---
title: "GutPath single-cell atlas reveals pathogen-specific reprogramming of the infected gut"
id: "nature-immunology-0-gutpath-links-immune-archetypes-and-single-cell-landscapes-in-the-infected-gut"
canonical_url: "https://medichelpline.com/clinical-feed/nature-immunology-0-gutpath-links-immune-archetypes-and-single-cell-landscapes-in-the-infected-gut"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "Nature Immunology"
source_url: "https://www.nature.com/articles/s41590-026-02719-9"
published_at: "2026-10-23T12:00:00.000Z"
evidence_level: "Journal Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# GutPath single-cell atlas reveals pathogen-specific reprogramming of the infected gut
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/nature-immunology-0-gutpath-links-immune-archetypes-and-single-cell-landscapes-in-the-infected-gut
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** Nature Immunology
- **Source URL:** [Original Journal Publication](https://www.nature.com/articles/s41590-026-02719-9)
- **Published At:** 2026-10-23T12:00:00.000Z
- **Evidence Rating:** Journal Feed
## Executive GIST (TL;DR)
- The research briefing summarizes a **single-cell** gene expression atlas, termed GutPath, profiling the intestinal epithelium across six phylogenetically diverse infections. - Investigators reported pathogen-specific transcriptional reprogramming of the **intestinal epithelium** rather than a single conserved injury response. - The cohort showed tuft and goblet cell hyperplasia during helminth infection, consistent with prior work describing epithelial–innate lymphoid cell circuits. - Data indicated a previously undescribed **Yersinia**-induced enterocyte state that the authors spatially linked to localized tissue pathology (pyogranuloma-associated signals were observed). - The study team applied spatial transcriptomics to map cell-state distributions within infected tissue sections and to correlate epithelial states with anatomical pathology. - Authors noted they used pseudotime and trajectory-based differential expression frameworks (tradeSeq is cited) to identify genes modulated along enterocyte maturation during infection. - References in the briefing supply methodological context (foundational single-cell atlases, enterocyte zonation, trajectory analyses), but the preview did not report full experimental parameters, sample sizes, or detailed protocols. - The briefing links observed myeloid infiltration in **Yersinia** infections to prior literature on inflammatory monocytes and granuloma control, providing a pathobiological context for the spatial signals. - The summary emphasizes atlas-level resources and cross-infection comparisons; the full resource, data, and more granular methods are available in the linked primary paper but are not detailed in the preview.
## Clinical Analysis & Structured Key Points
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[nature](https://www.nature.com/) 2. [nature immunology](https://www.nature.com/ni) 3. [research briefings](https://www.nature.com/ni/articles?type=research-briefing) 4. article * Research Briefing * Published: 23 October 2026 # GutPath links immune archetypes and single-cell landscapes in the infected gut [_Nature Immunology_](https://www.nature.com/ni) (2026) [Cite this article](https://www.nature.com/articles/s41590-026-02719-9#citeas) Save article [ View saved research ](https://www.nature.com/saved-research) A single-cell gene expression atlas, spanning six phylogenetically diverse infections, reveals pathogen-specific reprogramming of the intestinal epithelium and a novel _Yersinia_ -induced enterocyte state that is spatially linked to tissue pathology. This is a preview of subscription content, [access via your institution](https://wayf.springernature.com?redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-026-02719-9) ## Access options [ Access through your institution ](https://wayf.springernature.com?redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-026-02719-9) Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access subscription 27.99 € / 30 days cancel any time [Learn more](https://shop.nature.com/products/plus/?region=ROW) Subscribe to this journal Receive 12 print issues and online access 