The gut microbiota is associated with immune cell dynamics in humans.


Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
12 2020
Historique:
received: 03 05 2019
accepted: 30 09 2020
pubmed: 27 11 2020
medline: 2 3 2021
entrez: 26 11 2020
Statut: ppublish

Résumé

The gut microbiota influences development

Identifiants

pubmed: 33239790
doi: 10.1038/s41586-020-2971-8
pii: 10.1038/s41586-020-2971-8
pmc: PMC7725892
mid: NIHMS1634150
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

303-307

Subventions

Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : P01 CA023766
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA228308
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI124275
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI093808
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA209975
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI137269
Pays : United States
Organisme : NHLBI NIH HHS
ID : K08 HL143189
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA203950
Pays : United States

Commentaires et corrections

Type : CommentIn

Références

Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107–118 (2005).
pubmed: 16009137 doi: 10.1016/j.cell.2005.05.007 pmcid: 16009137
Gomez de Agüero, M. et al. The maternal microbiota drives early postnatal innate immune development. Science 351, 1296–1302 (2016).
pubmed: 26989247 doi: 10.1126/science.aad2571 pmcid: 26989247
Olin, A. et al. Stereotypic immune system development in newborn children. Cell 174, 1277–1292 (2018).
pubmed: 30142345 pmcid: 6108833 doi: 10.1016/j.cell.2018.06.045
Tan, T. G. et al. Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice. Proc. Natl Acad. Sci. USA 113, E8141–E8150 (2016).
pubmed: 27911839 doi: 10.1073/pnas.1617460113 pmcid: 27911839
Deshmukh, H. S. et al. The microbiota regulates neutrophil homeostasis and host resistance to Escherichia coli K1 sepsis in neonatal mice. Nat. Med. 20, 524–530 (2014).
pubmed: 24747744 pmcid: 4016187 doi: 10.1038/nm.3542
Ivanov, I. I. et al. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4, 337–349 (2008).
pubmed: 18854238 pmcid: 2597589 doi: 10.1016/j.chom.2008.09.009
Geva-Zatorsky, N. et al. Mining the human gut microbiota for immunomodulatory organisms. Cell 168, 928–943 (2017).
pubmed: 28215708 pmcid: 7774263 doi: 10.1016/j.cell.2017.01.022
Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019).
pubmed: 31142855 pmcid: 31142855 doi: 10.1038/s41586-019-1237-9
Markey, K. A. et al. The microbe-derived short-chain fatty acids butyrate and propionate are associated with protection from chronic GVHD. Blood 136, 130–136 (2020).
pubmed: 32430495 doi: 10.1182/blood.2019003369
Azzouz, D. et al. Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal. Ann. Rheum. Dis. 78, 947–956 (2019).
pubmed: 30782585 pmcid: 6585303 doi: 10.1136/annrheumdis-2018-214856
Routy, B. et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359, 91–97 (2018).
pubmed: 29097494 doi: 10.1126/science.aan3706 pmcid: 29097494
Gopalakrishnan, V. et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 359, 97–103 (2018).
pubmed: 29097493 doi: 10.1126/science.aan4236 pmcid: 29097493
Vétizou, M. et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science 350, 1079–1084 (2015).
pubmed: 26541610 pmcid: 4721659 doi: 10.1126/science.aad1329
Matson, V. et al. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 359, 104–108 (2018).
pubmed: 29302014 pmcid: 6707353 doi: 10.1126/science.aao3290
Tanoue, T. et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 565, 600–605 (2019).
pubmed: 30675064 doi: 10.1038/s41586-019-0878-z pmcid: 30675064
Brandi, G. & Frega, G. Microbiota: overview and implication in immunotherapy-based cancer treatments. Int. J. Mol. Sci. 20, 2699 (2019).
pmcid: 6600175 doi: 10.3390/ijms20112699
Xin Yu, J., Hubbard-Lucey, V. M. & Tang, J. The global pipeline of cell therapies for cancer. Nat. Rev. Drug Discov. 18, 821–822 (2019).
doi: 10.1038/d41573-019-00090-z
Morjaria, S. et al. Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation. Infect. Immun. 87, e00206-19 (2019).
pubmed: 31262981 pmcid: 6704593 doi: 10.1128/IAI.00206-19
Peled, J. U. et al. Microbiota as predictor of mortality in allogeneic hematopoietic-cell transplantation. N. Engl. J. Med. 382, 822–834 (2020).
pubmed: 32101664 pmcid: 7534690 doi: 10.1056/NEJMoa1900623
Taur, Y. et al. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci. Transl. Med. 10, eaap9489 (2018).
pubmed: 30257956 pmcid: 6468978 doi: 10.1126/scitranslmed.aap9489
Staffas, A. et al. Nutritional support from the intestinal microbiota improves hematopoietic reconstitution after bone marrow transplantation in mice. Cell Host Microbe 23, 447–457. (2018).
pubmed: 29576480 pmcid: 5897172 doi: 10.1016/j.chom.2018.03.002
Savani, B. N. et al. Absolute lymphocyte count on day 30 is a surrogate for robust hematopoietic recovery and strongly predicts outcome after T cell-depleted allogeneic stem cell transplantation. Biol. Blood Marrow Transplant. 13, 1216–1223 (2007).
pubmed: 17889359 pmcid: 3426353 doi: 10.1016/j.bbmt.2007.07.005
Scheiermann, C., Frenette, P. S. & Hidalgo, A. Regulation of leucocyte homeostasis in the circulation. Cardiovasc. Res. 107, 340–351 (2015).
pubmed: 25750191 pmcid: 4560027 doi: 10.1093/cvr/cvv099
