Examining the healthy human microbiome concept.


Journal

Nature reviews. Microbiology
ISSN: 1740-1534
Titre abrégé: Nat Rev Microbiol
Pays: England
ID NLM: 101190261

Informations de publication

Date de publication:
23 Oct 2024
Historique:
accepted: 04 09 2024
medline: 24 10 2024
pubmed: 24 10 2024
entrez: 24 10 2024
Statut: aheadofprint

Résumé

Human microbiomes are essential to health throughout the lifespan and are increasingly recognized and studied for their roles in metabolic, immunological and neurological processes. Although the full complexity of these microbial communities is not fully understood, their clinical and industrial exploitation is well advanced and expanding, needing greater oversight guided by a consensus from the research community. One of the most controversial issues in microbiome research is the definition of a 'healthy' human microbiome. This concept is complicated by the microbial variability over different spatial and temporal scales along with the challenge of applying a unified definition to the spectrum of healthy microbiome configurations. In this Perspective, we examine the progress made and the key gaps that remain to be addressed to fully harness the benefits of the human microbiome. We propose a road map to expand our knowledge of the microbiome-health relationship, incorporating epidemiological approaches informed by the unique ecological characteristics of these communities.

Identifiants

pubmed: 39443812
doi: 10.1038/s41579-024-01107-0
pii: 10.1038/s41579-024-01107-0
doi:

Types de publication

Journal Article Review

Langues

eng

Sous-ensembles de citation

IM

Investigateurs

Francesco Asnicar (F)
Athanasios Typas (A)
Fay Betsou (F)
Hervé Blottière (H)
Peer Bork (P)
Isabelle Boutron (I)
Federica Carraturo (F)
Marcus Claesson (M)
Magali Cordaillat-Simmons (M)
Celine Druart (C)
Alessio Fasano (A)
Yolanda Godoy (Y)
Dirk Haller (D)
Zahra Hassani (Z)
Diënty H M J Hazenbrink (DHMJ)
Mads Israelsen (M)
Anandhi Iyappan (A)
Alexander Jarde (A)
Stephan Kampshoff (S)
Aleksander Krag (A)
Aicha Kriaa (A)
Aonghus Lavelle (A)
Amira Metwaly (A)
Vitalina Morozova (V)
Federica Pinto (F)
Nicolas Pons (N)
Pierre-Louis Prost (PL)
Philippe Ravaud (P)
Moez Rhimi (M)
Julie Rodriquez (J)
Arjun Sarati (A)
Robert Schierwagen (R)
Nicola Segata (N)
Debora Serra (D)
Jonel Trebicka (J)
Corrado Vecchi (C)
Patrick Veiga (P)
Laurence Zitvogel (L)
Lisa Derosa (L)

Informations de copyright

© 2024. Springer Nature Limited.