251.40 € per year only 20.95 € per issue [Learn more](https://www.nature.com/ni/subscribe) Buy this article * Purchase on SpringerLink * Instant access to the full article PDF. 39,95 € Prices may be subject to local taxes which are calculated during checkout ### Additional access options: * [Log in](https://idp.nature.com/auth/personal/springernature?client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-026-02719-9) * [Learn about institutional subscriptions](https://www.springernature.com/gp/librarians/licensing/license-options) * [Read our FAQs](https://support.nature.com/en/support/home) * [Contact customer support](https://www.springernature.com/gp/contact) **Fig. 1: Spatial transcriptomics identifies epithelial cell signals induced by _Yersinia_ infection.** ![](https://media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fs41590-026-02719-9/MediaObjects/41590_2026_2719_Fig1_HTML.png) ## References 1. Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. _Nature_ **551** , 333–339 (2017). **A foundational single-cell study that defined small-intestinal epithelial cell types and states at homeostasis.** [Article](https://doi.org/10.1038%2Fnature24489) [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BC2sXhslygtLjK) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=29144463) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022292) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=A%20single-cell%20survey%20of%20the%20small%20intestinal%20epithelium&journal=Nature&doi=10.1038%2Fnature24489&volume=551&pages=333-339&publication_year=2017&author=Haber%2CAL) 2. Von Moltke, J., Ji, M., Liang, H. E. & Locksley, R. M. Tuft-cell-derived IL-25 regulates an intestinal ILC2–epithelial response circuit. _Nature_ **529** , 221–225 (2016). **This paper describes the tuft and goblet cell hyperplasia that our atlas captures during helminth infection.** [Article](https://doi.org/10.1038%2Fnature16161) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=Tuft-cell-derived%20IL-25%20regulates%20an%20intestinal%20ILC2%E2%80%93epithelial%20response%20circuit&journal=Nature&doi=10.1038%2Fnature16161&volume=529&pages=221-225&publication_year=2016&author=Moltke%2CJ&author=Ji%2CM&author=Liang%2CHE&author=Locksley%2CRM) 3. Sorobetea, D. et al. Inflammatory monocytes promote granuloma control of _Yersinia_ infection. _Nat. Microbiol._ **8** , 666–678 (2023). **This paper provides key context for the Yersinia-associated myeloid infiltration and pyogranuloma formation we observed.** [Article](https://doi.org/10.1038%2Fs41564-023-01338-6) [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BB3sXkslOqtr0%3D) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=36879169) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10653359) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=Inflammatory%20monocytes%20promote%20granuloma%20control%20of%20Yersinia%20infection&journal=Nat.%20Microbiol.&doi=10.1038%2Fs41564-023-01338-6&volume=8&pages=666-678&publication_year=2023&author=Sorobetea%2CD) 4. Moor, A. E. et al. 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Commun._ **11** , 1201 (2020). **This paper describes the tradeSeq generalized additive model framework we used to identify genes differentially expressed along enterocyte pseudotime during infection.** [Article](https://doi.org/10.1038%2Fs41467-020-14766-3) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=32139671) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058077) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=Trajectory-based%20differential%20expression%20analysis%20for%20single-cell%20sequencing%20data&journal=Nat.%20Commun.&doi=10.1038%2Fs41467-020-14766-3&volume=11&publication_year=2020&author=Berge%2CK) [Download references](https://citation-needed.springer.com/v2/references/10.1038/s41590-026-02719-9?format=refman&flavour=references) ## Additional information **Publisher’s note** Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. **This is a summary of:** Hart, A. et al. Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial–immune cell interactions. _Nat. Immunol_. (2026). ## Rights and permissions [Reprints and permissions](https://s100.copyright.com/AppDispatchServlet?title=GutPath%20links%20immune%20archetypes%20and%20single-cell%20landscapes%20in%20the%20infected%20gut&author=&contentID=10.1038%2Fs41590-026-02719-9&copyright=Springer%20Nature%20America%2C%20Inc.