{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T19:58:49Z","timestamp":1788897529203,"version":"build-2803163510"},"reference-count":92,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:00:00Z","timestamp":1773273600000},"content-version":"vor","delay-in-days":376,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100007658","name":"Crohn's and Colitis Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007658","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host & Microbe"],"published-print":{"date-parts":[[2025,3]]},"DOI":"10.1016\/j.chom.2025.02.008","type":"journal-article","created":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T10:47:50Z","timestamp":1741085270000},"page":"388-407.e9","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":9,"title":["Cross-kingdom-mediated detection of intestinal protozoa through NLRP6"],"prefix":"10.1016","volume":"33","author":[{"given":"Nathaniel J.","family":"Winsor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giuliano","family":"Bayer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ojas","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy K.","family":"Chan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu Yi","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandon Y.","family":"Lieng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Foerster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Popovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boyan K.","family":"Tsankov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather","family":"Maughan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Lemire","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elaine","family":"Tam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Streutker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lina","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacey L.","family":"Heaver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth E.","family":"Ley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Parkinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Rafael","family":"Montenegro-Burke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George M.H.","family":"Birchenough","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dana J.","family":"Philpott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9208-8879","authenticated-orcid":false,"given":"Stephen E.","family":"Girardin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2025.02.008_bib1","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1016\/j.cell.2015.10.048","article-title":"Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling","volume":"163","author":"Levy","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib2","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1016\/j.cell.2014.01.026","article-title":"NLRP6 inflammasome orchestrates the colonic host-microbial interface by regulating goblet cell mucus secretion","volume":"156","author":"Wlodarska","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib3","doi-asserted-by":"crossref","first-page":"2602","DOI":"10.1084\/jem.20190679","article-title":"The Nlrp6 inflammasome is not required for baseline colonic inner mucus layer formation or function","volume":"216","author":"Volk","year":"2019","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.chom.2025.02.008_bib4","doi-asserted-by":"crossref","first-page":"1782","DOI":"10.4049\/jimmunol.2100802","article-title":"NLRP1B and NLRP3 Control the Host Response following Colonization with the Commensal Protist Tritrichomonas musculis","volume":"208","author":"Chiaranunt","year":"2022","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.chom.2025.02.008_bib5","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1016\/j.cell.2018.09.047","article-title":"The NLRP6 Inflammasome Recognizes Lipoteichoic Acid and Regulates Gram-Positive Pathogen Infection","volume":"175","author":"Hara","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib6","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1073\/pnas.1817221116","article-title":"Molecular mechanism for NLRP6 inflammasome assembly and activation","volume":"116","author":"Shen","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.02.008_bib7","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.cell.2011.04.022","article-title":"NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis","volume":"145","author":"Elinav","year":"2011","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib8","doi-asserted-by":"crossref","first-page":"7187","DOI":"10.4049\/jimmunol.1100412","article-title":"A functional role for Nlrp6 in intestinal inflammation and tumorigenesis","volume":"186","author":"Chen","year":"2011","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.chom.2025.02.008_bib9","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.molcel.2014.03.039","article-title":"The Multifaceted Role of the Intestinal Microbiota in Colon Cancer","volume":"54","author":"Irraz\u00e1bal","year":"2014","journal-title":"Mol. Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib10","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1136\/gutjnl-2012-303207","article-title":"Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis","volume":"63","author":"Johansson","year":"2014","journal-title":"Gut"},{"key":"10.1016\/j.chom.2025.02.008_bib11","doi-asserted-by":"crossref","first-page":"15064","DOI":"10.1073\/pnas.0803124105","article-title":"The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria","volume":"105","author":"Johansson","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.02.008_bib12","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/s41575-022-00675-x","article-title":"The role of goblet cells and mucus in intestinal homeostasis","volume":"19","author":"Gustafsson","year":"2022","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10.1016\/j.chom.2025.02.008_bib13","doi-asserted-by":"crossref","DOI":"10.1126\/science.abb1590","article-title":"An intercrypt subpopulation of goblet cells is essential for colonic mucus barrier function","volume":"372","author":"Nystr\u00f6m","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.02.008_bib14","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1126\/science.aay7367","article-title":"Proximal colon-derived O-glycosylated mucus encapsulates and modulates the microbiota","volume":"370","author":"Bergstrom","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.02.008_bib15","doi-asserted-by":"crossref","first-page":"8527","DOI":"10.1038\/s41598-017-08938-3","article-title":"Mucus organisation is shaped by colonic content; A new view","volume":"7","author":"Kamphuis","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.chom.2025.02.008_bib16","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1038\/mi.2015.32","article-title":"New developments in goblet cell mucus secretion and function","volume":"8","author":"Birchenough","year":"2015","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.chom.2025.02.008_bib17","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-11811-8","article-title":"VAMP8-mediated MUC2 mucin exocytosis from colonic goblet cells maintains innate intestinal homeostasis","volume":"10","author":"Cornick","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.02.008_bib18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/19490976.2021.1902717","article-title":"Bifidobacterium dentium-derived y-glutamylcysteine suppresses ER-mediated goblet cell stress and reduces TNBS-driven colonic inflammation","volume":"13","author":"Engevik","year":"2021","journal-title":"Gut Microbes"},{"key":"10.1016\/j.chom.2025.02.008_bib19","doi-asserted-by":"crossref","DOI":"10.1172\/JCI153519","article-title":"The epithelial-specific ER stress sensor ERN2\/IRE1\u03b2 enables host-microbiota crosstalk to affect colon goblet cell development","volume":"132","author":"Grey","year":"2022","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.chom.2025.02.008_bib20","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1083\/jcb.85.3.626","article-title":"Mechanism of rapid mucus secretion in goblet cells stimulated by acetylcholine","volume":"85","author":"Specian","year":"1980","journal-title":"J.\u00a0Cell Biol."},{"key":"10.1016\/j.chom.2025.02.008_bib21","doi-asserted-by":"crossref","first-page":"232","DOI":"10.4161\/gmic.23866","article-title":"Goblet cell compound exocytosis in the defense against bacterial invasion in the colon exposed to ischemia-reperfusion","volume":"4","author":"Grootjans","year":"2013","journal-title":"Gut Microbes"},{"key":"10.1016\/j.chom.2025.02.008_bib22","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1126\/science.aaf7419","article-title":"A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion","volume":"352","author":"Birchenough","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.02.008_bib23","doi-asserted-by":"crossref","first-page":"3653","DOI":"10.1016\/j.celrep.2017.12.026","article-title":"The NLR Protein NLRP6 Does Not Impact Gut Microbiota Composition","volume":"21","author":"Lemire","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2025.02.008_bib24","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.immuni.2017.07.011","article-title":"Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition","volume":"47","author":"Mamantopoulos","year":"2017","journal-title":"Immunity"},{"key":"10.1016\/j.chom.2025.02.008_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.yfrne.2021.100912","article-title":"How biological sex of the host shapes its gut microbiota","volume":"61","author":"Valeri","year":"2021","journal-title":"Front. Neuroendocrinol."},{"key":"10.1016\/j.chom.2025.02.008_bib26","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.111454","article-title":"Estrogen receptor \u03b2 activation inhibits colitis by promoting NLRP6-mediated autophagy","volume":"41","author":"Fan","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2025.02.008_bib27","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.cell.2016.08.076","article-title":"Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome","volume":"167","author":"Chudnovskiy","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib28","doi-asserted-by":"crossref","first-page":"2841","DOI":"10.1084\/jem.20161776","article-title":"The common mouse protozoa Tritrichomonas muris alters mucosal T\u00a0cell homeostasis and colitis susceptibility","volume":"213","author":"Escalante","year":"2016","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.chom.2025.02.008_bib29","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1126\/science.aaf1648","article-title":"Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut","volume":"351","author":"Howitt","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.02.008_bib30","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.cell.2018.05.014","article-title":"A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling","volume":"174","author":"Schneider","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib31","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.cell.2023.11.018","article-title":"Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition","volume":"187","author":"Gerrick","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib32","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0041009","article-title":"Fast Renewal of the Distal Colonic Mucus Layers by the Surface Goblet Cells as Measured by In\u00a0Vivo Labeling of Mucin Glycoproteins","volume":"7","author":"Johansson","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2025.02.008_bib33","first-page":"15.25.1","article-title":"Dextran Sulfate Sodium (DSS)-Induced Colitis in Mice","volume":"104","author":"Chassaing","year":"2014","journal-title":"Curr. Protoc. Immunol."