Thompson, P. A. et al. Umbilical cord blood graft engineering: challenges and opportunities. Bone Marrow Transplant. 50 (Suppl 2), S55–S62 (2015).
pubmed: 26039209 doi: 10.1038/bmt.2015.97 pmcid: 26039209
Gabrilove, J. L. et al. Effect of granulocyte colony-stimulating factor on neutropenia and associated morbidity due to chemotherapy for transitional-cell carcinoma of the urothelium. N. Engl. J. Med. 318, 1414–1422 (1988).
pubmed: 2452983 doi: 10.1056/NEJM198806023182202 pmcid: 2452983
Belkaid, Y. & Hand, T. W. Role of the microbiota in immunity and inflammation. Cell 157, 121–141 (2014).
pubmed: 24679531 pmcid: 4056765 doi: 10.1016/j.cell.2014.03.011
Schirmer, M. et al. Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 167, 1125–1136 (2016).
pubmed: 27814509 pmcid: 5131922 doi: 10.1016/j.cell.2016.10.020
McLoughlin, K., Schluter, J., Rakoff-Nahoum, S., Smith, A. L. & Foster, K. R. Host selection of microbiota via differential adhesion. Cell Host Microbe 19, 550–559 (2016).
pubmed: 27053168 doi: 10.1016/j.chom.2016.02.021 pmcid: 27053168
Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).
pubmed: 22674334 pmcid: 4420145 doi: 10.1126/science.1223490
Palm, N. W. et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158, 1000–1010 (2014).
pubmed: 25171403 pmcid: 4174347 doi: 10.1016/j.cell.2014.08.006
Henke, M. T. et al. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide. Proc. Natl Acad. Sci. USA 116, 12672–12677 (2019).
pubmed: 31182571 doi: 10.1073/pnas.1904099116
Okba, A. M. et al. Neutrophil/lymphocyte ratio and lymphocyte/monocyte ratio in ulcerative colitis as non-invasive biomarkers of disease activity and severity. Auto Immun. Highlights 10, 4 (2019).
pubmed: 32257060 pmcid: 6909025 doi: 10.1186/s13317-019-0114-8
Choi, S.-J. et al. High neutrophil-to-lymphocyte ratio predicts short survival duration in amyotrophic lateral sclerosis. Sci. Rep. 10, 428 (2020).
pubmed: 31949271 pmcid: 6965090 doi: 10.1038/s41598-019-57366-y
Gao, Y. et al. Neutrophil/lymphocyte ratio is a more sensitive systemic inflammatory response biomarker than platelet/lymphocyte ratio in the prognosis evaluation of unresectable pancreatic cancer. Oncotarget 8, 88835–88844 (2017).
pubmed: 29179480 pmcid: 5687650 doi: 10.18632/oncotarget.21340
Hergott, C. B. et al. Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis. Blood 127, 2460–2471 (2016).
pubmed: 26989200 pmcid: 4874226 doi: 10.1182/blood-2015-10-675173
Smith, P. M. et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569–573 (2013).
pubmed: 23828891 doi: 10.1126/science.1241165 pmcid: 23828891
Balmer, M. L. et al. Microbiota-derived compounds drive steady-state granulopoiesis via MyD88/TICAM signaling. J. Immunol. 193, 5273–5283 (2014).
pubmed: 25305320 doi: 10.4049/jimmunol.1400762
Ze, X., Duncan, S. H., Louis, P. & Flint, H. J. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6, 1535–1543 (2012).
pubmed: 22343308 pmcid: 3400402 doi: 10.1038/ismej.2012.4
Foster, K. R., Schluter, J., Coyte, K. Z. & Rakoff-Nahoum, S. The evolution of the host microbiome as an ecosystem on a leash. Nature 548, 43–51 (2017).
pubmed: 5749636 pmcid: 5749636 doi: 10.1038/nature23292
Fu, Y.-Y. et al. T cell recruitment to the intestinal stem cell compartment drives immune-mediated intestinal damage after allogeneic transplantation. Immunity 51, 90–103 (2019).
pubmed: 31278057 pmcid: 7239328 doi: 10.1016/j.immuni.2019.06.003
Gerber, G. K. The dynamic microbiome. FEBS Lett. 588, 4131–4139 (2014).
pubmed: 24583074 doi: 10.1016/j.febslet.2014.02.037 pmcid: 24583074
Jobin, C. Precision medicine using microbiota. Science 359, 32–34 (2018).
pubmed: 29302001 doi: 10.1126/science.aar2946 pmcid: 29302001
The Integrative HMP (iHMP) Research Network Consortium. The integrative human microbiome project. Nature 569, 641–648 (2019).
doi: 10.1038/s41586-019-1238-8
Walter, J., Armet, A. M., Finlay, B. B. & Shanahan, F. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. Cell 180, 221–232 (2020).
doi: 10.1016/j.cell.2019.12.025
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).
pubmed: 22402401 pmcid: 3400413 doi: 10.1038/ismej.2012.8
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
pubmed: 27214047 pmcid: 4927377 doi: 10.1038/nmeth.3869
Murali, A., Bhargava, A. & Wright, E. S. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6, 140 (2018).
pubmed: 30092815 pmcid: 6085705 doi: 10.1186/s40168-018-0521-5
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
pubmed: 23193283 doi: 10.1093/nar/gks1219 pmcid: 23193283
Pinheiro, J. C., Bates, D. M., DebRoy, S. S. & Sarkar, D. nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-150 (2013).
Tibshirani, R. Regression shrinkage and selection via the lasso. J. R. Stat. Soc. B 58, 267–288 (1996).
Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825 (2011).
Salvatier, J., Wiecki, T. V. & Fonnesbeck, C. Probabilistic programming in Python using PyMC3. PeerJ Comput. Sci. 2, e55 (2016).
Hoffman, M. D. & Gelman, A. The No-U-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo. J. Mach. Learn. Res. 15, 1593–1623 (2014).
Franzosa, E. A. et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods 15, 962–968 (2018).
pubmed: 30377376 pmcid: 30377376 doi: 10.1038/s41592-018-0176-y