Références

Berg, G. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020).
pubmed: 32605663 pmcid: 7329523 doi: 10.1186/s40168-020-00875-0
Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. N. Engl. J. Med. 375, 2369–2379 (2016).
pubmed: 27974040 doi: 10.1056/NEJMra1600266
Turnbaugh, P. J. et al. The Human Microbiome Project. Nature 449, 804–810 (2007).
pubmed: 17943116 pmcid: 3709439 doi: 10.1038/nature06244
Larsen, N. et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 5, e9085 (2010).
pubmed: 20140211 pmcid: 2816710 doi: 10.1371/journal.pone.0009085
Qin, N. et al. Alterations of the human gut microbiome in liver cirrhosis. Nature 513, 59–64 (2014).
pubmed: 25079328 doi: 10.1038/nature13568
Wang, T. et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 6, 320–329 (2012).
pubmed: 21850056 doi: 10.1038/ismej.2011.109
Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15, 382–392 (2014).
pubmed: 24629344 pmcid: 4059512 doi: 10.1016/j.chom.2014.02.005
Jeffery, I. B. et al. Differences in fecal microbiomes and metabolomes of people with vs without irritable bowel syndrome and bile acid malabsorption. Gastroenterology 158, 1016–1028.e8 (2020).
pubmed: 31843589 doi: 10.1053/j.gastro.2019.11.301
McGuinness, A. J. et al. A systematic review of gut microbiota composition in observational studies of major depressive disorder, bipolar disorder and schizophrenia. Mol. Psychiatry 27, 1920–1935 (2022).
pubmed: 35194166 pmcid: 9126816 doi: 10.1038/s41380-022-01456-3
Nikolova, V. L. et al. Perturbations in gut microbiota composition in psychiatric disorders: a review and meta-analysis. JAMA Psychiatry 78, 1343–1354 (2021).
pubmed: 34524405 doi: 10.1001/jamapsychiatry.2021.2573
Zhang, X., Chen, B., Zhao, L. & Li, H. The gut microbiota: emerging evidence in autoimmune diseases. Trends Mol. Med. 26, 862–873 (2020).
pubmed: 32402849 doi: 10.1016/j.molmed.2020.04.001
Jansen, D. et al. Community types of the human gut virome are associated with endoscopic outcome in ulcerative colitis. J. Crohns Colitis 17, 1504–1513 (2023).
pubmed: 37052201 pmcid: 10588789 doi: 10.1093/ecco-jcc/jjad061
Salosensaari, A. et al. Taxonomic signatures of cause-specific mortality risk in human gut microbiome. Nat. Commun. 12, 2671 (2021).
pubmed: 33976176 pmcid: 8113604 doi: 10.1038/s41467-021-22962-y
US Food and Drug Administration. Approval letter—REBYOTA. FDA https://www.fda.gov/vaccines-blood-biologics/vaccines/rebyota (2022).
Walter, J. & Shanahan, F. Fecal microbiota-based treatment for recurrent Clostridioides difficile infection. Cell 186, 1087 (2023).
pubmed: 36931236 doi: 10.1016/j.cell.2023.02.034
Bibbò, S. et al. Fecal microbiota transplantation: screening and selection to choose the optimal donor. J. Clin. Med. 9, 1–14 (2020).
doi: 10.3390/jcm9061757
van Duijkeren, E. et al. Long-term carriage of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in the general population in the Netherlands. Clin. Infect. Dis. 66, 1368–1376 (2018).
pubmed: 29149242 doi: 10.1093/cid/cix1015
Piewngam, P. et al. Composition of the intestinal microbiota in extended-spectrum β-lactamase-producing Enterobacteriaceae carriers and non-carriers in Thailand. Int. J. Antimicrob. Agents 53, 435–441 (2019).
pubmed: 30578963 doi: 10.1016/j.ijantimicag.2018.12.006
Vandeputte, D. et al. Temporal variability in quantitative human gut microbiome profiles and implications for clinical research. Nat. Commun. 12, 6740 (2021).
pubmed: 34795283 pmcid: 8602282 doi: 10.1038/s41467-021-27098-7
Abdill, R. J., Adamowicz, E. M. & Blekhman, R. Public human microbiome data are dominated by highly developed countries. PLoS Biol. 20, e3001536 (2022).
pubmed: 35167588 pmcid: 8846514 doi: 10.1371/journal.pbio.3001536
Keohane, D. M. et al. Microbiome and health implications for ethnic minorities after enforced lifestyle changes. Nat. Med. 26, 1089–1095 (2020).
pubmed: 32632193 doi: 10.1038/s41591-020-0963-8
Makhalanyane, T. P. et al. African microbiomes matter. Nat. Rev. Microbiol. 21, 479–481 (2023).
pubmed: 37328673 doi: 10.1038/s41579-023-00925-y
Reynoso-García, J. et al. A complete guide to human microbiomes: body niches, transmission, development, dysbiosis, and restoration. Front. Syst. Biol. 2, 951403 (2022).
pubmed: 38993286 pmcid: 11238057 doi: 10.3389/fsysb.2022.951403
Huttenhower, C. et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).
doi: 10.1038/nature11234
Vemuri, R., Shankar, E. M., Chieppa, M., Eri, R. & Kavanagh, K. Beyond just bacteria: functional biomes in the gut ecosystem including virome, mycobiome, archaeome and helminths. Microorganisms 8, 483 (2020).
pubmed: 32231141 pmcid: 7232386 doi: 10.3390/microorganisms8040483
Stockdale, S. R. & Hill, C. Progress and prospects of the healthy human gut virome. Curr. Opin. Virol. 51, 164–171 (2021).
pubmed: 34742036 doi: 10.1016/j.coviro.2021.10.001
Laforest-Lapointe, I. & Arrieta, M.-C. Microbial eukaryotes: a missing link in gut microbiome studies. mSystems 3, e00201–e00217 (2018).
pubmed: 29556538 pmcid: 5850078 doi: 10.1128/mSystems.00201-17
Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med. 8, 51 (2016).
pubmed: 27122046 pmcid: 4848870 doi: 10.1186/s13073-016-0307-y
Shanahan, F., Ghosh, T. S. & O’Toole, P. W. The healthy microbiome—what is the definition of a healthy gut microbiome? Gastroenterology 160, 483–494 (2021).
pubmed: 33253682 doi: 10.1053/j.gastro.2020.09.057
Najmanová, L., Vídeňská, P. & Cahová, M. Healthy microbiome—a mere idea or a sound concept? Physiol. Res. 71, 719–738 (2022).
pubmed: 36426891 pmcid: 9814986 doi: 10.33549/physiolres.934967
Vandeputte, D., Tito, R. Y., Vanleeuwen, R., Falony, G. & Raes, J. Practical considerations for large-scale gut microbiome studies. FEMS Microbiol. Rev. 41, S154–S167 (2017).
pubmed: 28830090 pmcid: 7207147 doi: 10.1093/femsre/fux027
McBurney, M. I. et al. Establishing what constitutes a healthy human gut microbiome: state of the science, regulatory considerations, and future directions. J. Nutr. 149, 1882–1895 (2019).
