{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T03:52:05Z","timestamp":1784778725493,"version":"3.55.0"},"reference-count":158,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2023,12,21]],"date-time":"2023-12-21T00:00:00Z","timestamp":1703116800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,12,21]],"date-time":"2023-12-21T00:00:00Z","timestamp":1703116800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"USDA | National Institute of Food and Agriculture","award":["ME022102, ME022329"],"award-info":[{"award-number":["ME022102, ME022329"]}]},{"name":"USDA | National Institute of Food and Agriculture","award":["ME022303"],"award-info":[{"award-number":["ME022303"]}]},{"name":"USDA | National Institute of Food and Agriculture","award":["2018-67017-27520, 2018-67017-36797"],"award-info":[{"award-number":["2018-67017-27520, 2018-67017-36797"]}]},{"DOI":"10.13039\/100000062","name":"HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"crossref","award":["1R15DK133826-01"],"award-info":[{"award-number":["1R15DK133826-01"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2023,12,21]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Crohn\u2019s disease (CD) is a presentation of inflammatory bowel disease (IBD) that manifests in childhood and adolescence and involves chronic and severe enterocolitis, immune and gut microbial dysregulation, and other complications. Diet and gut-microbiota-produced metabolites are sources of anti-inflammatories that could ameliorate symptoms. However, questions remain on how IBD influences biogeographic patterns of microbial location and function in the gut, how early life transitional gut communities are affected by IBD and diet interventions, and how disruption to biogeography alters disease mediation by diet components or microbial metabolites. Many studies on diet and IBD use a chemically induced ulcerative colitis model, despite the availability of an immune-modulated CD model. Interleukin-10-knockout (IL-10-KO) mice on a C57BL\/6 background, beginning at age 4 or 7 weeks, were fed a control diet or one containing 10% (wt\/wt) raw broccoli sprouts, which was high in the sprout-sourced anti-inflammatory sulforaphane. Diets began 7 days prior to, and for 2 weeks after inoculation with\n                    <jats:italic>Helicobacter hepaticus,<\/jats:italic>\n                    which triggers Crohn\u2019s-like symptoms in these immune-impaired mice. The broccoli sprout diet increased sulforaphane in plasma; decreased weight stagnation, fecal blood, and diarrhea associated; and increased microbiota richness in the gut, especially in younger mice. Sprout diets resulted in some anatomically specific bacteria in younger mice and reduced the prevalence and abundance of pathobiont bacteria which trigger inflammation in the IL-10-KO mouse, for example,\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    and\n                    <jats:italic>Helicobacter<\/jats:italic>\n                    . Overall, the IL-10-KO mouse model is responsive to a raw broccoli sprout diet and represents an opportunity for more diet-host-microbiome research.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>To our knowledge, IL-10-KO mice have not previously been used to investigate the interactions of host, microbiota, and broccoli, broccoli sprouts, or broccoli bioactives in resolving symptoms of CD. We showed that a diet containing 10% raw broccoli sprouts increased the plasma concentration of the anti-inflammatory compound sulforaphane and protected mice to varying degrees against disease symptoms, including weight loss or stagnation, fecal blood, and diarrhea. Younger mice responded more strongly to the diet, further reducing symptoms, as well as increased gut bacterial richness, increased bacterial community similarity to each other, and more location-specific communities than older mice on the diet intervention. Crohn\u2019s disease disrupts the lives of patients and requires people to alter dietary and lifestyle habits to manage symptoms. The current medical treatment is expensive with significant side effects, and a dietary intervention represents an affordable, accessible, and simple strategy to reduce the burden of symptoms.