Hostname: page-component-586b7cd67f-gb8f7 Total loading time: 0 Render date: 2024-11-26T01:56:51.223Z Has data issue: false hasContentIssue false
  • English
  • Français

Practical guidelines for gut microbiome analysis in microbiota-gut-brain axis research

Published online by Cambridge University Press:  15 July 2019

Mireia Valles-Colomer Open the ORCID record for Mireia Valles-Colomer [Opens in a new window] ,
Gwen Falony Open the ORCID record for Gwen Falony [Opens in a new window] ,
Sara Vieira-Silva Open the ORCID record for Sara Vieira-Silva [Opens in a new window]  and
Jeroen Raes Open the ORCID record for Jeroen Raes [Opens in a new window]
Mireia Valles-Colomer
Affiliation:
Department of Microbiology, Immunology and Transplantation, KU Leuven, and Center for Microbiology, VIB–KU Leuven, 3000 Leuven, Belgium. [email protected]@[email protected]@kuleuven.vib.be
Gwen Falony
Affiliation:
Department of Microbiology, Immunology and Transplantation, KU Leuven, and Center for Microbiology, VIB–KU Leuven, 3000 Leuven, Belgium. [email protected]@[email protected]@kuleuven.vib.be
Sara Vieira-Silva
Affiliation:
Department of Microbiology, Immunology and Transplantation, KU Leuven, and Center for Microbiology, VIB–KU Leuven, 3000 Leuven, Belgium. [email protected]@[email protected]@kuleuven.vib.be
Jeroen Raes
Affiliation:
Department of Microbiology, Immunology and Transplantation, KU Leuven, and Center for Microbiology, VIB–KU Leuven, 3000 Leuven, Belgium. [email protected]@[email protected]@kuleuven.vib.be
Get access Rights & Permissions [Opens in a new window]

Abstract

The microbiota-gut-brain (MGB) axis field is at an exciting stage, but the most recent developments in microbiota research still have to find their way into MGB studies. Here we outline the standards for microbiome data generation, the appropriate statistical techniques, and the covariates that should be included in MGB studies to optimize discovery and translation to clinical applications.

