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Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls

, , , , ORCID Icon &
Article: 1941711 | Received 11 Dec 2020, Accepted 04 Jun 2021, Published online: 30 Jul 2021

References

  • Cryan JF, O'Riordan K, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–51.
  • Luczynski P, McVey Neufeld K, Seira Oriach C, Clarke G, Dinan TG, Cryan JF. Assess the influence of the gut microbiota on brain and behavior. Int J Neuropsychopharmacol. 2016;19(8):1–17. doi:10.1093/ijnp/pyw020.
  • Weingarden AR, Vaughn BP. Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease. Gut Microbes. 2017;8(3):238–252. doi:10.1080/19490976.2017.1290757.
  • Hartstra AV, Bouter KEC, Bäckhed F, Nieuwdorp M. Insights into the role of the microbiome in obesity and type 2 diabetes. Diabetes Care. 2015;38(1):159–165. doi:10.2337/dc14-0769.
  • Sun M-F, Zhu YL, Zhou ZL, Jia XB, Xu YD, Yang Q, Cui C, Shen YQ. Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson’s disease mice: gut microbiota, glial reaction and TLR4/TNF-α signaling pathway. Brain Behav Immun. 2018;70:48–60. doi:10.1016/j.bbi.2018.02.005.
  • Berer K, Gerdes LA, Cekanaviciute E, Jia X, Xiao L, Xia Z, Liu C, Klotz L, Stauffer U, Baranzini SE, et al.  Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice. Proc. Natl. Acad. Sci. U. S. A. 2017;114(40):10719–10724. doi:10.1073/pnas.1711233114.
  • Sun J, Xu J, Ling Y, Wang F, Gong T, Yang C, Ye S, Ye K, Wei D, Song Z et al. Fecal microbiota transplantation alleviated Alzheimer’s disease-like pathogenesis in APP/PS1 transgenic mice. Transl Psychiatry. 2019 5;9(1):189. doi: 10.1038/s41398-019-0525-3..
  • Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, et al. Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017;5(1):1–16. doi:10.1186/s40168-016-0225-7.
  • Zhu F, Guo R, Wang W, Ju Y, Wang Q, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, et al.  Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice. Mol Psychiatry. 2019;25(11):2905–2918. doi:10.1038/s41380-019-0475-4.
  • Kelly JR, Borre Y, O' Brien C, Patterson E, El Aidy S, Deane J, Kennedy PJ, Beers S, Scott K, Moloney G, et al.Transferring the blues: depression-associated gut microbiota induces neurobehavioural changes in the rat. J Psychiatr Res. 2016;82:109–118.
  • Choo JM, Rogers GB. Establishment of murine gut microbiota in gnotobiotic mice. iScience. 2021;24(102049):102049. doi:10.1016/j.isci.2021.102049.
  • Lange ME, Uwiera RRE, Inglis GD. Housing gnotobiotic mice in conventional animal facilities. Curr. Protoc. Mouse Biol. 2019;9(e59):e59. doi:10.1002/cpmo.59.
  • Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 2009;9(5):313–323. doi:10.1038/nri2515.
  • Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y.  Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. J. Physiol. 2004;558(1):263–275. doi:10.1113/jphysiol.2004.063388.
  • Mallapaty S. Gnotobiotics: getting a grip on the microbiome boom. Lab Anim. (NY). 2017;46(10):373–377. doi:10.1038/laban.1344.
  • Arvidsson C, Hallén A, Bäckhed F. Generating and analyzing germ-free mice. Curr. Protoc. Mouse Biol. 2012;2(4):307–316. doi:10.1002/9780470942390.mo120064.
  • Burman O, Buccarello L, Redaelli V, Cervo L. The effect of two different Individually Ventilated Cage systems on anxiety-related behaviour and welfare in two strains of laboratory mouse. Physiol Behav. 2014;124:92–99. doi:10.1016/j.physbeh.2013.10.019.
  • Dobson GP, Letson HL, Biros E, Morris J. Specific pathogen-free (SPF) animal status as a variable in biomedical research: have we come full circle? EBioMedicine. 2019;41:42–43. doi:10.1016/j.ebiom.2019.02.038.
  • Schaedler RW, Dubs R, Costello R. Association of germ free mice with bacteria isolated from normal mice. J. Exp. Med. 1965;122(1):77–82. doi:10.1084/jem.122.1.77.
  • Dewhirst FE, Chien CC, Paster BJ, Ericson RL, Orcutt RP, Schauer DB, Fox JG.  Phylogeny of the defined murine microbiota: altered schaedler flora. Appl Environ Microbiol. 1999;65(8):3287–3292. doi:10.1128/AEM.65.8.3287-3292.1999.
  • Wymore Brand M, Wannemuehler MJ, Phillips GJ, Proctor A, Overstreet AM, Jergens AE, Orcutt RP, Fox JG. The altered schaedler flora: continued applications of a defined murine microbial community. ILAR J. 2015;56(2):169–178. doi:10.1093/ilar/ilv012.
  • Stecher B, Chaffron S, Käppeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, von Mering C, et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 2010;6(e1000711):e1000711. doi:10.1371/journal.ppat.1000711.
  • Beura LK, Hamilton SE, Bi K, Schenkel JM, Odumade OA, Casey KA, Thompson EA, Fraser KA, Rosato PC, Filali-Mouhim A, et al. Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature. 2016;532(7600):512–516. doi:10.1038/nature17655.
  • Le Roy T, Debédat J, Marquet F, Da-Cunha C, Ichou F, Guerre-Millo M, Kapel N, Aron-Wisnewsky J, Clément K.  Comparative evaluation of microbiota engraftment following fecal microbiota transfer in mice models: age, kinetic and microbial status matter. Front. Microbiol. 2019;9. doi:10.3389/fmicb.2018.03289.
  • Kiraly DD, Walker DM, Calipari ES, Labonte B, Issler O, Pena CJ, Ribeiro EA, Russo SJ, Nestler EJ.  Alterations of the host microbiome affect behavioral responses to cocaine. Sci Rep. 2016;6(35455). doi:10.1038/srep35455.
  • Reikvam DH, Erofeev A, Sandvik A, Grcic V, Jahnsen FL, Gaustad P, McCoy KD, Macpherson AJ, Meza-Zepeda LA, Johansen FE. Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression. PLoS One. 2011;6(3):e17996.
  • Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, et al. Microbial metabolism modulates antibiotic susceptibility within the murine gut microbiome. Cell Metab. 2019;30(800–823.e7).
  • Baldridge MT, Nice TJ, McCune BT, Yokoyama CC, Kambal A, Wheadon M, Diamond MS, Ivanova Y, Artyomov M, Virgin HW. Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection. Science. 2015;347(6219):266–269. doi:10.1126/science.1258025.
  • Adamcak A, Otten B. Rodent Therapeutics. Rodent Ther. Vet. Clin. North Am. Exot. Anim. Pract. 2000;3(1):221–237. doi:10.1016/S1094-9194(17)30102-0.
  • Hu Z, Tawa R, Konishi T, Shibata N, Takada K. A novel emulsifier, labrasol, enhances gastrointestinal absorption of gentamicin. Life Sci. 2001;69(24):2899–2910. doi:10.1016/S0024-3205(01)01375-3.
  • Fröhlich EE, Farzi A, Mayerhofer R, Reichmann F, Jačan A, Wagner B, Zinser E, Bordag N, Magnes C, Fröhlich E, et al. Cognitive Impairment by Antibiotic-Induced Gut Dysbiosis: analysis of Gut Microbiota-Brain Communication. Brain Behav Immun. 2016;56:140–155. doi:10.1016/j.bbi.2016.02.020.
  • Spychala MS, Venna VR, Jandzinski M, Doran SJ, Durgan DJ, Ganesh BP, Ajami NJ, Putluri N, Graf J, Bryan RM, et al.  Age-related changes in the gut microbiota influence systemic inflammation and stroke outcome. Ann. Neurol. 2018;84(1):23–36. doi:10.1002/ana.25250.
  • Lai ZL, Tseng CH, Ho HJ, Cheung CKY, Lin JY, Chen YJ, Cheng FC, Hsu YC, Lin JT, El-Omar EM, et al.  Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice. Sci. Rep. 2018;8(1):15625. doi:10.1038/s41598-018-33893-y.
  • Kim SG, Becattini S, Moody TU, Shliaha PV, Littmann ER, Seok R, Gjonbalaj M, Eaton V, Fontana E, Amoretti L, et al. Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus. Nature. 2019;572(7771):665–669. doi:10.1038/s41586-019-1501-z.
  • Le Bastard Q, Ward T, Sidiropoulos D, Hillmann BM, Chun CL, Sadowsky MJ, Knights D, Montassier E. Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24342-x
  • Benakis C, Brea D, Caballero S, Faraco G, Moore J, Murphy M, Sita G, Racchumi G, Ling L, Pamer EG, Iadecola C, et al. Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδ T cells. Nat. Med. 2016;22(5):516–523. doi:10.1038/nm.4068.
  • Staley C, Kaiser T, Beura LK, Hamilton MJ, Weingarden AR, Bobr A, Kang J, Masopust D, Sadowsky MJ, Khoruts A. Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning. Microbiome. 2017;5(87). doi:10.1186/s40168-017-0306-2.
  • Hoyles L, Fernández-Real JM, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, et al. Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women. Nat. Med. 2018;24(7):1070–1080. doi:10.1038/s41591-018-0061-3.
  • . Assessing the viability of transplanted gut microbiota by sequential tagging with D-amino acid-based metabolic probes. Nat Commun. 2019;10(1317).
  • Ganal SC, Sanos SL, Kallfass C, Oberle K, Johner C, Kirschning C, Lienenklaus S, Weiss S, Staeheli P, Aichele P, et al. Priming of Natural Killer Cells by Nonmucosal Mononuclear Phagocytes Requires Instructive Signals from Commensal Microbiota. Immunity. 2012;37(1):171–186. doi:10.1016/j.immuni.2012.05.020.
  • Brown RL, Sequeira RP, Clarke TB. The microbiota protects against respiratory infection via GM-CSF signaling. Nat. Commun. 2017;8(1):1512. doi:10.1038/s41467-017-01803-x.
  • Burrello C, Garavaglia F, Cribiù FM, Ercoli G, Bosari S, Caprioli F, Facciotti F. Short-term oral antibiotics treatment promotes inflammatory activation of colonic invariant natural killer T and Conventional CD4(+) T Cells. Front Med. 2018;5:21. doi:10.3389/fmed.2018.00021.
  • Zhan G, Yang N, Li S, Huang N, Fang X, Zhang J, Zhu B, Yang L, Yang C, Luo A.  Abnormal gut microbiota composition contributes to cognitive dysfunction in SAMP8 mice. Aging (Albany NY). 2018;10(6):1257–1267. doi:10.18632/aging.101464.
  • Emal D, Rampanelli E, Stroo I, Butter LM, Teske GJ, Claessen N, Stokman G, Florquin S, Leemans JC, Dessing MC. Depletion of Gut Microbiota Protects against Renal Ischemia-Reperfusion Injury. J. Am. Soc. Nephrol. 2017;28(5):1450–1461. doi:10.1681/ASN.2016030255.
  • Guirro M, Costa A, Gual-Grau A, Herrero P, Torrell H, Canela N, Arola L. Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: a multiomics approach. PLoS One. 2019;14(9):e0218143. doi:10.1371/journal.pone.0218143.
  • Yang C, Fang X, Zhan G, Huang N, Li S, Bi J, Jiang R, Yang L, Miao L, Zhu B, et al. Key role of gut microbiota in anhedonia-like phenotype in rodents with neuropathic pain. Transl Psychiatry. 2019;9(1):57. doi:10.1038/s41398-019-0379-8.
  • Josefsdottir KS, Baldridge MT, Kadmon CS, King KY. Antibiotics impair murine hematopoiesis by depleting the intestinal microbiota. Blood. 2017;129(6):729–739. doi:10.1182/blood-2016-03-708594.
  • Vétizou M, Pitt JM, Daillère R, Lepage P, Waldschmitt N, Flament C, Rusakiewicz S, Routy B, Roberti MP, Duong CPet al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350(6264):1079–1084. doi:10.1126/science.aad1329.
  • Jacobson A, Lam L, Rajendram M, Tamburini F, Honeycutt J, Pham T, Van Treuren W, Pruss K, Stabler SR, Lugo K, et al. A gut commensal-produced metabolite mediates colonization resistance to salmonella infection. Cell Host Microbe. 2018;24(2):296–307.e7. doi:10.1016/j.chom.2018.07.002.
  • Shi Z, Zou J, Zhang Z, Zhao X, Noriega J, Zhang B, Zhao C, Ingle H, Bittinger K, Mattei LM, et al. Segmented Filamentous Bacteria Prevent and Cure Rotavirus Infection. Cell. 2019;179(3):644–658.e13. doi:10.1016/j.cell.2019.09.028.
  • Schuijt TJ, Lankelma JM, Scicluna BP, de Sousa e Melo F, Roelofs JJ, de Boer JD, Hoogendijk AJ, de Beer R, de Vos A, Belzer C, et al. The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut. 2016;65(4):575–583. doi:10.1136/gutjnl-2015-309728.
  • Gury-BenAri M, Thaiss CA, Serafini N, Winter DR, Giladi A, Lara-Astiaso D, Levy M, Salame TM, Weiner A, David E, et al. The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome. Cell. 2016;166(5):1231–1246.e13. doi:10.1016/j.cell.2016.07.043.
  • Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell. 2004;118(2):229–241. doi:10.1016/j.cell.2004.07.002.
  • Ivanov II, Frutos Rde L, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB, Littman DR. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe. 2008;4(4):337–349. doi:10.1016/j.chom.2008.09.009.
  • Johansson ME, Jakobsson HE, Holmén-Larsson J, Schütte A, Ermund A, Rodríguez-Piñeiro AM, Arike L, Wising C, Svensson F, Bäckhed F, et al. Normalization of host intestinal mucus layers requires long-term microbial colonization. Cell Host Microbe. 2015;18(5):582–592. doi:10.1016/j.chom.2015.10.007.
  • Kim S-H, Cho B-H, Kiyono H, Jang Y-S. Microbiota-derived butyrate suppresses group 3 innate lymphoid cells in terminal ileal Peyer’s patches. Sci. Rep. 2017;7(1):3980. doi:10.1038/s41598-017-02729-6.
  • Ye Z, Zhang N, Wu C, Zhang X, Wang Q, Huang X, Du L, Cao Q, Tang J, Zhou C, et al. A metagenomic study of the gut microbiome in Behcet’s disease. Microbiome. 2018;6(1):135. doi:10.1186/s40168-018-0520-6.
  • Park JH, Kotani T, Konno T, Setiawan J, Kitamura Y, Imada S, Usui Y, Hatano N, Shinohara M, Saito Y,  et al. Promotion of intestinal epithelial cell turnover by commensal bacteria: role of short-chain fatty acids. PLoS One. 2016;11(5):e0156334. doi:10.1371/journal.pone.0156334.
  • Yan J, Herzog JW, Tsang K, Brennan CA, Bower MA, Garrett WS, Sartor BR, Aliprantis AO, Charles JF.  Gut microbiota induce IGF-1 and promote bone formation and growth. Proc Natl Acad Sci. 2016;113(47):E7554–E7563. doi:10.1073/pnas.1607235113.
  • Khosravi A, Yáñez A, Price JG, Chow A, Merad M, Goodridge HS, Mazmanian SK. Gut microbiota promote hematopoiesis to control bacterial infection. Cell Host Microbe. 2014;15(3):374–381. doi:10.1016/j.chom.2014.02.006.
  • Zhang Y, Huang R, Cheng M, Wang L, Chao J, Li J, Zheng P, Xie P, Zhang Z, Yao H. Gut microbiota from NLRP3-deficient mice ameliorates depressive-like behaviors by regulating astrocyte dysfunction via circHIPK2. Microbiome. 2019;7(1):116. doi:10.1186/s40168-019-0733-3.
  • Bárcena C, Valdés-Mas R, Mayoral P, Garabaya C, Durand S, Rodríguez F, Fernández-García MT, Salazar N, Nogacka AM, Garatachea N, et al. Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice. Nat. Med. 2019;25(8):1234–1242. doi:10.1038/s41591-019-0504-5.
  • Cao H, Liu X, An Y, Zhou G, Liu Y, Xu M, Dong W, Wang S, Yan F, Jiang K,  et al. Dysbiosis contributes to chronic constipation development via regulation of serotonin transporter in the intestine. Sci. Rep. 2017;7(1):10322. doi:10.1038/s41598-017-10835-8.
  • Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, et al. Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors. Science (80-). 2018;359(6371):91–97. doi:10.1126/science.aan3706.
  • Hughes KR, Schofield Z, Dalby MJ, Caim S, Chalklen L, Bernuzzi F, Alcon-Giner C, Le Gall G, Watson AJM, Hall LJ. The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding. FASEB J. 2020;34(5):7075–7088. doi:10.1096/fj.202000042R.
  • Liu Z, Li N, Fang H, Chen X, Guo Y, Gong S, Niu M, Zhou H, Jiang Y, Chang P, et al. Enteric dysbiosis is associated with sepsis in patients. FASEB J. 2019;33(11):12299–12310. doi:10.1096/fj.201900398RR.
  • Ochoa-Repáraz J, Mielcarz DW, Ditrio LE, Burroughs AR, Foureau DM, Haque-Begum S, Kasper LH. Role of Gut Commensal Microflora in the Development of Experimental Autoimmune Encephalomyelitis. J Immunol. 2009;183(10):6041–6050. doi:10.4049/jimmunol.0900747.
  • Brandsma E, Kloosterhuis NJ, Koster M, Dekker DC, Gijbels MJJ, van der Velden S, Ríos-Morales M, van Faassen MJR, Loreti MG, de Bruin A, et al. A proinflammatory gut microbiota increases systemic inflammation and accelerates atherosclerosis. Circ. Res. 2019;124(1):94–100. doi:10.1161/CIRCRESAHA.118.313234.
  • Zhang J, Bi JJ, Guo GJ, Yang L, Zhu B, Zhan GF, Li S, Huang NN, Hashimoto K, Yang C, et al. Abnormal composition of gut microbiota contributes to delirium-like behaviors after abdominal surgery in mice. CNS Neurosci. Ther. 2019;25(6):685–696. doi:10.1111/cns.13103.