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00688-23","type":"journal-article","created":{"date-parts":[[2023,11,9]],"date-time":"2023-11-09T08:00:25Z","timestamp":1699516825000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":12,"title":["Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease"],"prefix":"10.1128","volume":"8","author":[{"given":"Lola","family":"Holcomb","sequence":"first","affiliation":[{"name":"Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna M.","family":"Holman","sequence":"additional","affiliation":[{"name":"School of Food and Agriculture, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly","family":"Hurd","sequence":"additional","affiliation":[{"name":"Larner College of Medicine, University of Vermont, Burlington, Vermont, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brigitte","family":"Lavoie","sequence":"additional","affiliation":[{"name":"Larner College of Medicine, University of Vermont, Burlington, Vermont, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louisa","family":"Colucci","sequence":"additional","affiliation":[{"name":"Department of Biology, Husson University, Bangor, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Hunt","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"Hunt","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marissa","family":"Kinney","sequence":"additional","affiliation":[{"name":"School of Food and Agriculture, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jahnavi","family":"Pathak","sequence":"additional","affiliation":[{"name":"Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary M.","family":"Mawe","sequence":"additional","affiliation":[{"name":"Larner College of Medicine, University of Vermont, Burlington, Vermont, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter L.","family":"Moses","sequence":"additional","affiliation":[{"name":"Larner College of Medicine, University of Vermont, Burlington, Vermont, USA"},{"name":"Finch Therapeutics, Somerville, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Perry","sequence":"additional","affiliation":[{"name":"Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allesandra","family":"Stratigakis","sequence":"additional","affiliation":[{"name":"School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2615-8055","authenticated-orcid":true,"given":"Suzanne L.","family":"Ishaq","sequence":"additional","affiliation":[{"name":"Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8139-6718","authenticated-orcid":false,"given":"Yanyan","family":"Li","sequence":"additional","affiliation":[{"name":"Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(17)32130-X"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1159\/000506364"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cgh.2019.07.022"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1177\/03000605221098868"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.28502"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1177\/2040622319899297"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jand.2013.12.019"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jnutbio.2022.109238"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005364"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2019.08.001"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-022-01930-9"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1053\/gast.2002.30294"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-01973-8"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05989-7"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1155\/2022\/7813278"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00665-20"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/advances\/nmac075"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2016.10.019"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1007\/s12664-018-0890-5"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1111\/joim.12945"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2012-303557"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1097\/00054725-199902000-00004"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1136\/gut.50.3.307"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1136\/flgastro-2020-101436"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1086\/510385"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1097\/MIB.0000000000000230"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41572-020-0156-2"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1038\/nri2660"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.28346"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41395-018-0239-9"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01396-12"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.3389\/fped.2021.626232"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-55290-9"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1097\/MIB.0000000000000382"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0134382"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2016-313235"},{"key":"e_1_3_5_38_2","article-title":"Crohn