pubmed: 31373365 pmcid: 6825832 doi: 10.1093/jn/nxz154
Constitution of the World Health Organization. A. J. Public Health Nations Health 36, 1315–1323 (1946).
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).
pubmed: 20203603 pmcid: 3779803 doi: 10.1038/nature08821
Herd, P., Palloni, A., Rey, F. & Dowd, J. B. Social and population health science approaches to understand the human microbiome. Nat. Hum. Behav. 2, 808–815 (2018).
pubmed: 31457107 pmcid: 6711373 doi: 10.1038/s41562-018-0452-y
Barton, W. et al. The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut 67, 625–633 (2018).
pubmed: 28360096
Raygoza Garay, J. A. et al. Gut microbiome composition is associated with future onset of Crohn’s disease in healthy first-degree relatives. Gastroenterology 165, 670–681 (2023).
pubmed: 37263307 doi: 10.1053/j.gastro.2023.05.032
Ferreiro, A. L. et al. Gut microbiome composition may be an indicator of preclinical Alzheimer’s disease. Sci. Transl. Med. 15, eabo2984 (2023).
pubmed: 37315112 pmcid: 10680783 doi: 10.1126/scitranslmed.abo2984
Ashton, J. J., Seaby, E. G., Beattie, R. M. & Ennis, S. NOD2 in Crohn’s disease—unfinished business. J. Crohns Colitis 17, 450–458 (2023).
pubmed: 36006803 doi: 10.1093/ecco-jcc/jjac124
Chowdhury, S. R., Chandra Das, D., Sunna, T. C., Beyene, J. & Hossain, A. Global and regional prevalence of multimorbidity in the adult population in community settings: a systematic review and meta-analysis. EClinicalMedicine 57, 101860 (2023).
pubmed: 36864977 pmcid: 9971315 doi: 10.1016/j.eclinm.2023.101860
Khezrian, M., McNeil, C. J., Murray, A. D. & Myint, P. K. An overview of prevalence, determinants and health outcomes of polypharmacy. Ther. Adv. Drug. Saf. 11, 2042098620933741 (2020).
pubmed: 32587680 pmcid: 7294476 doi: 10.1177/2042098620933741
Sonnenburg, E. D. & Sonnenburg, J. L. The ancestral and industrialized gut microbiota and implications for human health. Nat. Rev. Microbiol. 17, 383–390 (2019).
pubmed: 31089293 doi: 10.1038/s41579-019-0191-8
Le Bastard, Q., Vangay, P., Batard, E., Knights, D. & Montassier, E. US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut. Clin. Infect. Dis. 71, 419–421 (2020).
pubmed: 31679002 doi: 10.1093/cid/ciz1087
Pang, S. et al. Longevity of centenarians is reflected by the gut microbiome with youth-associated signatures. Nat. Aging 3, 436–449 (2023).
pubmed: 37117794 doi: 10.1038/s43587-023-00389-y
Foxman, B. & Riley, L. Molecular epidemiology of infection foxman and riley molecular epidemiology: focus on infection. Am. J. Epidemiol. 153, 1135–1141 (2001).
pubmed: 11415945 doi: 10.1093/aje/153.12.1135
Midha, S., Chawla, S. & Garg, P. K. Modifiable and non-modifiable risk factors for pancreatic cancer: a review. Cancer Lett. 381, 269–277 (2016).
pubmed: 27461582 doi: 10.1016/j.canlet.2016.07.022
Pradhan, A. D. et al. Inflammatory biomarkers, hormone replacement therapy, and incident coronary heart disease prospective analysis from the women’s health initiative observational study. JAMA 288, 980–987 (2002).
pubmed: 12190368 doi: 10.1001/jama.288.8.980
Zhernakova, A. et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352, 565–569 (2016).
pubmed: 27126040 pmcid: 5240844 doi: 10.1126/science.aad3369
Gacesa, R. et al. Environmental factors shaping the gut microbiome in a Dutch population. Nature 604, 732–739 (2022).
pubmed: 35418674 doi: 10.1038/s41586-022-04567-7
Winter, S. E. & Bäumler, A. J. Gut dysbiosis: ecological causes and causative effects on human disease. Proc. Natl Acad. Sci. USA 120, e2316579120 (2023).
pubmed: 38048456 pmcid: 10722970 doi: 10.1073/pnas.2316579120
Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013).
pubmed: 23985870 doi: 10.1038/nature12506
Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017).
pubmed: 29143816 doi: 10.1038/nature24460
Vieira-Silva, S. et al. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature 581, 310–315 (2020).
pubmed: 32433607 doi: 10.1038/s41586-020-2269-x
France, M. T. et al. VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. Microbiome 8, 166 (2020).
pubmed: 33228810 pmcid: 7684964 doi: 10.1186/s40168-020-00934-6
Wang, N. & Fang, J. Y. Fusobacterium nucleatum, a key pathogenic factor and microbial biomarker for colorectal cancer. Trends Microbiol. 31, 159–172 (2023).
pubmed: 36058786 doi: 10.1016/j.tim.2022.08.010
Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks
pubmed: 32106218 pmcid: 8142898 doi: 10.1038/s41586-020-2080-8
Wang, Z. et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472, 57–65 (2011).
pubmed: 21475195 pmcid: 3086762 doi: 10.1038/nature09922
Fu, J. et al. The gut microbiome contributes to a substantial proportion of the variation in blood lipids. Circ. Res. 117, 817–824 (2015).
pubmed: 26358192 pmcid: 4596485 doi: 10.1161/CIRCRESAHA.115.306807
Manor, O. et al. Health and disease markers correlate with gut microbiome composition across thousands of people. Nat. Commun. 11, 5206 (2020).
pubmed: 33060586 pmcid: 7562722 doi: 10.1038/s41467-020-18871-1
Frioux, C. et al. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 31, 1111–1125.e6 (2023).
pubmed: 37339626 doi: 10.1016/j.chom.2023.05.024
Anthamatten, L. et al. Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status. Preprint at bioRxiv https://doi.org/10.1101/2023.11.21.568118v1 (2023).
Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560–564 (2016).
pubmed: 27126039 doi: 10.1126/science.aad3503
Cotillard, A. et al. A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. Am. J. Clin. Nutr. 115, 432–443 (2022).
pubmed: 34617562 doi: 10.1093/ajcn/nqab332
Walker, R. L. et al. Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease. Genome Med. 13, 188 (2021).
pubmed: 34915914 pmcid: 8680346 doi: 10.1186/s13073-021-01007-5
Lu, J. et al. Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization. NPJ Biofilms Microbiomes 7, 71 (2021).