Auteurs

Jonas Schluter (J)

Institute for Computational Medicine, NYU Langone Health, New York, NY, USA. jonas.schluter@nyulangone.org.
Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. jonas.schluter@nyulangone.org.

Jonathan U Peled (JU)

Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Weill Cornell Medical College, New York, NY, USA.

Bradford P Taylor (BP)

Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Kate A Markey (KA)

Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Weill Cornell Medical College, New York, NY, USA.

Melody Smith (M)

Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Weill Cornell Medical College, New York, NY, USA.

Ying Taur (Y)

Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA.

Rene Niehus (R)

Harvard University, T. H. Chan School of Public Health, Boston, MA, USA.

Anna Staffas (A)

Sahlgrenska Cancer Center, Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.

Anqi Dai (A)

Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Emily Fontana (E)

Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA.

Luigi A Amoretti (LA)

Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA.

Roberta J Wright (RJ)

Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA.

Sejal Morjaria (S)

Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA.

Maly Fenelus (M)

Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Melissa S Pessin (MS)

Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Nelson J Chao (NJ)

Division of Hematologic Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA.

Meagan Lew (M)

Division of Hematologic Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA.

Lauren Bohannon (L)

Division of Hematologic Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA.

Amy Bush (A)

Division of Hematologic Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA.

Anthony D Sung (AD)

Division of Hematologic Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA.

Tobias M Hohl (TM)

Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA.

Miguel-Angel Perales (MA)

Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Weill Cornell Medical College, New York, NY, USA.

Marcel R M van den Brink (MRM)

Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Weill Cornell Medical College, New York, NY, USA.

Joao B Xavier (JB)

Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. xavierj@mskcc.org.

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