},{"key":"10.1016\/j.chom.2025.02.008_bib34","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.8681","article-title":"Expanding the utility of the dextran sulfate sodium (DSS) mouse model to induce a clinically relevant loss of intestinal barrier function","volume":"8","author":"Cochran","year":"2020","journal-title":"PeerJ"},{"key":"10.1016\/j.chom.2025.02.008_bib35","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1038\/mi.2015.140","article-title":"The goblet cell-derived mediator RELM-\u03b2 drives spontaneous colitis in Muc2-deficient mice by promoting commensal microbial dysbiosis","volume":"9","author":"Morampudi","year":"2016","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.chom.2025.02.008_bib36","doi-asserted-by":"crossref","first-page":"36","DOI":"10.3389\/fimmu.2017.00036","article-title":"Canonical and Non-Canonical Activation of NLRP3 Inflammasome at the Crossroad between Immune Tolerance and Intestinal Inflammation","volume":"8","author":"Pellegrini","year":"2017","journal-title":"Front. Immunol."},{"key":"10.1016\/j.chom.2025.02.008_bib37","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00017-20","article-title":"Salmonella enterica Infection of Murine and Human Enteroid-Derived Monolayers Elicits Differential Activation of Epithelium-Intrinsic Inflammasomes","volume":"88","author":"Holly","year":"2020","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.02.008_bib38","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.immuni.2018.06.016","article-title":"Detection of Succinate by Intestinal Tuft Cells Triggers a Type 2 Innate Immune Circuit","volume":"49","author":"Nadjsombati","year":"2018","journal-title":"Immunity"},{"key":"10.1016\/j.chom.2025.02.008_bib39","doi-asserted-by":"crossref","first-page":"5552","DOI":"10.1073\/pnas.1720758115","article-title":"Activation of intestinal tuft cell-expressed sucnr1 triggers type 2 immunity in the mouse small intestine","volume":"115","author":"Lei","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.02.008_bib40","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.chom.2019.04.002","article-title":"Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis","volume":"25","author":"Brown","year":"2019","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2025.02.008_bib41","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.00634-21","article-title":"Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron","volume":"10","author":"Sartorio","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.chom.2025.02.008_bib42","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1038\/s41564-022-01152-6","article-title":"Characterization of inositol lipid metabolism in gut-associated Bacteroidetes","volume":"7","author":"Heaver","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.02.008_bib43","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1007\/978-1-4419-6741-1_17","article-title":"Sphingolipids in Parasitic Protozoa","volume":"688","author":"Zhang","year":"2010","journal-title":"Adv. Exp. Med. Biol."},{"key":"10.1016\/j.chom.2025.02.008_bib44","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.carres.2015.11.001","article-title":"Novel structural features of the immunocompetent ceramide phospho-inositol glycan core from Trichomonas vaginalis","volume":"419","author":"Heiss","year":"2016","journal-title":"Carbohydr. Res."},{"key":"10.1016\/j.chom.2025.02.008_bib45","doi-asserted-by":"crossref","first-page":"3938","DOI":"10.1038\/s41598-018-22063-9","article-title":"Identifying inhibitors of the Leishmania inositol phosphorylceramide synthase with antiprotozoal activity using a yeast-based assay and ultra-high throughput screening platform","volume":"8","author":"Norcliffe","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.chom.2025.02.008_bib46","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/0166-6851(90)90021-D","article-title":"Fatty acid and sterol metabolism of cultured Trichomonas vaginalis and Tritrichomonas foetus","volume":"38","author":"Beach","year":"1990","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.chom.2025.02.008_bib47","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/glycob\/3.3.261","article-title":"Structural characterization of novel inositol phosphosphingolipids of Tritrichomonas foetus and Trichomonas vaginalis","volume":"3","author":"Costello","year":"1993","journal-title":"Glycobiology"},{"key":"10.1016\/j.chom.2025.02.008_bib48","doi-asserted-by":"crossref","first-page":"28200","DOI":"10.1074\/jbc.M600796200","article-title":"The protozoan inositol phosphorylceramide synthase: A novel drug target that defines a new class of sphingolipid synthase","volume":"281","author":"Denny","year":"2006","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.chom.2025.02.008_bib49","doi-asserted-by":"crossref","first-page":"17284","DOI":"10.1021\/acs.analchem.3c03343","article-title":"Computational Expansion of High-Resolution-MSn Spectral Libraries","volume":"95","author":"Lieng","year":"2023","journal-title":"Anal. Chem."