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<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">nogr</journal-id><journal-title-group><journal-title xml:lang="ru">Экспериментальная и клиническая гастроэнтерология</journal-title><trans-title-group xml:lang="en"><trans-title>Experimental and Clinical Gastroenterology</trans-title></trans-title-group></journal-title-group><issn pub-type="ppub">1682-8658</issn><publisher><publisher-name>«Global Media Technologies»</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.31146/1682-8658-ecg-220-12-164-182</article-id><article-id custom-type="elpub" pub-id-type="custom">nogr-2663</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>ОБЗОР</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>REVIEW</subject></subj-group></article-categories><title-group><article-title>Современные представления об этиологии и патогенезе воспалительных заболеваний кишечника (Часть 2): роль микробиома и нутритивных факторов</article-title><trans-title-group xml:lang="en"><trans-title>Current understanding of the aetiology and pathogenesis of inflammatory bowel diseases (Part 2): the role of the microbiome and nutritional factors</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-7308-7280</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Хавкин</surname><given-names>А. И.</given-names></name><name name-style="western" xml:lang="en"><surname>Khavkin</surname><given-names>A. I.</given-names></name></name-alternatives><email xlink:type="simple">khavkin@nikid.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-8364-6066</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Николайчук</surname><given-names>К. М.</given-names></name><name name-style="western" xml:lang="en"><surname>Nikolaychuk</surname><given-names>K. M.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-3606-4068</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Шрайнер</surname><given-names>Е. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Shrayner</surname><given-names>E. V.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-3"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0009-7816-5562</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Шаймарданова</surname><given-names>Д. Р.</given-names></name><name name-style="western" xml:lang="en"><surname>Shaimardanova</surname><given-names>D. R.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0002-9228-2350</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Веременко</surname><given-names>А. С.</given-names></name><name name-style="western" xml:lang="en"><surname>Veremenko</surname><given-names>A. S.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0002-7317-6077</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Левченко</surname><given-names>И. Д.</given-names></name><name name-style="western" xml:lang="en"><surname>Levchenko</surname><given-names>I. D.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0004-1880-9585</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Платонова</surname><given-names>П. Я.</given-names></name><name name-style="western" xml:lang="en"><surname>Platonova</surname><given-names>P. Ya.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0008-7479-8277</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Новикова</surname><given-names>М. Ф.</given-names></name><name name-style="western" xml:lang="en"><surname>Novikova</surname><given-names>M. F.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-6271-5218</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Дудурич</surname><given-names>В. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Dudurich</surname><given-names>V. V.</given-names></name></name-alternatives><email xlink:type="simple">noemail@neicon.ru</email><xref ref-type="aff" rid="aff-4"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru"><institution>Научно-исследовательский клинический институт детства Министерства здравоохранения Московской области; Белгородский государственный исследовательский университет Министерства науки и высшего образования Российской Федерации</institution><country>Россия</country></aff><aff xml:lang="en"><institution>Research Clinical Institute of Childhood, Ministry of Health of the Moscow Region; Belgorod State Research University</institution><country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru"><institution>Новосибирский государственный университет</institution><country>Россия</country></aff><aff xml:lang="en"><institution>Novosibirsk State University</institution><country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-3"><aff xml:lang="ru"><institution>Новосибирский государственный университет; Институт химической биологии и фундаментальной медицины СО РАН</institution><country>Россия</country></aff><aff xml:lang="en"><institution>Novosibirsk State University; Institute of Chemical Biology and Fundamental Medicine of the SB RAS</institution><country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-4"><aff xml:lang="ru"><institution>Федеральное государственное автономное образовательное учреждение высшего образования «Национальный исследовательский университет ИТМО»; «Сербалаб» генетическая лаборатория</institution><country>Россия</country></aff><aff xml:lang="en"><institution>ITMO National Research University; “Сerbalab” laboratory</institution><country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2023</year></pub-date><pub-date pub-type="epub"><day>18</day><month>12</month><year>2023</year></pub-date><volume>0</volume><issue>12</issue><fpage>164</fpage><lpage>182</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Хавкин А.И., Николайчук К.М., Шрайнер Е.В., Шаймарданова Д.Р., Веременко А.С., Левченко И.Д., Платонова П.Я., Новикова М.Ф., Дудурич В.В., 2023</copyright-statement><copyright-year>2023</copyright-year><copyright-holder xml:lang="ru">Хавкин А.И., Николайчук К.М., Шрайнер Е.В., Шаймарданова Д.Р., Веременко А.С., Левченко И.Д., Платонова П.Я., Новикова М.Ф., Дудурич В.В.</copyright-holder><copyright-holder xml:lang="en">Khavkin A.I., Nikolaychuk K.M., Shrayner E.V., Shaimardanova D.R., Veremenko A.S., Levchenko I.D., Platonova P.Y., Novikova M.F., Dudurich V.V.</copyright-holder><license xml:lang="ru" license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>Данная работа распространяется под лицензией Creative Commons Attribution 4.0.</license-p></license><license xml:lang="en" license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://www.nogr.org/jour/article/view/2663">https://www.nogr.org/jour/article/view/2663</self-uri><abstract><p>В рамках работы проведен обзор современных данных о структуре микробиоты и её взаимодействии с хозяином, а также оценено влияние микробного сообщества на иммунную систему и развитие хронического воспаления в желудочно-кишечном тракте. В обзоре представлены современные даные о влияние диеты на ход и терапию ВЗК. Изучение роли микробиоты и диеты в патогенезе ВЗК показало, что микробный дисбиоз и вирус Эпштейна-Барр могут усугублять течение ВЗК. Определённые продукты ухудшают симптомы, в то время как моносахаридная диета способствует ремиссии. Результаты подчёркивают важность индивидуального подхода к питанию для улучшения лечения ВЗК.</p></abstract><trans-abstract xml:lang="en"><p>This work reviews current data on the structure of the microbiota and its interaction with the host, and assesses the impact of the microbial community on the immune system and the development of chronic inflammation in the gastrointestinal tract. This review presents current evidence on the influence of diet on the course and therapy of GI tract inflammation. Studies on the role of microbiota and diet in the pathogenesis of ICD have shown that microbial dysbiosis and Epstein-Barr virus can exacerbate the course of ICD. Certain foods worsen symptoms, while a monosaccharide diet favours remission. The results emphasise the importance of an individualised nutritional approach to improve the treatment of IBS.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>воспалительные заболевания кишечника</kwd><kwd>болезнь Крона</kwd><kwd>язвенный колит</kwd><kwd>патогенезе</kwd><kwd>микробиота</kwd><kwd>питание и диета при ВЗК</kwd></kwd-group><kwd-group xml:lang="en"><kwd>Inflammatory bowel disease</kwd><kwd>Crohn’s disease</kwd><kwd>ulcerative colitis</kwd><kwd>pathogenesis</kwd><kwd>microbiota</kwd><kwd>nutrition and diet in IBD</kwd></kwd-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Selvamani S., Mehta V., Ali El Enshasy H., Thevarajoo S., El Adawi H., Zeini I., Pham K., Varzakas T., Abomoelak B. Efficacy of Probiotics-Based Interventions as Therapy for Inflammatory Bowel Disease: A Recent Update. Saudi J Biol Sci. 2022 May;29(5):3546-3567. doi: 10.1016/j.sjbs.2022.02.044.</mixed-citation><mixed-citation xml:lang="en">Selvamani S., Mehta V., Ali El Enshasy H., Thevarajoo S., El Adawi H., Zeini I., Pham K., Varzakas T., Abomoelak B. Efficacy of Probiotics-Based Interventions as Therapy for Inflammatory Bowel Disease: A Recent Update. Saudi J Biol Sci. 2022 May;29(5):3546-3567. doi: 10.1016/j.sjbs.2022.02.044.</mixed-citation></citation-alternatives></ref><ref id="cit2"><label>2</label><citation-alternatives><mixed-citation xml:lang="ru">Haneishi Y., Furuya Y., Hasegawa M., Picarelli A., Rossi M., Miyamoto J. Inflammatory Bowel Diseases and Gut Microbiota.Int J Mol Sci. 2023 Feb 14;24(4):3817. doi: 10.3390/ijms24043817.</mixed-citation><mixed-citation xml:lang="en">Haneishi Y., Furuya Y., Hasegawa M., Picarelli A., Rossi M., Miyamoto J. Inflammatory Bowel Diseases and Gut Microbiota.Int J Mol Sci. 2023 Feb 14;24(4):3817. doi: 10.3390/ijms24043817.</mixed-citation></citation-alternatives></ref><ref id="cit3"><label>3</label><citation-alternatives><mixed-citation xml:lang="ru">Jie Wang, Puxuan Zhang, Shujie Chen, Huimin Duan, Liwei Xie. Microbiota and Gut Health: Promising Pro-spects for Clinical Trials from Bench to Bedside. Advanced Gut &amp; Microbiome Research. 2022: Article ID 2290052. doi: 10.1155/2022/2290052.</mixed-citation><mixed-citation xml:lang="en">Jie Wang, Puxuan Zhang, Shujie Chen, Huimin Duan, Liwei Xie. Microbiota and Gut Health: Promising Pro-spects for Clinical Trials from Bench to Bedside. Advanced Gut &amp; Microbiome Research. 2022: Article ID 2290052. doi: 10.1155/2022/2290052.</mixed-citation></citation-alternatives></ref><ref id="cit4"><label>4</label><citation-alternatives><mixed-citation xml:lang="ru">Aldars-García L., Chaparro M., Gisbert J. P. Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease. Microorganisms. 2021 Apr 30;9(5):977. doi: 10.3390/microorganisms9050977.</mixed-citation><mixed-citation xml:lang="en">Aldars-García L., Chaparro M., Gisbert J. P. Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease. Microorganisms. 2021 Apr 30;9(5):977. doi: 10.3390/microorganisms9050977.