pubmed: 34489454 pmcid: 8421333 doi: 10.1038/s41522-021-00245-0
Armet, A. M. et al. Rethinking healthy eating in light of the gut microbiome. Cell Host Microbe 30, 764–785 (2022).
pubmed: 35679823 doi: 10.1016/j.chom.2022.04.016
Kates, A. E. et al. Household pet ownership and the microbial diversity of the human gut microbiota. Front. Cell Infect. Microbiol. 10, 73 (2020).
pubmed: 32185142 pmcid: 7058978 doi: 10.3389/fcimb.2020.00073
Tun, H. M. et al. Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios. Microbiome 5, 40 (2017).
pubmed: 28381231 pmcid: 5382463 doi: 10.1186/s40168-017-0254-x
Aasmets, O., Krigul, K. L., Lüll, K., Metspalu, A. & Org, E. Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort. Nat. Commun. 13, 869 (2022).
pubmed: 35169130 pmcid: 8847343 doi: 10.1038/s41467-022-28464-9
Procházková, N. et al. Advancing human gut microbiota research by considering gut transit time. Gut 72, 180–191 (2023).
pubmed: 36171079 doi: 10.1136/gutjnl-2022-328166
Roager, H. M. et al. Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nat. Microbiol. 1, 16093 (2016).
pubmed: 27562254 doi: 10.1038/nmicrobiol.2016.93
Vandeputte, D. et al. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut 65, 57–62 (2016).
pubmed: 26069274 doi: 10.1136/gutjnl-2015-309618
He, Y. et al. Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nat. Med. 24, 1532–1535 (2018).
pubmed: 30150716 doi: 10.1038/s41591-018-0164-x
Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5, 3654 (2014).
pubmed: 24736369 doi: 10.1038/ncomms4654
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).
pubmed: 22699611 pmcid: 3376388 doi: 10.1038/nature11053
De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl Acad. Sci. USA 107, 14691–14696 (2010).
pubmed: 20679230 pmcid: 2930426 doi: 10.1073/pnas.1005963107
Tamburini, F. B. et al. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nat. Commun. 13, 926 (2022).
pubmed: 35194028 pmcid: 8863827 doi: 10.1038/s41467-021-27917-x
Shad, N. S., Shaikh, N. I. & Cunningham, S. A. Migration spurs changes in the human microbiome: a review. J. Racial Ethn. Health Disparities https://doi.org/10.1007/s40615-023-01813-0 (2023).
Copeland, J. K. et al. The impact of migration on the gut metagenome of South Asian Canadians. Gut Microbes 13, 1–29 (2021).
pubmed: 33794735 doi: 10.1080/19490976.2021.1902705
Kaplan, R. C. et al. Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol. 20, 219 (2019).
pubmed: 31672155 pmcid: 6824043 doi: 10.1186/s13059-019-1831-z
Vangay, P. et al. US immigration westernizes the human gut microbiome. Cell 175, 962–972.e10 (2018).
pubmed: 30388453 pmcid: 6498444 doi: 10.1016/j.cell.2018.10.029
Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463 (2017).
pubmed: 28749457 doi: 10.1038/nri.2017.77
Browne, H. P. et al. Boosting microbiome science worldwide could save millions of children’s lives. Nature 625, 237–240 (2024).
pubmed: 38191714 pmcid: 10810019 doi: 10.1038/d41586-024-00017-8
Wang, H. et al. Global, regional, and national under-5 mortality, adult mortality, age-specific mortality, and life expectancy, 1970–2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet 390, 1084–1150 (2017).
doi: 10.1016/S0140-6736(17)31833-0
Brewster, R. et al. Surveying gut microbiome research in Africans: toward improved diversity and representation. Trends Microbiol. 27, 824–835 (2019).
pubmed: 31178123 pmcid: 6764420 doi: 10.1016/j.tim.2019.05.006
Smith, M. I. et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339, 548–554 (2013).
pubmed: 23363771 pmcid: 3667500 doi: 10.1126/science.1229000
Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production. Cell Host Microbe 27, 389–404.e6 (2020).
pubmed: 32004499 doi: 10.1016/j.chom.2020.01.006
Tebani, A. et al. Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat. Commun. 11, 4487 (2020).
pubmed: 32900998 pmcid: 7479148 doi: 10.1038/s41467-020-18148-7
Dekkers, K. F. et al. An online atlas of human plasma metabolite signatures of gut microbiome composition. Nat. Commun. 13, 5370 (2022).
pubmed: 36151114 pmcid: 9508139 doi: 10.1038/s41467-022-33050-0
Gou, W. et al. Westlake Gut Project: a consortium of microbiome epidemiology for the gut microbiome and health research in China. Med. Microecol. 14, 100064 (2022).
doi: 10.1016/j.medmic.2022.100064
Cernava, T. et al. Metadata harmonization—standards are the key for a better usage of omics data for integrative microbiome analysis. Environ. Microbiomes 17, 33 (2022).
doi: 10.1186/s40793-022-00425-1
Nagata, N. et al. Population-level metagenomics uncovers distinct effects of multiple medications on the human gut microbiome. Gastroenterology 163, 1038–1052 (2022).
pubmed: 35788347 doi: 10.1053/j.gastro.2022.06.070
Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662.e20 (2019).
pubmed: 30661755 pmcid: 6349461 doi: 10.1016/j.cell.2019.01.001
Allali, I. et al. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. Microbiome 9, 241 (2021).
pubmed: 34911583 pmcid: 8672519 doi: 10.1186/s40168-021-01195-7
Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018).
pubmed: 30356187 pmcid: 6415775 doi: 10.1038/s41586-018-0617-x
Claesson, M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178–184 (2012).
pubmed: 22797518 doi: 10.1038/nature11319
Amato, K. R. et al. The human gut microbiome and health inequities. Proc. Natl Acad. Sci. USA 118, e2017947118 (2021).
pubmed: 34161260 pmcid: 8237592 doi: 10.1073/pnas.2017947118
Dixon, M., Dunlop, A. L., Corwin, E. J. & Kramer, M. R. Joint effects of individual socioeconomic status and residential neighborhood context on vaginal microbiome composition. Front. Public. Health 11, 1029741 (2023).
pubmed: 36761121 pmcid: 9902942 doi: 10.3389/fpubh.2023.1029741
Bowyer, R. C. E. et al. Socioeconomic status and the gut microbiome: a TwinsUK cohort study. Microorganisms 7, 17 (2019).
pubmed: 30641975 pmcid: 6351927 doi: 10.3390/microorganisms7010017
