ArticleNature communications2025
A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- Orchestrating life's first community: molecular assembly by human milk oligosaccharides.Gut microbes · 2026Review
- Pathogenicity and virulence ofVirulence · 2026Review
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- Review
- Pathology-derived clinical micro-architectural diagnostics of tumour-microbiome interactions in colorectal cancer.Journal of translational medicine · 2026Article
- Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.Cell death and differentiation · 2026Review
- SpaMode: A Broadly Applicable Framework for Deciphering Spatial Multi-Omics Using Multimodal Mixture of Disentangled Experts.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- AI-driven big data analysis and predictive modeling of infectious disease immunity: from correlates to causal, multiscale understanding.Archives of microbiology · 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
- From triangle to pyramid: Understanding host-pathogen-microniome-environment interplay for sustainable, enviromics-empowered management of plant diseases.Plant communications · 2026Review
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 2026Article
- Intratumoral Microorganisms in Tumors: Current Understanding and Emerging Therapeutic Strategies.MedComm · 2026Review
- Article
- Review
- Uncovering Immune Niches in Health and Disease Using Spatial Transcriptomics.European journal of immunology · 2026Review
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- Harnessing Microbiome-Mediated and Macrophage-Driven Mechanisms for Oral Wound Healing.Microorganisms · 2026Review
- Gut microbiome-driven colorectal cancer via immune, metabolic, neural, and endocrine axes reprogramming.NPJ biofilms and microbiomes · 2026Review
- Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.The ISME journal · 2026Review
- Review
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
The intricate interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited by in situ approaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduce Microbiome Cartography (MicroCart), a framework for simultaneous in situ probing of host and microbiome across multiple spatial modalities. We demonstrate MicroCart by investigating gut host and microbiome changes in a murine colitis model, using spatial proteomics, transcriptomics, and glycomics. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multi-omics.
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What OpenQuestion holds
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.