</mixed-citation></citation-alternatives></ref><ref id="cit5"><label>5</label><citation-alternatives><mixed-citation xml:lang="ru">Elzayat H., Mesto G., Al-Marzooq F. Unraveling the Impact of Gut and Oral Microbiome on Gut Health in Inflammatory Bowel Diseases. Nutrients. 2023 Jul 29;15(15):3377. doi: 10.3390/nu15153377.</mixed-citation><mixed-citation xml:lang="en">Elzayat H., Mesto G., Al-Marzooq F. Unraveling the Impact of Gut and Oral Microbiome on Gut Health in Inflammatory Bowel Diseases. Nutrients. 2023 Jul 29;15(15):3377. doi: 10.3390/nu15153377.</mixed-citation></citation-alternatives></ref><ref id="cit6"><label>6</label><citation-alternatives><mixed-citation xml:lang="ru">Senapati T., Kothidar A., Banerjee S. K., DAS B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci. 2019 Oct;44(5):113. PMID: 31719222.</mixed-citation><mixed-citation xml:lang="en">Senapati T., Kothidar A., Banerjee S. K., DAS B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci. 2019 Oct;44(5):113. PMID: 31719222.</mixed-citation></citation-alternatives></ref><ref id="cit7"><label>7</label><citation-alternatives><mixed-citation xml:lang="ru">Pittayanon R., Lau J. T., Leontiadis G. I., Tse F., Yuan Y., Surette M., Moayyedi P. Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review. Gastroenterology. 2020 Mar;158(4):930-946.e1. doi: 10.1053/j.gastro.2019.11.294.</mixed-citation><mixed-citation xml:lang="en">Pittayanon R., Lau J. T., Leontiadis G. I., Tse F., Yuan Y., Surette M., Moayyedi P. Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review. Gastroenterology. 2020 Mar;158(4):930-946.e1. doi: 10.1053/j.gastro.2019.11.294.</mixed-citation></citation-alternatives></ref><ref id="cit8"><label>8</label><citation-alternatives><mixed-citation xml:lang="ru">Quévrain E., Maubert M. A., Michon C. et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn’s disease. Gut. 2016 Mar;65(3):415-425. doi: 10.1136/gutjnl-2014-307649.</mixed-citation><mixed-citation xml:lang="en">Quévrain E., Maubert M. A., Michon C. et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn’s disease. Gut. 2016 Mar;65(3):415-425. doi: 10.1136/gutjnl-2014-307649.</mixed-citation></citation-alternatives></ref><ref id="cit9"><label>9</label><citation-alternatives><mixed-citation xml:lang="ru">Parada Venegas D., De la Fuente M. K., Landskron G., González M. J., Quera R., Dijkstra G., Harmsen H. J.M., Faber K. N., Hermoso M. A. Corrigendum: Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol. 2019 Jun 28;10:1486. doi: 10.3389/fimmu.2019.01486.</mixed-citation><mixed-citation xml:lang="en">Parada Venegas D., De la Fuente M. K., Landskron G., González M. J., Quera R., Dijkstra G., Harmsen H. J.M., Faber K. N., Hermoso M. A. Corrigendum: Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol. 2019 Jun 28;10:1486. doi: 10.3389/fimmu.2019.01486.</mixed-citation></citation-alternatives></ref><ref id="cit10"><label>10</label><citation-alternatives><mixed-citation xml:lang="ru">Lal S., Kandiyal B., Ahuja V., Takeda K., Das B. Gut microbiome dysbiosis in inflammatory bowel disease. Prog Mol Biol Transl Sci. 2022;192(1):179-204. doi: 10.1016/bs.pmbts.2022.09.003.</mixed-citation><mixed-citation xml:lang="en">Lal S., Kandiyal B., Ahuja V., Takeda K., Das B. Gut microbiome dysbiosis in inflammatory bowel disease. Prog Mol Biol Transl Sci. 2022;192(1):179-204. doi: 10.1016/bs.pmbts.2022.09.003.</mixed-citation></citation-alternatives></ref><ref id="cit11"><label>11</label><citation-alternatives><mixed-citation xml:lang="ru">Pareek S., Kurakawa T., Das B. et al.Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi. NPJ Biofilms Microbiomes. 2019 Dec 20;5(1):37. doi: 10.1038/s41522-019-0110-9.</mixed-citation><mixed-citation xml:lang="en">Pareek S., Kurakawa T., Das B. et al.Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi. NPJ Biofilms Microbiomes. 2019 Dec 20;5(1):37. doi: 10.1038/s41522-019-0110-9.</mixed-citation></citation-alternatives></ref><ref id="cit12"><label>12</label><citation-alternatives><mixed-citation xml:lang="ru">Li X.V., Leonardi I., Iliev ID. Gut Mycobiota in Immunity and Inflammatory Disease. Immunity. 2019 Jun 18;50(6):1365-1379. doi: 10.1016/j.immuni.2019.05.023.</mixed-citation><mixed-citation xml:lang="en">Li X.V., Leonardi I., Iliev ID. Gut Mycobiota in Immunity and Inflammatory Disease. Immunity. 2019 Jun 18;50(6):1365-1379. doi: 10.1016/j.immuni.2019.05.023.</mixed-citation></citation-alternatives></ref><ref id="cit13"><label>13</label><citation-alternatives><mixed-citation xml:lang="ru">Limon J.J., Tang J., Li D. et al. Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models. Cell Host Microbe. 2019 Mar 13;25(3):377-388.e6. doi: 10.1016/j.chom.2019.01.007.</mixed-citation><mixed-citation xml:lang="en">Limon J.J., Tang J., Li D. et al. Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models. Cell Host Microbe. 2019 Mar 13;25(3):377-388.e6. doi: 10.1016/j.chom.2019.01.007.</mixed-citation></citation-alternatives></ref><ref id="cit14"><label>14</label><citation-alternatives><mixed-citation xml:lang="ru">Naglik J.R., Gaffen S. L., Hube B. Candidalysin: discovery and function in Candida albicans infections. Curr Opin Microbiol. 2019 Dec;52:100-109. doi: 10.1016/j.mib.2019.06.002.</mixed-citation><mixed-citation xml:lang="en">Naglik J.R., Gaffen S. L., Hube B. Candidalysin: discovery and function in Candida albicans infections. Curr Opin Microbiol. 2019 Dec;52:100-109. doi: 10.1016/j.mib.2019.06.002.</mixed-citation></citation-alternatives></ref><ref id="cit15"><label>15</label><citation-alternatives><mixed-citation xml:lang="ru">Sokol H., Leducq V., Aschard H., Pham H. P. et al. Fungal microbiota dysbiosis in IBD. Gut. 2017 Jun;66(6):1039-1048. doi: 10.1136/gutjnl-2015-310746.</mixed-citation><mixed-citation xml:lang="en">Sokol H., Leducq V., Aschard H., Pham H. P. et al. Fungal microbiota dysbiosis in IBD. Gut. 2017 Jun;66(6):1039-1048. doi: 10.1136/gutjnl-2015-310746.</mixed-citation></citation-alternatives></ref><ref id="cit16"><label>16</label><citation-alternatives><mixed-citation xml:lang="ru">Qiu X., Ma J., Jiao C., Mao X., Zhao X., Lu M., Wang K., Zhang H. Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Oncotarget. 2017 Nov 20;8(64):107577-107588. doi: 10.18632/oncotarget.22534.</mixed-citation><mixed-citation xml:lang="en">Qiu X., Ma J., Jiao C., Mao X., Zhao X., Lu M., Wang K., Zhang H. Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Oncotarget. 2017 Nov 20;8(64):107577-107588. doi: 10.18632/oncotarget.22534.</mixed-citation></citation-alternatives></ref><ref id="cit17"><label>17</label><citation-alternatives><mixed-citation xml:lang="ru">Li Q., Wang C., Tang C., He Q., Li N., Li J. Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn’s disease. J Clin Gastroenterol. 2014 Jul;48(6):513-23. doi: 10.1097/MCG.0000000000000035.</mixed-citation><mixed-citation xml:lang="en">Li Q., Wang C., Tang C., He Q., Li N., Li J. Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn’s disease. J Clin Gastroenterol. 2014 Jul;48(6):513-23. doi: 10.1097/MCG.0000000000000035.</mixed-citation></citation-alternatives></ref><ref id="cit18"><label>18</label><citation-alternatives><mixed-citation xml:lang="ru">Hoarau G., Mukherjee P. K., Gower-Rousseau C. et al. Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. mBio. 2016 Sep 20;7(5): e01250-16. doi: 10.1128/mBio.01250-16.</mixed-citation><mixed-citation xml:lang="en">Hoarau G., Mukherjee P. K., Gower-Rousseau C. et al. Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. mBio. 2016 Sep 20;7(5): e01250-16. doi: 10.1128/mBio.01250-16.</mixed-citation></citation-alternatives></ref><ref id="cit19"><label>19</label><citation-alternatives><mixed-citation xml:lang="ru">Imai T., Inoue R., Kawada Y., Morita Y., Inatomi O., Nishida A., Bamba S., Kawahara M., Andoh A. Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease. J Gastroenterol. 2019 Feb;54(2):149-159. doi: 10.1007/s00535-018-1530-7.</mixed-citation><mixed-citation xml:lang="en">Imai T., Inoue R., Kawada Y., Morita Y., Inatomi O., Nishida A., Bamba S., Kawahara M., Andoh A. Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease. J Gastroenterol. 2019 Feb;54(2):149-159. doi: 10.1007/s00535-018-1530-7.</mixed-citation></citation-alternatives></ref><ref id="cit20"><label>20</label><citation-alternatives><mixed-citation xml:lang="ru">Liguori G., Lamas B., Richard M. L. et al. Fungal Dysbiosis in Mucosa-associated Microbiota of Crohn’s Disease Patients. J Crohns Colitis. 2016 Mar;10(3):296-305. doi: 10.1093/ecco-jcc/jjv209.</mixed-citation><mixed-citation xml:lang="en">Liguori G., Lamas B., Richard M. L. et al. Fungal Dysbiosis in Mucosa-associated Microbiota of Crohn’s Disease Patients. J Crohns Colitis. 2016 Mar;10(3):296-305. doi: 10.1093/ecco-jcc/jjv209.</mixed-citation></citation-alternatives></ref><ref id="cit21"><label>21</label><citation-alternatives><mixed-citation xml:lang="ru">Shkoporov A.N., Clooney A. G., Sutton T. D.S. et al. The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific. Cell Host Microbe. 2019 Oct 9;26(4):527-541.e5. doi: 10.1016/j.chom.2019.09.009.</mixed-citation><mixed-citation xml:lang="en">Shkoporov A.N., Clooney A. G., Sutton T. D.S. et al. The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific. Cell Host Microbe. 2019 Oct 9;26(4):527-541.e5. doi: 10.1016/j.chom.2019.09.009.</mixed-citation></citation-alternatives></ref><ref id="cit22"><label>22</label><citation-alternatives><mixed-citation xml:lang="ru">Wang W., Jovel J., Halloran B. et al. Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria. Inflamm Bowel Dis. 2015 Jun;21(6):1419-27. doi: 10.1097/MIB.0000000000000344.</mixed-citation><mixed-citation xml:lang="en">Wang W., Jovel J., Halloran B. et al. Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria. Inflamm Bowel Dis. 2015 Jun;21(6):1419-27. doi: 10.1097/MIB.0000000000000344.</mixed-citation></citation-alternatives></ref><ref id="cit23"><label>23</label><citation-alternatives><mixed-citation xml:lang="ru">Norman J.M., Handley S. A., Baldridge M. T. et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015 Jan 29;160(3):447-60. doi: 10.1016/j.cell.2015.01.002.</mixed-citation><mixed-citation xml:lang="en">Norman J.M., Handley S. A., Baldridge M. T. et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015 Jan 29;160(3):447-60. doi: 10.1016/j.cell.2015.01.002.</mixed-citation></citation-alternatives></ref><ref id="cit24"><label>24</label><citation-alternatives><mixed-citation xml:lang="ru">Zuo T., Lu X. J., Zhang Y., Cheung C. P. et al. Gut mucosal virome alterations in ulcerative colitis. Gut. 2019 Jul;68(7):1169-1179. doi: 10.1136/gutjnl-2018-318131.</mixed-citation><mixed-citation xml:lang="en">Zuo T., Lu X. J., Zhang Y., Cheung C. P. et al. Gut mucosal virome alterations in ulcerative colitis. Gut. 2019 Jul;68(7):1169-1179. doi: 10.1136/gutjnl-2018-318131.