{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T16:41:19Z","timestamp":1784133679185,"version":"3.55.0"},"reference-count":172,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T00:00:00Z","timestamp":1769126400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012041","name":"Versus Arthritis","doi-asserted-by":"publisher","award":["UK Grant 22277"],"award-info":[{"award-number":["UK Grant 22277"]}],"id":[{"id":"10.13039\/501100012041","id-type":"DOI","asserted-by":"publisher"}]},{"name":"None","award":["Orthopedics Department Fund RUMC"],"award-info":[{"award-number":["Orthopedics Department Fund RUMC"]}]},{"name":"None","award":["Katz\/Rubschlager Endowed Chair at RUMC"],"award-info":[{"award-number":["Katz\/Rubschlager Endowed Chair at RUMC"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>Disrupted intestinal epithelial barrier function has been proposed to be integral to rheumatoid arthritis (RA) progression and pathogenesis. To further define the molecular pathways in synovial inflammation and the response of the intestinal tissues, we have used a rat model of mono-joint inflammatory arthritis, induced by intra-articular injection of Complete Freund\u2019s adjuvant (CFA). The predominant inflammatory response of a single injection of the adjuvant into the knee joint resulted in rapid and reproducible formation of a fibrotic myeloid-infiltrated synovial pannus. Our aim was to determine how intestinal tissues, including the proximal and distal ileum and distal colon, responded to inflammatory changes in the synovium in a temporally coordinated manner by comparing their transcriptomic landscapes using RNASeq analyses. We confirmed the timeline of joint inflammation by knee joint swelling measurement, increased synovial fluid levels of bikunin (a component of both the acute phase protein pre-alpha-inhibitor and inter-alpha-inhibitor) and demonstrated a self-correcting response of trabecular and cortical bone to the CFA challenge. Intestine-specific responses were monitored by 16S microbiome amplicon sequencing, histopathology for mucus layer integrity, and immune cell immunohistochemistry. We present data that shows the intestinal tissue displays an allostatic response to the acute joint inflammation and was region specific. The ileum primarily responded with increased mucus secretion and silencing of T-cell specific pathways, whereas the colon showed a transient upregulation of macrophages, with a broader suppression of immune related and metabolic pathway related transcripts. Interestingly, many neuropathways were activated early but then suppressed later in both the ileum and colon. There were only insignificant changes in the fecal microbiome composition in ileum or colon post-CFA administration. In summary, our data show for the first time a suppression of intestinal inflammatory and immune responses following the induction of joint inflammation and only minimal and transient changes in the microbiome. The results help clarify the molecular responses of intestinal tissues to inflammatory stresses that accompany the pathogenesis of inflammatory joint diseases.<\/jats:p>","DOI":"10.1371\/journal.pone.0338053","type":"journal-article","created":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T18:50:53Z","timestamp":1769194253000},"page":"e0338053","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Evidence of an allostatic response by intestinal tissues following induction of joint inflammation"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7801-4849","authenticated-orcid":true,"given":"Meghan M.","family":"Moran","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheona P.","family":"Drummond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline M.","family":"Milner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1415-3134","authenticated-orcid":true,"given":"Anthony J.","family":"Day","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankur","family":"Naqib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D. 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Maagensen","year":"2023","journal-title":"Curr Osteoporos Rep"},{"key":"pone.0338053.ref022","doi-asserted-by":"crossref","first-page":"454","DOI":"10.22203\/eCM.v041a29","article-title":"Gut microbial-derived short-chain fatty acids and bone: a potential role in fracture healing","volume":"41","author":"A Wallimann","year":"2021","journal-title":"Eur Cell Mater"},{"issue":"11","key":"pone.0338053.ref023","doi-asserted-by":"crossref","first-page":"14302","DOI":"10.1096\/fj.202001364R","article-title":"The gut microbiota may be a novel pathogenic mechanism in loosening of orthopedic implants in rats","volume":"34","author":"MM Moran","year":"2020","journal-title":"FASEB J"},{"issue":"3","key":"pone.0338053.ref024","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1002\/JLB.3MR0321-755R","article-title":"The microbiota-gut-bone axis and bone health","volume":"110","author":"Y Tu","year":"2021","journal-title":"J Leukoc 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experimental systems and insights","volume":"19","author":"BD Fischer","year":"2017","journal-title":"Arthritis Res Ther"},{"key":"pone.0338053.ref031","doi-asserted-by":"crossref","first-page":"1346054","DOI":"10.3389\/fphar.2023.1346054","article-title":"Mechanistic evaluation of antiarthritic and anti-inflammatory effect of campesterol ester derivatives in complete Freund\u2019s adjuvant-induced arthritic rats","volume":"14","author":"S Nazir","year":"2024","journal-title":"Front Pharmacol"},{"issue":"1","key":"pone.0338053.ref032","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s12986-023-00735-2","article-title":"Combined treatment with glucosamine and chondroitin sulfate improves rheumatoid arthritis in rats by regulating the