Kaisanlahti, A. et al. Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles. Microbiome 11, 249 (2023).
pubmed: 37953319 pmcid: 10642029 doi: 10.1186/s40168-023-01694-9
Mueller, N. T., Differding, M. K., Østbye, T., Hoyo, C. & Benjamin-Neelon, S. E. Association of birth mode of delivery with infant faecal microbiota, potential pathobionts, and short chain fatty acids: a longitudinal study over the first year of life. BJOG 128, 1293–1303 (2021).
pubmed: 33338292 pmcid: 8211907 doi: 10.1111/1471-0528.16633
Coker, M. O. et al. Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study. BJOG 127, 217–227 (2020).
pubmed: 31006170 doi: 10.1111/1471-0528.15799
Yang, B. et al. Bifidobacterium and Lactobacillus composition at species level and gut microbiota diversity in infants before 6 weeks. Int. J. Mol. Sci. 20, 3306 (2019).
pubmed: 31284413 pmcid: 6650860 doi: 10.3390/ijms20133306
Beller, L. et al. Successional stages in infant gut microbiota maturation. mBio 12, e0185721 (2021).
pubmed: 34903050 doi: 10.1128/mbio.01857-21
Laursen, M. F. et al. Maternal milk microbiota and oligosaccharides contribute to the infant gut microbiota assembly. ISME Commun. 1, 21 (2021).
pubmed: 36737495 pmcid: 9723702 doi: 10.1038/s43705-021-00021-3
Duranti, S. et al. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome 5, 66 (2017).
pubmed: 28651630 pmcid: 5485682 doi: 10.1186/s40168-017-0282-6
Feehily, C. et al. Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach. Nat. Commun. 14, 3015 (2023).
pubmed: 37230981 pmcid: 10213049 doi: 10.1038/s41467-023-38694-0
McKeen, S. et al. Adaptation of the infant gut microbiome during the complementary feeding transition. PLoS ONE 17, e0270213 (2022).
pubmed: 35834499 pmcid: 9282554 doi: 10.1371/journal.pone.0270213
Lim, E. S. et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat. Med. 21, 1228–1234 (2015).
pubmed: 26366711 pmcid: 4710368 doi: 10.1038/nm.3950
Laursen, M. F., Bahl, M. I. & Licht, T. R. Settlers of our inner surface-factors shaping the gut microbiota from birth to toddlerhood. FEMS Microbiol. Rev. 45, fuab001 (2021).
pubmed: 33428723 pmcid: 8371275 doi: 10.1093/femsre/fuab001
Warmink-Perdijk, W. D. B. et al. Lifelines NEXT: as prospective birth cohort adding the next generation to the three-generation Lifelines cohort study. Eur. J. Epidemiol. 35, 157–168 (2020).
pubmed: 32100173 pmcid: 7125065 doi: 10.1007/s10654-020-00614-7
Korpela, K. et al. Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort. BMJ Open. 9, e028500 (2019).
pubmed: 31253623 pmcid: 6609051 doi: 10.1136/bmjopen-2018-028500
Jeffery, I. B., Lynch, D. B. & O’Toole, P. W. Composition and temporal stability of the gut microbiota in older persons. ISME J. 10, 170–182 (2016).
pubmed: 26090993 doi: 10.1038/ismej.2015.88
Wilmanski, T., Gibbons, S. M. & Price, N. D. Healthy aging and the human gut microbiome: why we cannot just turn back the clock. Nat. Aging 2, 869–871 (2022).
pubmed: 37118282 pmcid: 10155257 doi: 10.1038/s43587-022-00294-w
Si, J. et al. Long-term life history predicts current gut microbiome in a population-based cohort study. Nat. Aging 2, 885–895 (2022).
pubmed: 37118287 pmcid: 10154234 doi: 10.1038/s43587-022-00286-w
Korpela, K. et al. Gut microbiota develop towards an adult profile in a sex-specific manner during puberty. Sci. Rep. 11, 23297 (2021).
pubmed: 34857814 pmcid: 8640005 doi: 10.1038/s41598-021-02375-z
McVey Neufeld, K. A., Luczynski, P., Dinan, T. G. & Cryan, J. F. Reframing the teenage wasteland: adolescent microbiota–gut–brain axis. Can. J. Psychiatry 61, 214–221 (2016).
pubmed: 27254413 pmcid: 4794958 doi: 10.1177/0706743716635536
Park, M. G., Cho, S. & Oh, M. M. Menopausal changes in the microbiome—a review focused on the genitourinary microbiome. Diagnostics 13, 1193 (2023).
pubmed: 36980501 pmcid: 10047399 doi: 10.3390/diagnostics13061193
Peters, B. A. et al. Menopause is associated with an altered gut microbiome and estrobolome, with implications for adverse cardiometabolic risk in the hispanic community health study/study of Latinos. mSystems 7, e0027322 (2022).
pubmed: 35675542 doi: 10.1128/msystems.00273-22
McDonald, D. et al. American Gut: an open platform for citizen science microbiome research. mBio 3, e00031-18 (2018).
McCallum, G. & Tropini, C. The gut microbiota and its biogeography. Nat. Rev. Microbiol. 22, 105–118 (2023).
pubmed: 37740073 doi: 10.1038/s41579-023-00969-0
Kennedy, K. M. et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613, 639–649 (2023).
pubmed: 36697862 pmcid: 11333990 doi: 10.1038/s41586-022-05546-8
Hayes, R. B. et al. Association of oral microbiome with risk for incident head and neck squamous cell cancer. JAMA Oncol. 4, 358–365 (2018).
pubmed: 29327043 pmcid: 5885828 doi: 10.1001/jamaoncol.2017.4777
Fan, X. et al. Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case–control study. Gut 67, 120–127 (2018).
pubmed: 27742762 doi: 10.1136/gutjnl-2016-312580
McClelland, R. S. et al. Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case–control study. Lancet Infect. Dis. 18, 554–564 (2018).
pubmed: 29396006 pmcid: 6445552 doi: 10.1016/S1473-3099(18)30058-6
Jie, Z. et al. A transomic cohort as a reference point for promoting a healthy human gut microbiome. Med. Microecol. 8, 100039 (2021).
doi: 10.1016/j.medmic.2021.100039
Liu, X. et al. Metagenome–genome-wide association studies reveal human genetic impact on the oral microbiome. Cell Discov. 7, 117 (2021).
pubmed: 34873157 pmcid: 8648780 doi: 10.1038/s41421-021-00356-0
Jie, Z. et al. Life history recorded in the vagino-cervical microbiome along with multi-omes. Genomics Proteom. Bioinforma. 20, 304–321 (2022).
doi: 10.1016/j.gpb.2021.01.005
Kurushima, Y. et al. Host genotype links to salivary and gut microbiota by periodontal status. J. Dent. Res. 102, 146–156 (2023).
pubmed: 36214094 doi: 10.1177/00220345221125402