</mixed-citation></citation-alternatives></ref><ref id="cit25"><label>25</label><citation-alternatives><mixed-citation xml:lang="ru">Clooney A.G., Sutton T. D.S., Shkoporov A. N., Holohan R. K. et al. Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease. Cell Host Microbe. 2019 Dec 11;26(6):764-778.e5. doi: 10.1016/j.chom.2019.10.009.</mixed-citation><mixed-citation xml:lang="en">Clooney A.G., Sutton T. D.S., Shkoporov A. N., Holohan R. K. et al. Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease. Cell Host Microbe. 2019 Dec 11;26(6):764-778.e5. doi: 10.1016/j.chom.2019.10.009.</mixed-citation></citation-alternatives></ref><ref id="cit26"><label>26</label><citation-alternatives><mixed-citation xml:lang="ru">Blais Lecours P., Marsolais D., Cormier Y., Berberi M., Haché C., Bourdages R., Duchaine C. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One. 2014 Feb 3;9(2): e87734. doi: 10.1371/journal.pone.0087734.</mixed-citation><mixed-citation xml:lang="en">Blais Lecours P., Marsolais D., Cormier Y., Berberi M., Haché C., Bourdages R., Duchaine C. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One. 2014 Feb 3;9(2): e87734. doi: 10.1371/journal.pone.0087734.</mixed-citation></citation-alternatives></ref><ref id="cit27"><label>27</label><citation-alternatives><mixed-citation xml:lang="ru">Sitkin S.I., Avalueva E. B., Bakulin I. G., Skalinskaya M. I., Vorobyev S. L., Pavlova E. Yu., Khavkin A. I. The role of bacterial, fungal, and viral infections in the pathogenesis of inflammatory bowel disease. Infekc. bolezni (Infectious Diseases). 2023; 21(2): 64-81. (In Russ.) doi: 10.20953/1729-9225-2023-2-64-81.@@ Ситкин С. И., Авалуева Е. Б., Бакулин И. Г., Скалинская М. И., Воробьёв С. Л., Павлова Е. Ю., Хавкин А. И. Роль бактериальных, грибковых и вирусных инфекций в патогенезе воспалительных заболеваний кишечника. Инфекционные болезни. 2023; 21(2): 64-81. doi: 10.20953/1729-9225-2023-2-64-81.</mixed-citation><mixed-citation xml:lang="en">Sitkin S.I., Avalueva E. B., Bakulin I. G., Skalinskaya M. I., Vorobyev S. L., Pavlova E. Yu., Khavkin A. I. The role of bacterial, fungal, and viral infections in the pathogenesis of inflammatory bowel disease. Infekc. bolezni (Infectious Diseases). 2023; 21(2): 64-81. (In Russ.) doi: 10.20953/1729-9225-2023-2-64-81.@@ Ситкин С. И., Авалуева Е. Б., Бакулин И. Г., Скалинская М. И., Воробьёв С. Л., Павлова Е. Ю., Хавкин А. И. Роль бактериальных, грибковых и вирусных инфекций в патогенезе воспалительных заболеваний кишечника. Инфекционные болезни. 2023; 21(2): 64-81. doi: 10.20953/1729-9225-2023-2-64-81.</mixed-citation></citation-alternatives></ref><ref id="cit28"><label>28</label><citation-alternatives><mixed-citation xml:lang="ru">Römkens T.E., Bulte G. J., Nissen L. H., Drenth J. P. Cytomegalovirus in inflammatory bowel disease: A systematic review. World J Gastroenterol. 2016 Jan 21;22(3):1321-30. doi: 10.3748/wjg.v22.i3.1321.</mixed-citation><mixed-citation xml:lang="en">Römkens T.E., Bulte G. J., Nissen L. H., Drenth J. P. Cytomegalovirus in inflammatory bowel disease: A systematic review. World J Gastroenterol. 2016 Jan 21;22(3):1321-30. doi: 10.3748/wjg.v22.i3.1321.</mixed-citation></citation-alternatives></ref><ref id="cit29"><label>29</label><citation-alternatives><mixed-citation xml:lang="ru">Mourad F.H., Hashash J. G., Kariyawasam V. C., Leong R. W. Ulcerative Colitis and Cytomegalovirus Infection: From A to Z. J Crohns Colitis. 2020 Sep 7;14(8):1162-1171. doi: 10.1093/ecco-jcc/jjaa036.</mixed-citation><mixed-citation xml:lang="en">Mourad F.H., Hashash J. G., Kariyawasam V. C., Leong R. W. Ulcerative Colitis and Cytomegalovirus Infection: From A to Z. J Crohns Colitis. 2020 Sep 7;14(8):1162-1171. doi: 10.1093/ecco-jcc/jjaa036.</mixed-citation></citation-alternatives></ref><ref id="cit30"><label>30</label><citation-alternatives><mixed-citation xml:lang="ru">Axelrad J.E., Cadwell K. H., Colombel J. F., Shah S. C. The role of gastrointestinal pathogens in inflammatory bowel disease: a systematic review. Therap Adv Gastroenterol. 2021 Mar 31;14:17562848211004493. doi: 10.1177/17562848211004493.</mixed-citation><mixed-citation xml:lang="en">Axelrad J.E., Cadwell K. H., Colombel J. F., Shah S. C. The role of gastrointestinal pathogens in inflammatory bowel disease: a systematic review. Therap Adv Gastroenterol. 2021 Mar 31;14:17562848211004493. doi: 10.1177/17562848211004493.</mixed-citation></citation-alternatives></ref><ref id="cit31"><label>31</label><citation-alternatives><mixed-citation xml:lang="ru">Linton M.S., Kroeker K., Fedorak D., Dieleman L., Fedorak R. N. Prevalence of Epstein-Barr Virus in a population of patients with inflammatory bowel disease: a prospective cohort study. Aliment Pharmacol Ther. 2013 Nov;38(10):1248-54. doi: 10.1111/apt.12503.</mixed-citation><mixed-citation xml:lang="en">Linton M.S., Kroeker K., Fedorak D., Dieleman L., Fedorak R. N. Prevalence of Epstein-Barr Virus in a population of patients with inflammatory bowel disease: a prospective cohort study. Aliment Pharmacol Ther. 2013 Nov;38(10):1248-54. doi: 10.1111/apt.12503.</mixed-citation></citation-alternatives></ref><ref id="cit32"><label>32</label><citation-alternatives><mixed-citation xml:lang="ru">Dimitroulia E., Pitiriga V. C., Piperaki E. T., Spanakis N. E., Tsakris A. Inflammatory bowel disease exacerbation associated with Epstein-Barr virus infection. Dis Colon Rectum. 2013 Mar;56(3):322-7. doi: 10.1097/DCR.0b013e31827cd02c.</mixed-citation><mixed-citation xml:lang="en">Dimitroulia E., Pitiriga V. C., Piperaki E. T., Spanakis N. E., Tsakris A. Inflammatory bowel disease exacerbation associated with Epstein-Barr virus infection. Dis Colon Rectum. 2013 Mar;56(3):322-7. doi: 10.1097/DCR.0b013e31827cd02c.</mixed-citation></citation-alternatives></ref><ref id="cit33"><label>33</label><citation-alternatives><mixed-citation xml:lang="ru">Nissen LH, Nagtegaal ID, de Jong DJ, Kievit W, Derikx LA, Groenen PJ, van Krieken JH, Hoentjen F. Epstein-Barr virus in inflammatory bowel disease: the spectrum of intestinal lymphoproliferative disorders. J Crohns Colitis. 2015 May;9(5):398-403. doi: 10.1093/ecco-jcc/jjv040.</mixed-citation><mixed-citation xml:lang="en">Nissen LH, Nagtegaal ID, de Jong DJ, Kievit W, Derikx LA, Groenen PJ, van Krieken JH, Hoentjen F. Epstein-Barr virus in inflammatory bowel disease: the spectrum of intestinal lymphoproliferative disorders. J Crohns Colitis. 2015 May;9(5):398-403. doi: 10.1093/ecco-jcc/jjv040.</mixed-citation></citation-alternatives></ref><ref id="cit34"><label>34</label><citation-alternatives><mixed-citation xml:lang="ru">Wei H.T., Xue X. W., Ling Q., Wang P. Y., Zhou W. X. Positive correlation between latent Epstein-Barr virus infection and severity of illness in inflammatory bowel disease patients. World J Gastrointest Surg. 2023 Mar 27;15(3):420-429. doi: 10.4240/wjgs.v15.i3.420.</mixed-citation><mixed-citation xml:lang="en">Wei H.T., Xue X. W., Ling Q., Wang P. Y., Zhou W. X. Positive correlation between latent Epstein-Barr virus infection and severity of illness in inflammatory bowel disease patients. World J Gastrointest Surg. 2023 Mar 27;15(3):420-429. doi: 10.4240/wjgs.v15.i3.420.</mixed-citation></citation-alternatives></ref><ref id="cit35"><label>35</label><citation-alternatives><mixed-citation xml:lang="ru">Axelrad J.E., Joelson A., Green P. H.R., Lawlor G., Lichtiger S., Cadwell K., Lebwohl B. Enteric Infections Are Common in Patients with Flares of Inflammatory Bowel Disease. Am J Gastroenterol. 2018 Oct;113(10):1530-1539. doi: 10.1038/s41395-018-0211-8.</mixed-citation><mixed-citation xml:lang="en">Axelrad J.E., Joelson A., Green P. H.R., Lawlor G., Lichtiger S., Cadwell K., Lebwohl B. Enteric Infections Are Common in Patients with Flares of Inflammatory Bowel Disease. Am J Gastroenterol. 2018 Oct;113(10):1530-1539. doi: 10.1038/s41395-018-0211-8.</mixed-citation></citation-alternatives></ref><ref id="cit36"><label>36</label><citation-alternatives><mixed-citation xml:lang="ru">Tarris G., de Rougemont A., Estienney M. et al. Specific Norovirus Interaction with Lewis x and Lewis a on Human Intestinal Inflammatory Mucosa during Refractory Inflammatory Bowel Disease. mSphere. 2021 Jan 13;6(1): e01185-20. doi: 10.1128/mSphere.01185-20.</mixed-citation><mixed-citation xml:lang="en">Tarris G., de Rougemont A., Estienney M. et al. Specific Norovirus Interaction with Lewis x and Lewis a on Human Intestinal Inflammatory Mucosa during Refractory Inflammatory Bowel Disease. mSphere. 2021 Jan 13;6(1): e01185-20. doi: 10.1128/mSphere.01185-20.</mixed-citation></citation-alternatives></ref><ref id="cit37"><label>37</label><citation-alternatives><mixed-citation xml:lang="ru">Adiliaghdam F., Amatullah H., Digumarthi S. et al. Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. Sci Immunol. 2022 Apr 8;7(70): eabn6660. doi: 10.1126/sciimmunol.abn6660.</mixed-citation><mixed-citation xml:lang="en">Adiliaghdam F., Amatullah H., Digumarthi S. et al. Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. Sci Immunol. 2022 Apr 8;7(70): eabn6660. doi: 10.1126/sciimmunol.abn6660.</mixed-citation></citation-alternatives></ref><ref id="cit38"><label>38</label><citation-alternatives><mixed-citation xml:lang="ru">Calabrese E., Zorzi F., Monteleone G., Del Vecchio Blanco G. Onset of ulcerative colitis during SARS-CoV-2 infection. Dig Liver Dis. 2020 Nov;52(11):1228-1229. doi: 10.1016/j.dld.2020.06.003.</mixed-citation><mixed-citation xml:lang="en">Calabrese E., Zorzi F., Monteleone G., Del Vecchio Blanco G. Onset of ulcerative colitis during SARS-CoV-2 infection. Dig Liver Dis. 2020 Nov;52(11):1228-1229. doi: 10.1016/j.dld.2020.06.003.</mixed-citation></citation-alternatives></ref><ref id="cit39"><label>39</label><citation-alternatives><mixed-citation xml:lang="ru">Taxonera C., Fisac J., Alba C. Can COVID-19 Trigger De Novo Inflammatory Bowel Disease? Gastroenterology. 2021 Mar;160(4):1029-1030. doi: 10.1053/j.gastro.2020.11.026.</mixed-citation><mixed-citation xml:lang="en">Taxonera C., Fisac J., Alba C. Can COVID-19 Trigger De Novo Inflammatory Bowel Disease? Gastroenterology. 2021 Mar;160(4):1029-1030. doi: 10.1053/j.gastro.2020.11.026.</mixed-citation></citation-alternatives></ref><ref id="cit40"><label>40</label><citation-alternatives><mixed-citation xml:lang="ru">Imperatore N., Bennato R., D’Avino A., Lombardi G., Manguso F. SARS-CoV-2 as a Trigger for De Novo Ulcerative Colitis. Inflamm Bowel Dis. 2021 Jun 15;27(7): e87-e88. doi: 10.1093/ibd/izab040.</mixed-citation><mixed-citation xml:lang="en">Imperatore N., Bennato R., D’Avino A., Lombardi G., Manguso F. SARS-CoV-2 as a Trigger for De Novo Ulcerative Colitis. Inflamm Bowel Dis. 2021 Jun 15;27(7): e87-e88. doi: 10.1093/ibd/izab040.