  • Du HX, Liu Y, Zhang LG, Zhan CS, Chen J, Zhang M, Chen XG, Zhang L, Liang CZ. Abnormal gut microbiota composition is associated with experimental autoimmune prostatitis-induced depressive-like behaviors in mice. Prostate. 2020;80(9):663–673. doi:10.1002/pros.23978.
  • Wong SH, Zhao L, Zhang X, Nakatsu G, Han J, Xu W, Xiao X, Kwong TNY, Tsoi H, Wu WKK, et al. Gavage of fecal samples from patients with colorectal cancer promotes intestinal carcinogenesis in germ-free and conventional mice. Gastroenterology. 2017;153(6):1621–1633.e6. doi:10.1053/j.gastro.2017.08.022.
  • Li N, Wang Q, Wang Y, Sun A, Lin Y, Jin Y, Li X. Fecal microbiota transplantation from chronic unpredictable mild stress mice donors affects anxiety-like and depression-like behavior in recipient mice via the gut microbiota-inflammation-brain axis. Stress. 2019;22(5):592–602. doi:10.1080/10253890.2019.1617267.
  • Lendrum J, Seebach B, Klein B, Liu S. Sleep and the gut microbiome: antibiotic-induced depletion of the gut microbiota reduces nocturnal sleep in mice. bioRxiv. 2017:199075. doi:10.1101/199075.
  • Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, Deshpande M, Jayaprakash A, Colombel JF, Lafaille JJ, et al. Diet Modifies Colonic Microbiota and CD4+ T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23. Gastroenterology. 2018;155(4):1177–1191.e16. doi:10.1053/j.gastro.2018.06.034.
  • Wang S, Huang M, You X, Zhao J, Chen L, Wang L, Luo Y, Chen Y.  Gut microbiota mediates the anti-obesity effect of calorie restriction in mice. Sci. Rep. 2018;8(1):13037. doi:10.1038/s41598-018-31353-1.
  • Olson CA, Vuong HE, Yano JM, Liang QY, Nusbaum DJ, Hsiao EY.  The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet. Cell. 2018;173(7):1728–1741.e13. doi:10.1016/j.cell.2018.04.027.
  • Medel-Matus J-S, Shin D, Dorfman E, Sankar R, Mazarati A. Facilitation of kindling epileptogenesis by chronic stress may be mediated by intestinal microbiome. Epilepsia Open. 2018;3(2):290–294. doi:10.1002/epi4.12114.
  • Steed AL, Christophi GP, Kaiko GE, Sun L, Goodwin VM, Jain U, Esaulova E, Artyomov MN, Morales DJ, Holtzman MJ, et al. The microbial metabolite desaminotyrosine protects from influenza through type I interferon. Science (80-). 2017;357(6350):498–502. doi:10.1126/science.aam5336.
  • Hintze KJ, Cox JE, Rompato G, Benninghoff AD, Ward RE, Broadbent J, Lefevre M.  Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer. Gut Microbes. 2014;5(2):183–191. doi:10.4161/gmic.28403.
  • Turner PV, Vaughn E, Sunohara-Neilson J, Ovari J, Leri F. Oral gavage in rats: animal welfare evaluation. J. Am. Assoc. Lab. Anim. Sci. 2012;51:25–30.
  • Turner PV, Brabb T, Pekow C, Vasbinder MA. Administration of substances to laboratory animals: routes of administration and factors to consider. J. Am. Assoc. Lab. Anim. Sci. 2011;50:600–613.
  • Hoggatt AF, Hoggatt J, Honerlaw M, Pelus LM. A spoonful of sugar helps the medicine go down: a novel technique to improve oral gavage in mice. J. Am. Assoc. Lab. Anim. Sci. 2010;49:329–334.
  • Morton DB, Jennings M, Buckwell A, Ewbank R, Godfrey C, Holgate B, Inglis I, James R, Page C, Sharman I, et al. Refining procedures for the administration of substances. Lab. Anim. 2001;35(1):1–41. doi:10.1258/0023677011911345.
  • Zarrinpar A, Chaix A, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S. Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun. 2018;9(2872). doi:10.1038/s41467-018-05336-9.
  • Möhle L, Mattei D, Heimesaat MM, Bereswill S, Fischer A, Alutis M, French T, Hambardzumyan D, Matzinger P, Dunay IR, et al. Ly6Chi monocytes provide a link between antibiotic-induced changes in gut microbiota and adult hippocampal neurogenesis. Cell Rep. 2016;15(9):1945–1956. doi:10.1016/j.celrep.2016.04.074.
  • Desbonnet L, Clarke G, Traplin A, O'Sullivan O, Crispie F, Moloney RD, Cotter PD, Dinan TG, Cryan JF. Gut microbiota depletion from early adolescence in mice: implications for brain and behaviour. Brain Behav Immun. 2015;48:165–173. doi:10.1016/j.bbi.2015.04.004.
  • Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. 2013;499(7457):219–222. doi:10.1038/nature12212.
  • Hibbing ME, Fuqua C, Parsek MR, Peterson SB. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol. 2010;8(1):15–25. doi:10.1038/nrmicro2259.
  • Ayres JS, Trinidad NJ, Vance RE. Lethal inflammasome activation by a multi-drug resistant pathobiont upon antibiotic disruption of the microbiota. Nat Med. 2012;18(5):799–806. doi:10.1038/nm.2729.
  • Martinez MN, Papich MG, Drusano GL. Dosing regimen matters: the importance of early intervention and rapid attainment of the pharmacokinetic/pharmacodynamic target. Antimicrob. Agents Chemother. 2012;56(6):2795–2805. doi:10.1128/AAC.05360-11.
  • Zhou W, Chow KH, Fleming E, Oh J. Selective colonization ability of human fecal microbes in different mouse gut environments. ISME J. 2019;13(3):805–823. doi:10.1038/s41396-018-0312-9.
  • Pearson-Leary J, Zhao C, Bittinger K, Eacret D, Luz S, Vigderman AS, Dayanim G, Bhatnagar S. The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats. Mol Psychiatry. 2019;1. doi:10.1038/s41380-019-0380-x.
  • Nicolas S, Blasco‐Baque V, Fournel A, Gilleron J, Klopp P, Waget A, Ceppo F, Marlin A, Padmanabhan R, Iacovoni JS, et al. Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism. Molecular Systems Biology. 2017;13(3):921. doi:10.15252/msb.20167356.
  • Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F. Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res. 2013;1411–1419. doi:10.1101/gr.107987.110.20.
  • Heimesaat MM, Plickert R, Fischer A, Göbel UB, Bereswill S. Can microbiota transplantation abrogate murine colonization resistance against Campylobacter jejuni ? Eur. J. Microbiol. Immunol. (Bp). 2013;3(1):36–43. doi:10.1556/EuJMI.3.2013.1.5.
  • Wrzosek L, Ciocan D, Borentain P, Spatz M, Puchois V, Hugot C, Ferrere G, Mayeur C, Perlemuter G, Cassard AM.  Transplantation of human microbiota into conventional mice durably reshapes the gut microbiota. Sci. Rep. 2018;8(1):6854.
  • Ji SK, Yan H, Jiang T, Guo CY, Liu JJ, Dong SZ, Yang KL, Wang YJ, Cao ZJ, Li SL. Preparing the gut with antibiotics enhances gut microbiota reprogramming efficiency by promoting xenomicrobiota colonization. Front Microbiol. 2017;8:1–9. doi:10.3389/fmicb.2017.01208.
  • Hirayama K, Miyaji K, Kawamura S, Itoh K, Takahashi E, Mitsuoka T. Development of intestinal flora of human-flora-associated mice in the intestine of their offspring. Exp. Anim. 1995;44(3):219–222. doi:10.1538/expanim.44.219.
  • Moeller AH, Suzuki TA, Phifer-Rixey M, Nachman MW. Transmission modes of the mammalian gut microbiota. Science. 2018;362(6413):453–457. doi:10.1126/science.aat7164.
  • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):6ra14–6ra14. doi:10.1126/scitranslmed.3000322.
  • Moreno-Indias I, Lundberg R, Krych L, Metzdorff SB, Kot W, Sørensen DB, Nielsen DS, Hansen CHF, Hansen AK.  A humanized diet profile may facilitate colonization and immune stimulation in human microbiota-colonized mice. Front Microbiol. 2020;11(1336). doi:10.3389/fmicb.2020.01336.
  • Moreno-Indias I, Lundberg R, Krych L, Metzdorff SB, Kot W, Sørensen DB, Nielsen DS, Hansen CHF, Hansen AK. Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nat Commun. 2020;11(2577). doi:10.1038/s41467-020-16431-1.
  • Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ,  et al. Human gut microbiota from autism spectrum disorder promote behavioral symptoms in mice. Cell. 2019;30;177(6):1600-1618.e17. doi: 10.1016/j.cell.2019.05.004. .
  • Kimura I,Kimura I, Miyamoto J, Ohue-Kitano R, Watanabe K, Yamada T, Onuki M, Aoki R, Isobe Y, Kashihara D, et al. Maternal gut microbiota in pregnancy influences offspring metabolic phenotype in mice. Science (80-). 2020;367(6481):eaaw8429. doi:10.1126/science.aaw8429.
  • Stebegg M, Silva-Cayetano A, Innocentin S, Jenkins TP, Cantacessi C, Gilbert C, Linterman MA.  Heterochronic faecal transplantation boosts gut germinal centres in aged mice. Nat. Commun. 2019;10(1):1–13. doi:10.1038/s41467-019-10430-7.
  • Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM,  et al. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science. 2016;351(6275):aad3311–aad3311. doi:10.1126/science.aad3311.
  • Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, et al. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome. 2015;3(10). doi:10.1186/s40168-015-0070-0.
  • Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, et al. Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Cell Host Microbe. 2018;23(229–240.e5):229–240.e5. doi:10.1016/j.chom.2018.01.003.
  • Staley C, Kelly CR, Brandt LJ, Khoruts A, Sadowsky MJ. Complete microbiota engraftment is not essential for recovery from recurrent Clostridium difficile infection following fecal microbiota transplantation. MBio. 2016;7(6):e01965–16. doi:10.1128/mBio.01965-16.
  • Bajaj JS, Salzman N, Acharya C, Takei H, Kakiyama G, Fagan A, White MB, Gavis EA, Holtz ML, Hayward M, et al. Microbial functional change is linked with clinical outcomes after capsular fecal transplant in cirrhosis. JCI Insight. 2019;4(24). doi:10.1172/jci.insight.133410.
  • Zhang W, Qu W, Wang H, Yan H. Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress. Transl Psychiatry. 2021;11(131). doi:10.1038/s41398-021-01254-5.
  • Hasan N, Yang H. Factors affecting the composition of the gut microbiota, and its modulation. PeerJ. 2019;7:e7502–e7502.
  • Kump P, Wurm P, Gröchenig HP, Wenzl H, Petritsch W, Halwachs B, Wagner M, Stadlbauer V, Eherer A, Hoffmann KM, et al. The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis. Aliment. Pharmacol. Ther. 2018;47(1):67–77. doi:10.1111/apt.14387.
  • Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, Gevers D, Ting A, Robson SC, Moss AC. Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn’s Disease. Inflamm. Bowel Dis. 2016;22(9):2182–2190. doi:10.1097/MIB.0000000000000893.
  • Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016;8(51). doi:10.1186/s13073-016-0307-y.
  • Zhao L, Zhang F, Ding X, Wu G, Lam YY, Wang X, Fu H, Xue X, Lu C, Ma J, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science. 2018;359(6380):1151–1156. doi:10.1126/science.aao5774.
  • Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174–180. doi:10.1038/nature09944.
  • Wilson BC, Vatanen T, Cutfield WS, O’Sullivan JM. The Super-Donor Phenomenon in Fecal Microbiota Transplantation. Front Cell Infect Microbiol. 2019;9(2). doi:10.3389/fcimb.2019.00002.
  • Vermeire S, Joossens M, Verbeke K, Wang J, Machiels K, Sabino J, Ferrante M, Van Assche G, Rutgeerts P, Raes J.  Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease. J Crohn’s Colitis. 2016;10(4):387–394. doi:10.1093/ecco-jcc/jjv203.
  • Nguyen TLA, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis. Model. Mech. 2015;8(1):1–16. doi:10.1242/dmm.017400.
  • Canibe N, O’Dea M, Abraham S. Potential relevance of pig gut content transplantation for production and research. J Anim Sci Biotechnol. 2019;10(55). doi:10.1186/s40104-019-0363-4.
  • Rawls JF, Mahowald MA, Ley RE, Gordon JI. Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection. Cell. 2006;127(2):423–433. doi:10.1016/j.cell.2006.08.043.
  • Valenzuela MJ, Caruffo M, Herrera Y, Medina DA, Coronado M, Feijóo CG, Muñoz S, Garrido D, Troncoso M, Figueroa G, et al. Evaluating the Capacity of Human Gut Microorganisms to Colonize the Zebrafish Larvae (Danio rerio). Front Microbiol. 2018;9(1032). doi:10.3389/fmicb.2018.01032.
  • Ericsson AC, Personett AR, Turner G, Dorfmeyer RA, Franklin CL. Variable Colonization after Reciprocal Fecal Microbiota Transfer between Mice with Low and High Richness Microbiota. Front Microbiol. 2017;8(196). doi:10.3389/fmicb.2017.00196.
  • Wos-Oxley M, Bleich A, Oxley AP, Kahl S, Janus LM, Smoczek A, Nahrstedt H, Pils MC, Taudien S, Platzer M, et al. Comparative evaluation of establishing a human gut microbial community within rodent models. Gut Microbes. 2012;3(3):1–16. doi:10.4161/gmic.19934.
  • Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, et al. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology. 2014;147:1055–63.e8. doi:10.1053/j.gastro.2014.07.020.
  • Li N, Zuo B, Huang S, Zeng B, Han D, Li T, Liu T, Wu Z, Wei H, Zhao J, Wang J. Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation. Microbiome. 2020;8(161). doi:10.1186/s40168-020-00917-7.
  • Kim YS, Unno T, Kim BY, Park MS. Sex differences in gut microbiota. World J. Men?s Heal. 2020;38(1):48–60. doi:10.5534/wjmh.190009.
  • Org E, Mehrabian M, Parks BW, Shipkova P, Liu X, Drake TA, Lusis AJ.  Sex differences and hormonal effects on gut microbiota composition in mice. Gut Microbes. 2016;7(4):313–322. doi:10.1080/19490976.2016.1203502.
  • Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS.  Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity. Science. 2013;339(6123):1084–1088. doi:10.1126/science.1233521.
  • Fransen F, van Beek AA, Borghuis T, Meijer B, Hugenholtz F, van der Gaast-de Jongh C, Savelkoul HF, de Jonge MI, Faas MM, Boekschoten MV, et al. The Impact of Gut Microbiota on Gender-Specific Differences in Immunity. Front Immunol. 2017;8(754). doi:10.3389/fimmu.2017.00754.
  • Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF. Stabilization of the murine gut microbiome following weaning. Gut Microbes. 2012;3(4):383–393. doi:10.4161/gmic.21008.
  • Laukens D, Brinkman BM, Raes J, De Vos M, Vandenabeele P. Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design. FEMS Microbiol. Rev. 2016;40(1):117–132. doi:10.1093/femsre/fuv036.
  • Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D,  et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell. 2014;158(4):705–721. doi:10.1016/j.cell.2014.05.052.
  • D'Amato A, Di Cesare Mannelli L, Lucarini E, Man AL, Le Gall G, Branca JJV, Ghelardini C, Amedei A, Bertelli E, Regoli M, et al. Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients. bioRxiv. 2020;866459. doi:10.1101/866459.
  • Kundu P, Lee HU, Garcia-Perez I, Tay EXY, Kim H, Faylon LE, Martin KA, Purbojati R, Drautz-Moses DI,  et al. Neurogenesis and prolongevity signaling in young germ-free mice transplanted with the gut microbiota of old mice. Sci. Transl. Med. 2019;11(eaau4760):eaau4760. doi:10.1126/scitranslmed.aau4760.
  • Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, et al. A catalog of the mouse gut metagenome. Nat. Biotechnol. 2015;33(10):1103. doi:10.1038/nbt.3353.
  • Bo TB, Zhang XY, Kohl KD, Wen J, Tian SJ, Wang DH.  Coprophagy prevention alters microbiome, metabolism, neurochemistry, and cognitive behavior in a small mammal. ISME J. 2020;14(10):2625–2645. doi:10.1038/s41396-020-0711-6.
  • Rausch P, Basic M, Batra A, Bischoff SC, Blaut M, Clavel T, Gläsner J, Gopalakrishnan S, Grassl GA, Günther C, et al. Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. Int. J. Med. Microbiol. 2016;306(5):343–355. doi:10.1016/j.ijmm.2016.03.004.
  • Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, et al. Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. Science (80-). 2013;339(6119):548–554. doi:10.1126/science.1229000.
  • Schroeder BO, Birchenough GMH, Ståhlman M, Arike L, Johansson MEV, Hansson GC, Bäckhed F. Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration. Cell Host Microbe. 2018;23(1):27–40.e7. doi:10.1016/j.chom.2017.11.004.
  • David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–563. doi:10.1038/nature12820.
  • Yanze L, Wenming C, Gao NL, Xing-Ming Zhao W-HC. Consistent alterations of human fecal microbes after transplanted to germ-free mice. Genomics ProteomicsBioinformatics 2018;III:224–234.
  • Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, Palumbo AV, Chesler EJ, Podar M. Host genetic and environmental effects on mouse intestinal microbiota. ISME J. 2012;6(11):2033–2044. doi:10.1038/ismej.2012.54.
  • Lee J, Venna VR, Durgan DJ, Shi H, Hudobenko J, Putluri N, Petrosino J, McCullough LD, Bryan RM.  Young versus aged microbiota transplants to germ-free mice: increased short-chain fatty acids and improved cognitive performance. Gut Microbes. 2020;12(1):1–14. doi:10.1080/19490976.2020.1814107.
  • Lee J, d'Aigle J, Atadja L, Quaicoe V, Honarpisheh P, Ganesh BP, Hassan A, Graf J, Petrosino J, Putluri N,  et al. Gut Microbiota-Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice. Circ. Res. 2020;127(4):453–465. doi:10.1161/CIRCRESAHA.119.316448.
