The gut microbiota is associated with immune cell dynamics in humans
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Gut microbiome plays critical roles in pathophysiological scenarios in the gut and can influence other organs such as the liver and the immune system.
“Gut microbiome 33 plays critical roles in the pathophysiological scenarios in the gut; they can influence other organs such as the liver 34,35 and the immune system 37 .”
From Gut-liver-axis microphysiological system for studying cellular fluidic shear stress and inter-tissue interaction (2022) · cites this paper as [37]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Regression shrinkage and selection via the lasso
Tibshirani, R. (1996) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1996.tb02080.x · Cited by 51,482 · see citing works
Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors
Routy, B., Le Chatelier, E., Derosa, L., Duong, C. P. M., Alou, M. T., Daillère, R., Fluckiger, A., Messaoudene, M., Rauber, C., Roberti, M. P., et al. (2018) · Science · doi:10.1126/science.aan3706 · Cited by 5,671 · see citing works
Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413 · see citing works
Role of the microbiota in immunity and inflammation.
Belkaid, Y., & Hand, T. W. (2014) · Cell · doi:10.1016/j.cell.2014.03.011 · Cited by 5,385 · see citing works
Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients
Gopalakrishnan, V., Spencer, C. N., Nezi, L., Reuben, A., Andrews, M. C., Karpinets, T. V., Prieto, P. A., Vicente, D., Hoffman, K., Wei, S. C., et al. (2018) · Science · doi:10.1126/science.aan4236 · Cited by 4,812 · see citing works
Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota
Vétizou, M., Pitt, J. M., Daillère, R., Lepage, P., Waldschmitt, N., Flament, C., Rusakiewicz, S., Routy, B., Roberti, M. P., Duong, C. P. M., et al. (2015) · Science · doi:10.1126/science.aad1329 · Cited by 3,488 · see citing works
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143 · see citing works
The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients
Matson, V., Fessler, J., Bao, R., Chongsuwat, T., Zha, Y., Alegre, M.-L., Luke, J. J., & Gajewski, T. F. (2018) · Science · doi:10.1126/science.aao3290 · Cited by 3,107 · see citing works
Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770 · see citing works
The Integrative Human Microbiome Project
The Integrative HMP (iHMP) Research Network Consortium, Proctor, L. M., Creasy, H. H., Fettweis, J. M., Lloyd-Price, J., Mahurkar, A., Zhou, W., Buck, G. A., Snyder, M. P., Strauss, J. F., et al. (2019) · Nature · doi:10.1038/s41586-019-1238-8 · Cited by 1,381 · see citing works
Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation
Peled, J. U., Gomes, A. L. C., Devlin, S. M., Littmann, E. R., Taur, Y., Sung, A. D., Weber, D., Hashimoto, D., Slingerland, A. E., Slingerland, J. B., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa1900623 · Cited by 765 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 43
- [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]Gomez de Agüero M The maternal microbiota drives early postnatal innate immune development. Science 351, 1296– 1302 (2016). 26989247
- [3]Olin A Stereotypic immune system development in newborn children. Cell 174, 1277– 1292.e14 (2018). 30142345 PMC6108833
- [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]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
- [7]Geva-Zatorsky N Mining the human gut microbiota for immunomodulatory organisms. Cell 168, 928– 943.e11 (2017). 28215708 PMC7774263
- [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
- [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
- [15]Tanoue T A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 565, 600– 605 (2019). 30675064
- [16]Brandi G & Frega G Microbiota: Overview and Implication in Immunotherapy-Based Cancer Treatments. Int. J. Mol. Sci 20, (2019). PMC6600175 31159348
- [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
- [18]Morjaria S Antibiotic-Induced Shifts in Fecal Microbiota Density and Composition during Hematopoietic Stem Cell Transplantation. Infect. Immun 87, (2019). PMC6704593 31262981
- [20]Taur Y Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci. Transl. Med 10, (2018). PMC6468978 30257956
- [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
- [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
- [23]Scheiermann C, Frenette PS & Hidalgo A Regulation of leucocyte homeostasis in the circulation. Cardiovasc. Res 107, 340– 351 (2015). 25750191 PMC4560027
- [24]Thompson PA Umbilical cord blood graft engineering: challenges and opportunities. Bone Marrow Transplant. 50 Suppl 2, S55– 62 (2015). 26039209
- [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
- [27]Schirmer M Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 167, 1125– 1136.e8 (2016). 27814509 PMC5131922
- [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
- [29]Hooper LV, Littman DR & Macpherson AJ Interactions between the microbiota and the immune system. Science 336, 1268– 1273 (2012). 22674334 PMC4420145
- [30]Palm NW Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158, 1000– 1010 (2014). 25171403 PMC4174347
- [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
- [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
- [33]Choi S-J High neutrophil-to-lymphocyte ratio predicts short survival duration in amyotrophic lateral sclerosis. Sci. Rep 10, 428 (2020). 31949271 PMC6965090
- [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
- [35]Hergott CB Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis. Blood 127, 2460– 2471 (2016). 26989200 PMC4874226
- [36]Smith PM The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569– 573 (2013). 23828891 PMC3807819
- [37]Balmer ML Microbiota-derived compounds drive steady-state granulopoiesis via MyD88/TICAM signaling. J. Immunol 193, 5273– 5283 (2014). 25305320
- [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
- [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
- [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
- [41]Gerber GK The dynamic microbiome. FEBS Lett. 588, 4131– 4139 (2014). 24583074
- [42]Jobin C Precision medicine using microbiota. Science 359, 32– 34 (2018). 29302001
- [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
- [45]Caporaso JG Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621– 1624 (2012). 22402401 PMC3400413
- [46]Callahan BJ DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581– 583 (2016). 27214047 PMC4927377
- [47]Murali A, Bhargava A & Wright ES IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6, 140 (2018). 30092815 PMC6085705
- [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
- [51]Pedregosa F Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research (2011).