disease","volume":"172940","author":"Ghazi LJ","year":"2023","unstructured":"Ghazi LJ. 2023. Crohn disease. Medscape 172940","journal-title":"Medscape"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jnutbio.2022.109215"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1002\/mnfr.201700991"},{"key":"e_1_3_5_41_2","first-page":"501","article-title":"Chemoprotective glucosinolates and isothiocyanates of broccoli sprouts: metabolism and excretion in humans","volume":"10","author":"Shapiro TA","year":"2001","unstructured":"Shapiro TA, Fahey JW, Wade KL, Stephenson KK, Talalay P. 2001. Chemoprotective glucosinolates and isothiocyanates of broccoli sprouts: metabolism and excretion in humans. Cancer Epidemiol Biomarkers Prev 10:501\u2013508.","journal-title":"Cancer Epidemiol Biomarkers Prev"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cgh.2013.09.063"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2021.151513"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1039\/d1fo03398k"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/710856"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/sigtrans.2017.23"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.canlet.2017.02.023"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00532-23"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.1093\/cdn\/nzac053.048"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13568-020-01053-z"},{"key":"e_1_3_5_51_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.112203099"},{"key":"e_1_3_5_52_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00394-020-02322-0"},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodchem.2020.128771"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules24193593"},{"key":"e_1_3_5_55_2","doi-asserted-by":"publisher","DOI":"10.1152\/ajpgi.2000.278.6.G829"},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1097\/MIB.0000000000000468"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1749-6632.2011.06339.x"},{"key":"e_1_3_5_58_2","doi-asserted-by":"publisher","DOI":"10.1152\/ajpgi.2001.281.3.G764"},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(93)80068-p"},{"key":"e_1_3_5_60_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2168.2000.01615.x"},{"key":"e_1_3_5_61_2","doi-asserted-by":"publisher","DOI":"10.1097\/00054725-200209000-00006"},{"key":"e_1_3_5_62_2","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aao1314"},{"key":"e_1_3_5_63_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0617-x"},{"key":"e_1_3_5_64_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.19.10367"},{"key":"e_1_3_5_65_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0044328"},{"key":"e_1_3_5_66_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-50216-x"},{"key":"e_1_3_5_67_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molimm.2022.07.010"},{"key":"e_1_3_5_68_2","doi-asserted-by":"publisher","DOI":"10.3390\/nu12072088"},{"key":"e_1_3_5_69_2","doi-asserted-by":"publisher","DOI":"10.3390\/nu13082750"},{"key":"e_1_3_5_70_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.01.023"},{"key":"e_1_3_5_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(12)60026-9"},{"key":"e_1_3_5_72_2","doi-asserted-by":"publisher","DOI":"10.3390\/nu10050537"},{"key":"e_1_3_5_73_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.041723-0"},{"key":"e_1_3_5_74_2","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.585431"},{"key":"e_1_3_5_75_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jnutbio.2018.01.002"},{"key":"e_1_3_5_76_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature12506"},{"key":"e_1_3_5_77_2","doi-asserted-by":"publisher","DOI":"10.5056\/jnm14008"},{"key":"e_1_3_5_78_2","doi-asserted-by":"publisher","DOI":"10.1097\/00054725-200409000-00009"},{"key":"e_1_3_5_79_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0007114512000657"},{"key":"e_1_3_5_80_2","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v23.i33.6016"},{"key":"e_1_3_5_81_2","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2017.044"},{"key":"e_1_3_5_82_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-5085(90)90290-h"},{"key":"e_1_3_5_83_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jss.2006.07.050"},{"key":"e_1_3_5_84_2","doi-asserted-by":"publisher","DOI":"10.1002\/0471142735.im1525s104"},{"key":"e_1_3_5_85_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00535-004-1492-9"},{"key":"e_1_3_5_86_2","doi-asserted-by":"publisher","DOI":"10.1016\/0016-5085(94)90803-6"},{"key":"e_1_3_5_87_2","doi-asserted-by":"publisher","DOI":"10.1002\/ibd.20821"},{"key":"e_1_3_5_88_2","doi-asserted-by":"publisher","DOI":"10.3389\/fnut.2022.895665"},{"key":"e_1_3_5_89_2","doi-asserted-by":"publisher","