de Vos WM, Tilg H, Van Hul M, Cani PD. Gut microbiome and health: mechanistic insights. Gut. 2022;71(5):1020–32.

Article  PubMed  Google Scholar 

The Integrative Human Microbiome Project. Nature 2019, 569(7758):641-648

Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Mbong Ngwese M, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, et al. Codiversification of gut microbiota with humans. Science. 2022;377(6612):1328–32.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ting NL, Lau HC, Yu J. Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes. Gut. 2022;71(7):1412–25.

Article  PubMed  Google Scholar 

Sepich-Poore GD, Zitvogel L, Straussman R, Hasty J, Wargo JA, Knight R. The microbiome and human cancer. Science. 2021;371(6536):eabc4552.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao LY, Mei JX, Yu G, Lei L, Zhang WH, Liu K, Chen XL, Kolat D, Yang K, Hu JK. Role of the gut microbiota in anticancer therapy: from molecular mechanisms to clinical applications. Signal Transduct Target Ther. 2023;8(1):201.

Article  PubMed  PubMed Central  Google Scholar 

Goto Y, Iwata S, Miyahara M, Miyako E. Discovery of intratumoral oncolytic bacteria toward targeted anticancer theranostics. Adv Sci. 2023;10(20):e2301679.

Article  Google Scholar 

Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489(7415):220–30.

Article  CAS  PubMed  PubMed Central  Google Scholar 

McNally L, Brown SP. Microbiome: ecology of stable gut communities. Nat Microbiol. 2016;1:15016.

Article  CAS  PubMed  Google Scholar 

Relman DA. The human microbiome: ecosystem resilience and health. Nutr Rev. 2012;70(Suppl 1):S2-9.

Article  PubMed  Google Scholar 

Shaw LP, Bassam H, Barnes CP, Walker AS, Klein N, Balloux F. Modelling microbiome recovery after antibiotics using a stability landscape framework. ISME J. 2019;13(7):1845–56.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: Networks, competition, and stability. Science. 2015;350(6261):663–6.

Article  CAS  PubMed  Google Scholar 

Claesson MJ, O’Sullivan O, Wang Q, Nikkila J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O’Toole PW. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE. 2009;4(8):e6669.

Article  PubMed  PubMed Central  Google Scholar 

Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009;3(2):179–89.

Article  CAS  PubMed  Google Scholar 

Fassarella M, Blaak EE, Penders J, Nauta A, Smidt H, Zoetendal EG. Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health. Gut. 2021;70(3):595–605.

Article  CAS  PubMed  Google Scholar 

Shi N, Li N, Duan X, Niu H. Interaction between the gut microbiome and mucosal immune system. Mil Med Res. 2017;4:14.

PubMed  PubMed Central  Google Scholar 

Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16(6):341–52.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Martin-Gallausiaux C, Marinelli L, Blottiere HM, Larraufie P, Lapaque N. SCFA: mechanisms and functional importance in the gut. Proc Nutr Soc. 2021;80(1):37–49.

Article  CAS  PubMed  Google Scholar 

Janeiro MH, Ramirez MJ, Milagro FI, Martinez JA, Solas M. Implication of trimethylamine N-oxide (TMAO) in disease: potential biomarker or new therapeutic target. Nutrients. 2018;10(10):1398.

Article  PubMed  PubMed Central  Google Scholar 

Fernandes MR, Aggarwal P, Costa RGF, Cole AM, Trinchieri G. Targeting the gut microbiota for cancer therapy. Nat Reviews Cancer. 2022;22:703–22.

Article  CAS  PubMed  Google Scholar 

Ignacio A, Shah K, Bernier-Latmani J, Köller Y, Coakley G, Moyat M, Hamelin R, Armand F, Wong NC, Ramay H, et al. Small intestinal resident eosinophils maintain gut homeostasis following microbial colonization. Immunity. 2022;55(7):1250-1267.e1212.