  • Pan F, Zhang L, Li M, Hu Y, Zeng B, Yuan H, Zhao L, Zhang C. Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice. Microbiome. 2018;6(54). doi:10.1186/s40168-018-0440-5.
  • Rogier R, Ederveen THA, Boekhorst J, Wopereis H, Scher JU, Manasson J, Frambach SJCM, Knol J, Garssen J, van der Kraan PM, et al. Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis. Microbiome. 2017;5(1):63. doi:10.1186/s40168-017-0278-2.
  • Binyamin D, Werbner N, Nuriel-Ohayon M, Uzan A, Mor H, Abbas A, Ziv O, Teperino R, Gutman R, Koren O. The aging mouse microbiome has obesogenic characteristics. Genome Med. 2020;12(1):87. doi:10.1186/s13073-020-00784-9.
  • Cui B, Su D, Li W, She X, Zhang M, Wang R, Zhai Q. Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer’s disease. J Neuroinflammation. 2018;15(1):190. doi:10.1186/s12974-018-1223-4.
  • Albouery M, Buteau B, Grégoire S, Cherbuy C, Pais de Barros JP, Martine L, Chain F, Cabaret S, Berdeaux O, Bron AM, et al. Age-Related Changes in the Gut Microbiota Modify Brain Lipid Composition. Front Cell Infect Microbiol. 2019;9:444. doi:10.3389/fcimb.2019.00444.
  • Mell B, Jala VR, Mathew AV, Byun J, Waghulde H, Zhang Y, Haribabu B, Vijay-Kumar M, Pennathur S, Joe B. Evidence for a link between gut microbiota and hypertension in the Dahl rat. Physiol Genomics. 2015;47(6):187–197. doi:10.1152/physiolgenomics.00136.2014.
  • Li Y, Ning L, Yin Y, Wang R, Zhang Z, Hao L, Wang B, Zhao X, Yang X, Yin L, et al. Age-related shifts in gut microbiota contribute to cognitive decline in aged rats. Aging (Albany NY). 2020;12(9):7801–7817. doi:10.18632/aging.103093.
  • Chen Y, Zhang S, Zeng B, Zhao J, Yang M, Zhang M, Li Y, Ni Q, Wu D, Li Y.  Transplant of microbiota from long-living people to mice reduces aging-related indices and transfers beneficial bacteria. Aging (Albany NY). 2020;12(6):4778–4793. doi:10.18632/aging.102872.
  • Planer JD, Peng Y, Kau AL, Blanton LV, Ndao IM, Tarr PI, Warner BB, Gordon JI. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature. 2016;534(7606):263–266. doi:10.1038/nature17940.
  • Fielding RA, Reeves AR, Jasuja R, Liu C, Barrett BB, Lustgarten MS.  Muscle strength is increased in mice that are colonized with microbiota from high-functioning older adults. Exp Gerontol. 2019;127:110722. doi:10.1016/j.exger.2019.110722.
  • Xiao HW, Ge C, Feng GX, Li Y, Luo D, Dong JL, Li H, Wang H, Cui M, Fan SJ. Gut microbiota modulates alcohol withdrawal-induced anxiety in mice. Toxicol Lett. 2018;287:23–30. doi:10.1016/j.toxlet.2018.01.021.
  • Samuelson DR, Shellito JE, Maffei VJ, Tague ED, Campagna SR, Blanchard EE, Luo M, Taylor CM, Ronis MJJ, Molina PE, et al. Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae. PLoS Pathog. 2017;13(6):e1006426. doi:10.1371/journal.ppat.1006426.
  • JJiang Y , Liu Y , Gao M , Xue M , Wang Z , Liang H . Nicotinamide riboside alleviates alcohol-induced depression-like behaviours in C57BL/6J mice by altering the intestinal microbiota associated with microglial activation and BDNF expression. Food Funct. 2020;11(1):378–391. doi:10.1039/C9FO01780A.
  • Uebanso T, Kano S, Yoshimoto A, Naito C, Shimohata T, Mawatari K, Takahashi A. Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice. Nutrients. 2017;14;9(7):756. doi: 10.3390/nu9070756..
  • Yu L, Wang L, Yi H, Wu X. Beneficial effects of LRP6-CRISPR on prevention of alcohol-related liver injury surpassed fecal microbiota transplant in a rat model. Gut Microbes. 2020;11(4):1015–1029. doi:10.1080/19490976.2020.1736457.
  • Zhao W, Hu Y, Li C, Li N, Zhu S, Tan X, Li M, Zhang Y, Xu Z, Ding Z, et al. Transplantation of fecal microbiota from patients with alcoholism induces anxiety/depression behaviors and decreases brain mGluR1/PKC ε levels in mouse. Biofactors. 2020;46(1):38–54. doi:10.1002/biof.1567.
  • Wrzosek L, Ciocan D, Hugot C, Spatz M, Dupeux M, Houron C, Lievin-Le Moal V, Puchois V, Ferrere G, Trainel N, et al. Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury. Gut. 2021;70(7):1299–1308. doi:10.1136/gutjnl-2020-321565.
  • Samuelson DR, Siggins RW, Ruan S, Amedee AM, Sun J, Zhu QK, Marasco WA, Taylor CM, Luo M, Welsh DA, Shellito JE. Alcohol consumption increases susceptibility to pneumococcal pneumonia in a humanized murine HIV model mediated by intestinal dysbiosis. Alcohol. 2019;80:33–43. doi:10.1016/j.alcohol.2018.08.012.
  • Kim MS, Kim Y, Choi H, Kim W, Park S, Lee D, Kim DK, Kim HJ, Choi H, Hyun DW, et al. Transfer of a healthy microbiota reduces amyloid and tau pathology in an Alzheimer’s disease animal model. Gut. 2020;69(2):283–294. doi:10.1136/gutjnl-2018-317431.
  • Zhou H, Tai J, Xu H, Lu X, Meng D. Xanthoceraside Could Ameliorate Alzheimer’s Disease Symptoms of Rats by Affecting the Gut Microbiota Composition and Modulating the Endogenous Metabolite Levels. Front Pharmacol. 2019;10:1035. doi:10.3389/fphar.2019.01035.
  • Fujii Y, Nguyen TTT, Fujimura Y, Kameya N, Nakamura S, Arakawa K, Morita H. Fecal metabolite of a gnotobiotic mouse transplanted with gut microbiota from a patient with Alzheimer’s disease. Biosci. Biotechnol. Biochem. 2019;83(11):2144–2152. doi:10.1080/09168451.2019.1644149.
  • Goo N, Bae HJ, Park K, Kim J, Jeong Y, Cai M, Cho K, Jung SY, Kim DH, Ryu JH. The effect of fecal microbiota transplantation on autistic-like behaviors in Fmr1 KO mice. Life Sci. 2020;262:118497. doi:10.1016/j.lfs.2020.118497.
  • Li Y, Luo ZY, Hu YY, Bi YW, Yang JM, Zou WJ, Song YL, Li S, Shen T, Li SJ, et al. The gut microbiota regulates autism-like behavior by mediating vitamin B(6) homeostasis in EphB6-deficient mice. Microbiome. 2020;8(1):120. doi:10.1186/s40168-020-00884-z.
  • Chen K, Fu Y, Wang Y, Liao L, Xu H, Zhang A, Zhang J, Fan L, Ren J, Fang B. Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder. Microb. Ecol. 2020;80(2):475–486. doi:10.1007/s00248-020-01494-w.
  • Lee B, Lee J, Woo MY, Lee MJ, Shin HJ, Kim K, Park S. Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner. Microorganisms. 2020;8(9):1395. doi:10.3390/microorganisms8091395.
  • Zhang X, Coker OO, Chu ES, Fu K, Lau HCH, Wang YX, Chan AWH, Wei H, Yang X, Sung JJY,  et al. Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites. Gut. 2020. doi:10.1136/gutjnl-2019-319664.
  • Almeida RR, Vieira RS, Castoldi A, Terra FF, Melo ACL, Canesso MCC, Lemos L, Cipelli M, Rana N, Hiyane MI, et al. Host dysbiosis negatively impacts IL-9-producing T-cell differentiation and antitumour immunity. Br J Cancer. 2020;123(4):534–541. doi:10.1038/s41416-020-0915-6.
  • Paik J, Meeker S, Hsu CC, Seamons A, Pershutkina O, Snyder JM, Brabb T, Maggio-Price L. Validation studies for germ-free Smad3-/- mice as a bio-assay to test the causative role of fecal microbiomes in IBD. Gut Microbes. 2020;11(1):21–31. doi:10.1080/19490976.2019.1611151.
  • Zhu Z, Huang J, Li X, Xing J, Chen Q, Liu R, Hua F, Qiu Z, Song Y, Bai C,  et al. Gut microbiota regulate tumor metastasis via circRNA/miRNA networks. Gut Microbes. 2020;12(1):1788891. doi:10.1080/19490976.2020.1788891.
  • Nie X, Li L, Yi M, Qin W, Zhao W, Li F, Wu B, Yuan X. et al. The Intestinal Microbiota Plays as a Protective Regulator Against Radiation Pneumonitis. Radiat. Res. 2020;194(1):52–60. doi:10.1667/RR15579.1.
  • Alrafas HR, Busbee PB, Chitrala KN, Nagarkatti M, Nagarkatti P. Alterations in the Gut Microbiome and Suppression of Histone Deacetylases by Resveratrol Are Associated with Attenuation of Colonic Inflammation and Protection Against Colorectal Cancer. J. Clin. Med. 2020;9(6):1796. doi:10.3390/jcm9061796.
  • Toubai T, Fujiwara H, Rossi C, Riwes M, Tamaki H, Zajac C, Liu C, Mathew AV, Byun J, Oravecz-Wilson K,  et al. Host NLRP6 exacerbates graft-versus-host disease independent of gut microbial composition. Nat. Microbiol. 2019;4(5):800–812. doi:10.1038/s41564-019-0373-1.
  • Sougiannis AT, VanderVeen BN, Enos RT, Velazquez KT, Bader JE, Carson M, Chatzistamou I, Walla M, Pena MM, Kubinak JL, et al. Impact of 5 fluorouracil chemotherapy on gut inflammation, functional parameters, and gut microbiota. Brain Behav Immun. 2019;80:44–55. doi:10.1016/j.bbi.2019.02.020.
  • Uribe-Herranz M, Bittinger K, Rafail S, Guedan S, Pierini S, Tanes C, Ganetsky A, Morgan MA, Gill S, Tanyi JL,  et al. Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. JCI Insight. 2018;3. doi:10.1172/jci.insight.94952
  • Jala VR, Maturu P, Bodduluri SR, Krishnan E, Mathis S, Subbarao K, Wang M, Jenson AB, Proctor ML, Rouchka EC, et al. Leukotriene B4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression. Oncoimmunology. 2017;6(e1361593):e1361593. doi:10.1080/2162402X.2017.1361593.
  • Sivan A, Corrales L, Hubert N, Williams JB, Aquino-Michaels K, Earley ZM, Benyamin FW, Lei YM, Jabri B, Alegre ML, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science. 2015;350(6264):1084–1089. doi:10.1126/science.aac4255.
  • Gong Y, Dong R, Gao X, Li J, Jiang L, Zheng J, Cui S, Ying M, Yang B, Cao J, He Q. Neohesperidin prevents colorectal tumorigenesis by altering the gut microbiota. Pharmacol. Res. 2019;148(104460):104460. doi:10.1016/j.phrs.2019.104460.
  • Cui M, Xiao H, Li Y, Zhou L, Zhao S, Luo D, Zheng Q, Dong J, Zhao Y, Zhang X, et al. Faecal microbiota transplantation protects against radiation-induced toxicity. EMBO Mol. Med. 2017;9(4):448–461. doi:10.15252/emmm.201606932.
  • Vicente-Dueñas C, Janssen S, Oldenburg M, Auer F, González-Herrero I, Casado-García A, Isidro-Hernández M, Raboso-Gallego J, Westhoff P, Pandyra AA, et al. An intact gut microbiome protects genetically predisposed mice against leukemia. Blood. 2020;136(18):2003–2017. doi:10.1182/blood.2019004381.
  • Ubeda C, Bucci V, Caballero S, Djukovic A, Toussaint NC, Equinda M, Lipuma L, Ling L, Gobourne A, No D,  et al. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect. Immun. 2013;81(3):965–973. doi:10.1128/IAI.01197-12.
  • Zhang P, Liu J, Xiong B, Zhang C, Kang B, Gao Y, Li Z, Ge W, Cheng S, Hao Y, et al. Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis. Microbiome. 2020;8(1):112. doi:10.1186/s40168-020-00886-x.
  • Poutahidis T, Varian BJ, Levkovich T, Lakritz JR, Mirabal S, Kwok C, Ibrahim YM, Kearney SM, Chatzigiagkos A, Alm EJ, et al. Dietary microbes modulate transgenerational cancer risk. Cancer Res. 2015;75(7):1197–1204. doi:10.1158/0008-5472.CAN-14-2732.
  • Shi L, Sheng J, Wang M, Luo H, Zhu J, Zhang B, Liu Z, Yang X. Combination Therapy of TGF-β Blockade and Commensal-derived Probiotics Provides Enhanced Antitumor Immune Response and Tumor Suppression. Theranostics. 2019;9(14):4115–4129. doi:10.7150/thno.35131.
  • Chang CW, Lee HC, Li LH, Chiang Chiau JS, Wang TE, Chuang WH, Chen MJ, Wang HY, Shih SC, Liu CY, et al. Fecal Microbiota Transplantation Prevents Intestinal Injury, Upregulation of Toll-Like Receptors, and 5-Fluorouracil/Oxaliplatin-Induced Toxicity in Colorectal Cancer. Int J Mol Sci. 2020 Jan 8;21(2):386. doi: 10.3390/ijms21020386.
  • Wang Z, Hua W, Li C, Chang H, Liu R, Ni Y, Sun H, Li Y, Wang X, Hou M, et al. Protective Role of Fecal Microbiota Transplantation on Colitis and Colitis-Associated Colon Cancer in Mice Is Associated With Treg Cells. Front Microbiol. 2019;10:2498. doi:10.3389/fmicb.2019.02498.
  • Zhang X, Zhao S, Song X, Jia J, Zhang Z, Zhou H, Fu H, Cui H, Hu S, Fang M, et al. Inhibition effect of glycyrrhiza polysaccharide (GCP) on tumor growth through regulation of the gut microbiota composition. . Journal of Pharmacological Sciences. 2018;137(4):324–332. doi:10.1016/j.jphs.2018.03.006.
  • Chen H, Zhang F, Li R, Liu Y, Wang X, Zhang X, Xu C, Li Y, Guo Y, Yao Q. Berberine regulates fecal metabolites to ameliorate 5-fluorouracil induced intestinal mucositis through modulating gut microbiota. Biomed Pharmacother. 2020;124:109829. doi:10.1016/j.biopha.2020.109829.
  • Wu R, Mei X, Ye Y, Xue T, Wang J, Sun W, Lin C, Xue R, Zhang J, Xu D. Zn(II)-curcumin solid dispersion impairs hepatocellular carcinoma growth and enhances chemotherapy by modulating gut microbiota-mediated zinc homeostasis. Pharmacol Res. 2018;3:104454. doi:10.1016/j.phrs.2019.104454.
  • Sui H, Zhang L, Gu K, Chai N, Ji Q, Zhou L, Wang Y, Ren J, Yang L, Zhang B, et al. YYFZBJS ameliorates colorectal cancer progression in Apc(Min/+) mice by remodeling gut microbiota and inhibiting regulatory T-cell generation. Cell Commun. Signal. 2020;18(1):113. doi:10.1186/s12964-020-00596-9.
  • Baxter NT, Zackular JP, Chen GY, Schloss PD. Structure of the gut microbiome following colonization with human feces determines colonic tumor burden. Microbiome. 2014;2(1):20. doi:10.1186/2049-2618-2-20.
  • Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, Quesada P, Sahin I, Chandra V, San Lucas A, et al. Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes. Cell. 2019;178(4):795–806.e12. doi:10.1016/j.cell.2019.07.008.
  • Li L, Li X, Zhong W, Yang M, Xu M, Sun Y, Ma J, Liu T, Song X, Dong W, et al. Gut microbiota from colorectal cancer patients enhances the progression of intestinal adenoma in Apc(min/+) mice. EBioMedicine. 2019;48:301–315. doi:10.1016/j.ebiom.2019.09.021.
  • Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature. 2019;565(7741):600–605. doi:10.1038/s41586-019-0878-z.
  • Jian X, Zhu Y, Ouyang J, Wang Y, Lei Q, Xia J, Guan Y, Zhang J, Guo J, He Y, et al. Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria. Microbiome. 2020;8(1):74. doi:10.1186/s40168-020-00854-5.
  • Sobhani I, Bergsten E, Couffin S, Amiot A, Nebbad B, Barau C, de'Angelis N, Rabot S, Canoui-Poitrine F, Mestivier D, et al. Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures. Proc. Natl. Acad. Sci. U. S. A. 2019;116(48):24285–24295. doi:10.1073/pnas.1912129116.
  • Su A, Yang W, Zhao L, Pei F, Yuan B, Zhong L, Ma G, Hu Q.  Flammulina velutipes polysaccharides improve scopolamine-induced learning and memory impairment in mice by modulating gut microbiota composition. Food Funct. 2018;9:1424–1432.
  • Li X, Li X, Shang Q, Gao Z, Hao F, Guo H, Guo C.  Fecal microbiota transplantation (FMT) could reverse the severity of experimental necrotizing enterocolitis (NEC) via oxidative stress modulation. Free Radic Biol Med. 2017;108:32–43. doi:10.1016/j.freeradbiomed.2017.03.011.
  • Brinkman BM, Becker A, Ayiseh RB, Hildebrand F, Raes J, Huys G, Vandenabeele P. Gut microbiota affects sensitivity to acute DSS-induced colitis independently of host genotype. Inflamm. Bowel Dis. 2013;19(12):2560–2567. doi:10.1097/MIB.0b013e3182a8759a.