Nearing, J. T., DeClercq, V., Van Limbergen, J. & Langille, M. G. I. Assessing the variation within the oral microbiome of healthy adults. mSphere 5, e00451-20 (2020).
pubmed: 32999079 pmcid: 7529435 doi: 10.1128/mSphere.00451-20
Willis, J. R. et al. Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors. NPJ Biofilms Microbiomes 8, 38 (2022).
pubmed: 35585074 pmcid: 9117221 doi: 10.1038/s41522-022-00279-y
Lebeer, S. et al. A citizen-science-enabled catalogue of the vaginal microbiome and associated factors. Nat. Microbiol. 8, 2183–2195 (2023).
pubmed: 37884815 pmcid: 10627828 doi: 10.1038/s41564-023-01500-0
Correia, G. D., Marchesi, J. R. & MacIntyre, D. A. Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods. Curr. Opin. Microbiol. 73, 102292 (2023).
pubmed: 36931094 doi: 10.1016/j.mib.2023.102292
Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018).
pubmed: 29332945 doi: 10.1038/nrmicro.2017.157
Jo, S. et al. Oral and gut dysbiosis leads to functional alterations in Parkinson’s disease. NPJ Parkinsons Dis. 8, 87 (2022).
pubmed: 35798742 pmcid: 9262988 doi: 10.1038/s41531-022-00351-6
De Filippis, F. et al. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host Microbe 25, 444–453.e3 (2019).
pubmed: 30799264 doi: 10.1016/j.chom.2019.01.004
Valles-Colomer, M. et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614, 125–135 (2023).
pubmed: 36653448 pmcid: 9892008 doi: 10.1038/s41586-022-05620-1
Zhernakova, D. V. et al. Host genetic regulation of human gut microbial structural variation. Nature 625, 813–821 (2024).
pubmed: 38172637 pmcid: 10808065 doi: 10.1038/s41586-023-06893-w
Zahavi, L. et al. Bacterial SNPs in the human gut microbiome associate with host BMI. Nat. Med. 29, 2785–2792 (2023).
pubmed: 37919437 pmcid: 10999242 doi: 10.1038/s41591-023-02599-8
Tedersoo, L., Albertsen, M., Anslan, S. & Callahan, B. Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Appl. Environ. Microbiol. 87, 1–19 (2021).
doi: 10.1128/AEM.00626-21
Chen, L. et al. The long-term genetic stability and individual specificity of the human gut microbiome. Cell 184, 2302–2315.e12 (2021).
pubmed: 33838112 doi: 10.1016/j.cell.2021.03.024
Jovel, J. et al. Characterization of the gut microbiome using 16S or shotgun metagenomics. Front. Microbiol. 7, 459 (2016).
pubmed: 27148170 pmcid: 4837688 doi: 10.3389/fmicb.2016.00459
Hu, D., Fuller, N. R., Caterson, I. D., Holmes, A. J. & Reeves, P. R. Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome. Cell Rep. 38, 1102339 (2022).
doi: 10.1016/j.celrep.2021.110239
Lloyd-Price, J. et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550, 61–66 (2017).
pubmed: 28953883 pmcid: 5831082 doi: 10.1038/nature23889
Carrow, H. C., Batachari, L. E. & Chu, H. Strain diversity in the microbiome: lessons from Bacteroides fragilis. PLoS Pathog. 16, e1009056 (2020).
pubmed: 33301530 pmcid: 7728264 doi: 10.1371/journal.ppat.1009056
Magnúsdóttir, S. et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat. Biotechnol. 35, 81–89 (2017).
pubmed: 27893703 doi: 10.1038/nbt.3703
Gehrig, J. L. et al. Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data. Microb. Genom. 8, 000794 (2022).
pubmed: 35302439 pmcid: 9176275
Pascal Andreu, V. et al. gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Nat. Biotechnol. 41, 1416–1423 (2023).
pubmed: 36782070 doi: 10.1038/s41587-023-01675-1
Lind, A. L. & Pollard, K. S. Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing. Microbiome 9, 58 (2021).
pubmed: 33658077 pmcid: 7931531 doi: 10.1186/s40168-021-01015-y
Shkoporov, A. N. et al. The human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe 26, 527–541.e5 (2019).
pubmed: 31600503 doi: 10.1016/j.chom.2019.09.009
Begum, N. et al. Host–mycobiome metabolic interactions in health and disease. Gut Microbes 14, 2121576 (2022).
pubmed: 36151873 pmcid: 9519009 doi: 10.1080/19490976.2022.2121576
Usyk, M. et al. Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies. Cell Rep. Methods 3, 100391 (2023).
pubmed: 36814836 pmcid: 9939430 doi: 10.1016/j.crmeth.2022.100391
Pollak, S. Plant DNA in feces as a nutritional crystal ball. Proc. Natl Acad. Sci. USA 120, e2309172120 (2023).
pubmed: 37406090 pmcid: 10629510 doi: 10.1073/pnas.2309172120
Quinn, R. A. et al. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 579, 123–129 (2020).
pubmed: 32103176 pmcid: 7252668 doi: 10.1038/s41586-020-2047-9
Guo, C. J. et al. Discovery of reactive microbiota-derived metabolites that inhibit host proteases. Cell 168, 517–526.e18 (2017).
pubmed: 28111075 pmcid: 5302092 doi: 10.1016/j.cell.2016.12.021
Hajjar, G. et al. Scaling-up metabolomics: current state and perspectives. Trends Anal. Chem. 167, 117225 (2023).
doi: 10.1016/j.trac.2023.117225
Wang, K. et al. The gut microbiome modifies the associations of short- and long-term physical activity with body weight changes. Microbiome 11, 121 (2023).
pubmed: 37254152 pmcid: 10228038 doi: 10.1186/s40168-023-01542-w
Mehta, R. S. et al. Stability of the human faecal microbiome in a cohort of adult men. Nat. Microbiol. 3, 347–355 (2018).
pubmed: 29335554 pmcid: 6016839 doi: 10.1038/s41564-017-0096-0
Yap, M. et al. Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome. Sci. Rep. 10, 21665 (2020).
pubmed: 33303873 pmcid: 7728742 doi: 10.1038/s41598-020-78773-6
Spreckels, J. E. et al. Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques. ISME Commun. 3, 116 (2023).
pubmed: 37945978 pmcid: 10636111 doi: 10.1038/s43705-023-00325-6
Rao, C. et al. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature 591, 633–638 (2021).
pubmed: 33627867 pmcid: 7990694 doi: 10.1038/s41586-021-03241-8
Galazzo, G. et al. How to count our microbes? The effect of different quantitative microbiome profiling approaches. Front. Cell. Infect. Microbiol. 10, 403 (2020).
pubmed: 32850498 pmcid: 7426659 doi: 10.3389/fcimb.2020.00403
Tito, R. Y. et al. Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development. Nat. Med. 30, 1339–1348 (2024).
