Cited by 534

The gut microbiota is associated with immune cell dynamics in humans

Schluter, Jonas, Peled, Jonathan U., Taylor, Bradford P., Markey, Kate A., Smith, Melody, Taur, Ying, Niehus, Rene, Staffas, Anna +16 more·2020·Nature

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  1. [1]Mazmanian SK, Liu CH, Tzianabos AO & Kasper DL An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107– 118 (2005). 16009137
  2. [2]Gomez de Agüero M The maternal microbiota drives early postnatal innate immune development. Science 351, 1296– 1302 (2016). 26989247
  3. [3]Olin A Stereotypic immune system development in newborn children. Cell 174, 1277– 1292.e14 (2018). 30142345 PMC6108833
  4. [4]Tan TG 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). 27911839 PMC5167147
  5. [5]Deshmukh HS The microbiota regulates neutrophil homeostasis and host resistance to Escherichia coli K1 sepsis in neonatal mice. Nat. Med 20, 524– 530 (2014). 24747744 PMC4016187
  6. [7]Geva-Zatorsky N Mining the human gut microbiota for immunomodulatory organisms. Cell 168, 928– 943.e11 (2017). 28215708 PMC7774263
  7. [9]Markey KA The microbe-derived short-chain fatty acids butyrate and propionate are associated with protection from chronic GVHD. Blood 136, 130– 136 (2020). 32430495 PMC7332893
  8. [10]Azzouz D Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal. Ann. Rheum. Dis 78, 947– 956 (2019). 30782585 PMC6585303
  9. [15]Tanoue T A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 565, 600– 605 (2019). 30675064
  10. [16]Brandi G & Frega G Microbiota: Overview and Implication in Immunotherapy-Based Cancer Treatments. Int. J. Mol. Sci 20, (2019). PMC6600175 31159348
  11. [17]Xin Yu J, Hubbard-Lucey VM & Tang J The global pipeline of cell therapies for cancer. Nat. Rev. Drug Discov 18, 821– 822 (2019). 31673124
  12. [18]Morjaria S Antibiotic-Induced Shifts in Fecal Microbiota Density and Composition during Hematopoietic Stem Cell Transplantation. Infect. Immun 87, (2019). PMC6704593 31262981
  13. [20]Taur Y Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci. Transl. Med 10, (2018). PMC6468978 30257956
  14. [21]Staffas A Nutritional Support from the Intestinal Microbiota Improves Hematopoietic Reconstitution after Bone Marrow Transplantation in Mice. Cell Host Microbe 23, 447– 457.e4 (2018). 29576480 PMC5897172
  15. [22]Savani BN 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). 17889359 PMC3426353
  16. [23]Scheiermann C, Frenette PS & Hidalgo A Regulation of leucocyte homeostasis in the circulation. Cardiovasc. Res 107, 340– 351 (2015). 25750191 PMC4560027
  17. [24]Thompson PA Umbilical cord blood graft engineering: challenges and opportunities. Bone Marrow Transplant. 50 Suppl 2, S55– 62 (2015). 26039209
  18. [25]Gabrilove JL 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). 2452983
  19. [27]Schirmer M Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 167, 1125– 1136.e8 (2016). 27814509 PMC5131922
  20. [28]McLoughlin K, Schluter J, Rakoff-Nahoum S, Smith AL & Foster KR Host selection of microbiota via differential adhesion. Cell Host Microbe 19, 550– 559 (2016). 27053168
  21. [29]Hooper LV, Littman DR & Macpherson AJ Interactions between the microbiota and the immune system. Science 336, 1268– 1273 (2012). 22674334 PMC4420145
  22. [30]Palm NW Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158, 1000– 1010 (2014). 25171403 PMC4174347
  23. [31]Henke MT 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). 31182571 PMC6601261
  24. [32]Okba AM 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). 32257060 PMC6909025
  25. [33]Choi S-J High neutrophil-to-lymphocyte ratio predicts short survival duration in amyotrophic lateral sclerosis. Sci. Rep 10, 428 (2020). 31949271 PMC6965090
  26. [34]Gao Y 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). 29179480 PMC5687650
  27. [35]Hergott CB Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis. Blood 127, 2460– 2471 (2016). 26989200 PMC4874226
  28. [36]Smith PM The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569– 573 (2013). 23828891 PMC3807819
  29. [37]Balmer ML Microbiota-derived compounds drive steady-state granulopoiesis via MyD88/TICAM signaling. J. Immunol 193, 5273– 5283 (2014). 25305320
  30. [38]Ze X, Duncan SH, Louis P & Flint HJ Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6, 1535– 1543 (2012). 22343308 PMC3400402
  31. [39]Foster KR, Schluter J, Coyte KZ & Rakoff-Nahoum S The evolution of the host microbiome as an ecosystem on a leash. Nature 548, 43– 51 (2017). 28770836 PMC5749636
  32. [40]Fu Y-Y T Cell Recruitment to the Intestinal Stem Cell Compartment Drives Immune-Mediated Intestinal Damage after Allogeneic Transplantation. Immunity 51, 90– 103.e3 (2019). 31278057 PMC7239328
  33. [41]Gerber GK The dynamic microbiome. FEBS Lett. 588, 4131– 4139 (2014). 24583074
  34. [42]Jobin C Precision medicine using microbiota. Science 359, 32– 34 (2018). 29302001
  35. [44]Walter J, Armet AM, Finlay BB & Shanahan F Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents. Cell 180, 221– 232 (2020). 31978342
  36. [45]Caporaso JG Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621– 1624 (2012). 22402401 PMC3400413
  37. [46]Callahan BJ DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581– 583 (2016). 27214047 PMC4927377
  38. [47]Murali A, Bhargava A & Wright ES IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6, 140 (2018). 30092815 PMC6085705
  39. [48]Quast C The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590– 6 (2013). 23193283 PMC3531112
  40. [51]Pedregosa F Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research (2011).
  41. [52]Salvatier J, Wiecki TV & Fonnesbeck C Probabilistic programming in Python using PyMC3. PeerJ Computer Science 2, e55 (2016). PMC10495961 37705656
  42. [53]Hoffman MD & Gelman A The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo. Journal of Machine Learning Research (2014).
  43. [54]Franzosa EA Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods 15, 962– 968 (2018). 30377376 PMC6235447

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Authors
Schluter, J., Peled, J. U., Taylor, B. P., Markey, K. A., Smith, M., Taur, Y., Niehus, R., Staffas, A., Dai, A., Fontana, E., Amoretti, L. A., Wright, R. J., Morjaria, S., Fenelus, M., Pessin, M. S., Chao, N. J., Lew, M., Bohannon, L., Bush, A., Sung, A. D., Hohl, T. M., Perales, M.-A., van den Brink, M. R. M., & Xavier, J. B.
Venue
Nature
Published
2020-11-25
Volume
588
Issue
7837
Pages
303-307
ISSN
  • 0028-0836
  • 1476-4687
Cited by
534
References
11
Language
en

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