  • Yin A, Luo Y, Chen W, He M, Deng JH, Zhao N, Cao L, Wang L. FAM96A Protects Mice From Dextran Sulfate Sodium (DSS)-Induced Colitis by Preventing Microbial Dysbiosis. Front Cell Infect Microbiol. 2019;9:381. doi:10.3389/fcimb.2019.00381.
  • Spalinger MR, Schwarzfischer M, Hering L, Shawki A, Sayoc A, Santos A, Gottier C, Lang S, Bäbler K, Geirnaert A, et al. Loss of PTPN22 abrogates the beneficial effect of cohousing-mediated fecal microbiota transfer in murine colitis. Mucosal Immunol. 2019;12(6):1336–1347. doi:10.1038/s41385-019-0201-1.
  • Lee C, Hong SN, Paik NY, Kim TJ, Kim ER, Chang DK, Kim YH. CD1d Modulates Colonic Inflammation in NOD2-/- Mice by Altering the Intestinal Microbial Composition Comprising Acetatifactor muris. J Crohns Colitis. 2019;13(8):1081–1091. doi:10.1093/ecco-jcc/jjz025.
  • Mishima Y, Oka A, Liu B, Herzog JW, Eun CS, Fan TJ, Bulik-Sullivan E, Carroll IM, Hansen JJ, Chen L, et al. Microbiota maintain colonic homeostasis by activating TLR2/MyD88/PI3K signaling in IL-10-producing regulatory B cells. J. Clin. Invest. 2019;129(9):3702–3716. doi:10.1172/JCI93820.
  • Burrello C, Giuffrè MR, Macandog AD, Diaz-Basabe A, Cribiù FM, Lopez G, Borgo F, Nezi L, Caprioli F, Vecchi M, et al. Fecal Microbiota Transplantation Controls Murine Chronic Intestinal Inflammation by Modulating Immune Cell Functions and Gut Microbiota Composition. Cells. 2019;8(6):517. doi:10.3390/cells8060517.
  • He Y, Yu H, Ge Y, Li X, Jiang M, Liu Y, Li X, Wang Y, Guo M, Qin X, et al. Bacterial β-glucuronidase alleviates dextran sulfate sodium-induced colitis in mice: a possible crucial new diagnostic and therapeutic target for inflammatory bowel disease. Biochem. Biophys. Res. Commun. 2019;513(2):426–433. doi:10.1016/j.bbrc.2019.03.196.
  • Goethel A, Turpin W, Rouquier S, Zanello G, Robertson SJ, Streutker CJ, Philpott DJ, Croitoru K.  Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure. Mucosal Immunol. 2019;12(3):720–732. doi:10.1038/s41385-018-0128-y.
  • Zhao M, Xiong X, Ren K, Xu B, Cheng M, Sahu C, Wu K, Nie Y, Huang Z, Blumberg RS, et al. Deficiency in intestinal epithelial O-GlcNAcylation predisposes to gut inflammation. EMBO Mol. Med. 2018;10(8). doi:10.15252/emmm.201708736.
  • Selvanantham T, Lin Q, Guo CX, Surendra A, Fieve S, Escalante NK, Guttman DS, Streutker CJ, Robertson SJ, Philpott DJ, et al. NKT Cell-Deficient Mice Harbor an Altered Microbiota That Fuels Intestinal Inflammation during Chemically Induced Colitis. J. Immunol. 2016;197(11):4464–4472. doi:10.4049/jimmunol.1601410.
  • Ward NL, Phillips CD, Nguyen DD, Shanmugam NK, Song Y, Hodin R, Shi HN, Cherayil BJ, Goldstein AM. Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis. Inflamm. Bowel Dis. 2016;22(10):2328–2340. doi:10.1097/MIB.0000000000000914.
  • Meisel M, Mayassi T, Fehlner-Peach H, Koval JC, O'Brien SL, Hinterleitner R, Lesko K, Kim S, Bouziat R, Chen L, et al. Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis. ISME J. 2017;11(1):15–30. doi:10.1038/ismej.2016.114.
  • Sun X, Winglee K, Gharaibeh RZ, Gauthier J, He Z, Tripathi P, Avram D, Bruner S, Fodor A, Jobin C. Microbiota-Derived Metabolic Factors Reduce Campylobacteriosis in Mice. Gastroenterology. 2018;154(6):1751–1763.e2. doi:10.1053/j.gastro.2018.01.042.
  • Schulfer AF, Battaglia T, Alvarez Y, Bijnens L, Ruiz VE, Ho M, Robinson S, Ward T, Cox LM, Rogers AB, et al. Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice. Nat. Microbiol. 2018;3(2):234–242. doi:10.1038/s41564-017-0075-5.
  • Darnaud M, Dos Santos A, Gonzalez P, Augui S, Lacoste C, Desterke C, De Hertogh G, Valentino E, Braun E, Zheng J, et al. Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis. Gastroenterology. 2018;154(4):1009–1023.e14. doi:10.1053/j.gastro.2017.11.003.
  • Levy M, Thaiss CA, Zeevi D, Dohnalová L, Zilberman-Schapira G, Mahdi JA, David E, Savidor A, Korem T, Herzig Y, et al. Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling. Cell. 2015;163(6):1428–1443. doi:10.1016/j.cell.2015.10.048.
  • Runtsch MC, Hu R, Alexander M, Wallace J, Kagele D, Petersen C, Valentine JF, Welker NC, Bronner MP, Chen X, et al. MicroRNA-146a constrains multiple parameters of intestinal immunity and increases susceptibility to DSS colitis. Oncotarget. 2015;6(30):28556–28572. doi:10.18632/oncotarget.5597.
  • He Y, Li X, Yu H, Ge Y, Liu Y, Qin X, Jiang M, Wang X. The Functional Role of Fecal Microbiota Transplantation on Dextran Sulfate Sodium-Induced Colitis in Mice. Front Cell Infect Microbiol. 2019;9:393. doi:10.3389/fcimb.2019.00393.
  • Nagy-Szakal D, Mir SA, Harris RA, Dowd SE, Yamada T, Lacorazza HD, Tatevian N, Smith CW, de Zoeten EF, Klein J,  et al. Loss of n-6 fatty acid induced pediatric obesity protects against acute murine colitis. FASEB J Off Publ Fed Am Soc Exp Biol. 2015;29:3151–3159.
  • Jacob N, Jacobs JP, Kumagai K, Ha CWY, Kanazawa Y, Lagishetty V, Altmayer K, Hamill AM, Von Arx A, Sartor RB, et al. Inflammation-independent TL1A-mediated intestinal fibrosis is dependent on the gut microbiome. Mucosal Immunol. 2018;11(5):1466–1476. doi:10.1038/s41385-018-0055-y.
  • Ihekweazu FD, Fofanova TY, Queliza K, Nagy-Szakal D, Stewart CJ, Engevik MA, Hulten KG, Tatevian N, Graham DY, Versalovic J,  et al. Bacteroides ovatus ATCC 8483 monotherapy is superior to traditional fecal transplant and multi-strain bacteriotherapy in a murine colitis model. Gut Microbes. 2019;10(4):504–520. doi:10.1080/19490976.2018.1560753.
  • Shanmugam NKN, Trebicka E, Fu -L-L, Shi HN, Cherayil BJ. Intestinal inflammation modulates expression of the iron-regulating hormone hepcidin depending on erythropoietic activity and the commensal microbiota. J. Immunol. 2014;193(3):1398–1407. doi:10.4049/jimmunol.1400278.
  • Ihara S, Hirata Y, Serizawa T, Suzuki N, Sakitani K, Kinoshita H, Hayakawa Y, Nakagawa H, Ijichi H, Tateishi K, et al. TGF-β Signaling in Dendritic Cells Governs Colonic Homeostasis by Controlling Epithelial Differentiation and the Luminal Microbiota. J. Immunol. 2016;196(11):4603–4613. doi:10.4049/jimmunol.1502548.
  • Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J, Eisenbarth SC, Gordon JI, et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell. 2011;145(5):745–757. doi:10.1016/j.cell.2011.04.022.
  • Lee JC, Lee HY, Kim TK, Kim MS, Park YM, Kim J, Park K, Kweon MN, Kim SH, Bae JW, et al. Obesogenic diet-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis. PLoS One. 2017;12(11):e0187515. doi:10.1371/journal.pone.0187515.
  • Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, Ajami NJ, Wong MC, Ghazaryan A, Valentine JF, et al. Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis. Cell Host Microbe. 2019;25(2):285–299.e8. doi:10.1016/j.chom.2019.01.008.
  • Gupta S, Basu S, Bal V, Rath S, George A. Gut IgA abundance in adult life is a major determinant of resistance to dextran sodium sulfate-colitis and can compensate for the effects of inadequate maternal IgA received by neonates. Immunology. 2019;158(1):19–34. doi:10.1111/imm.13091.
  • Wang L, An J, Song S, Mei M, Li W, Ding F, Liu S. Electroacupuncture preserves intestinal barrier integrity through modulating the gut microbiota in DSS-induced chronic colitis. Life Sci. 2020;261:118473. doi:10.1016/j.lfs.2020.118473.
  • Yan Y, Zhou X, Guo K, Zhou F, Yang H. Chlorogenic Acid Protects Against Indomethacin-Induced Inflammation and Mucosa Damage by Decreasing Bacteroides-Derived LPS. Front Immunol. 2020;11:1125. doi:10.3389/fimmu.2020.01125.
  • Liu Y, Luo L, Luo Y, Zhang J, Wang X, Sun K, Zeng L. Prebiotic Properties of Green and Dark Tea Contribute to Protective Effects in Chemical-Induced Colitis in Mice: a Fecal Microbiota Transplantation Study. J. Agric. Food Chem. 2020;68(23):6368–6380. doi:10.1021/acs.jafc.0c02336.
  • Pickert G, Wirtz S, Matzner J, Ashfaq-Khan M, Heck R, Rosigkeit S, Thies D, Surabattula R, Ehmann D, Wehkamp J, et al. Wheat Consumption Aggravates Colitis in Mice via Amylase Trypsin Inhibitor-mediated Dysbiosis. Gastroenterology. 2020;159(1):257–272.e17. doi:10.1053/j.gastro.2020.03.064.
  • Wu H, Rao Q, Ma GC, Yu XH, Zhang CE, Ma ZJ. Effect of Triptolide on Dextran Sodium Sulfate-Induced Ulcerative Colitis and Gut Microbiota in Mice. Front Pharmacol. 2019;10:1652. doi:10.3389/fphar.2019.01652.
  • Chen Y, Zhang L, Hong G, Huang C, Qian W, Bai T, Song J, Song Y, Hou X.  Probiotic mixtures with aerobic constituent promoted the recovery of multi-barriers in DSS-induced chronic colitis. Life Sci. 2020;240:117089.
  • Zou J, Zhao X, Shi Z, Zhang Z, Vijay-Kumar M, Chassaing B, Gewirtz AT. Critical role of innate immunity to flagellin in absence of adaptive immunity. J Infect Dis. 2020. doi:10.1093/infdis/jiaa521.
  • Hu S, Peng L, Kwak YT, Tekippe EM, Pasare C, Malter JS, Hooper LV, Zaki MH.  The DNA Sensor AIM2 Maintains Intestinal Homeostasis via Regulation of Epithelial Antimicrobial Host Defense. Cell Rep. 2015;13(9):1922–1936. doi:10.1016/j.celrep.2015.10.040.
  • Tian Z, et al. Beneficial Effects of Fecal Microbiota Transplantation on Ulcerative Colitis in Mice. Dig. Dis. Sci. 2016;61(8):2262–2271. doi:10.1007/s10620-016-4060-2.
  • Lee KW, Kim M, Lee CH. Treatment of Dextran Sulfate Sodium-Induced Colitis with Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Inhibitor MI-2 Is Associated with Restoration of Gut Immune Function and the Microbiota. Infect Immun. 2018;86(12). doi:10.1128/IAI.00091-18.
  • Kiyohara H, Sujino T, Teratani T, Miyamoto K, Arai MM, Nomura E, Harada Y, Aoki R, Koda Y, Mikami Y,  et al. Toll-Like Receptor 7 Agonist-Induced Dermatitis Causes Severe Dextran Sulfate Sodium Colitis by Altering the Gut Microbiome and Immune Cells. Cell. Mol. Gastroenterol. Hepatol. 2019;7(1):135–156. doi:10.1016/j.jcmgh.2018.09.010.
  • Reinoso Webb C, den Bakker H, Koboziev I, Jones-Hall Y, Rao Kottapalli K, Ostanin D, Furr KL, Mu Q, Luo XM, Grisham MB. Differential Susceptibility to T Cell-Induced Colitis in Mice: role of the Intestinal Microbiota. Inflamm. Bowel Dis. 2018;24(2):361–379. doi:10.1093/ibd/izx014.
  • Chen L, Wilson JE, Koenigsknecht MJ, Chou WC, Montgomery SA, Truax AD, Brickey WJ, Packey CD, Maharshak N, Matsushima GK, et al. NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth. Nat. Immunol. 2017;18(5):541–551. doi:10.1038/ni.3690.
  • Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat. Med. 2016;22(6):598–605. doi:10.1038/nm.4102.
  • Guo X-K, Ou J, Liang S, Zhou X, Hu X. Epithelial Hes1 maintains gut homeostasis by preventing microbial dysbiosis. Mucosal Immunol. 2018;11(3):716–726. doi:10.1038/mi.2017.111.
  • Wu J, Wei Z, Cheng P, Qian C, Xu F, Yang Y, Wang A, Chen W, Sun Z, Lu Y. Rhein modulates host purine metabolism in intestine through gut microbiota and ameliorates experimental colitis. Theranostics. 2020;10(23):10665–10679. doi:10.7150/thno.43528.
  • Shin JH, Lee YK, Shon WJ, Kim B, Jeon CO, Cho JY, Morse HC 3rd, Choi EY, Shin DM.  Gut microorganisms and their metabolites modulate the severity of acute colitis in a tryptophan metabolism-dependent manner. Eur. J. Nutr. 2020;59(8):3591–3601. doi:10.1007/s00394-020-02194-4.
  • Zachariassen LF, Hansen AK, Krych L, Nielsen DS, Holm TL, Tougaard P, Hansen CHF. Cesarean section increases sensitivity to oxazolone-induced colitis in C57BL/6 mice. Mucosal Immunol. 2019;12(6):1348–1357. doi:10.1038/s41385-019-0207-8.
  • Yoshimura T, McLean MH, Dzutsev AK, Yao X, Chen K, Huang J, Gong W, Zhou J, Xiang Y, H Badger J, et al. The Antimicrobial Peptide CRAMP is essential for colon homeostasis by maintaining microbiota Balance. J. Immunol. 2018;200(6):2174–2185. doi:10.4049/jimmunol.1602073.
  • Bernardazzi C, Xu H, Tong H, Laubitz D, Figliuolo da Paz V, Curiel L, Ghishan FK. An indisputable role of NHE8 in mucosal protection. Am. J. Physiol. Gastrointest. Liver Physiol. 2020;319(4):G421–G431. doi:10.1152/ajpgi.00246.2020.
  • Chassaing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, Ley RE, Gewirtz AT. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature. 2015;519(7541):92–96. doi:10.1038/nature14232.
  • Mir SA, Nagy-Szakal D, Dowd SE, Szigeti RG, Smith CW, Kellermayer R. Prenatal methyl-donor supplementation augments colitis in young adult mice. PLoS One. 2013;8(8):e73162. doi:10.1371/journal.pone.0073162.
  • Dziarski R, Park SY, Kashyap DR, Dowd SE, Gupta D. Pglyrp-regulated gut microflora prevotella falsenii, parabacteroides distasonis and bacteroides eggerthii enhance and alistipes finegoldii attenuates colitis in mice. PLoS One. 2016;11(1):e0146162. doi:10.1371/journal.pone.0146162.
  • Zhao D, Dai W, Tao H, Zhuang W, Qu M, Chang YN. Polysaccharide isolated from Auricularia auricular-judae (Bull.) prevents dextran sulfate sodium-induced colitis in mice through modulating the composition of the gut microbiota. J. Food Sci. 2020;85(9):2943–2951. doi:10.1111/1750-3841.15319.
  • Wu M, Li P, An Y, Ren J, Yan D, Cui J, Li D, Li M, Wang M, Zhong G. Phloretin ameliorates dextran sulfate sodium-induced ulcerative colitis in mice by regulating the gut microbiota. Pharmacol Res. 2019;150:104489. doi:10.1016/j.phrs.2019.104489.
  • Cui H, Cai Y, Wang L, Jia B, Li J, Zhao S, Chu X, Lin J, Zhang X, Bian Y, et al. Berberine regulates Treg/Th17 balance to treat ulcerative colitis through modulating the gut microbiota in the colon. Front Pharmacol. 2018;9:571. doi:10.3389/fphar.2018.00571.
  • Su C, Su L, Li Y, Long SR, Chang J, Zhang W, Walker WA, Xavier RJ, Cherayil BJ, Shi HN. Helminth-induced alterations of the gut microbiota exacerbate bacterial colitis. Mucosal Immunol. 2018;11(1):144–157. doi:10.1038/mi.2017.20.
  • Alrafas HR, Busbee PB, Nagarkatti M, Nagarkatti PS. Resveratrol modulates the gut microbiota to prevent murine colitis development through induction of Tregs and suppression of Th17 cells. J. Leukoc. Biol. 2019;106(2):467–480. doi:10.1002/JLB.3A1218-476RR.
  • Fan Q, Guan X, Hou Y, Liu Y, Wei W, Cai X, Zhang Y, Wang G, Zheng X, Hao H. Paeoniflorin modulates gut microbial production of indole-3-lactate and epithelial autophagy to alleviate colitis in mice. Phytomedicine. 2020;79:153345. doi:10.1016/j.phymed.2020.153345.
  • Ji J, Ge X, Chen Y, Zhu B, Wu Q, Zhang J, Shan J, Cheng H, Shi L. Daphnetin ameliorates experimental colitis by modulating microbiota composition and T(reg)/T(h)17 balance. FASEB J Off Publ Fed Am Soc Exp Biol. 2019;33:9308–9322.
  • Zhou J, Zhou Z, Ji P, Ma M, Guo J, Jiang S. Effect of fecal microbiota transplantation on experimental colitis in mice. Exp Ther Med. 2019;17:2581–2586. doi:10.3892/etm.2019.7263.