gut microbiota","volume":"20","author":"X Wang","year":"2023","journal-title":"Nutr Metab (Lond)"},{"key":"pone.0338053.ref033","doi-asserted-by":"crossref","first-page":"111090","DOI":"10.1016\/j.intimp.2023.111090","article-title":"Intestinal flora, intestinal metabolism, and intestinal immunity changes in complete Freud\u2019s adjuvant-rheumatoid arthritis C57BL\/6 mice","volume":"125","author":"M Liu","year":"2023","journal-title":"Int Immunopharmacol"},{"issue":"5","key":"pone.0338053.ref034","doi-asserted-by":"crossref","first-page":"988","DOI":"10.3390\/molecules23050988","article-title":"Sulforaphane modulates joint inflammation in a murine model of complete freund\u2019s adjuvant-induced mono-arthritis","volume":"23","author":"JF Silva Rodrigues","year":"2018","journal-title":"Molecules"},{"issue":"8","key":"pone.0338053.ref035","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1007\/s00011-010-0179-3","article-title":"Sensory and vascular changes in a rat monoarthritis model: prophylactic and therapeutic effects of meloxicam","volume":"59","author":"JA Hashmi","year":"2010","journal-title":"Inflamm Res"},{"issue":"20","key":"pone.0338053.ref036","article-title":"Collagen-induced arthritis: a model for murine autoimmune arthritis","volume":"5","author":"KM Pietrosimone","year":"2015","journal-title":"Bio Protoc"},{"issue":"12","key":"pone.0338053.ref037","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1369\/0022155420940067","article-title":"The Inter-\u03b1-Trypsin Inhibitor Family: Versatile Molecules in Biology and Pathology","volume":"68","author":"MS Lord","year":"2020","journal-title":"J Histochem Cytochem"},{"issue":"5","key":"pone.0338053.ref038","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1002\/oby.21485","article-title":"High-fat diet exacerbates pain-like behaviors and periarticular bone loss in mice with CFA-induced knee arthritis","volume":"24","author":"AA Loredo-P\u00e9rez","year":"2016","journal-title":"Obesity (Silver 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Bioinform"},{"issue":"644","key":"pone.0338053.ref042","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.abj9954","article-title":"Acute inflammatory response via neutrophil activation protects against the development of chronic pain","volume":"14","author":"M Parisien","year":"2022","journal-title":"Sci Transl Med"},{"key":"pone.0338053.ref043","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1007\/978-981-15-1580-4_3","article-title":"CLEC5A: a promiscuous pattern recognition receptor to microbes and beyond","volume":"1204","author":"P-S Sung","year":"2020","journal-title":"Adv Exp Med Biol"},{"issue":"6","key":"pone.0338053.ref044","first-page":"3048","article-title":"Immunolocalization of MMP-2 and MMP-9 in human rheumatoid synovium","volume":"7","author":"M Zhou","year":"2014","journal-title":"Int J Clin Exp Pathol"},{"key":"pone.0338053.ref045","doi-asserted-by":"crossref","first-page":"654839","DOI":"10.3389\/fimmu.2021.654839","article-title":"SLAM associated protein signaling in T cells: tilting the balance toward autoimmunity","volume":"12","author":"Y Gartshteyn","year":"2021","journal-title":"Front Immunol"},{"issue":"9","key":"pone.0338053.ref046","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0045478","article-title":"An inflammation loop orchestrated by S100A9 and calprotectin is critical for development of arthritis","volume":"7","author":"A Cesaro","year":"2012","journal-title":"PLoS One"},{"issue":"4","key":"pone.0338053.ref047","doi-asserted-by":"crossref","first-page":"470","DOI":"10.5114\/ceji.2021.111471","article-title":"Elevated macrophage-inducible C-type lectin expression in the synovial tissue of patients with rheumatoid arthritis","volume":"46","author":"K Takata","year":"2021","journal-title":"Cent Eur J Immunol"},{"issue":"3","key":"pone.0338053.ref048","doi-asserted-by":"crossref","first-page":"269","DOI":"10.5114\/ceji.2017.70969","article-title":"Lipocalin 2 as a clinical significance in rheumatoid arthritis","volume":"42","author":"A Gulkesen","year":"2017","journal-title":"Cent Eur J Immunol"},{"issue":"16","key":"pone.0338053.ref049","doi-asserted-by":"crossref","first-page":"2810","DOI":"10.1093\/hmg\/ddac061","article-title":"Understanding the complex genetic architecture connecting rheumatoid arthritis, osteoporosis and inflammation: discovering causal pathways","volume":"31","author":"CHARGE Inflammation Working Group","year":"2022","journal-title":"Hum Mol Genet"},{"issue":"9","key":"pone.0338053.ref050","doi-asserted-by":"crossref","DOI":"10.1111\/ijcp.13564","article-title":"The association between serum levels of growth differentiation factor-15 and rheumatoid arthritis activity","volume":"74","author":"K Esalatmanesh","year":"2020","journal-title":"Int J Clin Pract"},{"issue":"1","key":"pone.0338053.ref051","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13075-020-2130-5","article-title":"TGF\u03b2-mediated expression of TGF\u03b2-activating integrins in SSc monocytes: disturbed activation of latent TGF\u03b2?","volume":"22","author":"A van Caam","year":"2020","journal-title":"Arthritis Res Ther"},{"issue":"3","key":"pone.0338053.ref052","doi-asserted-by":"crossref","first-page":"502","DOI":"10.3390\/biom13030502","article-title":"Osteopontin: a bone-derived protein involved in rheumatoid arthritis and osteoarthritis immunopathology","volume":"13","author":"BT Mart\u00edn-M\u00e1rquez","year":"2023","journal-title":"Biomolecules"},{"key":"pone.0338053.ref053","doi-asserted-by":"crossref","first-page":"117592","DOI":"10.1016\/j.cca.2023.117592","article-title":"The pentraxin family in autoimmune disease","volume":"551","author":"Y Li","year":"2023","journal-title":"Clin Chim