&publication=1529-2908&publicationDate=2026-10-23&publisherName=SpringerNature&orderBeanReset=true) ## About this article [![Check for updates. Verify currency and authenticity via CrossMark](https://www.nature.com/articles/s41590-026-02719-9)](https://crossmark.crossref.org/dialog/?doi=10.1038/s41590-026-02719-9) ### Cite this article GutPath links immune archetypes and single-cell landscapes in the infected gut. _Nat Immunol_ (2026). https://doi.org/10.1038/s41590-026-02719-9 [Download citation](https://citation-needed.springer.com/v2/references/10.1038/s41590-026-02719-9?format=refman&flavour=citation) * Published: 23 October 2026 * Version of record: 23 October 2026 * DOI: https://doi.org/10.1038/s41590-026-02719-9 ### Share this article Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy shareable link to clipboard Provided by the Springer Nature SharedIt content-sharing initiative ### Subjects * [Bacteria](https://www.nature.com/subjects/bacteria) * [Infectious diseases](https://www.nature.com/subjects/infectious-diseases) [ Access through your institution ](https://wayf.springernature.com?redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41590-026-02719-9) [ Buy or subscribe ](https://www.nature.com/articles/s41590-026-02719-9#access-options) ## Associated content ### [Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial–immune cell interactions](https://www.nature.com/articles/s41590-026-02665-6) * Andrew Hart * Maria Merolle * on behalf of the MIST Consortium Nature Immunology Resource Open Access 07 Oct 2026 * Sections * Figures * References * [References](https://www.nature.com/articles/s41590-026-02719-9#Bib1) * [Additional information](https://www.nature.com/articles/s41590-026-02719-9#additional-information) * [Rights and permissions](https://www.nature.com/articles/s41590-026-02719-9#rightslink) * [About this article](https://www.nature.com/articles/s41590-026-02719-9#article-info) Advertisement * **Fig. 1: Spatial transcriptomics identifies epithelial cell signals induced by _Yersinia_ infection.** 1. Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. _Nature_ **551** , 333–339 (2017). **A foundational single-cell study that defined small-intestinal epithelial cell types and states at homeostasis.** [Article](https://doi.org/10.1038%2Fnature24489) [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BC2sXhslygtLjK) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=29144463) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022292) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=A%20single-cell%20survey%20of%20the%20small%20intestinal%20epithelium&journal=Nature&doi=10.1038%2Fnature24489&volume=551&pages=333-339&publication_year=2017&author=Haber%2CAL) 2. Von Moltke, J., Ji, M., Liang, H. E. & Locksley, R. M. Tuft-cell-derived IL-25 regulates an intestinal ILC2–epithelial response circuit. _Nature_ **529** , 221–225 (2016). **This paper describes the tuft and goblet cell hyperplasia that our atlas captures during helminth infection.** [Article](https://doi.org/10.1038%2Fnature16161) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=Tuft-cell-derived%20IL-25%20regulates%20an%20intestinal%20ILC2%E2%80%93epithelial%20response%20circuit&journal=Nature&doi=10.1038%2Fnature16161&volume=529&pages=221-225&publication_year=2016&author=Moltke%2CJ&author=Ji%2CM&author=Liang%2CHE&author=Locksley%2CRM) 3. Sorobetea, D. et al. Inflammatory monocytes promote granuloma control of _Yersinia_ infection. _Nat. Microbiol._ **8** , 666–678 (2023). **This paper provides key context for the Yersinia-associated myeloid infiltration and pyogranuloma formation we observed.** [Article](https://doi.org/10.1038%2Fs41564-023-01338-6) [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BB3sXkslOqtr0%3D) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=36879169) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10653359) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=Inflammatory%20monocytes%20promote%20granuloma%20control%20of%20Yersinia%20infection&journal=Nat.%20Microbiol.