Hostname: page-component-cd9895bd7-7cvxr Total loading time: 0 Render date: 2024-12-27T09:28:49.019Z Has data issue: false hasContentIssue false
  • English
  • Français

Causal clarity and deeper dimensions in microbiota-gut-brain research

Published online by Cambridge University Press:  15 July 2019

Katarzyna B. Hooks Open the ORCID record for Katarzyna B. Hooks [Opens in a new window] ,
Jan Pieter Konsman Open the ORCID record for Jan Pieter Konsman [Opens in a new window]  and
Maureen A. O'Malley Open the ORCID record for Maureen A. O'Malley [Opens in a new window]
Katarzyna B. Hooks
Affiliation:
University of Bordeaux, CBiB, 33076 Bordeaux, France. [email protected]://kbhooks.wordpress.com/ University of Bordeaux, CNRS/LaBRI, 33405 Talence, France
Jan Pieter Konsman
Affiliation:
University of Bordeaux, CNRS/INCIA, 33076 Bordeaux, France. [email protected]
Maureen A. O'Malley
Affiliation:
University of Bordeaux, CNRS/LaBRI, 33405 Talence, France School of History and Philosophy of Science, University of Sydney, Sydney, NSW 2006, Australia. [email protected]://www.maureenomalley.org/
Get access Rights & Permissions [Opens in a new window]

Abstract

Our analysis of microbiota-gut-brain (MGB) research took MGB to task for some of its methods, concepts, and interpretations. Commentators then raised numerous issues about the neuroscientific and microbiome aspects of MGB and how it can be understood as a field. We respond by addressing the dimensionality (scope and depth) and causal focus of MGB.

Type
Authors' Response
Information
Behavioral and Brain Sciences , Volume 42 , 2019 , e80
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

