in Alveolar Stem Cell Regeneration and Lung Repair.Microorganisms · 2026Review
- Microbiome-metabolite signaling networks in gastrointestinal disease: systems biology, network rewiring, and precision therapeutics.Archives of microbiology · 2026Review
- Spatial Heterogeneity of Intratumoral Microbiota and Its Roles in Tumor-Microbiota Interactions and Therapeutic Implications.Pathogens (Basel, Switzerland) · 2026Review
- Letter to the Editor: Deciphering macrophage heterogeneity and optimizing probioticsWorld journal of gastrointestinal pharmacology and therapeutics · 2026Article
- 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 Multifaceted Roles of Gut Microbiota and Their Metabolites in Metabolic Dysfunction-associated Steatotic Liver Disease: A Literature Review.Journal of clinical and translational hepatology · 2026Review
- Probiotics in colorectal cancer: mechanisms, biomarkers, and adjunct strategies.Cancer biology & medicine · 2026Review
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 2026Article
- The gut-tumor connection: the role of microbiota in cancer progression and treatment strategies.Journal of advanced research · 2026Review
- Review
- Strategies to control cellular spatial organization in microphysiological systems.Microsystems & nanoengineering · 2026Review
- Gut Microbiota-Non-Coding RNA Axis in Immune Modulation and Disease: From Mechanisms to Clinical Translation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.Cancer biology & medicine · 2026Review
32 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host-microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host-bacteria interactions. SHM-seq should enhance the study of native host-microbe interactions in 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.