</mixed-citation></citation-alternatives></ref><ref id="cit41"><label>41</label><citation-alternatives><mixed-citation xml:lang="ru">Tursi A., Nenna R. COVID-19 as a Trigger for De Novo Crohn’s Disease. Inflamm Bowel Dis. 2022 Jun 3;28(6): e76-e77. doi: 10.1093/ibd/izab298.</mixed-citation><mixed-citation xml:lang="en">Tursi A., Nenna R. COVID-19 as a Trigger for De Novo Crohn’s Disease. Inflamm Bowel Dis. 2022 Jun 3;28(6): e76-e77. doi: 10.1093/ibd/izab298.</mixed-citation></citation-alternatives></ref><ref id="cit42"><label>42</label><citation-alternatives><mixed-citation xml:lang="ru">Preziosi N.A., Rizvi A. H., Feerick J. D., Mandelia C. De Novo Pediatric Ulcerative Colitis Triggered by SARS-CoV-2 Infection: a Tale of 2 Sisters. Inflamm Bowel Dis. 2022 Oct 3;28(10):1623-1625. doi: 10.1093/ibd/izac142.</mixed-citation><mixed-citation xml:lang="en">Preziosi N.A., Rizvi A. H., Feerick J. D., Mandelia C. De Novo Pediatric Ulcerative Colitis Triggered by SARS-CoV-2 Infection: a Tale of 2 Sisters. Inflamm Bowel Dis. 2022 Oct 3;28(10):1623-1625. doi: 10.1093/ibd/izac142.</mixed-citation></citation-alternatives></ref><ref id="cit43"><label>43</label><citation-alternatives><mixed-citation xml:lang="ru">Morita A., Imagawa K., Tagawa M., Sakamoto N., Takada H. Case report: Immunological characteristics of de novo ulcerative colitis in a child post COVID-19. Front Immunol. 2023 Feb 16;14:1107808. doi: 10.3389/fimmu.2023.1107808.</mixed-citation><mixed-citation xml:lang="en">Morita A., Imagawa K., Tagawa M., Sakamoto N., Takada H. Case report: Immunological characteristics of de novo ulcerative colitis in a child post COVID-19. Front Immunol. 2023 Feb 16;14:1107808. doi: 10.3389/fimmu.2023.1107808.</mixed-citation></citation-alternatives></ref><ref id="cit44"><label>44</label><citation-alternatives><mixed-citation xml:lang="ru">Sweeny K.F., Zhang Y. J., Crume B., Martz C. A., Blessing M. M., Kahn S. A. Inflammatory Bowel Disease Presenting With Concurrent COVID-19 Multisystem Inflammatory Syndrome. Pediatrics. 2021 Apr;147(4): e2020027763. doi: 10.1542/peds.2020-027763.</mixed-citation><mixed-citation xml:lang="en">Sweeny K.F., Zhang Y. J., Crume B., Martz C. A., Blessing M. M., Kahn S. A. Inflammatory Bowel Disease Presenting With Concurrent COVID-19 Multisystem Inflammatory Syndrome. Pediatrics. 2021 Apr;147(4): e2020027763. doi: 10.1542/peds.2020-027763.</mixed-citation></citation-alternatives></ref><ref id="cit45"><label>45</label><citation-alternatives><mixed-citation xml:lang="ru">Krawiec P., Opoka-Winiarska V., Pac-Kożuchowska E. Is It Inflammatory Bowel Disease Flare or Pediatric Inflammatory Multisystem Syndrome Temporally Associated with COVID-19? J Clin Med. 2022 May 13;11(10):2765. doi: 10.3390/jcm11102765.</mixed-citation><mixed-citation xml:lang="en">Krawiec P., Opoka-Winiarska V., Pac-Kożuchowska E. Is It Inflammatory Bowel Disease Flare or Pediatric Inflammatory Multisystem Syndrome Temporally Associated with COVID-19? J Clin Med. 2022 May 13;11(10):2765. doi: 10.3390/jcm11102765.</mixed-citation></citation-alternatives></ref><ref id="cit46"><label>46</label><citation-alternatives><mixed-citation xml:lang="ru">Dvornikova K.A., Bystrova E. Y., Churilov L. P., Lerner A. Pathogenesis of the inflammatory bowel disease in context of SARS-COV-2 infection. Mol Biol Rep. 2021 Jul;48(7):5745-5758. doi: 10.1007/s11033-021-06565-w.</mixed-citation><mixed-citation xml:lang="en">Dvornikova K.A., Bystrova E. Y., Churilov L. P., Lerner A. Pathogenesis of the inflammatory bowel disease in context of SARS-COV-2 infection. Mol Biol Rep. 2021 Jul;48(7):5745-5758. doi: 10.1007/s11033-021-06565-w.</mixed-citation></citation-alternatives></ref><ref id="cit47"><label>47</label><citation-alternatives><mixed-citation xml:lang="ru">Zhao C., Zhao W. NLRP3 Inflammasome-A Key Player in Antiviral Responses. Front Immunol. 2020 Feb 18;11:211. doi: 10.3389/fimmu.2020.00211.</mixed-citation><mixed-citation xml:lang="en">Zhao C., Zhao W. NLRP3 Inflammasome-A Key Player in Antiviral Responses. Front Immunol. 2020 Feb 18;11:211. doi: 10.3389/fimmu.2020.00211.</mixed-citation></citation-alternatives></ref><ref id="cit48"><label>48</label><citation-alternatives><mixed-citation xml:lang="ru">Lin L., Jiang X., Zhang Z. et al. Gastrointestinal symptoms of 95 cases with SARS-CoV-2 infection. Gut. 2020 Jun;69(6):997-1001. doi: 10.1136/gutjnl-2020-321013.</mixed-citation><mixed-citation xml:lang="en">Lin L., Jiang X., Zhang Z. et al. Gastrointestinal symptoms of 95 cases with SARS-CoV-2 infection. Gut. 2020 Jun;69(6):997-1001. doi: 10.1136/gutjnl-2020-321013.</mixed-citation></citation-alternatives></ref><ref id="cit49"><label>49</label><citation-alternatives><mixed-citation xml:lang="ru">Buscarini E., Manfredi G., Brambilla G. et al. GI symptoms as early signs of COVID-19 in hospitalised Italian patients. Gut. 2020 Aug;69(8):1547-1548. doi: 10.1136/gutjnl-2020-321434.</mixed-citation><mixed-citation xml:lang="en">Buscarini E., Manfredi G., Brambilla G. et al. GI symptoms as early signs of COVID-19 in hospitalised Italian patients. Gut. 2020 Aug;69(8):1547-1548. doi: 10.1136/gutjnl-2020-321434.</mixed-citation></citation-alternatives></ref><ref id="cit50"><label>50</label><citation-alternatives><mixed-citation xml:lang="ru">Massimino L., Palmieri O., Facoetti A. et al. Gut virome-colonising Orthohepadnavirus genus is associated with ulcerative colitis pathogenesis and induces intestinal inflammation in vivo. Gut. 2023 Oct;72(10):1838-1847. doi: 10.1136/gutjnl-2022-328375.</mixed-citation><mixed-citation xml:lang="en">Massimino L., Palmieri O., Facoetti A. et al. Gut virome-colonising Orthohepadnavirus genus is associated with ulcerative colitis pathogenesis and induces intestinal inflammation in vivo. Gut. 2023 Oct;72(10):1838-1847. doi: 10.1136/gutjnl-2022-328375.</mixed-citation></citation-alternatives></ref><ref id="cit51"><label>51</label><citation-alternatives><mixed-citation xml:lang="ru">Ghavami S.B., Rostami E., Sephay A. A., Shahrokh S., Balaii H., Aghdaei H. A., Zali M. R. Alterations of the human gut Methanobrevibacter smithii as a biomarker for inflammatory bowel diseases. Microb Pathog. 2018 Apr;117:285-289. doi: 10.1016/j.micpath.2018.01.029.</mixed-citation><mixed-citation xml:lang="en">Ghavami S.B., Rostami E., Sephay A. A., Shahrokh S., Balaii H., Aghdaei H. A., Zali M. R. Alterations of the human gut Methanobrevibacter smithii as a biomarker for inflammatory bowel diseases. Microb Pathog. 2018 Apr;117:285-289. doi: 10.1016/j.micpath.2018.01.029.</mixed-citation></citation-alternatives></ref><ref id="cit52"><label>52</label><citation-alternatives><mixed-citation xml:lang="ru">Tong M., Li X., Wegener Parfrey L. et al. A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One. 2013 Nov 19;8(11): e80702. doi: 10.1371/journal.pone.0080702.</mixed-citation><mixed-citation xml:lang="en">Tong M., Li X., Wegener Parfrey L. et al. A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One. 2013 Nov 19;8(11): e80702. doi: 10.1371/journal.pone.0080702.</mixed-citation></citation-alternatives></ref><ref id="cit53"><label>53</label><citation-alternatives><mixed-citation xml:lang="ru">Vester-Andersen M.K., Mirsepasi-Lauridsen H.C., Prosberg M. V. et al. Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis. Sci Rep. 2019 Sep 17;9(1):13473. doi: 10.1038/s41598-019-49833-3.</mixed-citation><mixed-citation xml:lang="en">Vester-Andersen M.K., Mirsepasi-Lauridsen H.C., Prosberg M. V. et al. Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis. Sci Rep. 2019 Sep 17;9(1):13473. doi: 10.1038/s41598-019-49833-3.</mixed-citation></citation-alternatives></ref><ref id="cit54"><label>54</label><citation-alternatives><mixed-citation xml:lang="ru">Braun T., Di Segni A., BenShoshan M. et al. Individualized Dynamics in the Gut Microbiota Precede Crohn’s Disease Flares. Am J Gastroenterol. 2019 Jul;114(7):1142-1151. doi: 10.14309/ajg.0000000000000136.</mixed-citation><mixed-citation xml:lang="en">Braun T., Di Segni A., BenShoshan M. et al. Individualized Dynamics in the Gut Microbiota Precede Crohn’s Disease Flares. Am J Gastroenterol. 2019 Jul;114(7):1142-1151. doi: 10.14309/ajg.0000000000000136.</mixed-citation></citation-alternatives></ref><ref id="cit55"><label>55</label><citation-alternatives><mixed-citation xml:lang="ru">Sun M., Du B., Shi Y., Lu Y., Zhou Y., Liu B.Combined Signature of the Fecal Microbiome and Plasma Metabolome in Patients with Ulcerative Colitis. Med Sci Monit. 2019 May 5;25:3303-3315. doi: 10.12659/MSM.916009.</mixed-citation><mixed-citation xml:lang="en">Sun M., Du B., Shi Y., Lu Y., Zhou Y., Liu B.Combined Signature of the Fecal Microbiome and Plasma Metabolome in Patients with Ulcerative Colitis. Med Sci Monit. 2019 May 5;25:3303-3315. doi: 10.12659/MSM.916009.</mixed-citation></citation-alternatives></ref><ref id="cit56"><label>56</label><citation-alternatives><mixed-citation xml:lang="ru">Park S.K., Kim H. N., Choi C. H., Im J. P. et al. Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn’s Disease: Results from the IMPACT Study. J Clin Med. 2020 Jun 5;9(6):1748. doi: 10.3390/jcm9061748.</mixed-citation><mixed-citation xml:lang="en">Park S.K., Kim H. N., Choi C. H., Im J. P. et al. Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn’s Disease: Results from the IMPACT Study. J Clin Med. 2020 Jun 5;9(6):1748. doi: 10.3390/jcm9061748.</mixed-citation></citation-alternatives></ref><ref id="cit57"><label>57</label><citation-alternatives><mixed-citation xml:lang="ru">Zhang J., Chen S. L., Li L. B. Correlation between intestinal flora and serum inflammatory factors in patients with Crohn’s disease. Eur Rev Med Pharmacol Sci. 2017 Nov;21(21):4913-4917. PMID: 29164569.</mixed-citation><mixed-citation xml:lang="en">Zhang J., Chen S. L., Li L. B. Correlation between intestinal flora and serum inflammatory factors in patients with Crohn’s disease. Eur Rev Med Pharmacol Sci. 2017 Nov;21(21):4913-4917. PMID: 29164569.</mixed-citation></citation-alternatives></ref><ref id="cit58"><label>58</label><citation-alternatives><mixed-citation xml:lang="ru">Wang W., Chen L., Zhou R., Wang X., Song L., Huang S., Wang G., Xia B. Increased proportions of Bifidobacterium and the Lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease. J Clin Microbiol. 2014 Feb;52(2):398-406. doi: 10.1128/JCM.01500-13.</mixed-citation><mixed-citation xml:lang="en">Wang W., Chen L., Zhou R., Wang X., Song L., Huang S., Wang G., Xia B. Increased proportions of Bifidobacterium and the Lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease. J Clin Microbiol. 2014 Feb;52(2):398-406. doi: 10.1128/JCM.01500-13.</mixed-citation></citation-alternatives></ref><ref id="cit59"><label>59</label><citation-alternatives><mixed-citation xml:lang="ru">Galazzo G., Tedjo D. I., Wintjens D. S.J. et al. Faecal Microbiota Dynamics and their Relation to Disease Course in Crohn’s Disease. J Crohns Colitis. 