&doi=10.1038%2Fs41564-023-01338-6&volume=8&pages=666-678&publication_year=2023&author=Sorobetea%2CD) 4. Moor, A. E. et al. Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. _Cell_ **175** , 1156–1167.e15 (2018). **A pivotal single-cell study defining enterocyte maturation and the pseudotime analyses used in our study.** [Article](https://doi.org/10.1016%2Fj.cell.2018.08.063) [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BC1cXhvVahsb7P) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=30270040) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=Spatial%20reconstruction%20of%20single%20enterocytes%20uncovers%20broad%20zonation%20along%20the%20intestinal%20villus%20axis&journal=Cell&doi=10.1016%2Fj.cell.2018.08.063&volume=175&pages=1156-1167.e15&publication_year=2018&author=Moor%2CAE) 5. Van den Berge, K. et al. Trajectory-based differential expression analysis for single-cell sequencing data. _Nat. Commun._ **11** , 1201 (2020). **This paper describes the tradeSeq generalized additive model framework we used to identify genes differentially expressed along enterocyte pseudotime during infection.** [Article](https://doi.org/10.1038%2Fs41467-020-14766-3) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=32139671) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058077) [ Google Scholar](http://scholar.google.com/scholar_lookup?&title=Trajectory-based%20differential%20expression%20analysis%20for%20single-cell%20sequencing%20data&journal=Nat.%20Commun.&doi=10.1038%2Fs41467-020-14766-3&volume=11&publication_year=2020&author=Berge%2CK) Nature Immunology (_Nat Immunol_) ISSN 1529-2916 (online) ISSN 1529-2908 (print) ## nature.com footer links ### About Nature Portfolio * [About us](https://www.nature.com/npg_/company_info/index.html) * [Press releases](https://www.nature.com/npg_/press_room/press_releases.html) * [Press office](https://press.nature.com/) * [Contact us](https://support.nature.com/support/home) ### Discover content * [Journals A-Z](https://www.nature.com/siteindex) * [Articles by subject](https://www.nature.com/subjects) * [protocols.io](https://www.protocols.io/) * [Nature Index](https://www.natureindex.com/) ### Publishing policies * [Nature portfolio policies](https://www.nature.com/authors/editorial_policies) * [Open access](https://www.nature.com/nature-portfolio/for-authors/openaccess) ### Author & Researcher services * [Reprints & permissions](https://www.nature.com/reprints) * [Research data](https://www.springernature.com/gp/authors/research-data) * [Language editing](https://authorservices.springernature.com/language-editing/) * [Scientific editing](https://authorservices.springernature.com/scientific-editing/) * [Nature Masterclasses](https://masterclasses.nature.com/) * [Research Solutions](https://solutions.springernature.com/) ### Libraries & institutions * [Librarian service & tools](https://www.springernature.com/gp/librarians/tools-services) * [Librarian portal](https://www.springernature.com/gp/librarians/manage-your-account/librarianportal) * [Open research](https://www.nature.com/openresearch/about-open-access/information-for-institutions) * [Recommend to library](https://www.springernature.com/gp/librarians/recommend-to-your-library) ### Advertising & partnerships * [Advertising](https://partnerships.nature.com/product/digital-advertising/) * [Partnerships & Services](https://partnerships.nature.com/) * [Media kits](https://partnerships.nature.com/media-kits/) * [Branded content](https://partnerships.nature.com/product/branded-content-native-advertising/) ### Professional development * [Nature Awards](https://www.nature.com/immersive/natureawards/index.html) * [Nature Careers](https://www.nature.com/naturecareers/) * [Nature Conferences](https://conferences.nature.com) ### Regional websites * [Nature Africa](https://www.nature.com/natafrica) * [Nature China](http://www.naturechina.com) * [Nature India](https://www.nature.com/nindia) * [Nature Japan](https://www.natureasia.com/ja-jp) * [Nature Middle East](https://www.nature.com/nmiddleeast) * [Privacy Policy](https://www.nature.com/info/privacy) * [Use of cookies](https://www.nature.com/info/cookies) * Your privacy choices/Manage cookies * [Legal notice](https://www.nature
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