Notes
We should note here that in our target article we referred to ‘Clostridium difficile’, the spore-forming pathogen in intestines that can cause illness and death. However, in 2016, the genus this organism belongs to was renamed, and we should have said Clostridiodes difficile (Lawson et al. 2016). C. difficile throughout our response now refers accordingly, although it is commonly known as C. diff. Nomenclature may soon become even more complicated because C. difficile appears to be speciating (N. Kumar et al. 2019).
However, FMT risk calculations are likely to increase in practical importance after recent warnings of fatalities following FMTs in immunocompromised hosts (FDA 2019).
Here, we dispute Attah et al.’s (2020) characterization of our position as dichotomous: either individual microbes are causal, or emergent properties are causal. We do not think emergent causation is at work in microbiome-host relationships.
References
Abreu C, Lopez AO, Gore J (2018) Pairing off: a bottom-up approach to the human gut microbiome. Mol Syst Biol 14:e8425
Alexander MP, Naeser MA, Palumbo CL (1987) Correlations of subcortical lesion sites and aphasia profiles. Brain 110(4):961–988
Attah NO, DiMarco M, Plutynski A (2020) Microbiomes: proportional causes in context. Biol Philos 35:22
Buffie CG, Bucci V, Stein RR et al (2015) Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517:205–208
Donhauser J, Worley S, Bradie M, Bouzat JL (2019) The problem of mooted models for analyses of microbiome causality. Biol Philos 34:57
Douglas AE, Werren JH (2016) Holes in the hologenome: why host-microbe symbioses are not holobionts. mBio. https://doi.org/10.1128/mbio.02099-15
Dretske F (1995) Mental events as structuring causes of behaviour. In: Heil J, Mele A (eds) Mental causation. Clarendon Press, Oxford, pp 121–136
Eisen JA (2017) Microbiomania and ‘overselling the microbiome’. The tree of life. https://phylogenomics.blogspot.com/p/blog-page.html
Embick D, Marantz A, Miyashita Y, O’Neil W, Sakai KL (2000) A syntactic specialization for Broca’s area. Proc Natl Acad Sci USA 97(11):6150–6154
Fagan MB (2019) Commentary on ‘How causal are microbiomes?’. Biol Philos 34:58
FDA (2019) Important safety alert regarding use of fecal microbiota for transplantion and risk of serious adverse reactions due to transmission of multi-drug resistant organisms. https://www.fda.gov/vaccines-blood-biologics/safety-availability-biologics/important-safety-alert-regarding-use-fecal-microbiota-transplantation-and-risk-serious-adverse
Foster KR, Schluter J, Coyte KZ, Rakoff-Nahoum S (2017) The evolution of the host microbiome as an ecosystem on a leash. Nature 548:43–51
Gillies D (2019) Commentary on Kate E. Lynch, Emily C. Parke, and Maureen A. O'Malley: 'How causal are Microbiomes? A comparison with the helicobacter pylori explanation of ulcers'. Biol Philos 24:56.