pubmed: 38689063 pmcid: 11108775 doi: 10.1038/s41591-024-02963-2
Chadwick, R. & Zwart, H. From ELSA to responsible research and promisomics. Life Sci. Soc. Policy 9, 3 (2013).
pmcid: 4513009 doi: 10.1186/2195-7819-9-3
Nishijima, S. et al. Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort. Nat. Commun. 13, 5252 (2022).
pubmed: 36068216 pmcid: 9448778 doi: 10.1038/s41467-022-32832-w
Brandwein, M., Katz, I., Katz, A. & Kohen, R. Beyond the gut: skin microbiome compositional changes are associated with BMI. Hum. Microb. J. 13, 100063 (2019).
doi: 10.1016/j.humic.2019.100063
Hughes, D. A. et al. Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Nat. Microbiol. 5, 1079–1087 (2020).
pubmed: 32572223 pmcid: 7610462 doi: 10.1038/s41564-020-0743-8
Koponen, K. K. et al. Associations of healthy food choices with gut microbiota profiles. Am. J. Clin. Nutr. 114, 605–616 (2021).
pubmed: 34020448 pmcid: 8326043 doi: 10.1093/ajcn/nqab077
Palmu, J. et al. Association between the gut microbiota and blood pressure in a population cohort of 6953 individuals. J. Am. Heart Assoc. 9, e016641 (2020).
pubmed: 32691653 pmcid: 7792269 doi: 10.1161/JAHA.120.016641
Palmu, J. et al. Gut microbiome and atrial fibrillation—results from a large population-based study. EBioMedicine 91, 104583 (2023).
pubmed: 37119735 pmcid: 10165189 doi: 10.1016/j.ebiom.2023.104583
Peters, B. A. et al. Association of the gut microbiome with kidney function and damage in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Gut Microbes 15, 2186685 (2023).
pubmed: 36882941 pmcid: 10012940 doi: 10.1080/19490976.2023.2186685
Nash, A. K. et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome 5, 153 (2017).
pubmed: 29178920 pmcid: 5702186 doi: 10.1186/s40168-017-0373-4
Nogal, A. et al. Genetic and gut microbiome determinants of SCFA circulating and fecal levels, postprandial responses and links to chronic and acute inflammation. Gut Microbes 15, 2240050 (2023).
pubmed: 37526398 pmcid: 10395212 doi: 10.1080/19490976.2023.2240050
Armstrong, A. J. S., Parmar, V. & Blaser, M. J. Assessing saliva microbiome collection and processing methods. NPJ Biofilms Microbiomes 7, 81 (2021).
pubmed: 34795298 pmcid: 8602330 doi: 10.1038/s41522-021-00254-z
Robinson, C. K., Brotman, R. M. & Ravel, J. Intricacies of assessing the human microbiome in epidemiologic studies. Ann. Epidemiol. 26, 311–321 (2016).
pubmed: 27180112 pmcid: 4892937 doi: 10.1016/j.annepidem.2016.04.005
Hill, C. J. et al. Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. Microbiome 4, 19 (2016).
pubmed: 27160322 pmcid: 4862223 doi: 10.1186/s40168-016-0164-3
Tang, Q. et al. Current sampling methods for gut microbiota: a call for more precise devices. Front. Cell Infect. Microbiol. 10, 151 (2020).
pubmed: 32328469 pmcid: 7161087 doi: 10.3389/fcimb.2020.00151
Lourenço, M. et al. The spatial heterogeneity of the gut limits predation and fosters coexistence of bacteria and bacteriophages. Cell Host Microbe 28, 390–401.e5 (2020).
pubmed: 32615090 doi: 10.1016/j.chom.2020.06.002
Badawy, R. et al. Metadata concepts for advancing the use of digital health technologies in clinical research. Digit. Biomark. 3, 116–132 (2019).
pubmed: 32175520 pmcid: 7046173 doi: 10.1159/000502951
Berry, S. E. et al. Human postprandial responses to food and potential for precision nutrition. Nat. Med. 26, 964–973 (2020).
pubmed: 32528151 pmcid: 8265154 doi: 10.1038/s41591-020-0934-0
Koonin, E. V., Dolja, V. V. & Krupovic, M. The healthy human virome: from virus–host symbiosis to disease. Curr. Opin. Virol. 47, 86–94 (2021).
pubmed: 33652230 doi: 10.1016/j.coviro.2021.02.002
Kumata, R., Ito, J., Takahashi, K., Suzuki, T. & Sato, K. A tissue level atlas of the healthy human virome. BMC Biol. 18, 55 (2020).
pubmed: 32493363 pmcid: 7269688 doi: 10.1186/s12915-020-00785-5
Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498 (2014).
pubmed: 25058116 doi: 10.1038/ncomms5498
Yutin, N. et al. Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nat. Commun. 12, 1044 (2021).
pubmed: 33594055 pmcid: 7886860 doi: 10.1038/s41467-021-21350-w
Edwards, R. A. et al. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat. Microbiol. 4, 1727–1736 (2019).
pubmed: 31285584 pmcid: 7440971 doi: 10.1038/s41564-019-0494-6
Clooney, A. G. et al. Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe 26, 764–778.e5 (2019).
pubmed: 31757768 doi: 10.1016/j.chom.2019.10.009
Ma, Y., You, X., Mai, G., Tokuyasu, T. & Liu, C. A human gut phage catalog correlates the gut phageome with type 2 diabetes. Microbiome 6, 24 (2018).
pubmed: 29391057 pmcid: 5796561 doi: 10.1186/s40168-018-0410-y
Roux, S., Hallam, S. J., Woyke, T. & Sullivan, M. B. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes. eLife 4, e08490 (2015).
pubmed: 26200428 pmcid: 4533152 doi: 10.7554/eLife.08490
Beller, L. & Matthijnssens, J. What is (not) known about the dynamics of the human gut virome in health and disease. Curr. Opin. Virol. 37, 52–57 (2019).
pubmed: 31255903 doi: 10.1016/j.coviro.2019.05.013
Chibani, C. M. et al. A catalogue of 1,167 genomes from the human gut archaeome. Nat. Microbiol. 7, 48–61 (2022).
pubmed: 34969981 doi: 10.1038/s41564-021-01020-9
Koskinen, K. et al. First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin. mBio 8, e00824–17 (2017).
pubmed: 29138298 pmcid: 5686531 doi: 10.1128/mBio.00824-17
Beghini, F. et al. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME J. 11, 2848–2863 (2017).
pubmed: 28837129 pmcid: 5702742 doi: 10.1038/ismej.2017.139
Scanlan, P. D. et al. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. FEMS Microbiol. Ecol. 90, 326–330 (2014).
pubmed: 25077936 doi: 10.1111/1574-6941.12396
Marzano, V. et al. “Omic” investigations of protozoa and worms for a deeper understanding of the human gut “parasitome”. PLoS Negl. Trop. Dis. 11, e0005916 (2017).
pubmed: 29095820 pmcid: 5667730 doi: 10.1371/journal.pntd.0005916