Acta"},{"issue":"10","key":"pone.0338053.ref054","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1096\/fj.02-1036com","article-title":"Mucosal pentraxin (Mptx), a novel rat gene 10-fold down-regulated in colon by dietary heme","volume":"17","author":"C Van Der Meer-Van Kraaij","year":"2003","journal-title":"FASEB J"},{"issue":"13","key":"pone.0338053.ref055","doi-asserted-by":"crossref","first-page":"7196","DOI":"10.3390\/ijms22137196","article-title":"The Potential Role of REG Family Proteins in Inflammatory and Inflammation-Associated Diseases of the Gastrointestinal Tract","volume":"22","author":"C Sun","year":"2021","journal-title":"Int J Mol Sci"},{"issue":"1","key":"pone.0338053.ref056","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s41574-022-00774-4","article-title":"REG3G - a potential link between the intestinal microbiome and host physiology","volume":"19","author":"C Greenhill","year":"2023","journal-title":"Nat Rev Endocrinol"},{"key":"pone.0338053.ref057","doi-asserted-by":"crossref","first-page":"101231","DOI":"10.1016\/j.molmet.2021.101231","article-title":"Adhesion receptor ADGRG2\/GPR64 is in the GI-tract selectively expressed in mature intestinal tuft cells","volume":"51","author":"KV Grunddal","year":"2021","journal-title":"Mol Metab"},{"key":"pone.0338053.ref058","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/j.jad.2024.05.050","article-title":"In-silico functional analyses identify TMPRSS15-mediated intestinal absorption of lithium as a modulator of lithium response in bipolar disorder","volume":"358","author":"D Stacey","year":"2024","journal-title":"J Affect Disord"},{"key":"pone.0338053.ref059","doi-asserted-by":"crossref","first-page":"105779","DOI":"10.1016\/j.phrs.2021.105779","article-title":"Neutrophil extracellular traps in inflammatory bowel diseases: Implications in pathogenesis and therapeutic targets","volume":"171","author":"A Dos Santos Ramos","year":"2021","journal-title":"Pharmacol Res"},{"issue":"1","key":"pone.0338053.ref060","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/19336918.2023.2276616","article-title":"MST1\/2 in inflammation and immunity","volume":"17","author":"T Li","year":"2023","journal-title":"Cell Adh Migr"},{"key":"pone.0338053.ref061","first-page":"1317","article-title":"Changing intestinal connective tissue interactions alters homeobox gene expression in epithelial cells","author":"I Duluc","year":"1997","journal-title":"J Cell Sci"},{"key":"pone.0338053.ref062","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.mam.2012.10.007","article-title":"The SLC3 and SLC7 families of amino acid transporters","volume":"34","author":"D Fotiadis","year":"2013","journal-title":"Mol Aspects Med"},{"issue":"1","key":"pone.0338053.ref063","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s40659-020-00279-2","article-title":"Mast cells-derived MiR-223 destroys intestinal barrier function by inhibition of CLDN8 expression in intestinal epithelial cells","volume":"53","author":"M Li","year":"2020","journal-title":"Biol Res"},{"issue":"3","key":"pone.0338053.ref064","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.01214-23","article-title":"Intestinal lysozyme1 deficiency alters microbiota composition and impacts host metabolism through the emergence of NAD+-secreting ASTB Qing110 bacteria","volume":"9","author":"C Zhang","year":"2024","journal-title":"mSystems"},{"issue":"6","key":"pone.0338053.ref065","doi-asserted-by":"crossref","DOI":"10.1016\/j.immuni.2018.11.018","article-title":"Commensals suppress intestinal epithelial cell retinoic acid synthesis to regulate interleukin-22 activity and prevent microbial dysbiosis","volume":"49","author":"M Grizotte-Lake","year":"2018","journal-title":"Immunity"},{"issue":"1","key":"pone.0338053.ref066","doi-asserted-by":"crossref","first-page":"110179","DOI":"10.1016\/j.celrep.2021.110179","article-title":"Intestinal Gpr17 deficiency improves glucose metabolism by promoting GLP-1 secretion","volume":"38","author":"S Yan","year":"2022","journal-title":"Cell Rep"},{"key":"pone.0338053.ref067","doi-asserted-by":"crossref","first-page":"101807","DOI":"10.1016\/j.molmet.2023.101807","article-title":"Metformin increases the uptake of glucose into the gut from the circulation in high-fat diet-fed male mice, which is enhanced by a reduction in whole-body Slc2a2 expression","volume":"77","author":"N Morrice","year":"2023","journal-title":"Mol Metab"},{"key":"pone.0338053.ref068","doi-asserted-by":"crossref","first-page":"118974","DOI":"10.1016\/j.lfs.2020.118974","article-title":"Intestinal sodium\/glucose cotransporter 3 expression is epithelial and downregulated in obesity","volume":"267","author":"M Sot\u00e1k","year":"2021","journal-title":"Life Sci"},{"issue":"1","key":"pone.0338053.ref069","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1038\/s41598-023-28234-7","article-title":"Data mining combines bioinformatics discover immunoinfiltration-related gene SERPINE1 as a biomarker for diagnosis and prognosis of stomach adenocarcinoma","volume":"13","author":"Y Zhai","year":"2023","journal-title":"Sci Rep"},{"key":"pone.0338053.ref070","doi-asserted-by":"crossref","first-page":"2522","DOI":"10.3389\/fimmu.2018.02522","article-title":"ATF3 sustains IL-22-Induced STAT3 phosphorylation to maintain mucosal immunity through inhibiting phosphatases","volume":"9","author":"D Glal","year":"2018","journal-title":"Front Immunol"},{"issue":"13","key":"pone.0338053.ref071","doi-asserted-by":"crossref","first-page":"6286","DOI":"10.1073\/pnas.1818164116","article-title":"Transcriptional factor ATF3 protects against colitis by regulating follicular helper T cells in Peyer\u2019s patches","volume":"116","author":"Y Cao","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"pone.0338053.ref072","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2018.12.039","article-title":"Chronic