},{"key":"10.1016\/j.chom.2025.02.008_bib50","doi-asserted-by":"crossref","DOI":"10.1093\/ismejo\/wrae023","article-title":"Commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota","volume":"18","author":"Popovic","year":"2024","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2025.02.008_bib51","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-16431-1","article-title":"Intestinal fungi are causally implicated in microbiome assembly and immune development in mice","volume":"11","author":"van Tilburg Bernardes","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.02.008_bib52","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/j.chom.2015.10.007","article-title":"Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization","volume":"18","author":"Johansson","year":"2015","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2025.02.008_bib53","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/2049-2618-1-3","article-title":"Stool substitute transplant therapy for the eradication of Clostridium difficile infection: \u2018RePOOPulating\u2019 the gut","volume":"1","author":"Petrof","year":"2013","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2025.02.008_bib54","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1038\/s41564-019-0466-x","article-title":"Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci","volume":"4","author":"Brili\u016bt\u0117","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.02.008_bib55","doi-asserted-by":"crossref","first-page":"3705","DOI":"10.1016\/j.cell.2022.09.007","article-title":"Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease","volume":"185","author":"Hayase","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib56","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2007807118","article-title":"The intestinal parasite Cryptosporidium is controlled by an enterocyte intrinsic inflammasome that depends on NLRP6","volume":"118","author":"Sateriale","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.02.008_bib57","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1016\/j.celrep.2019.04.023","article-title":"Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models","volume":"27","author":"Robertson","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2025.02.008_bib58","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/s41590-020-0681-x","article-title":"Deubiquitination of NLRP6 inflammasome by Cyld critically regulates intestinal inflammation","volume":"21","author":"Mukherjee","year":"2020","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.chom.2025.02.008_bib59","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1053\/j.gastro.2006.04.020","article-title":"Muc2-Deficient Mice Spontaneously Develop Colitis, Indicating That MUC2 Is Critical for Colonic Protection","volume":"131","author":"Van der Sluis","year":"2006","journal-title":"Gastroenterology"},{"key":"10.1016\/j.chom.2025.02.008_bib60","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.1126\/science.1069094","article-title":"Colorectal Cancer in Mice Genetically Deficient in the Mucin Muc2","volume":"295","author":"Velcich","year":"2002","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.02.008_bib61","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1172\/JCI45538","article-title":"Loss of intestinal core 1\u2013derived O-glycans causes spontaneous colitis in mice","volume":"121","author":"Fu","year":"2011","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.chom.2025.02.008_bib62","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1084\/jem.20061929","article-title":"Increased susceptibility to colitis and colorectal tumors in mice lacking core 3\u2013derived O-glycans","volume":"204","author":"An","year":"2007","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.chom.2025.02.008_bib63","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1053\/j.gastro.2016.03.039","article-title":"Defective Intestinal Mucin-Type O-Glycosylation Causes Spontaneous Colitis-Associated Cancer in Mice","volume":"151","author":"Bergstrom","year":"2016","journal-title":"Gastroenterology"},{"key":"10.1016\/j.chom.2025.02.008_bib64","doi-asserted-by":"crossref","first-page":"2299","DOI":"10.1002\/ibd.21625","article-title":"Altered O-glycosylation profile of MUC2 mucin occurs in active ulcerative colitis and is associated with increased inflammation","volume":"17","author":"Larsson","year":"2011","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.chom.2025.02.008_bib65","doi-asserted-by":"crossref","DOI":"10.1016\/j.mce.2022.111554","article-title":"Ceramide signaling in the gut","volume":"544","author":"Li","year":"2022","journal-title":"Mol. Cell. Endocrinol."},{"key":"10.1016\/j.chom.2025.02.008_bib66","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1111\/j.1365-2567.2007.02612.x","article-title":"Acid sphingomyelinase inhibition suppresses lipopolysaccharide-mediated release of inflammatory cytokines from macrophages and protects against disease pathology in dextran sulphate sodium-induced colitis in mice","volume":"122","author":"Sakata","year":"2007","journal-title":"Immunology"},{"key":"10.1016\/j.chom.2025.02.008_bib67","doi-asserted-by":"crossref","first-page":"5217","DOI":"10.3748\/wjg.v13.i39.5217","article-title":"Exogenous sphingomyelinase causes impaired intestinal epithelial barrier function","volume":"13","author":"Bock","year":"2007","journal-title":"World J. Gastroenterol."},{"key":"10.1016\/j.chom.2025.02.008_bib68","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.abf6584","article-title":"Metabolomics activity screening of T cell\u2013induced colitis reveals anti-inflammatory metabolites","volume":"14","author":"Montenegro-Burke","year":"2021","journal-title":"Sci. Signal."