2019 Sep 27;13(10):1273-1282. doi: 10.1093/ecco-jcc/jjz049.</mixed-citation><mixed-citation xml:lang="en">Galazzo G., Tedjo D. I., Wintjens D. S.J. et al. Faecal Microbiota Dynamics and their Relation to Disease Course in Crohn’s Disease. J Crohns Colitis. 2019 Sep 27;13(10):1273-1282. doi: 10.1093/ecco-jcc/jjz049.</mixed-citation></citation-alternatives></ref><ref id="cit60"><label>60</label><citation-alternatives><mixed-citation xml:lang="ru">Boland K., Bedrani L., Turpin W., Kabakchiev B. et al. Persistent Diarrhea in Patients With Crohn’s Disease After Mucosal Healing Is Associated With Lower Diversity of the Intestinal Microbiome and Increased Dysbiosis. Clin Gastroenterol Hepatol. 2021 Feb;19(2):296-304.e3. doi: 10.1016/j.cgh.2020.03.044.</mixed-citation><mixed-citation xml:lang="en">Boland K., Bedrani L., Turpin W., Kabakchiev B. et al. Persistent Diarrhea in Patients With Crohn’s Disease After Mucosal Healing Is Associated With Lower Diversity of the Intestinal Microbiome and Increased Dysbiosis. Clin Gastroenterol Hepatol. 2021 Feb;19(2):296-304.e3. doi: 10.1016/j.cgh.2020.03.044.</mixed-citation></citation-alternatives></ref><ref id="cit61"><label>61</label><citation-alternatives><mixed-citation xml:lang="ru">Borren N.Z., Plichta D., Joshi A. D., Bonilla G., Sadreyev R., Vlamakis H., Xavier R. J., Ananthakrishnan A. N. Multi-”-Omics” Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse. Inflamm Bowel Dis. 2020 Sep 18;26(10):1524-1532. doi: 10.1093/ibd/izaa183.</mixed-citation><mixed-citation xml:lang="en">Borren N.Z., Plichta D., Joshi A. D., Bonilla G., Sadreyev R., Vlamakis H., Xavier R. J., Ananthakrishnan A. N. Multi-”-Omics” Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse. Inflamm Bowel Dis. 2020 Sep 18;26(10):1524-1532. doi: 10.1093/ibd/izaa183.</mixed-citation></citation-alternatives></ref><ref id="cit62"><label>62</label><citation-alternatives><mixed-citation xml:lang="ru">Tedjo D.I., Smolinska A., Savelkoul P. H., Masclee A. A., van Schooten F. J., Pierik M. J., Penders J., Jonkers D. M. The fecal microbiota as a biomarker for disease activity in Crohn’s disease. Sci Rep. 2016 Oct 13;6:35216. doi: 10.1038/srep35216.</mixed-citation><mixed-citation xml:lang="en">Tedjo D.I., Smolinska A., Savelkoul P. H., Masclee A. A., van Schooten F. J., Pierik M. J., Penders J., Jonkers D. M. The fecal microbiota as a biomarker for disease activity in Crohn’s disease. Sci Rep. 2016 Oct 13;6:35216. doi: 10.1038/srep35216.</mixed-citation></citation-alternatives></ref><ref id="cit63"><label>63</label><citation-alternatives><mixed-citation xml:lang="ru">Pascal V., Pozuelo M., Borruel N. et al. A microbial signature for Crohn’s disease. Gut. 2017 May;66(5):813-822. doi: 10.1136/gutjnl-2016-313235.</mixed-citation><mixed-citation xml:lang="en">Pascal V., Pozuelo M., Borruel N. et al. A microbial signature for Crohn’s disease. Gut. 2017 May;66(5):813-822. doi: 10.1136/gutjnl-2016-313235.</mixed-citation></citation-alternatives></ref><ref id="cit64"><label>64</label><citation-alternatives><mixed-citation xml:lang="ru">Rehman A., Rausch P., Wang J. et al. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut. 2016 Feb;65(2):238-48. doi: 10.1136/gutjnl-2014-308341.</mixed-citation><mixed-citation xml:lang="en">Rehman A., Rausch P., Wang J. et al. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut. 2016 Feb;65(2):238-48. doi: 10.1136/gutjnl-2014-308341.</mixed-citation></citation-alternatives></ref><ref id="cit65"><label>65</label><citation-alternatives><mixed-citation xml:lang="ru">Wisittipanit N., Rangwala H., Sikaroodi M., Keshavarzian A., Mutlu E. A., Gillevet P. Classification methods for the analysis of LH-PCR data associated with inflammatory bowel disease patients.Int J Bioinform Res Appl. 2015;11(2):111-29. doi: 10.1504/IJBRA.2015.068087.</mixed-citation><mixed-citation xml:lang="en">Wisittipanit N., Rangwala H., Sikaroodi M., Keshavarzian A., Mutlu E. A., Gillevet P. Classification methods for the analysis of LH-PCR data associated with inflammatory bowel disease patients.Int J Bioinform Res Appl. 2015;11(2):111-29. doi: 10.1504/IJBRA.2015.068087.</mixed-citation></citation-alternatives></ref><ref id="cit66"><label>66</label><citation-alternatives><mixed-citation xml:lang="ru">Lloyd-Price J., Arze C., Ananthakrishnan A. N., Schirmer M., Avila-Pacheco J., Poon T. W., Andrews E., Ajami N. J., Bonham K. S., Brislawn C. J., Casero D., Courtney H., Gonzalez A., Graeber T. G., Hall A. B., Lake K., Landers C. J., Mallick H., Plichta D. R., Prasad M., Rahnavard G., Sauk J., Shungin D., Vázquez-Baeza Y., White RA 3rd.; IBDMDB Investigators; Braun J., Denson L. A., Jansson J. K., Knight R., Kugathasan S., McGovern D.P.B., Petrosino J. F., Stappenbeck T. S., Winter H. S., Clish C. B., Franzosa E. A., Vlamakis H., Xavier R. J., Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 May;569(7758):655-662. doi: 10.1038/s41586-019-1237-9.</mixed-citation><mixed-citation xml:lang="en">Lloyd-Price J., Arze C., Ananthakrishnan A. N., Schirmer M., Avila-Pacheco J., Poon T. W., Andrews E., Ajami N. J., Bonham K. S., Brislawn C. J., Casero D., Courtney H., Gonzalez A., Graeber T. G., Hall A. B., Lake K., Landers C. J., Mallick H., Plichta D. R., Prasad M., Rahnavard G., Sauk J., Shungin D., Vázquez-Baeza Y., White RA 3rd.; IBDMDB Investigators; Braun J., Denson L. A., Jansson J. K., Knight R., Kugathasan S., McGovern D.P.B., Petrosino J. F., Stappenbeck T. S., Winter H. S., Clish C. B., Franzosa E. A., Vlamakis H., Xavier R. J., Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 May;569(7758):655-662. doi: 10.1038/s41586-019-1237-9.</mixed-citation></citation-alternatives></ref><ref id="cit67"><label>67</label><citation-alternatives><mixed-citation xml:lang="ru">Butera A., Di Paola M., Vitali F., De Nitto D. et al. IL-13 mRNA Tissue Content Identifies Two Subsets of Adult Ulcerative Colitis Patients With Different Clinical and Mucosa-Associated Microbiota Profiles. J Crohns Colitis. 2020 Mar 13;14(3):369-380. doi: 10.1093/ecco-jcc/jjz154.</mixed-citation><mixed-citation xml:lang="en">Butera A., Di Paola M., Vitali F., De Nitto D. et al. IL-13 mRNA Tissue Content Identifies Two Subsets of Adult Ulcerative Colitis Patients With Different Clinical and Mucosa-Associated Microbiota Profiles. J Crohns Colitis. 2020 Mar 13;14(3):369-380. doi: 10.1093/ecco-jcc/jjz154.</mixed-citation></citation-alternatives></ref><ref id="cit68"><label>68</label><citation-alternatives><mixed-citation xml:lang="ru">Rubbens P., Props R., Kerckhof F. M., Boon N., Waegeman W. Cytometric fingerprints of gut microbiota predict Crohn’s disease state. ISME J. 2021 Jan;15(1):354-358. doi: 10.1038/s41396-020-00762-4.</mixed-citation><mixed-citation xml:lang="en">Rubbens P., Props R., Kerckhof F. M., Boon N., Waegeman W. Cytometric fingerprints of gut microbiota predict Crohn’s disease state. ISME J. 2021 Jan;15(1):354-358. doi: 10.1038/s41396-020-00762-4.</mixed-citation></citation-alternatives></ref><ref id="cit69"><label>69</label><citation-alternatives><mixed-citation xml:lang="ru">Xun Z., Zhang Q., Xu T., Chen N., Chen F. Dysbiosis and Ecotypes of the Salivary Microbiome Associated With Inflammatory Bowel Diseases and the Assistance in Diagnosis of Diseases Using Oral Bacterial Profiles. Front Microbiol. 2018 May 30;9:1136. doi: 10.3389/fmicb.2018.01136.</mixed-citation><mixed-citation xml:lang="en">Xun Z., Zhang Q., Xu T., Chen N., Chen F. Dysbiosis and Ecotypes of the Salivary Microbiome Associated With Inflammatory Bowel Diseases and the Assistance in Diagnosis of Diseases Using Oral Bacterial Profiles. Front Microbiol. 2018 May 30;9:1136. doi: 10.3389/fmicb.2018.01136.</mixed-citation></citation-alternatives></ref><ref id="cit70"><label>70</label><citation-alternatives><mixed-citation xml:lang="ru">Said H.S., Suda W., Nakagome S. et al. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res. 2014 Feb;21(1):15-25. doi: 10.1093/dnares/dst037.</mixed-citation><mixed-citation xml:lang="en">Said H.S., Suda W., Nakagome S. et al. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res. 2014 Feb;21(1):15-25. doi: 10.1093/dnares/dst037.</mixed-citation></citation-alternatives></ref><ref id="cit71"><label>71</label><citation-alternatives><mixed-citation xml:lang="ru">Qi Y., Zang S. Q., Wei J., Yu H. C., Yang Z., Wu H. M., Kang Y., Tao H., Yang M. F., Jin L., Zen K., Wang F. Y. High-throughput sequencing provides insights into oral microbiota dysbiosis in association with inflammatory bowel disease. Genomics. 2021 Jan;113(1 Pt 2):664-676. doi: 10.1016/j.ygeno.2020.09.063.</mixed-citation><mixed-citation xml:lang="en">Qi Y., Zang S. Q., Wei J., Yu H. C., Yang Z., Wu H. M., Kang Y., Tao H., Yang M. F., Jin L., Zen K., Wang F. Y. High-throughput sequencing provides insights into oral microbiota dysbiosis in association with inflammatory bowel disease. Genomics. 2021 Jan;113(1 Pt 2):664-676. doi: 10.1016/j.ygeno.2020.09.063.</mixed-citation></citation-alternatives></ref><ref id="cit72"><label>72</label><citation-alternatives><mixed-citation xml:lang="ru">Zhang T., Kayani M. U.R., Hong L., Zhang C., Zhong J., Wang Z., Chen L. Dynamics of the Salivary Microbiome During Different Phases of Crohn’s Disease. Front Cell Infect Microbiol. 2020 Oct 6;10:544704. doi: 10.3389/fcimb.2020.544704.</mixed-citation><mixed-citation xml:lang="en">Zhang T., Kayani M. U.R., Hong L., Zhang C., Zhong J., Wang Z., Chen L. Dynamics of the Salivary Microbiome During Different Phases of Crohn’s Disease. Front Cell Infect Microbiol. 2020 Oct 6;10:544704. doi: 10.3389/fcimb.2020.544704.</mixed-citation></citation-alternatives></ref><ref id="cit73"><label>73</label><citation-alternatives><mixed-citation xml:lang="ru">Gevers D., Kugathasan S., Denson L. A. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014 Mar 12;15(3):382-392. doi: 10.1016/j.chom.2014.02.005.</mixed-citation><mixed-citation xml:lang="en">Gevers D., Kugathasan S., Denson L. A. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014 Mar 12;15(3):382-392. doi: 10.1016/j.chom.2014.02.005.</mixed-citation></citation-alternatives></ref><ref id="cit74"><label>74</label><citation-alternatives><mixed-citation xml:lang="ru">Molinero N., Taladrid D., Zorraquín-Peña I., de Celis M., Belda I., Mira A., Bartolomé B., Moreno-Arribas M. V. Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis. Curr Issues Mol Biol. 2022 Mar 30;44(4):1513-1527. doi: 10.3390/cimb44040103.</mixed-citation><mixed-citation xml:lang="en">Molinero N., Taladrid D., Zorraquín-Peña I., de Celis M., Belda I., Mira A., Bartolomé B., Moreno-Arribas M. V. Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis. Curr Issues Mol Biol. 2022 Mar 30;44(4):1513-1527. doi: 10.3390/cimb44040103.