inflammation permanently reshapes tissue-resident immunity in celiac disease","volume":"176","author":"T Mayassi","year":"2019","journal-title":"Cell"},{"issue":"12","key":"pone.0338053.ref073","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1016\/j.bbalip.2017.09.006","article-title":"FABP1 knockdown in human enterocytes impairs proliferation and alters lipid metabolism","volume":"1862","author":"L Rodriguez Sawicki","year":"2017","journal-title":"Biochim Biophys Acta Mol Cell Biol Lipids"},{"issue":"3","key":"pone.0338053.ref074","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/cdd.2013.163","article-title":"Type 2 cGMP-dependent protein kinase regulates homeostasis by blocking c-Jun N-terminal kinase in the colon epithelium","volume":"21","author":"R Wang","year":"2014","journal-title":"Cell Death Differ"},{"issue":"42","key":"pone.0338053.ref075","doi-asserted-by":"crossref","first-page":"11859","DOI":"10.1073\/pnas.1614057113","article-title":"Generation of an inducible colon-specific Cre enzyme mouse line for colon cancer research","volume":"113","author":"PW Tetteh","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"pone.0338053.ref076","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1002\/ibd.21473","article-title":"DMBT1 is a novel gene induced by IL-22 in ulcerative colitis","volume":"17","author":"H Fukui","year":"2011","journal-title":"Inflamm Bowel Dis"},{"issue":"3","key":"pone.0338053.ref077","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1111\/j.1365-2249.2011.04382.x","article-title":"Chemokine CXCL11 links microbial stimuli to intestinal inflammation","volume":"164","author":"Z Liu","year":"2011","journal-title":"Clin Exp Immunol"},{"issue":"3","key":"pone.0338053.ref078","doi-asserted-by":"crossref","DOI":"10.1152\/ajpgi.00338.2019","article-title":"Nr4A1 modulates inflammation-associated intestinal fibrosis and dampens fibrogenic signaling in myofibroblasts","volume":"321","author":"VK Pulakazhi Venu","year":"2021","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"issue":"1","key":"pone.0338053.ref079","doi-asserted-by":"crossref","first-page":"20","DOI":"10.3390\/genes9010020","article-title":"Wnt, RSPO and hippo signalling in the intestine and intestinal stem cells","volume":"9","author":"V Kriz","year":"2018","journal-title":"Genes (Basel)"},{"issue":"4","key":"pone.0338053.ref080","article-title":"Evidence for glucagon secretion and function within the human gut","volume":"162","author":"EW Sun","year":"2021","journal-title":"Endocrinology"},{"issue":"3","key":"pone.0338053.ref081","doi-asserted-by":"crossref","first-page":"189098","DOI":"10.1016\/j.bbcan.2024.189098","article-title":"All eyes on eya: a unique transcriptional co-activator and phosphatase in cancer","volume":"1879","author":"CJ Hughes","year":"2024","journal-title":"Biochim Biophys Acta Rev Cancer"},{"issue":"10","key":"pone.0338053.ref082","doi-asserted-by":"crossref","first-page":"540","DOI":"10.5483\/BMBRep.2014.47.10.177","article-title":"Cross-talk between Wnt\/\u03b2-catenin and hippo signaling pathways: a brief review","volume":"47","author":"M Kim","year":"2014","journal-title":"BMB Rep"},{"key":"pone.0338053.ref083","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.2147\/JIR.S444758","article-title":"The hippo-YAP signaling pathway in osteoarthritis and rheumatoid arthritis","volume":"17","author":"M Li","year":"2024","journal-title":"J Inflamm Res"},{"issue":"2","key":"pone.0338053.ref084","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1038\/s41401-022-00957-9","article-title":"PPAR-\u03b3 alleviates the inflammatory response in TNF-\u03b1-induced fibroblast-like synoviocytes by binding to p53 in rheumatoid arthritis","volume":"44","author":"X-F Li","year":"2023","journal-title":"Acta Pharmacol Sin"},{"issue":"10","key":"pone.0338053.ref085","article-title":"Intra-articular corticosteroid for knee osteoarthritis","volume":"2015","author":"P J\u00fcni","year":"2015","journal-title":"Cochrane Database Syst Rev"},{"issue":"5","key":"pone.0338053.ref086","article-title":"Joint lavage for osteoarthritis of the knee","author":"S Reichenbach","year":"2010","journal-title":"Cochrane Database Syst Rev"},{"key":"pone.0338053.ref087","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1186\/s12967-014-0293-z","article-title":"The triggering receptor expressed on myeloid cells (TREM) in inflammatory bowel disease pathogenesis","volume":"12","author":"M Genua","year":"2014","journal-title":"J Transl Med"},{"issue":"2","key":"pone.0338053.ref088","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.gastha.2022.09.006","article-title":"Age-dependent Microglial Disease Phenotype Results in Functional Decline in Gut Macrophages","volume":"2","author":"ES Bishop","year":"2023","journal-title":"Gastro Hep Adv"},{"issue":"10","key":"pone.0338053.ref089","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/nri.2016.88","article-title":"Immunological aspects of intestinal mucus and mucins","volume":"16","author":"MEV Johansson","year":"2016","journal-title":"Nat Rev Immunol"},{"issue":"4","key":"pone.0338053.ref090","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1002\/ijc.2910570420","article-title":"The lectin Griffonia simplicifolia I-A4 (GS I-A4) specifically recognizes terminal alpha-linked N-acetylgalactosaminyl groups and is cytotoxic to the human colon cancer cell lines LS174t and SW1116","volume":"57","author":"YF Chen","year":"1994","journal-title":"Int J Cancer"},{"issue":"7","key":"pone.0338053.ref091","article-title":"Mucus sialylation determines intestinal host-commensal homeostasis","volume":"185","author":"Y Yao","year":"2022","journal-title":"Cell"},{"key":"pone.0338053.ref092","doi-asserted-by":"crossref","first-page":"4943965","DOI":"10.1155\/2022\/4943965","article-title":"Evaluation