- [52]Salvatier J, Wiecki TV & Fonnesbeck C Probabilistic programming in Python using PyMC3. PeerJ Computer Science 2, e55 (2016). PMC10495961 37705656
- [53]Hoffman MD & Gelman A The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo. Journal of Machine Learning Research (2014).
- [54]Franzosa EA Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods 15, 962– 968 (2018). 30377376 PMC6235447
Cited by
Sorted by citations
The microbiome and human cancer
Sepich-Poore, G. D., Zitvogel, L., Straussman, R., Hasty, J., Wargo, J. A., & Knight, R. (2021) · Science · doi:10.1126/science.abc4552 · Cited by 1,332 · see citing works
Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases
Loh, J. S., Mak, W. Q., Tan, L. K. S., Ng, C. X., Chan, H. H., Yeow, S. H., Foo, J. B., Ong, Y. S., How, C. W., & Khaw, K. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01743-1 · Cited by 1,193 · see citing works
Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy
Smith, M., Dai, A., Ghilardi, G., Amelsberg, K. V., Devlin, S. M., Pajarillo, R., Slingerland, J. B., Beghi, S., Herrera, P. S., Giardina, P., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01702-9 · Cited by 349 · see citing works
Self-citation<i>Ruminococcus gnavus</i> : friend or foe for human health
Crost, E. H., Coletto, E., Bell, A., & Juge, N. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad014 · Cited by 335 · see citing works
The Microbiota–Gut–Brain Axis and Alzheimer’s Disease: Neuroinflammation Is to Blame?
Megur, A., Baltriukienė, D., Bukelskienė, V., & Burokas, A. (2020) · Nutrients · doi:10.3390/nu13010037 · Cited by 323 · see citing works
Stein-Thoeringer, C. K., Saini, N. Y., Zamir, E., Blumenberg, V., Schubert, M.-L., Mor, U., Fante, M. A., Schmidt, S., Hayase, E., Hayase, T., et al. (2023) · Nature Medicine · doi:10.1038/s41591-023-02234-6 · Cited by 255 · see citing works
Human immune diversity: from evolution to modernity
Liston, A., Humblet-Baron, S., Duffy, D., & Goris, A. (2021) · Nature Immunology · doi:10.1038/s41590-021-01058-1 · Cited by 187 · see citing works
Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology?
Derosa, L., Routy, B., Desilets, A., Daillère, R., Terrisse, S., Kroemer, G., & Zitvogel, L. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0236 · Cited by 170 · see citing works
Grajeda-Iglesias, C., Durand, S., Daillère, R., Iribarren, K., Lemaitre, F., Derosa, L., Aprahamian, F., Bossut, N., Nirmalathasan, N., Madeo, F., et al. (2021) · Aging · doi:10.18632/aging.202739 · Cited by 161 · see citing works
Roles of the intestinal microbiota and microbial metabolites in acute GVHD
Lin, D., Hu, B., Li, P., Zhao, Y., Xu, Y., & Wu, D. (2021) · Experimental Hematology & Oncology · doi:10.1186/s40164-021-00240-3 · Cited by 71 · see citing works
Lei, W., Cheng, Y., Liu, X., Gao, J., Zhu, Z., Ding, W., Xu, X., Li, Y., Ling, Z., Jiang, R., et al. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1582119 · Cited by 68 · see citing works
Computational methods and challenges in analyzing intratumoral microbiome data
Wang, Q., Liu, Z., Ma, A., Li, Z., Liu, B., & Ma, Q. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.01.011 · Cited by 37 · see citing works
Yang, J., Hirai, Y., Imamura, S., Tsuchiya, T., Tabata, O., & Kamei, K.-I. (2022) · doi:10.1101/2022.01.31.478467 · Cited by 21 · see citing works
Cantarelli, L., Gutiérrez Nicolás, F., García Gil, S., Morales Barrios, J. A., Oramas Rodriguez, J., & Nazco Casariego, G. J. (2024) · Journal of Immunotherapy · doi:10.1097/cji.0000000000000494 · Cited by 4 · see citing works
- 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.
- ORCID
- Venue
- Nature
- Published
- 2020-11-25
- Volume
- 588
- Issue
- 7837
- Pages
- 303-307
- ISSN
- 0028-0836
- 1476-4687
- PMC
- PMC7725892
- Cited by
- 534
- References
- 11
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review