Article  CAS  PubMed  Google Scholar 

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):1084–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baruch EN, Youngster I, Ben-Betzalel G, Ortenberg R, Lahat A, Katz L, Adler K, Dick-Necula D, Raskin S, Bloch N, et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science. 2021;371(6529):602–9.

Article  CAS  PubMed  Google Scholar 

Tomita Y, Goto Y, Sakata S, Imamura K, Minemura A, Oka K, Hayashi A, Jodai T, Akaike K, Anai M, et al. Clostridium butyricum therapy restores the decreased efficacy of immune checkpoint blockade in lung cancer patients receiving proton pump inhibitors. Oncoimmunology. 2022;11(1):2081010.

Article  PubMed  PubMed Central  Google Scholar 

Schupack DA, Mars RAT, Voelker DH, Abeykoon JP, Kashyap PC. The promise of the gut microbiome as part of individualized treatment strategies. Nat Rev Gastroenterol Hepatol. 2021;19:7–25.

Article  PubMed  PubMed Central  Google Scholar 

Hitch TCA, Hall LJ, Walsh SK, Leventhal GE, Slack E, de Wouters T, Walter J, Clavel T. Microbiome-based interventions to modulate gut ecology and the immune system. Mucosal Immunol. 2022;15:1095–113.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang H, Zhang Z, Liao Y, Zhang W, Tang D. The complex link and disease between the gut microbiome and the immune system in infants. Front Cell Infect Microbiol. 2022;12:924119.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Spiljar M, Merkler D, Trajkovski M. The immune system bridges the gut microbiota with systemic energy homeostasis: focus on TLRs, Mucosal Barrier, and SCFAs. Front Immunol. 2017;8:1353.

Article  PubMed  PubMed Central  Google Scholar 

Brown EM, Kenny DJ, Xavier RJ. Gut microbiota regulation of T cells during inflammation and autoimmunity. Annu Rev Immunol. 2019;37:599–624.

Article  CAS  PubMed  Google Scholar 

Kiner E, Willie E, Vijaykumar B, Chowdhary K, Schmutz H, Chandler J, Schnell A, Thakore PI, LeGros G, Mostafavi S, et al. Gut CD4(+) T cell phenotypes are a continuum molded by microbes, not by T(H) archetypes. Nat Immunol. 2021;22(2):216–28.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern PP, Merriman J, Cortez VS, Caparon MG, Donia MS, Gilfillan S, et al. Lactobacillus reuteri induces gut intraepithelial CD4(+)CD8αα(+) T cells. Science. 2017;357(6353):806–10.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nowosad CR, Mesin L, Castro TBR, Wichmann C, Donaldson GP, Araki T, Schiepers A, Lockhart AAK, Bilate AM, Mucida D, et al. Tunable dynamics of B cell selection in gut germinal centres. Nature. 2020;588(7837):321–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

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):582–92.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shono Y, Docampo MD, Peled JU, Perobelli SM, Velardi E, Tsai JJ, Slingerland AE, Smith OM, Young LF, Gupta J, et al. Increased GVHD-related mortality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci Transl Med. 2016;8(339):339–71.

Article  Google Scholar 

Routy B, Letendre C, Enot D, Chénard-Poirier M, Mehraj V, Séguin NC, Guenda K, Gagnon K, Woerther PL, Ghez D, et al. The influence of gut-decontamination prophylactic antibiotics on acute graft-versus-host disease and survival following allogeneic hematopoietic stem cell transplantation. Oncoimmunology. 2017;6(1):e1258506.

Article  PubMed  Google Scholar 

Staffas A, Burgos da Silva M, Slingerland AE, Lazrak A, Bare CJ, Holman CD, Docampo MD, Shono Y, Durham B, Pickard AJ, et al. Nutritional support from the intestinal microbiota improves hematopoietic reconstitution after bone marrow transplantation in mice. Cell Host Microbe. 2018;23(4):447–57.