Arrieta, M.-C., Walter, J. & Finlay, B. B. (2016) Human microbiota-associated mice: A model with challenges. Cell Host & Microbe 19:575–78. Available at: https://doi.org/10.1016/j.chom.2016.04.014.Google Scholar
Berer, K., Mues, M., Koutrolos, M., Rasbi, Z. Al, Boziki, M., Johner, C., Wekerle, H. & Krishnamoorthy, G. (2011) Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination. Nature 479(7374):538–41. Available at: https://doi.org/10.1038/nature10554.Google Scholar
Carlson, A. L., Xia, K., Azcarate-Peril, M. A., Goldman, B. D., Ahn, M., Styner, M. A., Thompson, A. L., Geng, X., Gilmore, J. H. & Knickmeyer, R. C. (2018) Infant gut microbiome associated with cognitive development. Biological Psychiatry 83(2):148–59. Available at: https://doi.org/10.1016/j.biopsych.2017.06.021.Google Scholar
Cowan, C. S. M., Hoban, A. E., Ventura-Silva, A. P., Dinan, T. G., Clarke, G. & Cryan, J. F. (2018) Gutsy moves: The amygdala as a critical node in microbiota to brain signaling. BioEssays 40:1700172. Available at: https://doi.org/10.1002/bies.201700172.Google Scholar
Dill-McFarland, K., Tang, Z.-Z., Kemis, J., Kerby, R., Chen, G., Palloni, A., Sorenson, T., Rey, F. & Herd, P. (2019) Close social relationships correlate with human gut microbiota composition. Scientific Reports 9(1):703. Available at: https://doi.org/10.1038/s41698-018-37298-9.Google Scholar
Duvallet, C., Gibbons, S. M., Gurry, T., Irizarry, R. A. & Alm, E. J. (2017) Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature Communications 8:1784. Available at: https://doi.org/10.1038/s41467-017-01973-8.Google Scholar
Eisen, J. A. (2017) Microbiomania and “overselling the microbiome.” The Tree of Life (blog). Available at: https://phylogenomics.blogspot.com/p/blog-page.html.Google Scholar
Foster, K. R., Schluter, J., Coyte, K. Z. & Rakoff-Nahoum, S. (2017) The evolution of the host microbiome as an ecosystem on a leash. Nature 548:43–51. Available at: https://doi.org/10.1038/nature23292.Google Scholar
Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N. & Huttenhower, C. (2018) Species-level functional profiling of metagenomes and metatranscriptomes. Nature Methods 15:962–68. Available at: https://doi.org/10.1038/s41592-018-0176-y.Google Scholar
Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V. & Knight, R. (2018) Current understanding of the human microbiome. Nature Medicine 24:392–400. Available at: https://doi.org/10.1038/nm.4517.Google Scholar
Griffiths, P. E. (2002) What is innateness? Monist 85:70–85. Available at: https://doi.org/10.5840/monist20028518.Google Scholar
Hooks, K. B. & O'Malley, M. A. (2017) Dysbiosis and its discontents. mBio 8:e01492-17. Available at: https://doi.org/10.1128/mBio.01492-17.Google Scholar
Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–14. Available at: https://doi.org/10.1038/nature11234.Google Scholar
Hunn, E. (1976) Toward a perceptual model of folk biological classification. American Ethnologist 3:508–24. Available at: https://doi.org/10.1525/ae.1976.3.3.02a00080.Google Scholar
Kell, D. B. & Oliver, S. G. (2004) Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 26:99–105. Available at: https://doi.org/10.1002/bies.10385.Google Scholar
Klein, C. (2010) Philosophical issues in neuroimaging. Philosophy Compass 5:186–98. Available at: https://doi.org/10.1111/j.1747-9991.2009.00275.x.Google Scholar
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., Melnik, A. V., Morton, J. T., Navas, J., Quinn, R. A., Sanders, J. G., Swafford, A. D., Thompson, L. R., Tripathi, A., Xu, Z. Z., Zaneveld, J. R., Zhu, Q., Caporaso, J. G. & Dorrestein, P. C. (2018) Best practices for analysing microbiomes. Nature Reviews Microbiology 16(7):410–22. Available at: https://doi.org/10.1038/s41579-018-0029-9.Google Scholar
Konsman, J. P., Parnet, P. & Dantzer, R. (2002) Cytokine-induced sickness behaviour: Mechanisms and implications. Trends in Neurosciences 25:154–59. Available at: http://www.ncbi.nlm.nih.gov/pubmed/11852148.Google Scholar
Logothetis, N. K. (2008) What we can do and what we cannot do with fMRI. Nature 453:869–78. Available at: https://doi.org/10.1038/nature06976.Google Scholar
Lynch, K., Parke, E. & O'Malley, M. (2019) How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biology and Philosophy. Available at: http://philsci-archive.pitt.edu/15777/.Google Scholar
Mahurin Smith, J. (2015) Breastfeeding and language outcomes: A review of the literature. Journal of Communication Disorders 57:29–40. Available at: https://doi.org/10.1016/j.jcomdis.2015.04.002.Google Scholar
Nguyen, T. L. A., Vieira-Silva, S., Liston, A. & Raes, J. (2015) How informative is the mouse for human gut microbiota research? Disease Models & Mechanisms 8:1–16. Available at: https://doi.org/10.1242/dmm.017400.Google Scholar
Nichols, S. (2004) Folk concepts and intuitions: From philosophy to cognitive science. Trends in Cognitive Sciences 8:514–18. Available at: https://doi.org/10.1016/j.tics.2004.09.001.Google Scholar
Norton, J. D. (2003) Causation as folk science. Philosophers' Imprint 3(4):1–22.Google Scholar
Olesen, S. W. & Alm, E. J. (2016) Dysbiosis is not an answer. Nature Microbiology 1:16228. Available at: https://doi.org/10.1038/nmicrobiol.2016.228.Google Scholar
Pfeiffer, J. K. & Virgin, H. W. (2016) Transkingdom control of viral infection and immunity in the mammalian intestine. Science 351(6270):aad5872. Available at: https://doi.org/10.1126/science.aad5872.Google Scholar
Popper, K.R. (1963) Science as falsification. In: Conjectures and refutations, ed. Popper, K. R., pp. 33–39. Routledge/Keagan Paul.Google Scholar
Rees, T., Bosch, T. & Douglas, A. E. (2018) How the microbiome challenges our concept of self. PLoS Biology 16:e2005358. Available at: https://doi.org/10.1371/journal.pbio.2005358.Google Scholar
Regan, J., Thompson, A. & DeFranco, E. (2013) The influence of mode of delivery on breastfeeding initiation in women with a prior cesarean delivery: A population-based study. Breastfeeding Medicine 8:181–86. Available at: https://doi.org/10.1089/bfm.2012.0049.Google Scholar
Shade, A. (2017) Diversity is the question, not the answer. ISME Journal 11:1–6. Available at: https://doi.org/10.1038/ismej.2016.118.Google Scholar
Sze, M. A. & Schloss, P. D. (2016) Looking for a signal in the noise: Revisiting obesity and the microbiome. mBio 7:e01018-16. Available at: https://doi.org/10.1128/mBio.01018-16.Google Scholar
Thornton, S. (2018) Karl Popper. In: The Stanford encyclopedia of philosophy (Fall 2018), ed. Zalta., E. N. Metaphysics Research Lab, Stanford University.Google Scholar
Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., Kotler, E., Zur, M., Regev-Lehavi, D., Brik, R. B., Federici, S., Cohen, Y., Linevsky, R., Rothschild, D., Moor, A. E., Ben-Moshe, S., Harmelin, A., Itzkovitz, S., Maharshak, N., Shibolet, O., Shapiro, H., Pevsner-Fischer, M., Sharon, I., Halpern, Z., Segal, E. & Elinav, E. (2018) Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174(6):1388–405. Available at: https://doi.org/10.1016/j.cell.2018.08.041.Google Scholar