  • Harrison CA, Laubitz D, Ohland CL, Midura-Kiela MT, Patil K, Besselsen DG, Jamwal DR, Jobin C, Ghishan FK, Kiela PR. Microbial dysbiosis associated with impaired intestinal Na(+)/H(+) exchange accelerates and exacerbates colitis in ex-germ free mice. Mucosal Immunol. 2018;11(5):1329–1341. doi:10.1038/s41385-018-0035-2.
  • Faivre B, Bellenger J, Rieu A, Guivier E, Galan M, Ollivier A, Poloni L, Sorci G. Disentangling the effect of host genetics and gut microbiota on resistance to an intestinal parasite. Int. J. Parasitol. 2019;49(11):873–883. doi:10.1016/j.ijpara.2019.06.001.
  • Sun Z, Li J, Dai Y, Wang W, Shi R, Wang Z, Ding P, Lu Q, Jiang H, Pei W, et al. Indigo naturalis alleviates dextran sulfate sodium-induced colitis in rats via altering gut microbiota. Front Microbiol. 2020;11(731). doi:10.3389/fmicb.2020.00731.
  • Wang MX, Lin L, Chen YD, Zhong YP, Lin YX, Li P, Tian X, Han B, Xie ZY, Liao QF. Evodiamine has therapeutic efficacy in ulcerative colitis by increasing Lactobacillus acidophilus levels and acetate production. Pharmacol Res. 2020;159:104978. doi:10.1016/j.phrs.2020.104978.
  • Yan ZX, Gao XJ, Li T, Wei B, Wang PP, Yang Y, Yan R.  Fecal Microbiota Transplantation in Experimental Ulcerative Colitis Reveals Associated Gut Microbial and Host Metabolic Reprogramming. Appl. Environ. Microbiol. 2018;84(14). doi:10.1128/AEM.00434-18.
  • Gao XJ, Li T, Wei B, Yan ZX, Hu N, Huang YJ, Han BL, Wai TS, Yang W, Yan R. Bacterial outer membrane vesicles from dextran sulfate sodium-induced colitis differentially regulate intestinal UDP-glucuronosyltransferase 1A1 partially through toll-like receptor 4/mitogen-activated protein kinase/phosphatidylinositol 3-kinase pathway. Drug Metab. Dispos. 2018;46(3):292–302. doi:10.1124/dmd.117.079046.
  • Natividad JM, Pinto-Sanchez MI, Galipeau HJ, Jury J, Jordana M, Reinisch W, Collins SM, Bercik P, Surette MG, Allen-Vercoe E, et al. Ecobiotherapy rich in firmicutes decreases susceptibility to colitis in a humanized gnotobiotic mouse model. Inflamm. Bowel Dis. 2015;21(8):1883–1893. doi:10.1097/MIB.0000000000000422.
  • Seishima J, Iida N, Kitamura K, Yutani M, Wang Z, Seki A, Yamashita T, Sakai Y, Honda M, Yamashita T, et al. Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host. Genome Biol. 2019;20(1):252. doi:10.1186/s13059-019-1879-9.
  • von Klitzing E, Ekmekciu I, Bereswill S, Heimesaat MM. Acute ileitis facilitates infection with multidrug resistant Pseudomonas aeruginosa in human microbiota-associated mice. Gut Pathog. 2017;9(1):4. doi:10.1186/s13099-017-0154-4.
  • Lleal M, Sarrabayrouse G, Willamil J, Santiago A, Pozuelo M, Manichanh C. A single faecal microbiota transplantation modulates the microbiome and improves clinical manifestations in a rat model of colitis. EBioMedicine. 2019;48:630–641. doi:10.1016/j.ebiom.2019.10.002.
  • Frisbee AL, Saleh MM, Young MK, Leslie JL, Simpson ME, Abhyankar MM, Cowardin CA, Ma JZ, Pramoonjago P, Turner SD, et al. IL-33 drives group 2 innate lymphoid cell-mediated protection during Clostridium difficile infection. Nat. Commun. 2019;10(1):2712. doi:10.1038/s41467-019-10733-9.
  • Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE. Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases. Cell Rep. 2016;14(5):1049–1061. doi:10.1016/j.celrep.2016.01.009.
  • Mullish BH, McDonald JAK, Pechlivanis A, Allegretti JR, Kao D, Barker GF, Kapila D, Petrof EO, Joyce SA, Gahan CGM, et al. Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut. 2019;68(10):1791–1800. doi:10.1136/gutjnl-2018-317842.
  • McDonald JAK, Mullish BH, Pechlivanis A, Liu Z, Brignardello J, Kao D, Holmes E, Li JV, Clarke TB, Thursz MR, et al. Inhibiting growth of clostridioides difficile by restoring valerate, produced by the intestinal microbiota. Gastroenterology. 2018;155(5):1495–1507.e15. doi:10.1053/j.gastro.2018.07.014.
  • Collins J, Auchtung JM, Schaefer L, Eaton KA, Britton RA. Humanized microbiota mice as a model of recurrent Clostridium difficile disease. Microbiome. 2015;3(1):35. doi:10.1186/s40168-015-0097-2.
  • Jiang ZD, Alexander A, Ke S, Valilis EM, Hu S, Li B, DuPont HL. Stability and efficacy of frozen and lyophilized fecal microbiota transplant (FMT) product in a mouse model of Clostridium difficile infection (CDI). Anaerobe. 2017;48:110–114. doi:10.1016/j.anaerobe.2017.08.003.
  • Liu H, Tian R, Wang H, Feng S, Li H, Xiao Y, Luan X, Zhang Z, Shi N, Niu H,  et al. Gut microbiota from coronary artery disease patients contributes to vascular dysfunction in mice by regulating bile acid metabolism and immune activation. J. Transl. Med. 2020;18(1):382. doi:10.1186/s12967-020-02539-x.
  • Yu F, Han W, Zhan G, Li S, Xiang S, Zhu B, Jiang X, Yang L, Luo A, Hua F, et al. Abnormal gut microbiota composition contributes to cognitive dysfunction in streptozotocin-induced diabetic mice. Aging (Albany NY). 2019;11(10):3262–3279. doi:10.18632/aging.101978.
  • Rasmussen TS, Mentzel CMJ, Kot W, Castro-Mejía JL, Zuffa S, Swann JR, Hansen LH, Vogensen FK, Hansen AK, Nielsen DS. Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model. Gut. 2020;69(12):2122–2130. gutjnl-2019-320005. doi:10.1136/gutjnl-2019-320005.
  • Wei Z, Shen P, Cheng P, Lu Y, Wang A, Sun Z. Gut Bacteria Selectively Altered by Sennoside A Alleviate Type 2 Diabetes and Obesity Traits. Oxid Med Cell Longev. 2020;2020:2375676. doi:10.1155/2020/2375676.
  • Wang H, Lu Y, Yan Y, Tian S, Zheng D, Leng D, Wang C, Jiao J, Wang Z, Bai Y. Promising treatment for type 2 diabetes: fecal microbiota transplantation reverses insulin resistance and impaired islets. Front Cell Infect Microbiol. 2020;9:1–10. doi:10.3389/fcimb.2019.00455.
  • Pearson JA, Tai N, Ekanayake-Alper DK, Peng J, Hu Y, Hager K, Compton S, Wong FS, Smith PC, Wen L. Norovirus changes susceptibility to Type 1 diabetes by altering intestinal microbiota and immune cell functions. Front Immunol. 2019;10:2654. doi:10.3389/fimmu.2019.02654.
  • Mullaney JA, Stephens JE, Geeling BE, Hamilton-Williams EE. Early-life exposure to gut microbiota from disease-protected mice does not impact disease outcome in type 1 diabetes susceptible NOD mice. Immunol. Cell Biol. 2019;97(1):97–103. doi:10.1111/imcb.12201.
  • Brown K, Godovannyi A, Ma C, Zhang Y, Ahmadi-Vand Z, Dai C, Gorzelak MA, Chan Y, Chan JM, Lochner A, et al. Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice. ISME J. 2016;10(2):321–332. doi:10.1038/ismej.2015.114.
  • Velmurugan G, Ramprasath T, Swaminathan K, Mithieux G, Rajendhran J, Dhivakar M, Parthasarathy A, Babu DD, Thumburaj LJ, Freddy AJ,  et al. Gut microbial degradation of organophosphate insecticides-induces glucose intolerance via gluconeogenesis. Genome Biol. 2017;18(8). doi:10.1186/s13059-016-1134-6.
  • Bauer PV, Duca FA, Waise TMZ, Dranse HJ, Rasmussen BA, Puri A, Rasti M, O'Brien CA, Lam TKT.  Lactobacillus gasseri in the Upper Small Intestine Impacts an ACSL3-Dependent Fatty Acid-Sensing Pathway Regulating Whole-Body Glucose Homeostasis. Cell Metab. 2018;27(3):572–587.e6. doi:10.1016/j.cmet.2018.01.013.
  • Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, et al. Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells. Cell. 2020;181(6):1263–1275.e16. doi:10.1016/j.cell.2020.04.027.
  • Neuman V, Cinek O, Funda DP, Hudcovic T, Golias J, Kramna L, Petruzelkova L, Pruhova S, Sumnik Z. Human gut microbiota transferred to germ-free NOD mice modulate the progression towards type 1 diabetes regardless of the pace of beta cell function loss in the donor. Diabetologia. 2019;62(7):1291–1296. doi:10.1007/s00125-019-4869-2.
  • Zhang PP, Li LL, Han X, Li QW, Zhang XH, Liu JJ, Wang Y. Fecal microbiota transplantation improves metabolism and gut microbiome composition in db/db mice. Acta Pharmacol. Sin. 2020;41(5):678–685. doi:10.1038/s41401-019-0330-9.
  • Yan T, Nian T, Liao Z, Xiao F, Wu B, Bi K, He B, Jia Y.  Antidepressant effects of a polysaccharide from okra (Abelmoschus esculentus (L) Moench) by anti-inflammation and rebalancing the gut microbiota. Int J Biol Macromol. 2020;144:427–440. doi:10.1016/j.ijbiomac.2019.12.138.
  • Wang S, Ishima T, Zhang J, Qu Y, Chang L, Pu Y, Fujita Y, Tan Y, Wang X, Hashimoto K. Ingestion of Lactobacillus intestinalis and Lactobacillus reuteri causes depression- and anhedonia-like phenotypes in antibiotic-treated mice via the vagus nerve. J Neuroinflammation. 2020;17(241). doi:10.1186/s12974-020-01916-z.
  • Siopi E, Chevalier G, Katsimpardi L, Saha S, Bigot M, Moigneu C, Eberl G, Lledo PM. Changes in gut microbiota by chronic stress impair the efficacy of fluoxetine. Cell Rep. 2020;30(11):3682–3690.e6. doi:10.1016/j.celrep.2020.02.099.
  • Chen P, Hei M, Kong L, Liu Y, Yang Y, Mu H, Zhang X, Zhao S, Duan J. One water-soluble polysaccharide from Ginkgo biloba leaves with antidepressant activities via modulation of the gut microbiome. Food Funct. 2019;10(12):8161–8171. doi:10.1039/C9FO01178A.
  • Lv WJ, Wu XL, Chen WQ, Li YF, Zhang GF, Chao LM, Zhou JH, Guo A, Liu C, Guo SN. The gut microbiome modulates the changes in liver metabolism and in inflammatory processes in the brain of chronic unpredictable mild stress rats. Oxid Med Cell Longev. 2019;2019:7902874. doi:10.1155/2019/7902874.
  • Zhang F, Chen H, Zhang R, Liu Y, Kong N, Guo Y, Xu M.5-Fluorouracil induced dysregulation of the microbiome-gut-brain axis manifesting as depressive like behaviors in rats. Biochim. Biophys. Acta. Mol. Basis Dis. 2020;1866(10):165884. doi:10.1016/j.bbadis.2020.165884.
  • Pearson-Leary J, Zhao C, Bittinger K, Eacret D, Luz S, Vigderman AS, Dayanim G, Bhatnagar S. The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats. Mol Psychiatry. 2020;25(5):1068–1079. doi:10.1038/s41380-019-0380-x.
  • Tillmann S, Abildgaard A, Winther G, Wegener G. Altered fecal microbiota composition in the Flinders sensitive line rat model of depression. Psychopharmacology (Berl). 2019;236(5):1445–1457. doi:10.1007/s00213-018-5094-2.
  • Schmidt EKA, Torres-Espin A, Raposo PJF, Madsen KL, Kigerl KA, Popovich PG, Fenrich KK, Fouad K. Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats. PLoS One. 2020;15(1):e0226128. doi:10.1371/journal.pone.0226128.
  • Marcondes Ávila PR, Fiorot M, Michels M, Dominguini D, Abatti M, Vieira A, de Moura AB, Behenck JP, Borba LA, Botelho MEM, et al. Effects of microbiota transplantation and the role of the vagus nerve in gut-brain axis in animals subjected to chronic mild stress. J Affect Disord. 2020;277:410–416. doi:10.1016/j.jad.2020.08.013.
  • Wang H, Liu L, Rao X, Zeng B, Yu Y, Zhou C, Zeng L, Zheng P, Pu J, Xu S, et al. Integrated phosphoproteomic and metabolomic profiling reveals perturbed pathways in the hippocampus of gut microbiota dysbiosis mice. Transl Psychiatry. 2020;10(1):346. doi:10.1038/s41398-020-01024-9.
  • Qi X, Zhong X, Xu S, Zeng B, Chen J, Zang G, Zeng L, Bai S, Zhou C, Wei H, et al. Extracellular matrix and oxidative phosphorylation: important role in the regulation of hypothalamic function by gut microbiota. Front Genet. 2020;11:520. doi:10.3389/fgene.2020.00520.
  • Okamoto T, Morino K, Ugi S, Nakagawa F, Lemecha M, Ida S, Ohashi N, Sato D, Fujita Y, Maegawa H.  Microbiome potentiates endurance exercise through intestinal acetate production. Am. J. Physiol. Endocrinol. Metab. 2019;316(5):E956–E966. doi:10.1152/ajpendo.00510.2018.
  • Liu YJ, Tang B, Wang FC, Tang L, Lei YY, Luo Y, Huang SJ, Yang M, Wu LY, Wang W, et al. Parthenolide ameliorates colon inflammation through regulating Treg/Th17 balance in a gut microbiota-dependent manner. Theranostics. 2020;10(12):5225–5241. doi:10.7150/thno.43716.
  • Ma J, Li J, Qian M, He N, Cao Y, Liu Y, Wu K, He S.  The comprehensive pathophysiological changes in a novel rat model of postinflammatory visceral hypersensitivity. FASEB J Off Publ Fed Am Soc Exp Biol. 2019;33:13560–13571.
  • Botschuijver S, Roeselers G, Levin E, Jonkers DM, Welting O, Heinsbroek SEM, de Weerd HH, Boekhout T, Fornai M, Masclee AA, et al. Intestinal Fungal Dysbiosis Is Associated With Visceral Hypersensitivity in Patients With Irritable Bowel Syndrome and Rats. Gastroenterology. 2017;153(4):1026–1039. doi:10.1053/j.gastro.2017.06.004.
  • Li J, Cui H, Cai Y, Lin J, Song X, Zhou Z, Xiong W, Zhou H, Bian Y, Wang L.  Tong-Xie-Yao-Fang Regulates 5-HT Level in Diarrhea Predominant Irritable Bowel Syndrome Through Gut Microbiota Modulation. Front Pharmacol. 2018;9:1110. doi:10.3389/fphar.2018.01110.
  • Touw K, Ringus DL, Hubert N, Wang Y, Leone VA, Nadimpalli A, Theriault BR, Huang YE, Tune JD, Herring PB, et al. Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models. Physiol. Rep. 2017;5(6):e13182. doi:10.14814/phy2.13182.
  • Britton GJ, Contijoch EJ, Spindler MP, Aggarwala V, Dogan B, Bongers G, San Mateo L, Baltus A, Das A, Gevers D, et al. Defined microbiota transplant restores Th17/RORγt + regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas. Proc. Natl. Acad. Sci. U. S. A. 2020;117(35):21536–21545. doi:10.1073/pnas.1922189117.
  • Torres J, Hu J, Seki A, Eisele C, Nair N, Huang R, Tarassishin L, Jharap B, Cote-Daigneault J, Mao Q, et al. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut. 2020;69(1):42–51. doi:10.1136/gutjnl-2018-317855.
  • Chen YJ, Wu H, Wu SD, Lu N, Wang YT, Liu HN, Dong L, Liu TT, Shen XZ.  Parasutterella, in association with irritable bowel syndrome and intestinal chronic inflammation. J. Gastroenterol. Hepatol. 2018;33(11):1844–1852. doi:10.1111/jgh.14281.
  • Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H, Chun E, Michaud M, Lang JK, Gallini Comeau CA, et al. The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response. Elife. 2019;8. doi:10.7554/eLife.39982
  • Jia Q, Zhang L, Zhang J, Pei F, Zhu S, Sun Q, Duan L. Fecal Microbiota of Diarrhea-Predominant Irritable Bowel Syndrome Patients Causes Hepatic Inflammation of Germ-Free Rats and Berberine Reverses It Partially. Biomed Res Int. 2019;2019:4530203. doi:10.1155/2019/4530203.
  • Crouzet L, Gaultier E, Del'Homme C, Cartier C, Delmas E, Dapoigny M, Fioramonti J, Bernalier-Donadille A. The hypersensitivity to colonic distension of IBS patients can be transferred to rats through their fecal microbiota. Neurogastroenterol. Motil. Off. J. Eur. Gastrointest. Motil. Soc. 2013;25(4):e272–82. doi:10.1111/nmo.12103.
  • Liu R, Kang JD, Sartor RB, Sikaroodi M, Fagan A, Gavis EA, Zhou H, Hylemon PB, Herzog JW, Li X, et al. Neuroinflammation in Murine Cirrhosis Is Dependent on the Gut Microbiome and Is Attenuated by Fecal Transplant. Hepatology. 2020;71(2):611–626. doi:10.1002/hep.30827.