</mixed-citation></citation-alternatives></ref><ref id="cit75"><label>75</label><citation-alternatives><mixed-citation xml:lang="ru">Abdullah N., Al-Marzooq F., Mohamad S., Abd Rahman N., Chi Ngo H., Perera Samaranayake L.Intraoral appliances for in situ oral biofilm growth: a systematic review. J Oral Microbiol. 2019 Aug 6;11(1):1647757. doi: 10.1080/20002297.2019.1647757.</mixed-citation><mixed-citation xml:lang="en">Abdullah N., Al-Marzooq F., Mohamad S., Abd Rahman N., Chi Ngo H., Perera Samaranayake L.Intraoral appliances for in situ oral biofilm growth: a systematic review. J Oral Microbiol. 2019 Aug 6;11(1):1647757. doi: 10.1080/20002297.2019.1647757.</mixed-citation></citation-alternatives></ref><ref id="cit76"><label>76</label><citation-alternatives><mixed-citation xml:lang="ru">Elmaghrawy K., Hussey S., Moran G. P. The Oral Microbiome in Pediatric IBD: A Source of Pathobionts or Biomarkers? Front Pediatr. 2021 Jan 21;8:620254. doi: 10.3389/fped.2020.620254.</mixed-citation><mixed-citation xml:lang="en">Elmaghrawy K., Hussey S., Moran G. P. The Oral Microbiome in Pediatric IBD: A Source of Pathobionts or Biomarkers? Front Pediatr. 2021 Jan 21;8:620254. doi: 10.3389/fped.2020.620254.</mixed-citation></citation-alternatives></ref><ref id="cit77"><label>77</label><citation-alternatives><mixed-citation xml:lang="ru">Read E., Curtis M. A., Neves J. F. The role of oral bacteria in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol. 2021 Oct;18(10):731-742. doi: 10.1038/s41575-021-00488-4.</mixed-citation><mixed-citation xml:lang="en">Read E., Curtis M. A., Neves J. F. The role of oral bacteria in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol. 2021 Oct;18(10):731-742. doi: 10.1038/s41575-021-00488-4.</mixed-citation></citation-alternatives></ref><ref id="cit78"><label>78</label><citation-alternatives><mixed-citation xml:lang="ru">Cecoro G., Annunziata M., Iuorio M. T., Nastri L., Guida L. Periodontitis, Low-Grade Inflammation and Systemic Health: A Scoping Review. Medicina (Kaunas). 2020 May 30;56(6):272. doi: 10.3390/medicina56060272.</mixed-citation><mixed-citation xml:lang="en">Cecoro G., Annunziata M., Iuorio M. T., Nastri L., Guida L. Periodontitis, Low-Grade Inflammation and Systemic Health: A Scoping Review. Medicina (Kaunas). 2020 May 30;56(6):272. doi: 10.3390/medicina56060272.</mixed-citation></citation-alternatives></ref><ref id="cit79"><label>79</label><citation-alternatives><mixed-citation xml:lang="ru">Kitamoto S., Nagao-Kitamoto H., Jiao Y. et al. The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis. Cell. 2020 Jul 23;182(2):447-462.e14. doi: 10.1016/j.cell.2020.05.048.</mixed-citation><mixed-citation xml:lang="en">Kitamoto S., Nagao-Kitamoto H., Jiao Y. et al. The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis. Cell. 2020 Jul 23;182(2):447-462.e14. doi: 10.1016/j.cell.2020.05.048.</mixed-citation></citation-alternatives></ref><ref id="cit80"><label>80</label><citation-alternatives><mixed-citation xml:lang="ru">Atarashi K., Suda W., Luo C. et al. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science. 2017 Oct 20;358(6361):359-365. doi: 10.1126/science.aan4526.</mixed-citation><mixed-citation xml:lang="en">Atarashi K., Suda W., Luo C. et al. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science. 2017 Oct 20;358(6361):359-365. doi: 10.1126/science.aan4526.</mixed-citation></citation-alternatives></ref><ref id="cit81"><label>81</label><citation-alternatives><mixed-citation xml:lang="ru">Al-Rawi N., Al-Marzooq F. The Relation between Periodontopathogenic Bacterial Levels and Resistin in the Saliva of Obese Type 2 Diabetic Patients. J Diabetes Res. 2017;2017:2643079. doi: 10.1155/2017/2643079.</mixed-citation><mixed-citation xml:lang="en">Al-Rawi N., Al-Marzooq F. The Relation between Periodontopathogenic Bacterial Levels and Resistin in the Saliva of Obese Type 2 Diabetic Patients. J Diabetes Res. 2017;2017:2643079. doi: 10.1155/2017/2643079.</mixed-citation></citation-alternatives></ref><ref id="cit82"><label>82</label><citation-alternatives><mixed-citation xml:lang="ru">Al-Rawi N.H., Al-Marzooq F., Al-Nuaimi A.S., Hachim M. Y., Hamoudi R. Salivary microRNA 155, 146a/b and 203: A pilot study for potentially non-invasive diagnostic biomarkers of periodontitis and diabetes mellitus. PLoS One. 2020 Aug 5;15(8): e0237004. doi: 10.1371/journal.pone.0237004.</mixed-citation><mixed-citation xml:lang="en">Al-Rawi N.H., Al-Marzooq F., Al-Nuaimi A.S., Hachim M. Y., Hamoudi R. Salivary microRNA 155, 146a/b and 203: A pilot study for potentially non-invasive diagnostic biomarkers of periodontitis and diabetes mellitus. PLoS One. 2020 Aug 5;15(8): e0237004. doi: 10.1371/journal.pone.0237004.</mixed-citation></citation-alternatives></ref><ref id="cit83"><label>83</label><citation-alternatives><mixed-citation xml:lang="ru">van der Sloot K. W.J., Voskuil M. D., Blokzijl T., Dinkla A. et al. Isotype-specific Antibody Responses to Mycobacterium avium paratuberculosis Antigens Are Associated With the Use of Biologic Therapy in Inflammatory Bowel Disease. J Crohns Colitis. 2021 Aug 2;15(8):1253-1263. doi: 10.1093/ecco-jcc/jjaa263.</mixed-citation><mixed-citation xml:lang="en">van der Sloot K. W.J., Voskuil M. D., Blokzijl T., Dinkla A. et al. Isotype-specific Antibody Responses to Mycobacterium avium paratuberculosis Antigens Are Associated With the Use of Biologic Therapy in Inflammatory Bowel Disease. J Crohns Colitis. 2021 Aug 2;15(8):1253-1263. doi: 10.1093/ecco-jcc/jjaa263.</mixed-citation></citation-alternatives></ref><ref id="cit84"><label>84</label><citation-alternatives><mixed-citation xml:lang="ru">Fernandes J., Su W., Rahat-Rozenbloom S., Wolever T. M., Comelli E. M. Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans. Nutr Diabetes. 2014 Jun 30;4(6): e121. doi: 10.1038/nutd.2014.23.</mixed-citation><mixed-citation xml:lang="en">Fernandes J., Su W., Rahat-Rozenbloom S., Wolever T. M., Comelli E. M. Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans. Nutr Diabetes. 2014 Jun 30;4(6): e121. doi: 10.1038/nutd.2014.23.</mixed-citation></citation-alternatives></ref><ref id="cit85"><label>85</label><citation-alternatives><mixed-citation xml:lang="ru">Khatib M. The Impact of Food Structure and Promoting Short Chain Fatty Acids Production on Energy Home-ostasis and Appetite Regulation. London. Imperial College. 2019.</mixed-citation><mixed-citation xml:lang="en">Khatib M. The Impact of Food Structure and Promoting Short Chain Fatty Acids Production on Energy Home-ostasis and Appetite Regulation. London. Imperial College. 2019.</mixed-citation></citation-alternatives></ref><ref id="cit86"><label>86</label><citation-alternatives><mixed-citation xml:lang="ru">Deleu S., Machiels K., Raes J., Verbeke K., Vermeire S. Short chain fatty acids and its producing organisms: An overlooked therapy for IBD? EBioMedicine. 2021 Apr;66:103293. doi: 10.1016/j.ebiom.2021.103293.</mixed-citation><mixed-citation xml:lang="en">Deleu S., Machiels K., Raes J., Verbeke K., Vermeire S. Short chain fatty acids and its producing organisms: An overlooked therapy for IBD? EBioMedicine. 2021 Apr;66:103293. doi: 10.1016/j.ebiom.2021.103293.</mixed-citation></citation-alternatives></ref><ref id="cit87"><label>87</label><citation-alternatives><mixed-citation xml:lang="ru">Huda-Faujan N., Abdulamir A. S., Fatimah A. B., Anas O. M., Shuhaimi M., Yazid A. M., Loong Y. Y. The impact of the level of the intestinal short chain Fatty acids in inflammatory bowel disease patients versus healthy subjects. Open Biochem J. 2010 May 13;4:53-8. doi: 10.2174/1874091X01004010053.</mixed-citation><mixed-citation xml:lang="en">Huda-Faujan N., Abdulamir A. S., Fatimah A. B., Anas O. M., Shuhaimi M., Yazid A. M., Loong Y. Y. The impact of the level of the intestinal short chain Fatty acids in inflammatory bowel disease patients versus healthy subjects. Open Biochem J. 2010 May 13;4:53-8. doi: 10.2174/1874091X01004010053.</mixed-citation></citation-alternatives></ref><ref id="cit88"><label>88</label><citation-alternatives><mixed-citation xml:lang="ru">Gonçalves P., Araújo J. R., Di Santo J. P. A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease. Inflamm Bowel Dis. 2018 Feb 15;24(3):558-572. doi: 10.1093/ibd/izx029.</mixed-citation><mixed-citation xml:lang="en">Gonçalves P., Araújo J. R., Di Santo J. P. A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease. Inflamm Bowel Dis. 2018 Feb 15;24(3):558-572. doi: 10.1093/ibd/izx029.</mixed-citation></citation-alternatives></ref><ref id="cit89"><label>89</label><citation-alternatives><mixed-citation xml:lang="ru">Tan J., McKenzie C., Potamitis M., Thorburn A. N., Mackay C. R., Macia L. The role of short-chain fatty acids in health and disease. Adv Immunol. 2014;121:91-119. doi: 10.1016/B978-0-12-800100-4.00003-9.</mixed-citation><mixed-citation xml:lang="en">Tan J., McKenzie C., Potamitis M., Thorburn A. N., Mackay C. R., Macia L. The role of short-chain fatty acids in health and disease. Adv Immunol. 2014;121:91-119. doi: 10.1016/B978-0-12-800100-4.00003-9.</mixed-citation></citation-alternatives></ref><ref id="cit90"><label>90</label><citation-alternatives><mixed-citation xml:lang="ru">Tan Y., Zou K. F., Qian W., Chen S., Hou X. H. Expression and implication of toll-like receptors TLR2, TLR4 and TLR9 in colonic mucosa of patients with ulcerative colitis. J Huazhong Univ Sci Technolog Med Sci. 2014 Oct;34(5):785-790. doi: 10.1007/s11596-014-1353-6.</mixed-citation><mixed-citation xml:lang="en">Tan Y., Zou K. F., Qian W., Chen S., Hou X. H. Expression and implication of toll-like receptors TLR2, TLR4 and TLR9 in colonic mucosa of patients with ulcerative colitis. J Huazhong Univ Sci Technolog Med Sci. 2014 Oct;34(5):785-790. doi: 10.1007/s11596-014-1353-6.</mixed-citation></citation-alternatives></ref><ref id="cit91"><label>91</label><citation-alternatives><mixed-citation xml:lang="ru">Parada Venegas D., De la Fuente M. K., Landskron G., González M. J., Quera R., Dijkstra G., Harmsen H. J.M., Faber K. N., Hermoso M. A. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol. 2019 Mar 11;10:277. doi: 10.3389/fimmu.2019.00277.</mixed-citation><mixed-citation xml:lang="en">Parada Venegas D., De la Fuente M. K., Landskron G., González M. J., Quera R., Dijkstra G., Harmsen H. J.M., Faber K. N., Hermoso M. A. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol. 2019 Mar 11;10:277. doi: 10.3389/fimmu.2019.00277.</mixed-citation></citation-alternatives></ref><ref id="cit92"><label>92</label><citation-alternatives><mixed-citation xml:lang="ru">Kussmann M., Stover P. J. Nutrigenomics and Proteomics in Health and Disease: Towards a Systems-Level Un-derstanding of Gene-Diet Interactions. Oxford. John Wiley &amp; Sons. 2017.</mixed-citation><mixed-citation xml:lang="en">Kussmann M., Stover P. J. Nutrigenomics and Proteomics in Health and Disease: Towards a Systems-Level Un-derstanding of Gene-Diet Interactions. Oxford. John Wiley &amp; Sons. 2017.