Shen ZH, Zhu CX, Quan YS, Yang ZY, Wu S, Luo WW, et al. Relationship between intestinal microbiota and ulcerative colitis: mechanisms and clinical application of probiotics and fecal microbiota transplantation. World J Gastroentero. 2018;24(1):5–14.

Article  CAS  Google Scholar 

Hudcovic T, Stepankova R, Cebra J, Tlaskalova-Hogenova H. The role of microflora in the development of intestinal inflammation: acute and chronic colitis induced by dextran sulfate in germ-free and conventionally reared immunocompetent and immunodeficient mice. Folia Microbiol (Praha). 2001;46(6):565–72.

Article  CAS  PubMed  Google Scholar 

Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, et al. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nat Commun. 2019;10(1):38.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nemoto H, Kataoka K, Ishikawa H, Ikata K, Arimochi H, Iwasaki T, et al. Reduced diversity and imbalance of fecal microbiota in patients with ulcerative colitis. Dig Dis Sci. 2012;57(11):2955–64.

Article  PubMed  Google Scholar 

Machiels K, Joossens M, Sabino J, De Preter V, Arijs I, Eeckhaut V, et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut. 2014;63(8):1275–83.

Article  CAS  PubMed  Google Scholar 

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2018.

Garrett WS, Gallini CA, Yatsunenko T, Michaud M, DuBois A, Delaney ML, et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe. 2010;8(3):292–300.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shmuel-Galia L, Humphries F, Lei X, Ceglia S, Wilson R, Jiang Z, et al. Dysbiosis exacerbates colitis by promoting ubiquitination and accumulation of the innate immune adaptor STING in myeloid cells. Immunity. 2021;54(6):1137–53e8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tran HQ, Ley RE, Gewirtz AT, Chassaing B. Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nat Commun. 2019;10(1):5650.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bernardo D, Vallejo-Díez S, Mann ER, Al-Hassi HO, Martínez-Abad B, Montalvillo E, et al. IL-6 promotes immune responses in human ulcerative colitis and induces a skin-homing phenotype in the dendritic cells and tcells they stimulate. Eur J Immunol. 2012;42(5):1337–53.

Article  CAS  PubMed  Google Scholar 

van der Lelie D, Oka A, Taghavi S, Umeno J, Fan TJ, Merrell KE, et al. Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis. Nat Commun. 2021;12(1):3105.

Article  PubMed  PubMed Central  Google Scholar 

Fan L, Qi Y, Qu S, Chen X, Li A, Hendi M, et al. B. adolescentis ameliorates chronic colitis by regulating Treg/Th2 response and gut microbiota remodeling. Gut Microbes. 2021;13(1):1–17.

Article  CAS  PubMed  Google Scholar 

Costello SP, Hughes PA, Waters O, Bryant RV, Vincent AD, Blatchford P, et al. Effect of fecal microbiota transplantation on 8-Week remission in patients with Ulcerative Colitis: a Randomized Clinical Trial. JAMA. 2019;321(2):156–64.

Article  PubMed  PubMed Central  Google Scholar 

Wang T, Zheng N, Luo Q, Jiang L, He B, Yuan X, et al. Probiotics Lactobacillus reuteri abrogates Immune Checkpoint Blockade-Associated Colitis by Inhibiting Group 3 innate lymphoid cells. Front Immunol. 2019;10:1235.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen Y, Jin Y, Stanton C, Paul Ross R, Zhao J, Zhang H, et al. Alleviation effects of Bifidobacterium breve on DSS-induced colitis depends on intestinal tract barrier maintenance and gut microbiota modulation. Eur J Nutr. 2021;60(1):369–87.

Article  CAS  PubMed  Google Scholar 

Zhai R, Xue X, Zhang L, Yang X, Zhao L, Zhang C. Strain-specific anti-inflammatory properties of two Akkermansia muciniphila strains on Chronic Colitis in mice. Front Cell Infect Microbiol. 2019;9:239.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bian X, Wu W, Yang L, Lv L, Wang Q, Li Y, et al. Administration of Akkermansia muciniphila ameliorates Dextran Sulfate Sodium-Induced Ulcerative Colitis in mice. Front Microbiol. 2019;10:2259.

Article  PubMed  PubMed Central  Google Scholar 

Yoshimatsu Y, Yamada A, Furukawa R, Sono K, Osamura A, Nakamura K, et al. Effectiveness of probiotic therapy for the prevention of relapse in patients with inactive ulcerative colitis. World J Gastroentero. 2015;21(19):5985–94.