  • Wang Y, Zhao W, Shi J, Wang J, Hao J, Pang X, Huang X, Chen X, Li Y, Jin R, et al. Intestinal microbiota contributes to altered glucose metabolism in simulated microgravity mouse model. FASEB J Off Publ Fed Am Soc Exp Biol. 2019;33:10140–10151.
  • Xie Y, Matsumoto H, Kennedy S, Newberry EP, Moritz W, DeBosch BJ, Moley KH, Rubin DC, Warner BW, Kau AL, et al. Impaired Chylomicron Assembly Modifies Hepatic Metabolism Through Bile Acid-Dependent and Transmissible Microbial Adaptations. Hepatology. 2019;70(4):1168–1184. doi:10.1002/hep.30669.
  • Sheng L, Jena PK, Hu Y, Liu HX, Nagar N, Kalanetra KM, French SW, French SW, Mills DA, Wan YY. Hepatic inflammation caused by dysregulated bile acid synthesis is reversible by butyrate supplementation. J. Pathol. 2017;243(4):431–441. doi:10.1002/path.4983.
  • Zhou D, Pan Q, Shen F, Cao HX, Ding WJ, Chen YW, Fan JG. Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota. Sci. Rep. 2017;7(1):1529. doi:10.1038/s41598-017-01751-y.
  • Khan N, Vidyarthi A, Nadeem S, Negi S, Nair G, Agrewala JN.  Alteration in the Gut Microbiota Provokes Susceptibility to Tuberculosis. Front Immunol. 2016;7:529. doi:10.3389/fimmu.2016.00529.
  • Cao X, Han Y, Gu M, Du H, Song M, Zhu X, Ma G, Pan C, Wang W, Zhao E, Foodborne Titanium Dioxide Nanoparticles Induce Stronger Adverse Effects in Obese Mice than Non-Obese Mice: gut Microbiota Dysbiosis, Colonic Inflammation, and Proteome Alterations. Small. 2020;16(36):e2001858. doi:10.1002/smll.202001858.
  • Wang P, Wang J, Li D, Ke W, Chen F, Hu X. Targeting the gut microbiota with resveratrol: a demonstration of novel evidence for the management of hepatic steatosis. J Nutr Biochem. 2020;81:108363. doi:10.1016/j.jnutbio.2020.108363.
  • Bereswill S, Escher U, Grunau A, Kühl AA, Dunay IR, Tamas A, Reglodi D, Heimesaat MM. Pituitary Adenylate Cyclase-Activating Polypeptide-A Neuropeptide as Novel Treatment Option for Subacute Ileitis in Mice Harboring a Human Gut Microbiota. Front Immunol. 2019;10:554. doi:10.3389/fimmu.2019.00554.
  • Ferrere G, Wrzosek L, Cailleux F, Turpin W, Puchois V, Spatz M, Ciocan D, Rainteau D, Humbert L, Hugot C, et al. Fecal microbiota manipulation prevents dysbiosis and alcohol-induced liver injury in mice. J. Hepatol. 2017;66(4):806–815. doi:10.1016/j.jhep.2016.11.008.
  • Murakami M, Tognini P, Liu Y, Eckel-Mahan KL, Baldi P, Sassone-Corsi P.  Gut microbiota directs PPAR γ-driven reprogramming of the liver circadian clock by nutritional challenge. EMBO Rep. 2016;17(9):1292–1303. doi:10.15252/embr.201642463.
  • Shen TC, Chehoud C, Ni J, Hsu E, Chen YY, Bailey A, Laughlin A, Bittinger K, Bushman FD, Wu GD. Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium. PLoS One. 2016;11(5):e0155620. doi:10.1371/journal.pone.0155620.
  • Ahn IS, Lang JM, Olson CA, Diamante G, Zhang G, Ying Z, Byun HR, Cely I, Ding J, Cohn P, et al. Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to Fructose Consumption in Mice. J. Nutr. 2020;150(10):2716–2728. doi:10.1093/jn/nxaa239.
  • Yang M, Fukui H, Eda H, Xu X, Kitayama Y, Hara K, Kodani M, Tomita T, Oshima T, Watari J, et al. Involvement of gut microbiota in association between GLP-1/GLP-1 receptor expression and gastrointestinal motility. Am. J. Physiol. Gastrointest. Liver Physiol. 2017;312(4):G367–G373. doi:10.1152/ajpgi.00232.2016.
  • Celaj S, Gleeson MW, Deng J, O'Toole GA, Hampton TH, Toft MF, Morrison HG, Sogin ML, Putra J, Suriawinata AA, et al. The microbiota regulates susceptibility to Fas-mediated acute hepatic injury. Lab. Invest. 2014;94(9):938–949. doi:10.1038/labinvest.2014.93.
  • Qin C, Zhang H, Zhao L, Zeng M, Huang W, Fu G, Zhou W, Wang H, Yan H. Microbiota transplantation reveals beneficial impact of berberine on hepatotoxicity by improving gut homeostasis. Sci. China. Life Sci. 2018;61(12):1537–1544. doi:10.1007/s11427-017-9202-0.
  • Zhao Y, Tang Y, Chen L, Lv S, Liu S, Nie P, Aguilar ZP, Xu H.  Restraining the TiO(2) nanoparticles-induced intestinal inflammation mediated by gut microbiota in juvenile rats via ingestion of Lactobacillus rhamnosus GG. Ecotoxicol Environ Saf. 2020;206:111393. doi:10.1016/j.ecoenv.2020.111393.
  • Escher U, Giladi E, Dunay IR, Bereswill S, Gozes I, Heimesaat MM.  Anti-inflammatory Effects of the Octapeptide NAP in Human Microbiota-Associated Mice Suffering from Subacute Ileitis. Eur. J. Microbiol. Immunol. (Bp). 2018;8(2):34–40. doi:10.1556/1886.2018.00006.
  • Llopis M, Cassard AM, Wrzosek L, Boschat L, Bruneau A, Ferrere G, Puchois V, Martin JC, Lepage P, Le Roy T, et al. Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease. Gut. 2016;65(5):830–839. doi:10.1136/gutjnl-2015-310585.
  • Basson AR, Gomez-Nguyen A, Menghini P, Buttó LF, Di Martino L, Aladyshkina N, Osme A, LaSalla A, Fischer D, Ezeji JC, et al. Human Gut Microbiome Transplantation in Ileitis Prone Mice: a Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients. Inflamm. Bowel Dis. 2020;26(3):347–359. doi:10.1093/ibd/izz242.
  • Galvão MF, Bastos RW, Acurcio LB, Nascimento BB, Sandes SHC, Arantes RME, Souza MR, Martins FS, Vieira LQ, Nicoli JR. Evaluation of colonisation resistance in stool of human donors using ex vivo, in vitro and in vivo assays. Benef Microbes. 2017;8(2):217–230. doi:10.3920/BM2016.0027.
  • Wang WW, Zhang Y, Huang XB, You N, Zheng L, Li J. Fecal microbiota transplantation prevents hepatic encephalopathy in rats with carbon tetrachloride-induced acute hepatic dysfunction. World J. Gastroenterol. 2017;23(38):6983–6994. doi:10.3748/wjg.v23.i38.6983.
  • Rungapamestry V, Rabot S, Fuller Z, Ratcliffe B, Duncan AJ. Influence of cooking duration of cabbage and presence of colonic microbiota on the excretion of N-acetylcysteine conjugates of allyl isothiocyanate and bioactivity of phase 2 enzymes in F344 rats. Br. J. Nutr. 2008;99(4):773–781. doi:10.1017/S0007114507841134.
  • Lin DM, Koskella B, Ritz NL, Lin D, Carroll-Portillo A, Lin HC.  Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice. Front Cell Infect Microbiol. 2019;9:348. doi:10.3389/fcimb.2019.00348.
  • SSafari Z, Bruneau A, Monnoye M, Mariadassou M, Philippe C, Zatloukal K, Gérard P. Murine Genetic Background Overcomes Gut Microbiota Changes to Explain Metabolic Response to High-Fat Diet. Nutrients. 2020;12(287):287. doi:10.3390/nu12020287.
  • Kau AL, Planer JD, Liu J, Rao S, Yatsunenko T, Trehan I, Manary MJ, Liu TC, Stappenbeck TS, Maleta KM, et al. Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Sci. Transl. Med. 2015;7(276):276ra24. doi:10.1126/scitranslmed.aaa4877.
  • Cowardin CA, Ahern PP, Kung VL, Hibberd MC, Cheng J, Guruge JL, Sundaresan V, Head RD, Barile D, Mills DA, et al. Mechanisms by which sialylated milk oligosaccharides impact bone biology in a gnotobiotic mouse model of infant undernutrition. Proc. Natl. Acad. Sci. U. S. A. 2019;116(24):11988–11996. doi:10.1073/pnas.1821770116.
  • Zeng SL, Li SZ, Xiao PT, Cai YY, Chu C, Chen BZ, Li P, Li J, Liu EH. Citrus polymethoxyflavones attenuate metabolic syndrome by regulating gut microbiome and amino acid metabolism. Sci. Adv. 2020;6(1):eaax6208. doi:10.1126/sciadv.aax6208.
  • Su CW, Chen CY, Jiao L, Long SR, Mao T, Ji Q, O'Donnell S, Stanton C, Zheng S, Walker WA, et al. Helminth-Induced and Th2-Dependent Alterations of the Gut Microbiota Attenuate Obesity Caused by High-Fat Diet. Cell. Mol. Gastroenterol. Hepatol. 2020;10(4):763–778. doi:10.1016/j.jcmgh.2020.06.010.
  • Kaliannan K, Robertson RC, Murphy K, Stanton C, Kang C, Wang B, Hao L, Bhan AK, Kang JX. Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice. Microbiome. 2018;6(1):205. doi:10.1186/s40168-018-0587-0.
  • Kapur R, Kim M, Rebetz J, Hallström B, Björkman JT, Takabe-French A, Kim N, Liu J, Shanmugabhavananthan S, Milosevic S, et al. Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury. Blood Adv. 2018;2(13):1651–1663. doi:10.1182/bloodadvances.2018018903.
  • Chen S, Li X, Liu L, Liu C, Han X. Ophiopogonin D alleviates high-fat diet-induced metabolic syndrome and changes the structure of gut microbiota in mice. FASEB J Off Publ Fed Am Soc Exp Biol. 2018;32:1139–1153.
  • Xie Z, Jiang H, Liu W, Zhang X, Chen D, Sun S, Zhou C, Liu J, Bao S, Wang X, et al. The triterpenoid sapogenin (2α-OH-Protopanoxadiol) ameliorates metabolic syndrome via the intestinal FXR/GLP-1 axis through gut microbiota remodelling. Cell Death Dis. 2020;11(9):770. doi:10.1038/s41419-020-02974-0.
  • Kim TT, Parajuli N, Sung MM, Bairwa SC, Levasseur J, Soltys CM, Wishart DS, Madsen K, Schertzer JD, Dyck JRB. Fecal transplant from resveratrol-fed donors improves glycaemia and cardiovascular features of the metabolic syndrome in mice. Am. J. Physiol. Endocrinol. Metab. 2018;315(4):E511–E519. doi:10.1152/ajpendo.00471.2017.
  • Han J, Wang X, Tang S, Lu C, Wan H, Zhou J, Li Y, Ming T, Wang ZJ, Su X. Protective effects of tuna meat oligopeptides (TMOP) supplementation on hyperuricemia and associated renal inflammation mediated by gut microbiota. FASEB J Off Publ Fed Am Soc Exp Biol. 2020;34:5061–5076.
  • Zhan J, Ma X, Liu D, Liang Y, Li P, Cui J, Zhou Z, Wang P. Gut microbiome alterations induced by tributyltin exposure are associated with increased body weight, impaired glucose and insulin homeostasis and endocrine disruption in mice. Environ Pollut. 2020;266:115276. doi:10.1016/j.envpol.2020.115276.
  • Thaiss CA, Zeevi D, Levy M, Zilberman-Schapira G, Suez J, Tengeler AC, Abramson L, Katz MN, Korem T, Zmora N, et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell. 2014;159(3):514–529. doi:10.1016/j.cell.2014.09.048.
  • Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O, Israeli D, Zmora N, Gilad S, Weinberger A, et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014;514(7521):181–186. doi:10.1038/nature13793.
  • Xu Y, Ai C, Jiang P, Sun X, Liu Y, Jiang G, Song S. Oligosaccharides from Gracilaria lemaneiformis better attenuated high fat diet-induced metabolic syndrome by promoting the Bacteroidales proliferation. Food Funct. 2020;11(1):1049–1062. doi:10.1039/C9FO01996K.
  • Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami P, Ganewatta MS, Tang C, Chatterjee S, Nagarkatti P, et al. CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice. Eur. J. Immunol. 2017;47(7):1188–1199. doi:10.1002/eji.201646792.
  • Takata K, Tomita T, Okuno T, Kinoshita M, Koda T, Honorat JA, Takei M, Hagihara K, Sugimoto T, Mochizuki H,et al. Dietary Yeasts Reduce Inflammation in Central Nerve System via Microflora. Ann. Clin. Transl. Neurol. 2015;2(1):56–66. doi:10.1002/acn3.153.
  • Chen H, Chen Z, Shen L, Wu X, Ma X, Lin D, Zhang M, Ma X, Liu Y, Wang Z, et al. Fecal microbiota transplantation from patients with autoimmune encephalitis modulates Th17 response and relevant behaviors in mice. Cell Death Discov. 2020;6(1):75. doi:10.1038/s41420-020-00309-8.
  • Liu S, Rezende RM, Moreira TG, Tankou SK, Cox LM, Wu M, Song A, Dhang FH, Wei Z, Costamagna G, et al. Oral Administration of miR-30d from Feces of MS Patients Suppresses MS-like Symptoms in Mice by Expanding Akkermansia muciniphila. Cell Host Microbe. 2019;26(6):779–794.e8. doi:10.1016/j.chom.2019.10.008.
  • Stanisavljević S, Dinić M, Jevtić B, Đedović N, Momčilović M, Đokić J, Golić N, Mostarica Stojković M, Miljković Đ. Gut Microbiota Confers Resistance of Albino Oxford Rats to the Induction of Experimental Autoimmune Encephalomyelitis. Front Immunol. 2018;9:942. doi:10.3389/fimmu.2018.00942.
  • Li K, Wei S, Hu L, Yin X, Mai Y, Jiang C, Peng X, Cao X, Huang Z, Zhou H, et al. Protection of Fecal Microbiota Transplantation in a Mouse Model of Multiple Sclerosis. Mediators Inflamm. 2020;2020:2058272. doi:10.1155/2020/2058272.
  • Yuan J, Chen C, Cui J, Lu J, Yan C, Wei X, Zhao X, Li N, Li S, Xue G,  et al. Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae. Cell Metab. 2019;30(4):675–688.e7. doi:10.1016/j.cmet.2019.08.018.
  • Petrov PD, García-Mediavilla MV, Guzmán C, Porras D, Nistal E, Martínez-Flórez S, Castell JV, González-Gallego J, Sánchez-Campos S, Jover R.  A Network Involving Gut Microbiota, Circulating Bile Acids, and Hepatic Metabolism Genes That Protects Against Non-Alcoholic Fatty Liver Disease. Mol. Nutr. Food Res. 2019;63(20):e1900487. doi:10.1002/mnfr.201900487.
  • Porras D, Nistal E, Martínez-Flórez S, Olcoz JL, Jover R, Jorquera F, González-Gallego J, García-Mediavilla MV, Sánchez-Campos S. Functional Interactions between Gut Microbiota Transplantation, Quercetin, and High-Fat Diet Determine Non-Alcoholic Fatty Liver Disease Development in Germ-Free Mice. Mol. Nutr. Food Res. 2019;63(8):e1800930. doi:10.1002/mnfr.201800930.
  • Mouries J, Brescia P, Silvestri A, Spadoni I, Sorribas M, Wiest R, Mileti E, Galbiati M, Invernizzi P, Adorini L, et al. Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development. J. Hepatol. 2019;71(6):1216–1228. doi:10.1016/j.jhep.2019.08.005.
  • Morissette A, Kropp C, Songpadith JP, Junges Moreira R, Costa J, Mariné-Casadó R, Pilon G, Varin TV, Dudonné S, Boutekrabt L, et al. Blueberry proanthocyanidins and anthocyanins improve metabolic health through a gut microbiota-dependent mechanism in diet-induced obese mice. Am. J. Physiol. Endocrinol. Metab. 2020;318(6):E965–E980. doi:10.1152/ajpendo.00560.2019.
  • Chagwedera DN, Ang QY, Bisanz JE, Leong YA, Ganeshan K, Cai J, Patterson AD, Turnbaugh PJ, Chawla A.  Nutrient Sensing in CD11c Cells Alters the Gut Microbiota to Regulate Food Intake and Body Mass. Cell Metab. 2019;30(2):364–373.e7. doi:10.1016/j.cmet.2019.05.002.
  • Lu JF, Zhu MQ, Zhang H, Liu H, Xia B, Wang YL, Shi X, Peng L, Wu JW. Neohesperidin attenuates obesity by altering the composition of the gut microbiota in high-fat diet-fed mice. FASEB J Off Publ Fed Am Soc Exp Biol. 2020. doi:10.1096/fj.201903102RR.
  • Luo Y, Chen GL, Hannemann N, Ipseiz N, Krönke G, Bäuerle T, Munos L, Wirtz S, Schett G, Bozec A. Microbiota from Obese Mice Regulate Hematopoietic Stem Cell Differentiation by Altering the Bone Niche. Cell Metab. 2015;22(5):886–894. doi:10.1016/j.cmet.2015.08.020.
  • Tashiro H, Cho Y, Kasahara DI, Brand JD, Bry L, Yeliseyev V, Abu-Ali G, Huttenhower C, Shore SA. Microbiota Contribute to Obesity-related Increases in the Pulmonary Response to Ozone. Am. J. Respir. Cell Mol. Biol. 2019;61(6):702–712. doi:10.1165/rcmb.2019-0144OC.
  • Ji Y, Sun S, Goodrich JK, Kim H, Poole AC, Duhamel GE, Ley RE, Qi L. Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice. Cell Rep. 2014;8(1):137–149. doi:10.1016/j.celrep.2014.05.040.