Gomez-Lavin J (2019) Why expect causation at all? A pessimistic parallel with neuroscience. Biol Philos 34:61
Greslehner GP, Lemoine M (2020) A dual decomposition strategy of both microbial and phenotypic components for a better understanding of causal claims. Biol Philos 35:1
Griffiths PE, Pocheville A, Calcott B, Stotz K, Kim H, Knight R (2015) Measuring causal specificity. Philos Sci 82:529–555
Halfvarson J, Brislawn CJ, Lamendella R et al (2017) Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol 2:17004
Hooks KB, O’Malley MA (2017) Dysbiosis and its discontents. mBio. https://doi.org/10.1128/mBio.01492-17
Hooks KB, Konsman JP, O’Malley MA (2019) Microbiota-gut-brain research: a critical analysis. Behav Brain Sci 42:e60
Humeau Y, Doussau F, Grant NJ, Poulain B (2000) How botulinum and tetanus neurotoxins block neurotransmitter release. Biochimie 82:427–446
Johns NI, Blazejewski T, Gomes ALC, Wang HH (2016) Principles for designing synthetic microbial communities. Curr Opin Microbiol 31:146–153
Johnson EL, Heaver SL, Walters WA, Ley RE (2016) Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes. J Mol Med. https://doi.org/10.1007/s00109016-1492-2
Klassen JL (2020) Ecology helps bound causal explanations in microbiology. Biol Philos 35:3
Kumar N, Browne HP, Vciani E et al (2019) Adaptation of host transmission cycle during Clostridium difficile speciation. Nat Genet 51:1315–1320
Kumar M, Ji B, Zengler K, Nielsen J (2019) Modelling approaches for studying the microbiome. Nat Microbiol 4:1253–1267
Lawson PA, Citron DM, Tyrrell KL, Finegold SM (2016) Reclassification of Clostridium difficile as Clostridiodes difficile (Hall and O’Toole 1935) Prévot 1938. Anaerobe 40:95–99
Lean CH (2019) Can communities cause? Biol Philos 34:59
Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Genome Med 8:51
Lynch KE, Parke EC, O’Malley MA (2019) How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biol Philos 34:62
Menzies P (2004) Difference making in context. In: Collins JD, Hall N, Paul LA (eds) Causation and counterfactuals. Cambridge, pp 139-180
Moran NA, Sloan DB (2015) The hologenome concept: helpful or hollow? PLoS Biol. https://doi.org/10.1371/journal.pbio.1002311
Neal JP (2019) When causal specificity does not matter (much): insights from HIV treatment. Philos Sci 86:836–846
O’Malley MA, Parke EC (2018) Microbes, mathematics, and models. Stud Hist Philos Biol Biomed Sci 72:1–10
Oftedal G (2020) Problems with using stability, specificity, and proportionality as criteria for evaluating strength of scientific causal explanations: commentary on Lynch et al. Biol Philos 35:26
Olesen SW, Alm EJ (2016) Dysbiosis is not an answer. Nat Microbiol 1:16228
Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), 17th October 2019. https://omim.org/
Perez-Muñoz ME, Arrieta M-C, Ramer-Tait AE, Walter J (2017) A critical assessment of the ‘sterile womb’ and ‘in utero colonization’ hypotheses: implications for research on the pioneer infant microbiome. Microbiome 5:48
Petersen C, Bell R, Klag KA et al (2019) T cell-mediated regulation of the microbiota protects against obesity. Science 365:eaat9351
Queller DC, Strassmann JE (2016) Problems of multi-species organisms: endosymbionts to holobionts. Biol Philos 31:855–873
Raman AS, Gehrig JL, Venkatesh S et al (2019) A sparse covarying unit that describes healthy and impaired human gut microbiota development. Science 365:eaau4735
Schneider T (2020) Microbial activities are dependent on background conditions. Biol Philos 35:23
Schulfer AF, Battaglia T, Alvarez Y et al (2018) Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice. Nat Microbiol 3:234–242
Skillings D (2016) Holobionts and the ecology of organisms: multi-species communities or integrated individuals? Biol Philos 31:875–892
Skillings D (2019) Trojan horses and Black Queens: ‘causal core’ explanations in microbiome research. Biol Philos 34:60
Vásquez-Castellanos JF, Biclot A, Vrancken G, Huys GRB, Raes J (2019) Design of synthetic microbial consortia for gut microbiota modulation. Curr Opin Pharmacol 49:52–59
Venturelli OS, Carr AV, Fisher G et al (2018) Deciphering microbial interactions in synthetic human gut microbiome communities. Mol Syst Biol 14:e8157
Vrancken G, Gregory AC, Huys GRB, Faust K, Raes J (2019) Synthetic ecology of the human gut microbiota. Nat Rev Microbiol 17:754–763
Waters CK (2007) Causes that make a difference. J Philos 104:551–579
Watkins A, Bocchi F (2020) Pathogen versus microbiome causation in the holobiont. Biol Philos 35:7
Woodward J (2003) Making things happen: a theory of causal explanation. Oxford University Press, Oxford
Woodward J (2018) Explanatory autonomy: the role of proportionality, stability, and conditional irrelevance. Synthese. https://doi.org/10.1007/s11229-018-01998-6
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Lynch, K.E., Parke, E.C. & O’Malley, M.A. Microbiome causality: further reflections (a response to our commentators). Biol Philos 35, 29 (2020). https://doi.org/10.1007/s10539-020-9742-7
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10539-020-9742-7