of antiarthritic and antinociceptive effects of cedrol in a rat model of arthritis","volume":"2022","author":"F Forouzanfar","year":"2022","journal-title":"Oxid Med Cell Longev"},{"issue":"1","key":"pone.0338053.ref093","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1186\/s12906-018-2408-1","article-title":"Therapeutic benefits of Indole-3-Carbinol in adjuvant-induced arthritis and its protective effect against methotrexate induced-hepatic toxicity","volume":"18","author":"H Hasan","year":"2018","journal-title":"BMC Complement Altern Med"},{"key":"pone.0338053.ref094","doi-asserted-by":"crossref","first-page":"841662","DOI":"10.3389\/fmicb.2022.841662","article-title":"Analgesic and anxiolytic effects of gastrodin and its influences on ferroptosis and jejunal microbiota in complete freund\u2019s adjuvant-injected mice","volume":"13","author":"X Chen","year":"2022","journal-title":"Front Microbiol"},{"issue":"5","key":"pone.0338053.ref095","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1097\/j.pain.0000000000002467","article-title":"Behavioral outcomes of complete Freund adjuvant-induced inflammatory pain in the rodent hind paw: a systematic review and meta-analysis","volume":"163","author":"DJ Burek","year":"2022","journal-title":"Pain"},{"issue":"5","key":"pone.0338053.ref096","doi-asserted-by":"crossref","first-page":"3429","DOI":"10.1007\/s10787-024-01553-5","article-title":"In vitro and in vivo modulatory effects of fluoxetine on gene expression and antioxidant enzymes in CFA-induced chronic inflammatory model: drug repurposing for arthritis","volume":"32","author":"Alamgeer","year":"2024","journal-title":"Inflammopharmacology"},{"issue":"7","key":"pone.0338053.ref097","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1002\/jor.23412","article-title":"Nociception contributes to the formation of myogenic contracture in the early phase of adjuvant-induced arthritis in a rat knee","volume":"35","author":"A Kaneguchi","year":"2017","journal-title":"J Orthop Res"},{"issue":"3","key":"pone.0338053.ref098","doi-asserted-by":"crossref","first-page":"173","DOI":"10.18869\/nirp.bcn.8.3.173","article-title":"The impact of synovial NF-\u03baB activation on apoptosis pattern change during adjuvant-induced inflammation","volume":"8","author":"S Golabi","year":"2017","journal-title":"Basic Clin Neurosci"},{"key":"pone.0338053.ref099","first-page":"25","article-title":"Synovial interlukin-6 affects apoptosis induction via nuclear factor kappa-B and fractalkine pathway during adjuvant arthritis","volume":"34","author":"S Golabi","year":"2020","journal-title":"Med J Islam Repub Iran"},{"issue":"6","key":"pone.0338053.ref100","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1007\/s10753-018-0861-0","article-title":"Therapeutic effect of penta-acetyl geniposide on adjuvant-induced arthritis in rats: involvement of inducing synovial apoptosis and inhibiting NF-\u03baB signal pathway","volume":"41","author":"L Cai","year":"2018","journal-title":"Inflammation"},{"issue":"3","key":"pone.0338053.ref101","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1007\/s00774-018-0944-x","article-title":"1,25-Dihydroxyvitamin D3 attenuates disease severity and induces synoviocyte apoptosis in a concentration-dependent manner in rats with adjuvant-induced arthritis by inactivating the NF-\u03baB signaling pathway","volume":"37","author":"H-Q Sun","year":"2019","journal-title":"J Bone Miner Metab"},{"issue":"11","key":"pone.0338053.ref102","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1016\/j.joca.2008.04.004","article-title":"Superficial zone chondrocytes in normal and osteoarthritic human articular cartilages synthesize novel truncated forms of inter-alpha-trypsin inhibitor heavy chains which are attached to a chondroitin sulfate proteoglycan other than bikunin","volume":"16","author":"Y Yoshihara","year":"2008","journal-title":"Osteoarthritis Cartilage"},{"issue":"2","key":"pone.0338053.ref103","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1046\/j.1365-3083.1997.d01-103.x","article-title":"Alpha1-microglobulin and bikunin in rats with collagen II-induced arthritis: plasma levels and liver mRNA content","volume":"46","author":"C Falkenberg","year":"1997","journal-title":"Scand J Immunol"},{"issue":"6","key":"pone.0338053.ref104","first-page":"1230","article-title":"The SHAP-HA complex in sera from patients with rheumatoid arthritis and osteoarthritis","volume":"26","author":"D Kida","year":"1999","journal-title":"J Rheumatol"},{"issue":"3","key":"pone.0338053.ref105","doi-asserted-by":"crossref","DOI":"10.1002\/pgr2.70003","article-title":"A novel method to quantify TSG-6 protein levels in synovial fluid from osteoarthritis patients","volume":"2","author":"JL Scott","year":"2024","journal-title":"Proteoglycan Research"},{"key":"pone.0338053.ref106","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.matbio.2018.01.011","article-title":"TSG-6: A multifunctional protein with anti-inflammatory and tissue-protective properties","author":"AJ Day","year":"2019","journal-title":"Matrix Biol"},{"issue":"4","key":"pone.0338053.ref107","article-title":"Hyaluronan-protein interactions: lilliput revisited","volume":"2","author":"AJ Day","year":"2024","journal-title":"Proteoglycan Res"},{"issue":"4","key":"pone.0338053.ref108","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1021\/acs.analchem.3c04387","article-title":"Targeted analysis of the size distribution of heavy chain-modified hyaluronan with solid-state nanopores","volume":"96","author":"DA Erxleben","year":"2024","journal-title":"Anal Chem"},{"issue":"35","key":"pone.0338053.ref109","first-page":"32710","article-title":"Molecular heterogeneity of the SHAP-hyaluronan complex. Isolation and characterization of the