DOI":"10.1161\/CIRCEP.117.006040"},{"key":"e_1_3_5_90_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00125-010-2020-5"},{"key":"e_1_3_5_91_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.36521"},{"key":"e_1_3_5_92_2","doi-asserted-by":"publisher","DOI":"10.1152\/ajpregu.00072.2020"},{"key":"e_1_3_5_93_2","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.137943"},{"key":"e_1_3_5_94_2","doi-asserted-by":"publisher","DOI":"10.4161\/gmic.21008"},{"key":"e_1_3_5_95_2","doi-asserted-by":"publisher","DOI":"10.3390\/pharmaceutics13101624"},{"key":"e_1_3_5_96_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.05.012"},{"key":"e_1_3_5_97_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1237439"},{"key":"e_1_3_5_98_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2017.03.010"},{"key":"e_1_3_5_99_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-90303-9_9"},{"key":"e_1_3_5_100_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0163720"},{"key":"e_1_3_5_101_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-21440-8"},{"key":"e_1_3_5_102_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-1-r4"},{"key":"e_1_3_5_103_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00301871"},{"key":"e_1_3_5_104_2","doi-asserted-by":"publisher","DOI":"10.1084\/jem.132.2.251"},{"key":"e_1_3_5_105_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2022.2123677"},{"key":"e_1_3_5_106_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0225079"},{"key":"e_1_3_5_107_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jff.2017.08.038"},{"key":"e_1_3_5_108_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0804812105"},{"key":"e_1_3_5_109_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2019.1618173"},{"key":"e_1_3_5_110_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1109051"},{"key":"e_1_3_5_111_2","doi-asserted-by":"publisher","DOI":"10.1002\/ibd.21895"},{"key":"e_1_3_5_112_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jare.2022.11.003"},{"key":"e_1_3_5_113_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00284-016-1079-8"},{"key":"e_1_3_5_114_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00114-008-0452-2"},{"key":"e_1_3_5_115_2","doi-asserted-by":"publisher","DOI":"10.1177\/17562848211004493"},{"key":"e_1_3_5_116_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2013-306226"},{"key":"e_1_3_5_117_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2567.2008.02834.x"},{"key":"e_1_3_5_118_2","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.86907"},{"key":"e_1_3_5_119_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00335-021-09863-7"},{"key":"e_1_3_5_120_2","first-page":"534","article-title":"Helicobacter typhlonius and Helicobacter rodentium differentially affect the severity of colon inflammation and inflammation-associated neoplasia in IL10-deficient mice","volume":"58","author":"Chichlowski M","year":"2008","unstructured":"Chichlowski M, Sharp JM, Vanderford DA, Myles MH, Hale LP. 2008. Helicobacter typhlonius and Helicobacter rodentium differentially affect the severity of colon inflammation and inflammation-associated neoplasia in IL10-deficient mice. Comp Med 58:534\u2013541.","journal-title":"Comp Med"},{"key":"e_1_3_5_121_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.05.012"},{"key":"e_1_3_5_122_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cgh.2015.12.029"},{"key":"e_1_3_5_123_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2022.09.034"},{"key":"e_1_3_5_124_2","doi-asserted-by":"publisher","DOI":"10.1002\/mnfr.201800427"},{"key":"e_1_3_5_125_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.clnu.2022.10.024"},{"key":"e_1_3_5_126_2","doi-asserted-by":"publisher","DOI":"10.1097\/00054725-200303000-00005"},{"key":"e_1_3_5_127_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00140-18"},{"key":"e_1_3_5_128_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2017.06.007"},{"key":"e_1_3_5_129_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12974-019-1588-z"},{"key":"e_1_3_5_130_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10753-015-0180-7"},{"key":"e_1_3_5_131_2","doi-asserted-by":"publisher","DOI":"10.1210\/en.2015-1177"},{"key":"e_1_3_5_132_2","doi-asserted-by":"publisher","DOI":"10.1093\/ibd\/izaa081"},{"key":"e_1_3_5_133_2","doi-asserted-by":"publisher","DOI":"10.1093\/ibd\/izab074"},{"key":"e_1_3_5_134_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2018.08.063"},{"key":"e_1_3_5_135_2","first-page":"99","article-title":"Role of animal models for the pathogenesis and treatment of inflammatory bowel disease","volume":"223","author":"Dieleman LA","year":"1997","unstructured":"Dieleman LA, Pe\u00f1a AS, Meuwissen