  • Liu MT, Huang YJ, Zhang TY, Tan LB, Lu XF, Qin J. Lingguizhugan decoction attenuates diet-induced obesity and hepatosteatosis via gut microbiota. World J. Gastroenterol. 2019;25(27):3590–3606. doi:10.3748/wjg.v25.i27.3590.
  • Andriessen EM, Wilson AM, Mawambo G, Dejda A, Miloudi K, Sennlaub F, Sapieha P. Gut microbiota influences pathological angiogenesis in obesity-driven choroidal neovascularization. EMBO Mol. Med. 2016;8(12):1366–1379. doi:10.15252/emmm.201606531.
  • Parséus A, Sommer N, Sommer F, Caesar R, Molinaro A, Ståhlman M, Greiner TU, Perkins R, Bäckhed F.  Microbiota-induced obesity requires farnesoid X receptor. Gut. 2017;66(3):429–437. doi:10.1136/gutjnl-2015-310283.
  • Wu TR, Lin CS, Chang CJ, Lin TL, Martel J, Ko YF, Ojcius DM, Lu CC, Young JD, Lai HC. Gut commensal Parabacteroides goldsteinii plays a predominant role in the anti-obesity effects of polysaccharides isolated from Hirsutella sinensis. Gut. 2019;68(2):248–262. doi:10.1136/gutjnl-2017-315458.
  • Liou AP, Paziuk M, Luevano JM Jr, Machineni S, Turnbaugh PJ, Kaplan LM. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci. Transl. Med. 2013;5(178):178ra41. doi:10.1126/scitranslmed.3005687.
  • Kang C, Wang B, Kaliannan K, Wang X, Lang H, Hui S, Huang L, Zhang Y, Zhou M, Chen M, et al. Gut Microbiota Mediates the Protective Effects of Dietary Capsaicin against Chronic Low-Grade Inflammation and Associated Obesity Induced by High-Fat Diet.
  • Wang J, Wang P, Li D, Hu X, Chen F. Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice. Eur. J. Nutr. 2020;59(2):699–718. doi:10.1007/s00394-019-01938-1.
  • Arita S, Inagaki-Ohara K. High-fat-diet-induced modulations of leptin signaling and gastric microbiota drive precancerous lesions in the stomach. Nutrition. 2019;6768:110556. doi:10.1016/j.nut.2019.110556.
  • Li X, Chen P, Zhang P, Chang Y, Cui M, Duan J. Protein-Bound β-glucan from Coriolus Versicolor has Potential for Use Against Obesity. Mol. Nutr. Food Res. 2019;63(7):e1801231. doi:10.1002/mnfr.201801231.
  • Ba Q, Li M, Chen P, Huang C, Duan X, Lu L, Li J, Chu R, Xie D, Song H, et al. Sex-Dependent Effects of Cadmium Exposure in Early Life on Gut Microbiota and Fat Accumulation in Mice. Environ. Health Perspect. 2017;125(3):437–446. doi:10.1289/EHP360.
  • Rabot S, Membrez M, Blancher F, Berger B, Moine D, Krause L, Bibiloni R, Bruneau A, Gérard P, Siddharth J, et al. High fat diet drives obesity regardless the composition of gut microbiota in mice. Sci. Rep. 2016;6(1):32484. doi:10.1038/srep32484.
  • Soto M, Herzog C, Pacheco JA, Fujisaka S, Bullock K, Clish CB, Kahn CR. Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism. Mol Psychiatry. 2018;23(12):2287–2301. doi:10.1038/s41380-018-0086-5.
  • Chaplin A, Parra P, Laraichi S, Serra F, Palou A. Calcium supplementation modulates gut microbiota in a prebiotic manner in dietary obese mice. Mol. Nutr. Food Res. 2016;60(2):468–480. doi:10.1002/mnfr.201500480.
  • Ussar S, Griffin NW, Bezy O, Fujisaka S, Vienberg S, Softic S, Deng L, Bry L, Gordon JI, Kahn CR.  Interactions between gut microbiota, host genetics and diet modulate the predisposition to obesity and metabolic syndrome. Cell Metab. 2015;22(3):516–530. doi:10.1016/j.cmet.2015.07.007.
  • Liu Z, Wang N, Ma Y, Wen D. Hydroxytyrosol improves obesity and insulin resistance by modulating gut microbiota in high-fat diet-induced obese mice. Front Microbiol. 2019;10:390. doi:10.3389/fmicb.2019.00390.
  • Xu Y, Wang N, Tan HY, Li S, Zhang C, Zhang Z, Feng Y.  Panax notoginseng saponins modulate the gut microbiota to promote thermogenesis and beige adipocyte reconstruction via leptin-mediated AMPKα/STAT3 signaling in diet-induced obesity. Theranostics. 2020;10(24):11302–11323. doi:10.7150/thno.47746.
  • Foley KP, Zlitni S, Duggan BM, Barra NG, Anhê FF, Cavallari JF, Henriksbo BD, Chen CY, Huang M, Lau TC, et al. Gut microbiota impairs insulin clearance in obese mice. Mol. Metab. 2020;42(101067):101067. doi:10.1016/j.molmet.2020.101067.
  • Jing N, Liu X, Jin M, Yang X, Hu X, Li C, Zhao K. Fubrick tea attenuates high-fat diet induced fat deposition and metabolic disorder by regulating gut microbiota and caffeine metabolism. Food Funct. 2020;11(8):6971–6986. doi:10.1039/D0FO01282C.
  • Pérez-Matute P, Íñiguez M, de Toro M, Recio-Fernández E, Oteo JA. Autologous fecal transplantation from a lean state potentiates caloric restriction effects on body weight and adiposity in obese mice. Sci. Rep. 2020;10(1):9388. doi:10.1038/s41598-020-64961-x.
  • Zoll J, Read MN, Heywood SE, Estevez E, Marshall JPS, Kammoun HL, Allen TL, Holmes AJ, Febbraio MA, Henstridge DC. Fecal microbiota transplantation from high caloric-fed donors alters glucose metabolism in recipient mice, independently of adiposity or exercise status. Am. J. Physiol. Endocrinol. Metab. 2020;319(1):E203–E216. doi:10.1152/ajpendo.00037.2020.
  • Pereira FV, Melo ACL, Silva MB, de Melo FM, Terra FF, Castro IA, Perandini LA, Miyagi MT, Sato FT, Origassa CST, et al. Interleukin-6 and the gut microbiota influence melanoma progression in obese mice. Nutr Cancer. 2020;1–10. doi:10.1080/01635581.2020.1764982.
  • Wang P, Gao J, Ke W, Wang J, Li D, Liu R, Jia Y, Wang X, Chen X, Chen F, et al. Resveratrol reduces obesity in high-fat diet-fed mice via modulating the composition and metabolic function of the gut microbiota. Free Radic Biol Med. 2020;156:83–98. doi:10.1016/j.freeradbiomed.2020.04.013.
  • Anhê FF, Nachbar RT, Varin TV, Trottier J, Dudonné S, Le Barz M, Feutry P, Pilon G, Barbier O, Desjardins Y, et al. Treatment with camu camu (Myrciaria dubia) prevents obesity by altering the gut microbiota and increasing energy expenditure in diet-induced obese mice. Gut. 2019;68(3):453–464. doi:10.1136/gutjnl-2017-315565.
  • Lee H, Lee Y, Kim J, An J, Lee S, Kong H, Song Y, Lee CK, Kim K. Modulation of the gut microbiota by metformin improves metabolic profiles in aged obese mice. Gut Microbes. 2018;9(2):155–165. doi:10.1080/19490976.2017.1405209.
  • Kim J, Lee H, An J, Song Y, Lee CK, Kim K, Kong H. Alterations in Gut Microbiota by Statin Therapy and Possible Intermediate Effects on Hyperglycemia and Hyperlipidemia. Front Microbiol. 2019;10:1947. doi:10.3389/fmicb.2019.01947.
  • Sung MM, Kim TT, Denou E, Soltys CM, Hamza SM, Byrne NJ, Masson G, Park H, Wishart DS, Madsen KL, et al. Improved glucose homeostasis in obese mice treated with resveratrol is associated with alterations in the gut microbiome. Diabetes. 2017;66(2):418–425. doi:10.2337/db16-0680.
  • Lützhøft DO, Sánchez-Alcoholado L, Tougaard P, Junker Mentzel CM, Kot W, Nielsen DS, Hansen AK.  Short communication: gut microbial colonization of the mouse colon using faecal transfer was equally effective when comparing rectal inoculation and oral inoculation based on 16S rRNA sequencing. Res Vet Sci. 2019;126:227–232. doi:10.1016/j.rvsc.2019.09.009.
  • Rinott E, Youngster I, Yaskolka Meir A, Tsaban G, Zelicha H, Kaplan A, Knights D, Tuohy K, Fava F, Scholz MU, et al. Effects of diet-modulated autologous fecal microbiota transplantation on weight regain. Gastroenterology. 2020;160(1):158–173.e10. doi:10.1053/j.gastro.2020.08.041.
  • Duan Y, Zhong Y, Xiao H, Zheng C, Song B, Wang W, Guo Q, Li Y, Han H, Gao J, et al. Gut microbiota mediates the protective effects of dietary β-hydroxy-β-methylbutyrate (HMB) against obesity induced by high-fat diets. FASEB J Off Publ Fed Am Soc Exp Biol. 2019;33:10019–10033.
  • Sun -S-S, Wang K, Ma K, Bao L, Liu H-W. An insoluble polysaccharide from the sclerotium of Poria cocos improves hyperglycemia, hyperlipidemia and hepatic steatosis in ob/ob mice via modulation of gut microbiota. Chin. J. Nat. Med. 2019;17(1):3–14. doi:10.1016/S1875-5364(19)30003-2.
  • Yang JY, Lee YS, Kim Y, Lee SH, Ryu S, Fukuda S, Hase K, Yang CS, Lim HS, Kim MS, et al. Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice. Mucosal Immunol. 2017;10(1):104–116. doi:10.1038/mi.2016.42.
  • Nettleton JE, Cho NA, Klancic T, Nicolucci AC, Shearer J, Borgland SL, Johnston LA, Ramay HR, Noye Tuplin E, Chleilat F, et al. Maternal low-dose aspartame and stevia consumption with an obesogenic diet alters metabolism, gut microbiota and mesolimbic reward system in rat dams and their offspring. Gut. 2020;69(10):1807–1817. doi:10.1136/gutjnl-2018-317505.
  • Klancic T, Laforest-Lapointe I, Choo A, Nettleton JE, Chleilat F, Noye Tuplin EW, Alukic E, Cho NA, Nicolucci AC, Arrieta MC, et al. Prebiotic oligofructose prevents antibiotic-induced obesity risk and improves metabolic and gut microbiota profiles in rat dams and offspring. Mol. Nutr. Food Res. 2020;64(16):e2000288. doi:10.1002/mnfr.202000288.
  • Sun W, Guo Y, Zhang S, Chen Z, Wu K, Liu Q, Liu K, Wen L, Wei Y, Wang B, et al. Fecal Microbiota Transplantation Can Alleviate Gastrointestinal Transit in Rats with High-Fat Diet-Induced Obesity via Regulation of Serotonin Biosynthesis. Biomed Res Int. 2018;2018:8308671. doi:10.1155/2018/8308671.
  • Wang J-H, Kim B-S, Han K, Kim H. Ephedra-treated donor-derived gut microbiota transplantation ameliorates high fat diet-induced obesity in rats. Int J Environ Res Public Health.
  • Di Luccia B, Crescenzo R, Mazzoli A, Cigliano L, Venditti P, Walser JC, Widmer A, Baccigalupi L, Ricca E, Iossa S. Rescue of fructose-induced metabolic syndrome by antibiotics or faecal transplantation in a rat model of obesity. PLoS One. 2015;10(8):e0134893. doi:10.1371/journal.pone.0134893.
  • Zhu Y, Zhang JY, Wei YL, Hao JY, Lei YQ, Zhao WB, Xiao YH, Sun AD. The polyphenol-rich extract from chokeberry (Aronia melanocarpa L.) modulates gut microbiota and improves lipid metabolism in diet-induced obese rats. Nutr. Metab. (Lond). 2020;17(1):54. doi:10.1186/s12986-020-00473-9.
  • Zhang L, Zhou W, Zhan L, Hou S, Zhao C, Bi T, Lu X. Fecal microbiota transplantation alters the susceptibility of obese rats to type 2 diabetes mellitus. Aging (Albany NY). 2020;12(17):17480–17502. doi:10.18632/aging.103756.
  • Yang H, Xiang Y, Robinson K, Wang J, Zhang G, Zhao J, Xiao Y. Gut Microbiota Is a Major Contributor to Adiposity in Pigs. Front Microbiol. 2018;9:3045. doi:10.3389/fmicb.2018.03045.
  • Rodriguez DM, Benninghoff AD, Aardema NDJ, Phatak S, Hintze KJ. Basal diet determined long-term composition of the gut microbiome and mouse phenotype to a greater extent than fecal microbiome transfer from lean or obese human donors. Nutrients. 2019;11(7):1630. doi:10.3390/nu11071630.
  • Fouladi F, Brooks AE, Fodor AA, Carroll IM, Bulik-Sullivan EC, Tsilimigras MCB, Sioda M, Steffen KJ.  The Role of the Gut Microbiota in Sustained Weight Loss Following Roux-en-Y Gastric Bypass Surgery. Obes. Surg. 2019;29(4):1259–1267. doi:10.1007/s11695-018-03653-y.
  • Dugas LR, Bernabé BP, Priyadarshini M, Fei N, Park SJ, Brown L, Plange-Rhule J, Nelson D, Toh EC, Gao X,  et al. Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women. Sci. Rep. 2018;8(1):17135. doi:10.1038/s41598-018-35230-9.
  • Arnoriaga-Rodríguez M, Mayneris-Perxachs J, Burokas A, Pérez-Brocal V, Moya A, Portero-Otin M, Ricart W, Maldonado R, Fernández-Real JM. Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile. Microbiome. 2020;8(1):59. doi:10.1186/s40168-020-00837-6.
  • Rodriguez J, Hiel S, Neyrinck AM, Le Roy T, Pötgens SA, Leyrolle Q, Pachikian BD, Gianfrancesco MA, Cani PD, Paquot N,  et al. Discovery of the gut microbial signature driving the efficacy of prebiotic intervention in obese patients. Gut. 2020;69(11):1975–1987. doi:10.1136/gutjnl-2019-319726.
  • Liu Y, Wang Y, Ni Y, Cheung CKY, Lam KSL, Wang Y, Xia Z, Ye D, Guo J, Tse MA, et al. Gut microbiome fermentation determines the efficacy of exercise for diabetes prevention. Cell Metab. 2020;31(1):77–91.e5. doi:10.1016/j.cmet.2019.11.001.
  • Arnoriaga-Rodríguez M, Mayneris-Perxachs J, Burokas A, Contreras-Rodríguez O, Blasco G, Coll C, Biarnés C, Miranda-Olivos R, Latorre J, Moreno-Navarrete JM,  et al. Obesity impairs short-term and working memory through gut microbial metabolism of aromatic amino acids. Cell Metab. 2020;32(4):548–560.e7. doi:10.1016/j.cmet.2020.09.002.
  • Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, et al. Human genetics shape the gut microbiome. Cell. 2014;159(4):789–799. doi:10.1016/j.cell.2014.09.053.
  • Olsson LM, Poitou C, Tremaroli V, Coupaye M, Aron-Wisnewsky J, Bäckhed F, Clément K, Caesar R. Gut microbiota of obese subjects with Prader-Willi syndrome is linked to metabolic health. Gut. 2020;69(7):1229–1238. doi:10.1136/gutjnl-2019-319322.
  • van den Berg FF, van Dalen D, Hyoju SK, van Santvoort HC, Besselink MG, Wiersinga WJ, Zaborina O, Boermeester MA, Alverdy J. Western-type diet influences mortality from necrotising pancreatitis and demonstrates a central role for butyrate. Gut. 2020. doi:10.1136/gutjnl-2019-320430.
  • Li X, He C, Li N, Ding L, Chen H, Wan J, Yang X, Xia L, He W, Xiong H, et al. The interplay between the gut microbiota and NLRP3 activation affects the severity of acute pancreatitis in mice. Gut Microbes. 2020;11(6):1774–1789. doi:10.1080/19490976.2020.1770042.
  • Zhu Y, He C, Li X, Cai Y, Hu J, Liao Y, Zhao J, Xia L, He W, Liu L, et al. Gut microbiota dysbiosis worsens the severity of acute pancreatitis in patients and mice. J. Gastroenterol. 2019;54(4):347–358. doi:10.1007/s00535-018-1529-0.
  • Wang J, Wang P, Tian H, Tian F, Zhang Y, Zhang L, Gao X, Wang X. Aryl hydrocarbon receptor/IL-22/Stat3 signaling pathway is involved in the modulation of intestinal mucosa antimicrobial molecules by commensal microbiota in mice. Innate Immunity. 2018;24(5):297–306. doi:10.1177/1753425918785016.
  • Couturier-Maillard A, Froux N, Piotet-Morin J, Michaudel C, Brault L, Le Bérichel J, Sénéchal A, Robinet P, Chenuet P, Jejou S, et al. Interleukin-22-deficiency and microbiota contribute to the exacerbation of Toxoplasma gondii-induced intestinal inflammation. Mucosal Immunol. 2018;11(4):1181–1190. doi:10.1038/s41385-018-0005-8.
  • Kamata K, Watanabe T, Minaga K, Hara A, Yoshikawa T, Okamoto A, Yamao K, Takenaka M, Park A-M, Kudo M, et al. Intestinal dysbiosis mediates experimental autoimmune pancreatitis via activation of plasmacytoid dendritic cells. International Immunology. 2019;31(12):795–809. doi:10.1093/intimm/dxz050.
  • Hansen CHF, Larsen CS, Petersson HO, Zachariassen LF, Vegge A, Lauridsen C, Kot W, Krych Ł, Nielsen DS, Hansen AK, et al. Targeting gut microbiota and barrier function with prebiotics to alleviate autoimmune manifestations in NOD mice. Diabetologia. 2019;62(9):1689–1700. doi:10.1007/s00125-019-4910-5.