complex in synovial fluid from patients with rheumatoid arthritis","volume":"278","author":"W Yingsung","year":"2003","journal-title":"J Biol Chem"},{"issue":"29","key":"pone.0338053.ref110","doi-asserted-by":"crossref","first-page":"20303","DOI":"10.1074\/jbc.M506703200","article-title":"SHAP potentiates the CD44-mediated leukocyte adhesion to the hyaluronan substratum","volume":"281","author":"L Zhuo","year":"2006","journal-title":"J Biol Chem"},{"issue":"1","key":"pone.0338053.ref111","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/S0002-9440(10)63636-X","article-title":"Mononuclear leukocytes bind to specific hyaluronan structures on colon mucosal smooth muscle cells treated with polyinosinic acid:polycytidylic acid: inter-alpha-trypsin inhibitor is crucial to structure and function","volume":"163","author":"CA de la Motte","year":"2003","journal-title":"Am J Pathol"},{"issue":"10","key":"pone.0338053.ref112","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1007\/s11926-019-0858-1","article-title":"Synovial Tissue: Cellular and Molecular Phenotyping","volume":"21","author":"S Shanaj","year":"2019","journal-title":"Curr Rheumatol Rep"},{"issue":"7987","key":"pone.0338053.ref113","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/s41586-023-06708-y","article-title":"Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes","volume":"623","author":"F Zhang","year":"2023","journal-title":"Nature"},{"key":"pone.0338053.ref114","doi-asserted-by":"crossref","first-page":"1394108","DOI":"10.3389\/fimmu.2024.1394108","article-title":"Macrophage polarization in rheumatoid arthritis: signaling pathways, metabolic reprogramming, and crosstalk with synovial fibroblasts","volume":"15","author":"Y Zheng","year":"2024","journal-title":"Front Immunol"},{"issue":"12","key":"pone.0338053.ref115","doi-asserted-by":"crossref","first-page":"3694","DOI":"10.1111\/febs.15715","article-title":"More than just protein building blocks: how amino acids and related metabolic pathways fuel macrophage polarization","volume":"288","author":"M Kieler","year":"2021","journal-title":"FEBS J"},{"issue":"1890","key":"pone.0338053.ref116","doi-asserted-by":"crossref","first-page":"20220240","DOI":"10.1098\/rstb.2022.0240","article-title":"Protein citrullination: inhibition, identification and insertion","volume":"378","author":"L Barasa","year":"2023","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"pone.0338053.ref117","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.jot.2022.02.007","article-title":"An osteoarthritis subtype characterized by synovial lipid metabolism disorder and fibroblast-like synoviocyte dysfunction","volume":"33","author":"X Cao","year":"2022","journal-title":"J Orthop Translat"},{"issue":"5","key":"pone.0338053.ref118","first-page":"661","article-title":"Biomarkers identification of early rheumatoid arthritis via bioinformatics approach and experimental verification","volume":"54","author":"C Shen","year":"2024","journal-title":"Ann Clin Lab Sci"},{"key":"pone.0338053.ref119","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1111\/nyas.12389","article-title":"Glucocorticoid metabolism in rheumatoid arthritis","volume":"1318","author":"RS Hardy","year":"2014","journal-title":"Ann N Y Acad Sci"},{"issue":"3","key":"pone.0338053.ref120","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1002\/jbmr.4773","article-title":"Macrophages and bone remodeling","volume":"38","author":"MM Weivoda","year":"2023","journal-title":"J Bone Miner Res"},{"key":"pone.0338053.ref121","doi-asserted-by":"crossref","first-page":"1274679","DOI":"10.3389\/fimmu.2023.1274679","article-title":"Mechanism of regulating macrophages\/osteoclasts in attenuating wear particle-induced aseptic osteolysis","volume":"14","author":"Z Yin","year":"2023","journal-title":"Front Immunol"},{"issue":"1","key":"pone.0338053.ref122","first-page":"46","article-title":"Propionate and butyrate attenuate macrophage pyroptosis and osteoclastogenesis induced by CoCrMo alloy particles","volume":"9","author":"Y-L Wu","year":"2022","journal-title":"Mil Med Res"},{"issue":"15","key":"pone.0338053.ref123","doi-asserted-by":"crossref","first-page":"12307","DOI":"10.3390\/ijms241512307","article-title":"Circadian regulation of macrophages and osteoclasts in rheumatoid arthritis","volume":"24","author":"N Kikyo","year":"2023","journal-title":"Int J Mol Sci"},{"key":"pone.0338053.ref124","doi-asserted-by":"crossref","first-page":"1462","DOI":"10.3389\/fimmu.2019.01462","article-title":"The metabolic signature of macrophage responses","volume":"10","author":"A Viola","year":"2019","journal-title":"Front Immunol"},{"key":"pone.0338053.ref125","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.matbio.2023.06.007","article-title":"TSG6 hyaluronan matrix remodeling dampens the inflammatory response during colitis","volume":"121","author":"N Albtoush","year":"2023","journal-title":"Matrix Biol"},{"issue":"36","key":"pone.0338053.ref126","doi-asserted-by":"crossref","first-page":"25792","DOI":"10.1074\/jbc.M113.479584","article-title":"Immobilized heavy chain-hyaluronic acid polarizes lipopolysaccharide-activated macrophages toward M2 phenotype","volume":"288","author":"H He","year":"2013","journal-title":"J Biol Chem"},{"issue":"8","key":"pone.0338053.ref127","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1093\/rheumatology\/kex258","article-title":"Effects of tofacitinib in early arthritis-induced bone loss in an adjuvant-induced arthritis rat model","volume":"57","author":"B Vidal","year":"2018","journal-title":"Rheumatology (Oxford)"},{"issue":"2","key":"pone.0338053.ref128","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/s00223-017-0270-7","article-title":"Bone matrix maturation in a rat model of intra-cortical bone remodeling","volume":"101","author":"RD