},{"key":"10.1016\/j.chom.2025.02.008_bib69","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.cell.2013.11.042","article-title":"Sphingolipids from a symbiotic microbe regulate homeostasis of host intestinal natural killer T\u00a0cells","volume":"156","author":"An","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib70","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2021108080","article-title":"SNX10-mediated LPS sensing causes intestinal barrier dysfunction via a caspase-5-dependent signaling cascade","volume":"40","author":"Wang","year":"2021","journal-title":"EMBO J."},{"key":"10.1016\/j.chom.2025.02.008_bib71","doi-asserted-by":"crossref","first-page":"1508","DOI":"10.1111\/cmi.12655","article-title":"Mechanisms of outer membrane vesicle entry into host cells","volume":"18","author":"O\u2019Donoghue","year":"2016","journal-title":"Cell. Microbiol."},{"key":"10.1016\/j.chom.2025.02.008_bib72","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s40168-020-00868-z","article-title":"Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease","volume":"8","author":"Durant","year":"2020","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2025.02.008_bib73","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2306314120","article-title":"Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet-And host-derived glycans","volume":"120","author":"Sartorio","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.02.008_bib74","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.cell.2019.12.002","article-title":"Adrenergic Signaling in Muscularis Macrophages Limits Infection-Induced Neuronal Loss","volume":"180","author":"Matheis","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.02.008_bib75","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1126\/science.abd6176","article-title":"Microbiota-modulated CART+ enteric neurons autonomously regulate blood glucose","volume":"370","author":"Muller","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.02.008_bib77","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.02.008_bib78","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"10.1016\/j.chom.2025.02.008_bib79","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1093\/bioinformatics\/bts252","article-title":"SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes","volume":"28","author":"Pruesse","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.02.008_bib81","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.02.008_bib82","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.02.008_bib83","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J.\u00a0Comput. Biol."},{"key":"10.1016\/j.chom.2025.02.008_bib76","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/s40168-018-0612-3","article-title":"Design and application of a novel two-amplicon approach for defining eukaryotic microbiota","volume":"6","author":"Popovic","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2025.02.008_bib80","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.02.008_bib84","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.02.008_bib85","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nmeth.2276","article-title":"Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing","volume":"10","author":"Bokulich","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.02.008_bib86","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00191-16","article-title":"Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns","volume":"2","author":"Amir","year":"2017","journal-title":"mSystems"},{"key":"10.1016\/j.chom.2025.02.008_bib87","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s40168-018-0470-z","article-title":"Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2019s q2-feature-classifier plugin","volume":"6","author":"Bokulich","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2025.02.008_bib88","article-title":"Analysis of composition of microbiomes: a novel method for studying microbial composition","volume":"26","author":"Mandal","year":"2015","journal-title":"Microb. Ecol. Health Dis."},{"key":"10.1016\/j.chom.2025.02.008_bib89","first-page":"32","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","author":"Anderson","year":"2001","journal-title":"Austral Ecol."},{"key":"10.1016\/j.chom.2025.02.008_bib90","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.02.008_bib91","doi-asserted-by":"crossref","first-page":"G430","DOI":"10.1152\/ajpgi.00405.2011","article-title":"An ex\u00a0vivo method for studying mucus formation, properties, and thickness in human colonic biopsies and mouse small and large intestinal explants","volume":"302","author":"Gustafsson","year":"2012","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"10.1016\/j.chom.2025.02.008_bib92","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.jim.2014.01.014","article-title":"Optimization of murine small intestine leukocyte isolation for global immune phenotype analysis","volume":"405","author":"Goodyear","year":"2014","journal-title":"J.\u00a0Immunol. Methods"}],"container-title":["Cell Host & Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312825000563?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312825000563?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T03:41:58Z","timestamp":1773286918000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312825000563"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":92,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3]]}},"alternative-id":["S1931312825000563"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2025.02.008","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2025,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Cross-kingdom-mediated detection of intestinal protozoa through NLRP6","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2025.02.008","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}