Article  Google Scholar 

Philippe D, Heupel E, Blum-Sperisen S, Riedel CU. Treatment with Bifidobacterium bifidum 17 partially protects mice from Th1-driven inflammation in a chemically induced model of colitis. Int J Food Microbiol. 2011;149(1):45–9.

Article  CAS  PubMed  Google Scholar 

Yin M, Yan X, Weng W, Yang Y, Gao R, Liu M, et al. Micro Integral Membrane Protein (MIMP), a newly discovered anti-inflammatory protein of Lactobacillus Plantarum, enhances the gut barrier and modulates microbiota and inflammatory cytokines. Cell Physiol Biochem. 2018;45(2):474–90.

Article  CAS  PubMed  Google Scholar 

Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M et al. A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. Cell Host Microbe. 2021.

Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009;461(7268):1282–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly YM, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013;341(6145):569–73.

Article  CAS  PubMed  Google Scholar 

Praveschotinunt P, Duraj-Thatte AM, Gelfat I, Bahl F, Chou DB, Joshi NS. Engineered E. Coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut. Nat Commun. 2019;10(1):5580.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Paramsothy S, Nielsen S, Kamm MA, Deshpande NP, Faith JJ, Clemente JC, et al. Specific Bacteria and metabolites Associated with response to fecal microbiota transplantation in patients with Ulcerative Colitis. Gastroenterology. 2019;156(5):1440–54. e2.

Article  PubMed  Google Scholar 

Fuentes S, Rossen NG, van der Spek MJ, Hartman JH, Huuskonen L, Korpela K, et al. Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation. ISME J. 2017;11(8):1877–89.

Article  PubMed  PubMed Central  Google Scholar 

Manfredo Vieira S, Hiltensperger M, Kumar V, Zegarra-Ruiz D, Dehner C, Khan N, et al. Translocation of a gut pathobiont drives autoimmunity in mice and humans. Science. 2018;359(6380):1156–61.

Article  CAS  PubMed  Google Scholar 

Mishra S, Mandavdhare HS, Singh H, Choudhury A, Shah J, Ram S, et al. Adjuvant use of combination of antibiotics in acute severe ulcerative colitis: a placebo controlled randomized trial. Expert Rev Anti Infect Ther. 2021;19(7):949–55.

Article  CAS  PubMed  Google Scholar 

Ledder O, Turner D. Antibiotics in IBD: still a role in the Biological era? Inflamm Bowel Dis. 2018;24(8):1676–88.

Article  PubMed  Google Scholar 

Miyoshi J, Bobe AM, Miyoshi S, Huang Y, Hubert N, Delmont TO, et al. Peripartum Antibiotics promote gut dysbiosis, loss of Immune Tolerance, and inflammatory bowel disease in genetically prone offspring. Cell Rep. 2017;20(2):491–504.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yoon H, Schaubeck M, Lagkouvardos I, Blesl A, Heinzlmeir S, Hahne H, et al. Increased pancreatic protease activity in response to Antibiotics impairs gut barrier and triggers colitis. Cell Mol Gastroenterol Hepatol. 2018;6(3):370–88. e3.

Article  PubMed  PubMed Central  Google Scholar 

Hernandez-Chirlaque C, Aranda CJ, Ocon B, Capitan-Canadas F, Ortega-Gonzalez M, Carrero JJ, et al. Germ-free and antibiotic-treated mice are highly susceptible to Epithelial Injury in DSS Colitis. J Crohns Colitis. 2016;10(11):1324–35.

Article  PubMed  Google Scholar 

Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by Probiotics and improved by autologous FMT. Cell. 2018;174(6):1406–23e16.

Article  CAS  PubMed  Google Scholar 

Wang JJ, Wang J, Pang XY, Zhao LP, Tian L, Wang XP. Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin-supplemented diet in germ-free mice. Sci Rep. 2016;6:36137.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang J, Lang T, Shen J, Dai J, Tian L, Wang X. Core Gut Bacteria Analysis of Healthy Mice. Front Microbiol. 2019;10:887.

Article  PubMed  PubMed Central  Google Scholar 

Isani M, Bell BA, Delaplain PT, Bowling JD, Golden JM, Elizee M, et al. Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. PLoS ONE. 2018;13(6):e0196710.