Auteurs

Raphaela Joos (R)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
School of Microbiology, University College Cork, Cork, Ireland.

Katy Boucher (K)

APC Microbiome Ireland, University College Cork, Cork, Ireland.

Aonghus Lavelle (A)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.

Manimozhiyan Arumugam (M)

Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Martin J Blaser (MJ)

Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.

Marcus J Claesson (MJ)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
School of Microbiology, University College Cork, Cork, Ireland.

Gerard Clarke (G)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland.

Paul D Cotter (PD)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
Teagasc Food Research Centre and VistaMilk SFI Research Centre, Moorepark, Fermoy, Moorepark, Ireland.

Luisa De Sordi (L)

Centre de Recherche Saint Antoine, Sorbonne Université, INSERM, Paris, France.

Maria G Dominguez-Bello (MG)

Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.

Bas E Dutilh (BE)

Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands.

Stanislav D Ehrlich (SD)

Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France.
Department of Clinical and Movement Neurosciences, University College London, London, UK.

Tarini Shankar Ghosh (TS)

Department of Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), New Delhi, India.

Colin Hill (C)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
School of Microbiology, University College Cork, Cork, Ireland.

Christophe Junot (C)

Département Médicaments et Technologies pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, Gif-sur-Yvette, France.

Leo Lahti (L)

Department of Computing, University of Turku, Turku, Finland.

Trevor D Lawley (TD)

Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.

Tine R Licht (TR)

National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.

Emmanuelle Maguin (E)

Université Paris-Saclay, INRAE, AgroParisTech, MICALIS, Jouy-en-Josas, France.

Thulani P Makhalanyane (TP)

Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa.

Julian R Marchesi (JR)

Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.

Jelle Matthijnssens (J)

KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium.

Jeroen Raes (J)

KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium.
Vlaams Instituut voor Biotechnologie (VIB) Center for Microbiology, Leuven, Belgium.

Jacques Ravel (J)

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.

Anne Salonen (A)

Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.

Pauline D Scanlan (PD)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
School of Microbiology, University College Cork, Cork, Ireland.

Andrey Shkoporov (A)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
School of Microbiology, University College Cork, Cork, Ireland.

Catherine Stanton (C)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
Teagasc Food Research Centre and VistaMilk SFI Research Centre, Moorepark, Fermoy, Moorepark, Ireland.

Ines Thiele (I)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
School of Medicine, University of Ireland, Galway, Ireland.

Igor Tolstoy (I)

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

Jens Walter (J)

APC Microbiome Ireland, University College Cork, Cork, Ireland.
School of Microbiology, University College Cork, Cork, Ireland.
Department of Medicine, University College Cork, Cork, Ireland.

Bo Yang (B)

State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China.
School of Food Science and Technology, Jiangnan University, Wuxi, China.

Natalia Yutin (N)

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

Alexandra Zhernakova (A)

Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

Hub Zwart (H)

Erasmus School of Philosophy, Erasmus University Rotterdam, Rotterdam, The Netherlands.

Joël Doré (J)

Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France.
Université Paris-Saclay, INRAE, AgroParisTech, MICALIS, Jouy-en-Josas, France.

R Paul Ross (RP)

APC Microbiome Ireland, University College Cork, Cork, Ireland. p.ross@ucc.ie.
School of Microbiology, University College Cork, Cork, Ireland. p.ross@ucc.ie.

Classifications MeSH