Type
Open Peer Commentary
Information
Behavioral and Brain Sciences , Volume 42 , 2019 , e78
Check for updates
Copyright
Copyright © Cambridge University Press 2019 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C., Ghalith, G. A. Al, Alexander, H., Alm, E. J., Arumugam, M., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, T.C., Callahan, B. J., Mauricio, A., Rodríguez, C., Chase, J., Cope, E., Da Silva, R., Dorrestein, P.C., Douglas, G. M., Duvallet, C., Edwardson, C. F., Ernst, M., Fouquier, J., Gauglitz, J. M., Gibson, D. L., Gonzalez, A., Huttley, G. A., Janssen, S., Jarmusch, A. K., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Ley, R., Loftfield, E., Marotz, C., Martin, B., Mcdonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R, Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. JJ., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C. HD., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Knight, R., Caporaso, G. J. (2018) QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v2. Available at: https://doi.org/10.7287/peerj.preprints.27295v1.Google Scholar
Cenit, M. C., Sanz, Y. & Codoñer-Franch, P. (2017) Influence of gut microbiota on neuropsychiatric disorders. World Journal of Gastroenterology 23(30):5486–98. Available at: https://doi.org/10.3748/wjg.v23.i30.5486.Google Scholar
Costea, P. I., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F. E., Kultima, J. R., Hayward, M. R., Coelho, L. P., Allen-Vercoe, E., Bertrand, L., Blaut, M., Brown, J. R.M., Carton, T., Cools-Portier, S., Daigneault, M., Derrien, M., Druesne, A., De Vos, W. M., Finlay, B. B., Flint, H. J., Guarner, F., Hattori, M., Heilig, H., Luna, R. A., Van Hylckama Vlieg, J., Junick, J., Klymiuk, I., Langella, P., Le Chatelier, E., Mai, V., Manichanh, C., Martin, J. C., Mery, C., Morita, H., O'Toole, P. W., Orvain, C., Patil, K. R., Penders, J., Persson, S., Pons, N., Popova, M., Salonen, A., Saulnier, D., Scott, K. P., Singh, B., Slezak, K., Veiga, P., Versalovic, J., Zhao, L., Zoetendal, E. G., Ehrlich, S. D., Dore, J., Bork, P. (2017) Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology 35(11), 1069–1076.Google Scholar
Cussotto, S., Strain, C. R., Fouhy, F., Strain, R. G., Peterson, V. L., Clarke, G., Stanton, C., Dinan, T. G. & Cryan, J. F. (2018) Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function. Psychopharmacology. Published online August 28, 2018. Available at: https://doi.org/10.1007/s00213-018-5006-5.Google Scholar
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J. & Turnbaugh, P. J. (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505(7484):559–63. Available at: https://doi.org/10.1038/nature12820.Google Scholar
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., Tito, R. Y., Chaffron, S., Rymenans, L., Verspecht, C., De Sutter, L., Lima-Mendez, G., D'Hoe, K., Jonckheere, K., Homola, D., Garcia, R., Tigchelaar, E. F., Eeckhaudt, L., Fu, J., Henckaerts, L., Zhernakova, A., Wijmenga, C. & Raes, J. (2016) Population-level analysis of gut microbiome variation. Science 352(6285):560–64. Available at: https://doi.org/10.1126/science.aad3503.Google Scholar
Falony, G., Vieira-Silva, S. & Raes, J. (2018) Richness and ecosystem development across faecal snapshots of the gut microbiota. Nature Microbiology 3(5):526–28. Available at: https://doi.org/10.1038/s41564-018-0143-5.Google Scholar
Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Sunagawa, S., Prifti, Edi, Vieira-Silva, S., Gudmundsdottir, V., Krogh Pedersen, H., Arumugam, M., Kristiansen, K., Voigt, A., Vestergaard, H., Hercog, R., Costea, P., Kultima, J., Li, J., Jorgensen, T., Levenez, F., Dore, J., Nielsen, B. H., Brunak, S., Raes, J., Hansen, T., Wang, J., Dusko, E. S., Bork, P. & Pedersen, O. (2015) Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528(7581):262–66. Available at: https://doi.org/10.1038/nature15766.Google Scholar
Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. (2017) Microbiome datasets are compositional: And this is not optional. Frontiers in Microbiology 8:2224. Available at: https://doi.org/10.3389/fmicb.2017.02224.Google Scholar
Gorard, D., Gomborone, J., Libby, G. & Farthing, M. (1996) Intestinal transit in anxiety and depression. Gut 39:551–55.Google Scholar
Knudsen, K., Haase, A., Fedorova, T. D. & Charlotte, A. (2017) Gastrointestinal transit time in Parkinson's disease using a magnetic tracking system. Journal of Parkinsons Disease 7:471–79. Available at: https://doi.org/10.3233/JPD-171131.Google Scholar
Lewis, S. J. & Heaton, K. W. (1997) Stool form scale as a useful guide to intestinal transit time. Scandinavian Journal of Gastroenterology 32(9):920–24. Available at: https://doi.org/10.3109/00365529709011203.Google Scholar
Lyte, M. & Cryan, J. F. (2014) Microbial endocrinology: The microbiota-gut-brain axis in health and disease. Springer.Google Scholar
Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E. E., Brochado, A. R., Fernandez, K. C., Dose, H., Mori, H., Patil, K. R., Bork, P. & Typas, A. (2018) Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555(7698):623–28. Available at: https://doi.org/10.1038/nature25979.Google Scholar
Sinha, R., Abu-Ali, G., Vogtmann, E., Fodor, A. A., Ren, B., Amir, A., Schwager, E., Crabtree, J., Ma, S., Abnet, C. C., Knight, R., White, O. & Huttenhower, C. (2017) Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nature Biotechnology 35(11):1077–86. Available at: https://doi.org/10.1038/nbt.3981.Google Scholar
Valles-Colomer, M., Darzi, Y., Vieira-Silva, S., Falony, G., Raes, J. & Joossens, M. (2016) Meta-omics in inflammatory bowel disease research: Applications, challenges, and guidelines. Journal of Crohn's and Colitis 10(6):735–46. Available at: https://doi.org/10.1093/ecco-jcc/jjw024.Google Scholar
Valles-Colomer, M., Falony, G., Darzi, Y., Tigchelaar, E. F., Wang, J., Tito, R. Y., Schiweck, C., Kurilshikov, A., Joossens, M., Wijmenga, C., Claes, S., Van Oudenhove, L., Zhernakova, A., Vieira-Silva, S. & Raes, J. (2019) The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology 4:623–32. Available at: https://doi.org/10.1038/s41564-018-0337-x.Google Scholar
Vandeputte, D., Falony, G., Vieira-Silva, S., Tito, R. Y., Joossens, M. & Raes, J. (2015) Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut 65:57–62. Available at: https://doi.org/10.1136/gutjnl-2015-309618.Google Scholar
Vandeputte, D., Kathagen, G., D'Hoe, K., Vieira-Silva, S., Valles-Colomer, M., Sabino, J., Wang, J., Tito, R. Y., De Commer, L., Darzi, Y., Vermeire, S., Falony, G. & Raes, J. (2017b) Quantitative microbiome profiling links gut community variation to microbial load. Nature 551(7681):507–11. Available at: https://doi.org/10.1038/nature24460.Google Scholar
Vandeputte, D., Tito, R. Y., Vanleeuwen, R., Falony, G. & Raes, J. (2017c) Practical considerations for large-scale gut microbiome studies. FEMS Microbiology Reviews 41(1):S154–67. Available at: https://doi.org/10.1093/femsre/fux027.Google Scholar