</mixed-citation></citation-alternatives></ref><ref id="cit93"><label>93</label><citation-alternatives><mixed-citation xml:lang="ru">Suskind D. L. Nutrition in Immune Balance (NIMBAL) Therapy: Using Diet to Treat Inflammatory Bowel Dis-ease. Nimbal Publishing. 2015.</mixed-citation><mixed-citation xml:lang="en">Suskind D. L. Nutrition in Immune Balance (NIMBAL) Therapy: Using Diet to Treat Inflammatory Bowel Dis-ease. Nimbal Publishing. 2015.</mixed-citation></citation-alternatives></ref><ref id="cit94"><label>94</label><citation-alternatives><mixed-citation xml:lang="ru">Kakodkar S., Farooqui A. J., Mikolaitis S. L., Mutlu E. A. The Specific Carbohydrate Diet for Inflammatory Bowel Disease: A Case Series. J Acad Nutr Diet. 2015 Aug;115(8):1226-32. doi: 10.1016/j.jand.2015.04.016.</mixed-citation><mixed-citation xml:lang="en">Kakodkar S., Farooqui A. J., Mikolaitis S. L., Mutlu E. A. The Specific Carbohydrate Diet for Inflammatory Bowel Disease: A Case Series. J Acad Nutr Diet. 2015 Aug;115(8):1226-32. doi: 10.1016/j.jand.2015.04.016.</mixed-citation></citation-alternatives></ref><ref id="cit95"><label>95</label><citation-alternatives><mixed-citation xml:lang="ru">Elsaygh H., Alhafez I., Jaber M., Al-Rasheed M., Zaher A., ElSaygh J. A Literature Review of Major Clinical Trials That Contributed to Treatment Protocols of Irritable Bowel Syndrome With Diarrhea. Cureus. 2022 Jun 19;14(6): e26092. doi: 10.7759/cureus.26092.</mixed-citation><mixed-citation xml:lang="en">Elsaygh H., Alhafez I., Jaber M., Al-Rasheed M., Zaher A., ElSaygh J. A Literature Review of Major Clinical Trials That Contributed to Treatment Protocols of Irritable Bowel Syndrome With Diarrhea. Cureus. 2022 Jun 19;14(6): e26092. doi: 10.7759/cureus.26092.</mixed-citation></citation-alternatives></ref><ref id="cit96"><label>96</label><citation-alternatives><mixed-citation xml:lang="ru">Gibson P. R. The evidence base for efficacy of the low FODMAP diet in irritable bowel syndrome: is it ready for prime time as a first-line therapy? J Gastroenterol Hepatol. 2017 Mar;32 Suppl 1:32-35. doi: 10.1111/jgh.13693.</mixed-citation><mixed-citation xml:lang="en">Gibson P. R. The evidence base for efficacy of the low FODMAP diet in irritable bowel syndrome: is it ready for prime time as a first-line therapy? J Gastroenterol Hepatol. 2017 Mar;32 Suppl 1:32-35. doi: 10.1111/jgh.13693.</mixed-citation></citation-alternatives></ref><ref id="cit97"><label>97</label><citation-alternatives><mixed-citation xml:lang="ru">Barrett J. S. How to institute the low-FODMAP diet. J Gastroenterol Hepatol. 2017 Mar;32 Suppl 1:8-10. doi: 10.1111/jgh.13686.</mixed-citation><mixed-citation xml:lang="en">Barrett J. S. How to institute the low-FODMAP diet. J Gastroenterol Hepatol. 2017 Mar;32 Suppl 1:8-10. doi: 10.1111/jgh.13686.</mixed-citation></citation-alternatives></ref><ref id="cit98"><label>98</label><citation-alternatives><mixed-citation xml:lang="ru">Adamji M., Day A. S. An overview of the role of exclusive enteral nutrition for complicated Crohn’s disease.Intest Res. 2019 Apr;17(2):171-176. doi: 10.5217/ir.2018.00079.</mixed-citation><mixed-citation xml:lang="en">Adamji M., Day A. S. An overview of the role of exclusive enteral nutrition for complicated Crohn’s disease.Intest Res. 2019 Apr;17(2):171-176. doi: 10.5217/ir.2018.00079.</mixed-citation></citation-alternatives></ref><ref id="cit99"><label>99</label><citation-alternatives><mixed-citation xml:lang="ru">Gubatan J., Boye T. L., Temby M., Sojwal R. S., Holman D. R., Sinha S. R., Rogalla S. R., Nielsen O. H. Gut Microbiome in Inflammatory Bowel Disease: Role in Pathogenesis, Dietary Modulation, and Colitis-Associated Colon Cancer. Microorganisms. 2022 Jul 7;10(7):1371. doi: 10.3390/microorganisms10071371.</mixed-citation><mixed-citation xml:lang="en">Gubatan J., Boye T. L., Temby M., Sojwal R. S., Holman D. R., Sinha S. R., Rogalla S. R., Nielsen O. H. Gut Microbiome in Inflammatory Bowel Disease: Role in Pathogenesis, Dietary Modulation, and Colitis-Associated Colon Cancer. Microorganisms. 2022 Jul 7;10(7):1371. doi: 10.3390/microorganisms10071371.</mixed-citation></citation-alternatives></ref><ref id="cit100"><label>100</label><citation-alternatives><mixed-citation xml:lang="ru">Rizzello F., Spisni E., Giovanardi E., Imbesi V., Salice M., Alvisi P., Valerii M. C., Gionchetti P. Implications of the Westernized Diet in the Onset and Progression of IBD. Nutrients. 2019 May 8;11(5):1033. doi: 10.3390/nu11051033.</mixed-citation><mixed-citation xml:lang="en">Rizzello F., Spisni E., Giovanardi E., Imbesi V., Salice M., Alvisi P., Valerii M. C., Gionchetti P. Implications of the Westernized Diet in the Onset and Progression of IBD. Nutrients. 2019 May 8;11(5):1033. doi: 10.3390/nu11051033.</mixed-citation></citation-alternatives></ref><ref id="cit101"><label>101</label><citation-alternatives><mixed-citation xml:lang="ru">Chiba M., Nakane K., Komatsu M. Westernized Diet is the Most Ubiquitous Environmental Factor in Inflammatory Bowel Disease. Perm J. 2019;23:18-107. doi: 10.7812/TPP/18-107.</mixed-citation><mixed-citation xml:lang="en">Chiba M., Nakane K., Komatsu M. Westernized Diet is the Most Ubiquitous Environmental Factor in Inflammatory Bowel Disease. Perm J. 2019;23:18-107. doi: 10.7812/TPP/18-107.</mixed-citation></citation-alternatives></ref><ref id="cit102"><label>102</label><citation-alternatives><mixed-citation xml:lang="ru">Lee J.E., Kim K. S., Koh H., Lee D. W., Kang N. J. Diet-Induced Host-Microbe Interactions: Personalized Diet Strategies for Improving Inflammatory Bowel Disease. Curr Dev Nutr. 2022 Jun 25;6(8): nzac110. doi: 10.1093/cdn/nzac110.</mixed-citation><mixed-citation xml:lang="en">Lee J.E., Kim K. S., Koh H., Lee D. W., Kang N. J. Diet-Induced Host-Microbe Interactions: Personalized Diet Strategies for Improving Inflammatory Bowel Disease. Curr Dev Nutr. 2022 Jun 25;6(8): nzac110. doi: 10.1093/cdn/nzac110.</mixed-citation></citation-alternatives></ref><ref id="cit103"><label>103</label><citation-alternatives><mixed-citation xml:lang="ru">Constante M., Fragoso G., Calvé A., Samba-Mondonga M., Santos M. M. Dietary Heme Induces Gut Dysbiosis, Aggravates Colitis, and Potentiates the Development of Adenomas in Mice. Front Microbiol. 2017 Sep 21;8:1809. doi: 10.3389/fmicb.2017.01809.</mixed-citation><mixed-citation xml:lang="en">Constante M., Fragoso G., Calvé A., Samba-Mondonga M., Santos M. M. Dietary Heme Induces Gut Dysbiosis, Aggravates Colitis, and Potentiates the Development of Adenomas in Mice. Front Microbiol. 2017 Sep 21;8:1809. doi: 10.3389/fmicb.2017.01809.</mixed-citation></citation-alternatives></ref><ref id="cit104"><label>104</label><citation-alternatives><mixed-citation xml:lang="ru">Hu S., Mok J., Gowans M., Ong D. E.H., Hartono J. L., Lee J. W.J. Oral Microbiome of Crohn’s Disease Patients With and Without Oral Manifestations. J Crohns Colitis. 2022 Nov 1;16(10):1628-1636. doi: 10.1093/ecco-jcc/jjac063.</mixed-citation><mixed-citation xml:lang="en">Hu S., Mok J., Gowans M., Ong D. E.H., Hartono J. L., Lee J. W.J. Oral Microbiome of Crohn’s Disease Patients With and Without Oral Manifestations. J Crohns Colitis. 2022 Nov 1;16(10):1628-1636. doi: 10.1093/ecco-jcc/jjac063.</mixed-citation></citation-alternatives></ref><ref id="cit105"><label>105</label><citation-alternatives><mixed-citation xml:lang="ru">Abdelbary M.M.H., Hatting M., Bott A., Dahlhausen A., Keller D., Trautwein C., Conrads G. The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease. Front Cell Infect Microbiol. 2022 Oct 7;12:1010853. doi: 10.3389/fcimb.2022.1010853.</mixed-citation><mixed-citation xml:lang="en">Abdelbary M.M.H., Hatting M., Bott A., Dahlhausen A., Keller D., Trautwein C., Conrads G. The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease. Front Cell Infect Microbiol. 2022 Oct 7;12:1010853. doi: 10.3389/fcimb.2022.1010853.</mixed-citation></citation-alternatives></ref><ref id="cit106"><label>106</label><citation-alternatives><mixed-citation xml:lang="ru">Brito F., Zaltman C., Carvalho A. T., Fischer R. G., Persson R., Gustafsson A., Figueredo C. M. Subgingival microflora in inflammatory bowel disease patients with untreated periodontitis. Eur J Gastroenterol Hepatol. 2013 Feb;25(2):239-45. doi: 10.1097/MEG.0b013e32835a2b70.</mixed-citation><mixed-citation xml:lang="en">Brito F., Zaltman C., Carvalho A. T., Fischer R. G., Persson R., Gustafsson A., Figueredo C. M. Subgingival microflora in inflammatory bowel disease patients with untreated periodontitis. Eur J Gastroenterol Hepatol. 2013 Feb;25(2):239-45. doi: 10.1097/MEG.0b013e32835a2b70.</mixed-citation></citation-alternatives></ref><ref id="cit107"><label>107</label><citation-alternatives><mixed-citation xml:lang="ru">Kelsen J., Bittinger K., Pauly-Hubbard H., Posivak L., Grunberg S., Baldassano R., Lewis J. D., Wu G. D., Bushman F. D. Alterations of the Subgingival Microbiota in Pediatric Crohn’s Disease Studied Longitudinally in Discovery and Validation Cohorts. Inflamm Bowel Dis. 2015 Dec;21(12):2797-805. doi: 10.1097/MIB.0000000000000557.</mixed-citation><mixed-citation xml:lang="en">Kelsen J., Bittinger K., Pauly-Hubbard H., Posivak L., Grunberg S., Baldassano R., Lewis J. D., Wu G. D., Bushman F. D. Alterations of the Subgingival Microbiota in Pediatric Crohn’s Disease Studied Longitudinally in Discovery and Validation Cohorts. Inflamm Bowel Dis. 2015 Dec;21(12):2797-805. doi: 10.1097/MIB.0000000000000557.</mixed-citation></citation-alternatives></ref><ref id="cit108"><label>108</label><citation-alternatives><mixed-citation xml:lang="ru">Elmaghrawy K., Fleming P., Fitzgerald K., Cooper S., Dominik A., Hussey S., Moran G. P. The Oral Microbiome in Treatment-Naïve Paediatric IBD Patients Exhibits Dysbiosis Related to Disease Severity that Resolves Following Therapy. J Crohns Colitis. 2023 Apr 19;17(4):553-564. doi: 10.1093/ecco-jcc/jjac155.</mixed-citation><mixed-citation xml:lang="en">Elmaghrawy K., Fleming P., Fitzgerald K., Cooper S., Dominik A., Hussey S., Moran G. P. The Oral Microbiome in Treatment-Naïve Paediatric IBD Patients Exhibits Dysbiosis Related to Disease Severity that Resolves Following Therapy. J Crohns Colitis. 2023 Apr 19;17(4):553-564. doi: 10.1093/ecco-jcc/jjac155.</mixed-citation></citation-alternatives></ref><ref id="cit109"><label>109</label><citation-alternatives><mixed-citation xml:lang="ru">Davenport M., Poles J., Leung J. M., Wolff M. J., Abidi W. M., Ullman T., Mayer L., Cho I., Loke P. Metabolic alterations to the mucosal microbiota in inflammatory bowel disease. Inflamm Bowel Dis. 2014 Apr;20(4):723-31. doi: 10.1097/MIB.0000000000000011.