Ross","year":"2017","journal-title":"Calcif Tissue Int"},{"issue":"4","key":"pone.0338053.ref129","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.joca.2021.06.013","article-title":"Fundamentals of OA. An initiative of Osteoarthritis and Cartilage. Obesity and metabolic factors in OA","volume":"30","author":"A Batushansky","year":"2022","journal-title":"Osteoarthritis Cartilage"},{"issue":"1","key":"pone.0338053.ref130","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1038\/s41598-024-52322-x","article-title":"All-trans retinoic acid alleviates collagen-induced arthritis and promotes intestinal homeostasis","volume":"14","author":"Y Zhang","year":"2024","journal-title":"Sci Rep"},{"key":"pone.0338053.ref131","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.freeradbiomed.2016.12.048","article-title":"Redox signaling in the gastrointestinal tract","volume":"104","author":"S P\u00e9rez","year":"2017","journal-title":"Free Radic Biol Med"},{"issue":"2","key":"pone.0338053.ref132","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1152\/physrev.00040.2012","article-title":"Oxidative stress: an essential factor in the pathogenesis of gastrointestinal mucosal diseases","volume":"94","author":"A Bhattacharyya","year":"2014","journal-title":"Physiol Rev"},{"issue":"2","key":"pone.0338053.ref133","doi-asserted-by":"crossref","first-page":"480","DOI":"10.3390\/antiox12020480","article-title":"Role of mitophagy in regulating intestinal oxidative damage","volume":"12","author":"X Wen","year":"2023","journal-title":"Antioxidants (Basel)"},{"issue":"1","key":"pone.0338053.ref134","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1038\/s41420-025-02313-2","article-title":"Regulatory role of PPAR in colorectal cancer","volume":"11","author":"C Wang","year":"2025","journal-title":"Cell Death Discov"},{"key":"pone.0338053.ref135","doi-asserted-by":"crossref","first-page":"745","DOI":"10.3389\/fimmu.2018.00745","article-title":"Crosstalk between peroxisome proliferator-activated receptor gamma and the canonical WNT\/\u03b2-Catenin pathway in chronic inflammation and oxidative stress during carcinogenesis","volume":"9","author":"A Vall\u00e9e","year":"2018","journal-title":"Front Immunol"},{"issue":"12","key":"pone.0338053.ref136","doi-asserted-by":"crossref","first-page":"4685","DOI":"10.1172\/JCI45797","article-title":"Crosstalk between the canonical NF-\u03baB and Notch signaling pathways inhibits Ppar\u03b3 expression and promotes pancreatic cancer progression in mice","volume":"121","author":"E Maniati","year":"2011","journal-title":"J Clin Invest"},{"issue":"3","key":"pone.0338053.ref137","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/j.taap.2003.12.020","article-title":"Simultaneous, bidirectional inhibitory crosstalk between PPAR and STAT5b","volume":"199","author":"JM Shipley","year":"2004","journal-title":"Toxicol Appl Pharmacol"},{"issue":"5","key":"pone.0338053.ref138","doi-asserted-by":"crossref","first-page":"823","DOI":"10.2174\/1874467214666210301121432","article-title":"Connection between JAK\/STAT and PPAR\u03b3 signaling during the progression of multiple sclerosis: insights into the modulation of T-Cells and immune responses in the brain","volume":"14","author":"N Kumar","year":"2021","journal-title":"Curr Mol Pharmacol"},{"issue":"6","key":"pone.0338053.ref139","first-page":"416","article-title":"Transcriptional crosstalk between nuclear receptors and cytokine signal transduction pathways in immunity","volume":"1","author":"L Wang","year":"2004","journal-title":"Cell Mol Immunol"},{"issue":"6","key":"pone.0338053.ref140","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1038\/s41596-022-00692-9","article-title":"Chromatin accessibility profiling by ATAC-seq","volume":"17","author":"FC Grandi","year":"2022","journal-title":"Nat Protoc"},{"issue":"3","key":"pone.0338053.ref141","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1556\/2060.106.2019.19","article-title":"The gut-kidney-heart axis in chronic kidney disease","volume":"106","author":"K Sumida","year":"2019","journal-title":"Physiol Int"},{"issue":"11","key":"pone.0338053.ref142","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1161\/CIRCRESAHA.125.325516","article-title":"Gut-Heart Axis: The Role of Gut Microbiota and Metabolites in Heart Failure","volume":"136","author":"M Snelson","year":"2025","journal-title":"Circ Res"},{"issue":"4","key":"pone.0338053.ref143","article-title":"Gut-liver axis calibrates intestinal stem cell fitness","volume":"187","author":"G Kim","year":"2024","journal-title":"Cell"},{"issue":"6571","key":"pone.0338053.ref144","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1126\/science.abi6087","article-title":"Signaling inflammation across the gut-brain axis","volume":"374","author":"G Agirman","year":"2021","journal-title":"Science"},{"issue":"10","key":"pone.0338053.ref145","doi-asserted-by":"crossref","first-page":"4713","DOI":"10.1007\/s00018-021-03812-y","article-title":"The enteric nervous system in gastrointestinal disease etiology","volume":"78","author":"AM Holland","year":"2021","journal-title":"Cell Mol Life Sci"},{"key":"pone.0338053.ref146","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.brainres.2018.01.011","article-title":"Enteric nervous system manifestations of neurodegenerative disease","volume":"1693","author":"A Chalazonitis","year":"2018","journal-title":"Brain Res"},{"issue":"13","key":"pone.0338053.ref147","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2023.05.001","article-title":"The enteric nervous system relays psychological stress to intestinal inflammation","volume":"186","author":"KM Schneider","year":"2023","journal-title":"Cell"},{"key":"pone.0338053.ref148","doi-asserted-by":"crossref","first-page":"2470547017692328","DOI":"10.1177\/2470547017692328","article-title":"Neurobiological