SG, van Rees EP. 1997. Role of animal models for the pathogenesis and treatment of inflammatory bowel disease. Scand J Gastroenterol Suppl 223:99\u2013104.","journal-title":"Scand J Gastroenterol"},{"key":"e_1_3_5_136_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mrfmmm.2007.04.003"},{"key":"e_1_3_5_137_2","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2022.946065"},{"key":"e_1_3_5_138_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaim.2022.100544"},{"key":"e_1_3_5_139_2","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.01242"},{"key":"e_1_3_5_140_2","doi-asserted-by":"publisher","DOI":"10.1101\/pdb.prot073411"},{"key":"e_1_3_5_141_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2016.07.032"},{"key":"e_1_3_5_142_2","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-6"},{"key":"e_1_3_5_143_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1000080107"},{"key":"e_1_3_5_144_2","doi-asserted-by":"crossref","unstructured":"The earth Microbiome project. 2011. The earth microbiome project. http:\/\/www.earthmicrobiome.org.","DOI":"10.69645\/GFOT9303"},{"key":"e_1_3_5_145_2","unstructured":"Callahan B. 2022. DADA2: fast and accurate sample inference from amplicon data with single-nucleotide resolution (1.16). Available from: https:\/\/benjjneb.github.io\/dada2\/tutorial.html"},{"key":"e_1_3_5_146_2","unstructured":"RCoreTeam. 2022. R: a language and environment for statistical computing (4.2.2). R foundation for statistical computing Vienna Austria. Available from: https:\/\/www.r-project.org"},{"key":"e_1_3_5_147_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm864"},{"key":"e_1_3_5_148_2","doi-asserted-by":"crossref","unstructured":"Wickham H Francois R Henry L M\u00fcller K. 2015. dplyr: a grammar of data manipulation. R package version 0.4. 3. R found stat comput vienna. Available from: https:\/\/CRAN R-project org\/package= dplyr","DOI":"10.32614\/CRAN.package.dplyr"},{"key":"e_1_3_5_149_2","unstructured":"Ishaq SL. 2017. Github. Phyloseq_dealing_with_neg_controls_ Ishaq_example.R. Github. Available from: https:\/\/github.com\/SueIshaq\/Examples-DADA2-Phyloseq. Retrieved 5 Mar 2019."},{"key":"e_1_3_5_150_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217"},{"key":"e_1_3_5_151_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0237-y"},{"key":"e_1_3_5_152_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-01636-1"},{"key":"e_1_3_5_153_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v067.i01"},{"key":"e_1_3_5_154_2","unstructured":"Oksanen J Guillaume Blanchet F Friendly M Kindt R Legendre P McGlinn D Minchin PR O\u2019Hara RB Simpson GL Solymos P Stevens MHH Szoecs E Wagner H. 2020. Vegan: community ecology package (2.5-7). Available from: https:\/\/cran.r-project.org\/web\/packages\/vegan\/vignettes\/diversity-vegan.pdf"},{"key":"e_1_3_5_155_2","unstructured":"Archer E. 2022. rfpermute: estimate permutation P-values for random forest importance metrics (2.5.1). Available from: https:\/\/github.com\/EricArcher\/rfPermute"},{"key":"e_1_3_5_156_2","unstructured":"Wickham H. 2016. ggplot2: elegant graphics for data analysis. Springer Publishing Company New York. Available from: https:\/\/dl.acm.org\/citation.cfm?id=1795559."},{"key":"e_1_3_5_157_2","unstructured":"Kassambara A. 2022. ggpubr:\u201cggplot2\u201d based publication ready plots (0.1.7). Available from: https:\/\/rpkgs.datanovia.com\/ggpubr"},{"key":"e_1_3_5_158_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1650"},{"key":"e_1_3_5_159_2","unstructured":"Galey M. 2021. Mi-Seq analysis. GitHub. Available from: https:\/\/mgaley-004.github.io\/MiSeq-Analysis\/Tutorials\/SourceSink.html https:\/\/github.com\/mgaley-004\/MiSeq-Analysis. Retrieved 7 Dec 2022."}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00688-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00688-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T15:05:29Z","timestamp":1730473529000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.00688-23"}},"subtitle":[],"editor":[{"given":"Hiutung","family":"Chu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,12,21]]},"references-count":158,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,12,21]]}},"alternative-id":["10.1128\/msystems.00688-23"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00688-23","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.01.27.525953","asserted-by":"object"}]},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,21]]},"assertion":[{"value":"2023-07-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-10-02","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-11-09","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00688-23"}}