  • Zhou ZL, Jia XB, Sun MF, Zhu YL, Qiao CM, Zhang BP, Zhao LP, Yang Q, Cui C, Chen X, et al. Neuroprotection of Fasting Mimicking Diet on MPTP-Induced Parkinson’s Disease Mice via Gut Microbiota and Metabolites. Neurother J Am Soc Exp Neurother. 2019;16:741–760.
  • Lindheim L, Manti M, Fornes R, Bashir M, Czarnewski P, Diaz OE, Seifert M, Engstrand L, Villablanca EJ, Obermayer-Pietsch B, et al. Reproductive and behavior dysfunction induced by maternal androgen exposure and obesity is likely not gut microbiome-mediated. . Journal of the Endocrine Society. 2018;2(12):1363–1380. doi:10.1210/js.2018-00266.
  • Guo Y, Qi Y, Yang X, Zhao L, Wen S, Liu Y, Tang L. Association between polycystic ovary syndrome and gut microbiota. PLoS One. 2016;11(4):e0153196. doi:10.1371/journal.pone.0153196.
  • Qi X, Yun C, Sun L, Xia J, Wu Q, Wang Y, Wang L, Zhang Y, Liang X, Wang L, et al. Gut microbiota–bile acid–interleukin-22 axis orchestrates polycystic ovary syndrome. Nature Medicine. 2019;25(8):1225–1233. doi:10.1038/s41591-019-0509-0.
  • Zhu F, Guo R, Wang W, Ju Y, Wang Q, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, et al. Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice. . Molecular Psychiatry. 2020;25(11):2905–2918. doi:10.1038/s41380-019-0475-4.
  • Zhu F, Ju Y, Wang W, Wang Q, Guo R, Ma Q, Sun Q, Fan Y, Xie Y, Yang Z, et al. Metagenome-wide association of gut microbiome features for schizophrenia. . Nature Communications. 2020;11(1):1612. doi:10.1038/s41467-020-15457-9.
  • Zheng P, Zeng B, Liu M, Chen J, Pan J, Han Y, Liu Y, Cheng K, Zhou C, Wang H, et al. The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice. . Science Advances. 2019;5(2):eaau8317. doi:10.1126/sciadv.aau8317.
  • Kim SM, DeFazio JR, Hyoju SK, Sangani K, Keskey R, Krezalek MA, Khodarev NN, Sangwan N, Christley S, Harris KG, et al. Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity. Nature Communications. 2020;11(1):2354. doi:10.1038/s41467-020-15545-w.
  • Fay KT, Klingensmith NJ, Chen CW, Zhang W, Sun Y, Morrow KN, Liang Z, Burd EM, Ford ML, Coopersmith CM.  The gut microbiome alters immunophenotype and survival from sepsis. FASEB J Off Publ Fed Am Soc Exp Biol. 2019;33:11258–11269.
  • Gong S, Yan Z, Liu Z, Niu M, Fang H, Li N, Huang C, Li L, Chen G, Luo H, et al. Intestinal microbiota mediates the susceptibility to polymicrobial sepsis-induced liver injury by granisetron generation in mice. Hepatology. 2019;69(4):1751–1767. doi:10.1002/hep.30361.
  • Morffy Smith CD, Gong M, Andrew AK, Russ BN, Ge Y, Zadeh M, Cooper CA, Mohamadzadeh M, Moore JM. Composition of the gut microbiota transcends genetic determinants of malaria infection severity and influences pregnancy outcome. EBioMedicine. 2019;44:639–655. doi:10.1016/j.ebiom.2019.05.052.
  • Bradley KC, Finsterbusch K, Schnepf D, Crotta S, Llorian M, Davidson S, Fuchs SY, Staeheli P, Wack A. Microbiota-driven tonic interferon signals in lung stromal cells protect from influenza virus infection. Cell Rep. 2019;28(1):245–256.e4. doi:10.1016/j.celrep.2019.05.105.
  • Li S, Xu N, Hua R, Niu X, Lyu C, Li M, Li J. [Fecal microbiota transplantation regulates the cholinergic anti-inflammatory pathway in cerebral cortex of septic rats through intestinal microbiota]. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue. 2019;31(9):1102–1107. doi:10.3760/cma.j..2095-4352.2019.09.009.
  • Li S, Lv J, Li J, Zhao Z, Guo H, Zhang Y, Cheng S, Sun J, Pan H, Fan S, et al. Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve. Neurosci Lett. 2018;662:98–104. doi:10.1016/j.neulet.2017.10.008.
  • Ávila PRM, Michels M, Vuolo F, Bilésimo R, Burger H, Milioli MVM, Sonai B, Borges H, Carneiro C, Abatti M, et al. Protective effects of fecal microbiota transplantation in sepsis are independent of the modulation of the intestinal flora. Nutrition. 2020;73:110727. doi:10.1016/j.nut.2020.110727.
  • Assimakopoulos SF, Papadopoulou I, Bantouna D, de Lastic AL, Rodi M, Mouzaki A, Gogos CA, Zolota V, Maroulis I. Fecal Microbiota Transplantation and Hydrocortisone Ameliorate Intestinal Barrier Dysfunction and Improve Survival in a Rat Model of Cecal Ligation and Puncture-Induced Sepsis. Shock. 2020. doi:10.1097/SHK.0000000000001566.
  • Zaborin A, Krezalek M, Hyoju S, Defazio JR, Setia N, Belogortseva N, Bindokas VP, Guo Q, Zaborina O, Alverdy JC.  Critical role of microbiota within cecal crypts on the regenerative capacity of the intestinal epithelium following surgical stress. Am. J. Physiol. Gastrointest. Liver Physiol. 2017;312(2):G112–G122. doi:10.1152/ajpgi.00294.2016.
  • Jang H-M, Lee K-E, Lee H-J, Kim D-H. Immobilization stress-induced Escherichia coli causes anxiety by inducing NF-κB activation through gut microbiota disturbance. Sci. Rep. 2018;8(1):13897. doi:10.1038/s41598-018-31764-0.
  • Yoshikawa K, Kurihara C, Furuhashi H, Takajo T, Maruta K, Yasutake Y, Sato H, Narimatsu K, Okada Y, Higashiyama M, et al. Psychological stress exacerbates NSAID-induced small bowel injury by inducing changes in intestinal microbiota and permeability via glucocorticoid receptor signaling. J. Gastroenterol. 2017;52(1):61–71. doi:10.1007/s00535-016-1205-1.
  • Rehaume LM, Mondot S, Aguirre de Cárcer D, Velasco J, Benham H, Hasnain SZ, Bowman J, Ruutu M, Hansbro PM, McGuckin MA, et al. ZAP-70 genotype disrupts the relationship between microbiota and host, leading to spondyloarthritis and ileitis in SKG mice. Arthritis Rheumatol (Hoboken, N J). 2014;66(10):2780–2792. doi:10.1002/art.38773.
  • Toral M, Robles-Vera I, de la Visitación N, Romero M, Yang T, Sánchez M, Gómez-Guzmán M, Jiménez R, Raizada MK, Duarte J. Critical Role of the Interaction Gut Microbiota - Sympathetic Nervous System in the Regulation of Blood Pressure. Front Physiol. 2019;10:231. doi:10.3389/fphys.2019.00231.
  • Nishimura N, Tanabe H, Komori E, Sasaki Y, Inoue R, Yamamoto T. Transplantation of high hydrogen-producing microbiota leads to generation of large amounts of colonic hydrogen in recipient rats fed high amylose maize starch. Nutrients. 2018;10(2):144. doi:10.3390/nu10020144.
  • Yang CQ, Guo XS, Ji-Li, Wei ZB, Zhao L, Zhao GT, Sheng ST. Rifaximin improves visceral hyperalgesia via trpv1 by modulating intestinal flora in the water avoidance stressed rat. Gastroenterol. Res. Pract. 2020;2020(4078681):1–9. doi:10.1155/2020/4078681.
  • Shan B, Ai Z, Zeng S, Song Y, Song J, Zeng Q, Liao Z, Wang T, Huang C, Su D.  Gut microbiome-derived lactate promotes to anxiety-like behaviors through GPR81 receptor-mediated lipid metabolism pathway. Psychoneuroendocrinology. 2020;117:104699. doi:10.1016/j.psyneuen.2020.104699.
  • Zhou W, Chow K-H, Fleming E, Oh J. Selective colonization ability of human fecal microbes in different mouse gut environments. ISME J. 2019;13:805–823.
  • Buchta Rosean C, Bostic RR, Ferey JCM, Feng TY, Azar FN, Tung KS, Dozmorov MG, Smirnova E, Bos PD, Rutkowski MR. Preexisting commensal dysbiosis is a host-intrinsic regulator of tissue inflammation and tumor cell dissemination in hormone receptor-positive breast cancer. Cancer Res. 2019;79(14):3662–3675. doi:10.1158/0008-5472.CAN-18-3464.
  • Singh V, Roth S, Llovera G, Sadler R, Garzetti D, Stecher B, Dichgans M, Liesz A.  Microbiota dysbiosis controls the neuroinflammatory response after stroke. J Neurosci. 2016;36:7428–7440.
  • Cheung MK, Yue GGL, Tsui KY, Gomes AJ, Kwan HS, Chiu PWY, Lau CBS. Discovery of an interplay between the gut microbiota and esophageal squamous cell carcinoma in mice. Am. J. Cancer Res. 2020;10(8):2409–2427.
  • Zhang F, Zhai M, Wu Q, Jia X, Wang Y, Wang N. Protective effect of tong-qiao-huo-xue decoction on inflammatory injury caused by intestinal microbial disorders in stroke rats. Biol. Pharm. Bull. 2020;43(5):788–800. doi:10.1248/bpb.b19-00847.
  • Chen R, Xu Y, Wu P, Zhou H, Lasanajak Y, Fang Y, Tang L, Ye L, Li X, Cai Z, et al. Transplantation of fecal microbiota rich in short chain fatty acids and butyric acid treat cerebral ischemic stroke by regulating gut microbiota. Pharmacol Res. 2019;148:104403. doi:10.1016/j.phrs.2019.104403.
  • Zhou GF, Jiang YH, Ma DF, Wang YC, Yang JL, Chen JY, Chi CY, Han XW, Li ZY, Li X. Xiao-Qing-Long Tang Prevents Cardiomyocyte Hypertrophy, Fibrosis, and the Development of Heart Failure with Preserved Ejection Faction in Rats by Modulating the Composition of the Gut Microbiota. Biomed Res Int. 2019;2019:9637479.
  • Xia GH, You C, Gao XX, Zeng XL, Zhu JJ, Xu KY, Tan CH, Xu RT, Wu QH, Zhou HW,  et al. Stroke Dysbiosis Index (SDI) in gut microbiome are associated with brain injury and prognosis of stroke. Front Neurol. 2019;10(397). doi:10.3389/fneur.2019.00397.
  • Cammarota G, Ianiro G, Kelly CR, Mullish BH, Allegretti JR, Kassam Z, Putignani L, Fischer M, Keller JJ, Costello SP, et al. International consensus conference on stool banking for faecal microbiota transplantation in clinical practice.
  • Yang J, Park S, Park S, Baek I, Chun J. Introducing Murine Microbiome Database (MMDB): a curated database with taxonomic profiling of the healthy mouse gastrointestinal microbiome. Microorganisms. 2019;7(11):480. doi:10.3390/microorganisms7110480.
  • Deloris Alexander A, Orcutt RP, Henry JC, Baker J Jr, Bissahoyo AC, Threadgill DW. Quantitative PCR assays for mouse enteric flora reveal strain-dependent differences in composition that are influenced by the microenvironment. Mamm Genome. 2006;17(11):1093–1104. doi:10.1007/s00335-006-0063-1.
  • Korach-Rechtman H, Freilich S, Gerassy-Vainberg S, Buhnik-Rosenblau K, Danin-Poleg Y, Bar H, Kashi Y. Murine genetic background has a stronger impact on the composition of the gut microbiota than maternal inoculation or exposure to unlike exogenous microbiota. Appl. Environ. Microbiol. 2019;85(18). doi:10.1128/AEM.00826-19.
  • Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl. Acad. Sci. U. S. A. 2010;107(44):18933–18938. doi:10.1073/pnas.1007028107.
  • Buhnik-Rosenblau K, Danin-Poleg Y, Kashi Y. Predominant effect of host genetics on levels of Lactobacillus johnsonii bacteria in the mouse gut. Appl. Environ. Microbiol. 2011;77(18):6531–6538. doi:10.1128/AEM.00324-11.
  • Bercik P, Denou E, Collins J, Jackson W, Lu J, Jury J, Deng Y, Blennerhassett P, Macri J, McCoy KD, et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology. 2011;141(599–609.e3):599–609.e3. doi:10.1053/j.gastro.2011.04.052.
  • Lundberg R, Toft MF, Metzdorff SB, Hansen CHF, Licht TR, Bahl MI, Hansen AK. Human microbiota-transplanted C57BL/6 mice and offspring display reduced establishment of key bacteria and reduced immune stimulation compared to mouse microbiota-transplantation. Sci Rep. 2020;10(7805). doi:10.1038/s41598-020-64703-z.
  • Montgomery TL, Künstner A, Kennedy JJ, Fang Q, Asarian L, Culp-Hill R, D'Alessandro A, Teuscher C, Busch H, Krementsov DN. Interactions between host genetics and gut microbiota determine susceptibility to CNS autoimmunity. Proc Natl Acad Sci. 2020;117(44):27516–27527. doi:10.1073/pnas.2002817117.
  • Pu Y, Tan Y, Qu Y, Chang L, Wang S, Wei Y, Wang X, Hashimoto K.  A role of the subdiaphragmatic vagus nerve in depression-like phenotypes in mice after fecal microbiota transplantation from Chrna7 knock-out mice with depression-like phenotypes. Brain. Behav. Immun. 2021;94:318–326. doi:10.1016/j.bbi.2020.12.032.
  • Kootte RS, Levin E, Salojärvi J, Smits LP, Hartstra AV, Udayappan SD, Hermes G, Bouter KE, Koopen AM, Holst JJ, et al. Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition. Cell Metab. 2017;26(611–619.e6):611–619.e6. doi:10.1016/j.cmet.2017.09.008.
  • El Aidy S, van Baarlen P, Derrien M, Lindenbergh-Kortleve DJ, Hooiveld G, Levenez F, Doré J, Dekker J, Samsom JN, Nieuwenhuis EE, et al. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol. 2012;5(5):567–579. doi:10.1038/mi.2012.32.
  • Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. U. S. A. 2004;101(44):15718–15723. doi:10.1073/pnas.0407076101.
  • Lewis SJ, Heaton KW. Stool form scale as a useful guide to intestinal transit time. Scand. J. Gastroenterol. 1997;32(9):920–924. doi:10.3109/00365529709011203.
  • Dore J, Ehrlich SD, Levenez F, Pelletier E, Alberti A, Bertrand L, Bork P, Costea PI, Sunagawa S, Guarner F, et al. IHMS Sop 02 V1 : standard operating procedure for fecal samples self ‐ collection. Int Hum Microbiome Stand. 2015;2(12).
  • Gratton J, Phetcharaburanin J, Mullish BH, Williams HR, Thursz M, Nicholson JK, Holmes E, Marchesi JR, Li JV.  Optimized sample handling strategy for metabolic profiling of human feces. Anal. Chem. 2016;88(9):4661–4668. doi:10.1021/acs.analchem.5b04159.
  • Papanicolas LE, Choo JM, Wang Y, Leong LEX, Costello SP, Gordon DL, Wesselingh SL, Rogers GB. Bacterial viability in faecal transplants: which bacteria survive? EBioMedicine. 2019;41:509–516. doi:10.1016/j.ebiom.2019.02.023.
  • O'Donnell MM, Rea MC, O'Sullivan Ó, Flynn C, Jones B, McQuaid A, Shanahan F, Ross RP. Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias. J Microbiol Methods. 2016;129:109–116. doi:10.1016/j.mimet.2016.08.002.
  • Béal C, Fonseca F. Freezing of Probiotic Bacteria. Adv Probiotic Technol. 2015;978-14987:179–212.
  • Burz SD, Abraham AL, Fonseca F, David O, Chapron A, Béguet-Crespel F, Cénard S, Le Roux K, Patrascu O, Levenez F, et al. A guide for ex vivo handling and storage of stool samples intended for fecal microbiota transplantation. Sci. Rep. 2019;9(1):1–16. doi:10.1038/s41598-019-45173-4.
  • Shaw AG, Sim K, Powell E, Cornwell E, Cramer T, McClure ZE, Li MS, Kroll JS. Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? Microbiome. 2016;4(1):1–14. doi:10.1186/s40168-016-0186-x.
  • Kia E, Wagner Mackenzie B, Middleton D, Lau A, Waite DW, Lewis G, Chan YK, Silvestre M, Cooper GJ, Poppitt SD,  et al. Integrity of the human faecal microbiota following long-term sample storage. PLoS One. 2016;11(e0163666):e0163666. doi:10.1371/journal.pone.0163666.
  • Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat. Commun. 2019;10(1):1–11. doi:10.1038/s41467-019-13036-1.
  • Walter J, Armet AM, Finlay BB, Shanahan F. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. Cell. 2020;180(2):221–232. doi:10.1016/j.cell.2019.12.025.
  • Thomas V, Clark J, Doré J. Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies. Future Microbiol. 2015;10(9):1485–1504. doi:10.2217/fmb.15.87.
  • Deng L, Silins R, Castro-Mejía JL, Kot W, Jessen L, Thorsen J, Shah S, Stokholm J, Bisgaard H, Moineau S, et al. A protocol for extraction of infective viromes suitable for metagenomics sequencing from low volume fecal samples. Viruses. 2019;11(667):667. doi:10.3390/v11070667.
  • Sausset R, Petit MA, Gaboriau-Routhiau V, De Paepe M. New insights into intestinal phages. Mucosal Immunol. 2020;13(2):205–215. doi:10.1038/s41385-019-0250-5.
  • Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK. Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model. Cell Host Microbe. 2019;25(803–814.e5):803–814.e5. doi:10.1016/j.chom.2019.05.001.
  • Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Front Microbiol. 2017;8:1–6. doi:10.3389/fmicb.2017.02224.
  • McLaren MR, Willis AD, Callahan BJ. Consistent and correctable bias in metagenomic sequencing experiments. Elife. 2019;8:1–31. doi:10.7554/eLife.46923.