</mixed-citation><mixed-citation xml:lang="en">Davenport M., Poles J., Leung J. M., Wolff M. J., Abidi W. M., Ullman T., Mayer L., Cho I., Loke P. Metabolic alterations to the mucosal microbiota in inflammatory bowel disease. Inflamm Bowel Dis. 2014 Apr;20(4):723-31. doi: 10.1097/MIB.0000000000000011.</mixed-citation></citation-alternatives></ref><ref id="cit110"><label>110</label><citation-alternatives><mixed-citation xml:lang="ru">Chen L., Wang W., Zhou R., Ng S. C., Li J., Huang M., Zhou F., Wang X., Shen B., A Kamm M., Wu K., Xia B. Characteristics of fecal and mucosa-associated microbiota in Chinese patients with inflammatory bowel disease. Medicine (Baltimore). 2014 Aug;93(8): e51. doi: 10.1097/MD.0000000000000051.</mixed-citation><mixed-citation xml:lang="en">Chen L., Wang W., Zhou R., Ng S. C., Li J., Huang M., Zhou F., Wang X., Shen B., A Kamm M., Wu K., Xia B. Characteristics of fecal and mucosa-associated microbiota in Chinese patients with inflammatory bowel disease. Medicine (Baltimore). 2014 Aug;93(8): e51. doi: 10.1097/MD.0000000000000051.</mixed-citation></citation-alternatives></ref><ref id="cit111"><label>111</label><citation-alternatives><mixed-citation xml:lang="ru">Santoru M.L., Piras C., Murgia A., Palmas V. et al. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci Rep. 2017 Aug 25;7(1):9523. doi: 10.1038/s41598-017-10034-5.</mixed-citation><mixed-citation xml:lang="en">Santoru M.L., Piras C., Murgia A., Palmas V. et al. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci Rep. 2017 Aug 25;7(1):9523. doi: 10.1038/s41598-017-10034-5.</mixed-citation></citation-alternatives></ref><ref id="cit112"><label>112</label><citation-alternatives><mixed-citation xml:lang="ru">Imhann F., Vich Vila A., Bonder M. J., Fu J. et al.Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. 2018 Jan;67(1):108-119. doi: 10.1136/gutjnl-2016-312135.</mixed-citation><mixed-citation xml:lang="en">Imhann F., Vich Vila A., Bonder M. J., Fu J. et al.Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. 2018 Jan;67(1):108-119. doi: 10.1136/gutjnl-2016-312135.</mixed-citation></citation-alternatives></ref><ref id="cit113"><label>113</label><citation-alternatives><mixed-citation xml:lang="ru">Zakrzewski M., Simms L. A., Brown A., Appleyard M., Irwin J., Waddell N., Radford-Smith G.L. IL23R-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease. J Crohns Colitis. 2019 Mar 30;13(4):451-461. doi: 10.1093/ecco-jcc/jjy188.</mixed-citation><mixed-citation xml:lang="en">Zakrzewski M., Simms L. A., Brown A., Appleyard M., Irwin J., Waddell N., Radford-Smith G.L. IL23R-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease. J Crohns Colitis. 2019 Mar 30;13(4):451-461. doi: 10.1093/ecco-jcc/jjy188.</mixed-citation></citation-alternatives></ref><ref id="cit114"><label>114</label><citation-alternatives><mixed-citation xml:lang="ru">Altomare A., Putignani L., Del Chierico F., Cocca S. et al. Gut mucosal-associated microbiota better discloses inflammatory bowel disease differential patterns than faecal microbiota. Dig Liver Dis. 2019 May;51(5):648-656. doi: 10.1016/j.dld.2018.11.021.</mixed-citation><mixed-citation xml:lang="en">Altomare A., Putignani L., Del Chierico F., Cocca S. et al. Gut mucosal-associated microbiota better discloses inflammatory bowel disease differential patterns than faecal microbiota. Dig Liver Dis. 2019 May;51(5):648-656. doi: 10.1016/j.dld.2018.11.021.</mixed-citation></citation-alternatives></ref><ref id="cit115"><label>115</label><citation-alternatives><mixed-citation xml:lang="ru">Franzosa E.A., Sirota-Madi A., Avila-Pacheco J., Fornelos N. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 Feb;4(2):293-305. doi: 10.1038/s41564-018-0306-4.</mixed-citation><mixed-citation xml:lang="en">Franzosa E.A., Sirota-Madi A., Avila-Pacheco J., Fornelos N. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019 Feb;4(2):293-305. doi: 10.1038/s41564-018-0306-4.</mixed-citation></citation-alternatives></ref><ref id="cit116"><label>116</label><citation-alternatives><mixed-citation xml:lang="ru">Li E., Zhang Y., Tian X., Wang X. et al. Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome. PLoS One. 2019 Feb 28;14(2): e0213108. doi: 10.1371/journal.pone.0213108.</mixed-citation><mixed-citation xml:lang="en">Li E., Zhang Y., Tian X., Wang X. et al. Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome. PLoS One. 2019 Feb 28;14(2): e0213108. doi: 10.1371/journal.pone.0213108.</mixed-citation></citation-alternatives></ref><ref id="cit117"><label>117</label><citation-alternatives><mixed-citation xml:lang="ru">Yilmaz B., Juillerat P., Øyås O., Ramon C., Bravo F. D., Franc Y., Fournier N., Michetti P., Mueller C., Geuking M., Pittet V. E.H., Maillard M. H., Rogler G.; Swiss IBD Cohort Investigators; Wiest R, Stelling J, Macpherson AJ. Microbial network disturbances in relapsing refractory Crohn’s disease. Nat Med. 2019 Feb;25(2):323-336. doi: 10.1038/s41591-018-0308-z.</mixed-citation><mixed-citation xml:lang="en">Yilmaz B., Juillerat P., Øyås O., Ramon C., Bravo F. D., Franc Y., Fournier N., Michetti P., Mueller C., Geuking M., Pittet V. E.H., Maillard M. H., Rogler G.; Swiss IBD Cohort Investigators; Wiest R, Stelling J, Macpherson AJ. Microbial network disturbances in relapsing refractory Crohn’s disease. Nat Med. 2019 Feb;25(2):323-336. doi: 10.1038/s41591-018-0308-z.</mixed-citation></citation-alternatives></ref><ref id="cit118"><label>118</label><citation-alternatives><mixed-citation xml:lang="ru">Magro D.O., Santos A., Guadagnini D. et al. Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production. Sci Rep. 2019 Sep 13;9(1):13263. doi: 10.1038/s41598-019-49893-5.</mixed-citation><mixed-citation xml:lang="en">Magro D.O., Santos A., Guadagnini D. et al. Remission in Crohn’s disease is accompanied by alterations in the gut microbiota and mucins production. Sci Rep. 2019 Sep 13;9(1):13263. doi: 10.1038/s41598-019-49893-5.</mixed-citation></citation-alternatives></ref><ref id="cit119"><label>119</label><citation-alternatives><mixed-citation xml:lang="ru">Zhang Y.L., Cai L. T., Qi J. Y. et al. Gut microbiota contributes to the distinction between two traditional Chinese medicine syndromes of ulcerative colitis. World J Gastroenterol. 2019 Jul 7;25(25):3242-3255. doi: 10.3748/wjg.v25.i25.3242.</mixed-citation><mixed-citation xml:lang="en">Zhang Y.L., Cai L. T., Qi J. Y. et al. Gut microbiota contributes to the distinction between two traditional Chinese medicine syndromes of ulcerative colitis. World J Gastroenterol. 2019 Jul 7;25(25):3242-3255. doi: 10.3748/wjg.v25.i25.3242.</mixed-citation></citation-alternatives></ref><ref id="cit120"><label>120</label><citation-alternatives><mixed-citation xml:lang="ru">Alam M.T., Amos G. C.A., Murphy A. R.J., Murch S., Wellington E. M.H., Arasaradnam R. P. Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut Pathog. 2020 Jan 4;12:1. doi: 10.1186/s13099-019-0341-6.</mixed-citation><mixed-citation xml:lang="en">Alam M.T., Amos G. C.A., Murphy A. R.J., Murch S., Wellington E. M.H., Arasaradnam R. P. Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut Pathog. 2020 Jan 4;12:1. doi: 10.1186/s13099-019-0341-6.</mixed-citation></citation-alternatives></ref><ref id="cit121"><label>121</label><citation-alternatives><mixed-citation xml:lang="ru">Ryan F.J., Ahern A. M., Fitzgerald R. S. et al. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease. Nat Commun. 2020 Mar 23;11(1):1512. doi: 10.1038/s41467-020-15342-5.</mixed-citation><mixed-citation xml:lang="en">Ryan F.J., Ahern A. M., Fitzgerald R. S. et al. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease. Nat Commun. 2020 Mar 23;11(1):1512. doi: 10.1038/s41467-020-15342-5.</mixed-citation></citation-alternatives></ref><ref id="cit122"><label>122</label><citation-alternatives><mixed-citation xml:lang="ru">Olaisen M., Flatberg A., Granlund A. V.B., Røyset E. S., Martinsen T. C., Sandvik A. K., Fossmark R. Bacterial Mucosa-associated Microbiome in Inflamed and Proximal Noninflamed Ileum of Patients With Crohn’s Disease. Inflamm Bowel Dis. 2021 Jan 1;27(1):12-24. doi: 10.1093/ibd/izaa107.</mixed-citation><mixed-citation xml:lang="en">Olaisen M., Flatberg A., Granlund A. V.B., Røyset E. S., Martinsen T. C., Sandvik A. K., Fossmark R. Bacterial Mucosa-associated Microbiome in Inflamed and Proximal Noninflamed Ileum of Patients With Crohn’s Disease. Inflamm Bowel Dis. 2021 Jan 1;27(1):12-24. doi: 10.1093/ibd/izaa107.</mixed-citation></citation-alternatives></ref><ref id="cit123"><label>123</label><citation-alternatives><mixed-citation xml:lang="ru">Shahir N.M., Wang J. R., Wolber E. A. et al. Crohn’s Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis. 2020 Nov 19;26(12):1843-1855. doi: 10.1093/ibd/izaa103.</mixed-citation><mixed-citation xml:lang="en">Shahir N.M., Wang J. R., Wolber E. A. et al. Crohn’s Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis. 2020 Nov 19;26(12):1843-1855. doi: 10.1093/ibd/izaa103.</mixed-citation></citation-alternatives></ref><ref id="cit124"><label>124</label><citation-alternatives><mixed-citation xml:lang="ru">Clooney A.G., Eckenberger J., Laserna-Mendieta E. et al. Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study. Gut. 2021 Mar;70(3):499-510. doi: 10.1136/gutjnl-2020-321106.</mixed-citation><mixed-citation xml:lang="en">Clooney A.G., Eckenberger J., Laserna-Mendieta E. et al. Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study. Gut. 2021 Mar;70(3):499-510. doi: 10.1136/gutjnl-2020-321106.</mixed-citation></citation-alternatives></ref><ref id="cit125"><label>125</label><citation-alternatives><mixed-citation xml:lang="ru">Park Y.M., Ha E., Gu K. N., Shin G. Y., Lee C. K., Kim K., Kim H. J. Host Genetic and Gut Microbial Signatures in Familial Inflammatory Bowel Disease. Clin Transl Gastroenterol. 2020 Jul;11(7): e00213. doi: 10.14309/ctg.0000000000000213.</mixed-citation><mixed-citation xml:lang="en">Park Y.M., Ha E., Gu K. N., Shin G. Y., Lee C. K., Kim K., Kim H. J. Host Genetic and Gut Microbial Signatures in Familial Inflammatory Bowel Disease. Clin Transl Gastroenterol. 2020 Jul;11(7): e00213. doi: 10.14309/ctg.0000000000000213.</mixed-citation></citation-alternatives></ref><ref id="cit126"><label>126</label><citation-alternatives><mixed-citation xml:lang="ru">Lo Sasso G., Khachatryan L., Kondylis A. et al. Inflammatory Bowel Disease-Associated Changes in the Gut: Focus on Kazan Patients. Inflamm Bowel Dis. 2021 Feb 16;27(3):418-433. doi: 10.1093/ibd/izaa188.</mixed-citation><mixed-citation xml:lang="en">Lo Sasso G., Khachatryan L., Kondylis A. et al. Inflammatory Bowel Disease-Associated Changes in the Gut: Focus on Kazan Patients. Inflamm Bowel Dis. 2021 Feb 16;27(3):418-433. doi: 10.1093/ibd/izaa188.</mixed-citation></citation-alternatives></ref></ref-list><fn-group><fn fn-type="conflict"><p>The authors declare that there are no conflicts of interest present.</p></fn></fn-group></back></article>