and systemic effects of chronic stress","volume":"1","author":"BS McEwen","year":"2017","journal-title":"Chronic Stress (Thousand Oaks)"},{"key":"pone.0338053.ref149","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.conb.2019.01.002","article-title":"Pumping the brakes: suppression of synapse development by MDGA-neuroligin interactions","volume":"57","author":"SA Connor","year":"2019","journal-title":"Curr Opin Neurobiol"},{"key":"pone.0338053.ref150","doi-asserted-by":"crossref","first-page":"28653","DOI":"10.1038\/srep28653","article-title":"Growth differentiation factor-15 promotes glutamate release in medial prefrontal cortex of mice through upregulation of T-type calcium channels","volume":"6","author":"D-D Liu","year":"2016","journal-title":"Sci Rep"},{"issue":"14","key":"pone.0338053.ref151","doi-asserted-by":"crossref","DOI":"10.1212\/WNL.0000000000200927","article-title":"The phenotypic continuum of ATP1A3-related disorders","volume":"99","author":"A Vezyroglou","year":"2022","journal-title":"Neurology"},{"issue":"1","key":"pone.0338053.ref152","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1159\/000510696","article-title":"Allostatic load and its impact on health: a systematic review","volume":"90","author":"J Guidi","year":"2021","journal-title":"Psychother Psychosom"},{"issue":"8","key":"pone.0338053.ref153","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1111\/apt.18217","article-title":"Allostatic load increases the incidence and risk of adverse prognosis in inflammatory bowel disease","volume":"60","author":"J Zhao","year":"2024","journal-title":"Aliment Pharmacol Ther"},{"key":"pone.0338053.ref154","doi-asserted-by":"crossref","first-page":"101630","DOI":"10.1016\/j.mex.2022.101630","article-title":"Improved swiss-rolling method for histological analyses of colon tissue","volume":"9","author":"J Le Naour","year":"2022","journal-title":"MethodsX"},{"issue":"7","key":"pone.0338053.ref155","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.3390\/cells9071681","article-title":"Addition of high molecular weight hyaluronic acid to fibroblast-like stromal cells modulates endogenous hyaluronic acid metabolism and enhances proteolytic processing and secretion of versican","volume":"9","author":"J Xue","year":"2020","journal-title":"Cells"},{"issue":"2","key":"pone.0338053.ref156","doi-asserted-by":"crossref","first-page":"221","DOI":"10.3390\/biom13020221","article-title":"Statistical power analysis for designing bulk, single-cell, and spatial transcriptomics experiments: review, tutorial, and perspectives","volume":"13","author":"H Jeon","year":"2023","journal-title":"Biomolecules"},{"issue":"1","key":"pone.0338053.ref157","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1002\/jor.23635","article-title":"Pirfenidone reduces subchondral bone loss and fibrosis after murine knee cartilage injury","volume":"36","author":"DD Chan","year":"2018","journal-title":"J Orthop Res"},{"key":"pone.0338053.ref158","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M Martin","year":"2011","journal-title":"EMBnet.journal"},{"issue":"1","key":"pone.0338053.ref159","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"issue":"7","key":"pone.0338053.ref160","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Y Liao","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0338053.ref161","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"issue":"10","key":"pone.0338053.ref162","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"DJ McCarthy","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"pone.0338053.ref163","first-page":"325","article-title":"Calculating average power for the benjamini-hochberg procedure","volume":"8","author":"WJ Feser","year":"2009","journal-title":"J Stat Theory Appl"},{"key":"pone.0338053.ref164","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1007\/978-1-4939-7834-2_7","article-title":"Making and sequencing heavily multiplexed, high-throughput 16s ribosomal RNA gene amplicon libraries using a flexible, two-stage PCR protocol","volume":"1783","author":"A Naqib","year":"2018","journal-title":"Methods Mol Biol"},{"issue":"8","key":"pone.0338053.ref165","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":"E Bolyen","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"5","key":"pone.0338053.ref166","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","article-title":"PEAR: a fast and accurate Illumina Paired-End reAd mergeR","volume":"30","author":"J Zhang","year":"2014","journal-title":"Bioinformatics"},{"issue":"7","key":"pone.0338053.ref167","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"BJ Callahan","year":"2016","journal-title":"Nat Methods"},{"issue":"1","key":"pone.0338053.ref168","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0006-3207(92)91201-3","article-title":"Conservation evaluation and phylogenetic diversity","volume":"61","author":"DP Faith","year":"1992","journal-title":"Biological Conservation"},{"issue":"3","key":"pone.0338053.ref169","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"CE Shannon","year":"1948","journal-title":"Bell System Technical Journal"},{"issue":"4148","key":"pone.0338053.ref170","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/163688a0","article-title":"Measurement of Diversity","volume":"163","author":"EH SIMPSON","year":"1949","journal-title":"Nature"},{"issue":"1","key":"pone.0338053.ref171","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":"NA Bokulich","year":"2018","journal-title":"Microbiome"},{"key":"pone.0338053.ref172","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"C Quast","year":"2013","journal-title":"Nucleic Acids Res"}],"container-title":["PLOS 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