Gilbert SF, Sapp J, Tauber AI. A symbiotic view of life: we have never been individuals. Q Rev Biol. 2012; 87(4):325–41. https://doi.org/10.1086/668166.
Article
PubMed
Google Scholar
Pradeu T. Organisms or biological individuals? Combining physiological and evolutionary individuality. Biol Philos. 2016; 31(6):797–817. https://doi.org/10.1007/s10539-016-9551-1.
Article
Google Scholar
Doolittle WF, Booth A. It’s the song, not the singer: an exploration of holobiosis and evolutionary theory. Biol Philos. 2017; 32(1):5–24. https://doi.org/10.1007/s10539-016-9542-2.
Article
Google Scholar
Gilbert SF. Evolutionary transitions revisited: holobiont evo-devo. J Exp Zool B Mol Dev Evol. 2019; 332(8):307–14. https://doi.org/10.1002/jez.b.22903.
Article
PubMed
Google Scholar
Pradeu T. Philosophy of biology: immunology and individuality. eLife. 2019; 8:47384. https://doi.org/10.7554/eLife.47384.
Article
Google Scholar
McFall-Ngai M, Hadfield MG, Bosch TCG, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci. 2013; 110(9):3229–36. https://doi.org/10.1073/pnas.1218525110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rees T, Bosch T, Douglas AE. How the microbiome challenges our concept of self. PLOS Biol. 2018; 16(2):1–7. https://doi.org/10.1371/journal.pbio.2005358.
Article
CAS
Google Scholar
Suárez J, Triviño V. What is a hologenomic adaptation? Emergent individuality and inter-identity in multispecies systems. Front Psychol. 2020; 11:187. https://doi.org/10.3389/fpsyg.2020.00187.
Article
PubMed
PubMed Central
Google Scholar
Lidgard S, Nyhart LK. Biological individuality: integrating biological, historical, and philosophical perspectives. Chicago and London: The University of Chicago Press; 2017.
Book
Google Scholar
Laplane L, Mantovani P, Adolphs R, Chang H, Mantovani A, McFall-Ngai M, Rovelli C, Sober E, Pradeu T. Opinion: why science needs philosophy. Proc Natl Acad Sci. 2019; 116(10):3948–52. https://doi.org/10.1073/pnas.1900357116.
Article
CAS
PubMed Central
Google Scholar
Bosch TCG, Miller DJ. The holobiont imperative. Wien: Springer; 2016. https://doi.org/10.1007/978-3-7091-1896-2.
Book
Google Scholar
Nyholm SV, McFall-Ngai M. The winnowing: establishing the squid–vibrio symbiosis. Nat Rev Microbiol. 2004; 2(8):632–42. https://doi.org/10.1038/nrmicro957.
Article
CAS
PubMed
Google Scholar
Reshef L, Koren O, Loya Y, Zilber-Rosenberg I, Rosenberg E. The coral probiotic hypothesis. Environ Microbiol. 2006; 8(12):2068–73. https://doi.org/10.1111/j.1462-2920.2006.01148.x.
Article
CAS
PubMed
Google Scholar
Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol. 2007; 5(5):355–62. https://doi.org/10.1038/nrmicro1635.
Article
CAS
PubMed
Google Scholar
Moree WJ, McConnell OJ, Nguyen DD, Sanchez LM, Yang Y-L, Zhao X, Liu W-T, Boudreau PD, Srinivasan J, Atencio L, Ballesteros J, Gavilán RG, Torres-Mendoza D, Guzmán HM, Gerwick WH, Gutiérrez M, Dorrestein PC. Microbiota of healthy corals are active against fungi in a light-dependent manner. ACS Chem Biol. 2014; 9(10):2300–8. https://doi.org/10.1021/cb500432j.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carrier TJ, Reitzel AM. The hologenome across environments and the implications of a host-associated microbial repertoire. Front Microbiol. 2017; 8:802. https://doi.org/10.3389/fmicb.2017.00802.
Article
PubMed
PubMed Central
Google Scholar
Pradeu T. The many faces of biological individuality. Biol Philos. 2016; 31(6):761–73. https://doi.org/10.1007/s10539-016-9553-z.
Article
Google Scholar
Pradeu T. Philosophy of immunology. Elements in the Philosophy of Biology. Cambridge: Cambridge University Press; 2020. https://doi.org/10.1017/9781108616706.
Google Scholar
Pradeu T. The limits of the self: immunology and biological identity. Oxford; New York: Oxford University Press; 2012. https://doi.org/10.1093/acprof:oso/9780199775286.001.0001.
Book
Google Scholar
Pradeu T. What is an organism? An immunological answer. Hist Philos Life Sci. 2010; 32(2-3):247–67.
PubMed
Google Scholar
Gilbert SF. Developmental symbiosis facilitates the multiple origins of herbivory. Evol Dev. 2020; 22(1-2):154–64. https://doi.org/10.1111/ede.12291.
Article
PubMed
Google Scholar
Chiu L, Gilbert SF. The birth of the holobiont: multi-species birthing through mutual scaffolding and niche construction. Biosemiotics. 2015; 8(2):191–210. https://doi.org/10.1007/s12304-015-9232-5.
Article
Google Scholar
Martens J. L’évolution des organismes: Une perspective épistémologique. Paris: éditions MATERIOLOGIQUES; 2018.
Google Scholar
Martens J. Organisms in evolution. Hist Philos Life Sci. 2010; 32(2/3):373–400.
PubMed
Google Scholar
Hooks KB, Konsman JP, O’Malley MA. Microbiota-gut-brain research: a critical analysis. Behav Brain Sci. 2019; 42:60. https://doi.org/10.1017/S0140525X18002133.
Article
Google Scholar
Hooks KB, Konsman JP, O’Malley MA. Causal clarity and deeper dimensions in microbiota-gut-brain research. Behav Brain Sci. 2019; 42:80. https://doi.org/10.1017/S0140525X19000050.
Article
Google Scholar
Finlay BB, Pettersson S, Melby MK, Bosch TCG. The microbiome mediates environmental effects on aging. BioEssays. 2019; 41(10):1800257. https://doi.org/10.1002/bies.201800257.
Article
Google Scholar
Deines P, Lachnit T, Bosch TCG. Competing forces maintain the Hydra metaorganism. Immunol Rev. 2017; 279(1):123–36. https://doi.org/10.1111/imr.12564.
Article
CAS
PubMed
Google Scholar
Cekanaviciute E, Yoo BB, Runia TF, Debelius JW, Singh S, Nelson CA, Kanner R, Bencosme Y, Lee YK, Hauser SL, Crabtree-Hartman E, Sand IK, Gacias M, Zhu Y, Casaccia P, Cree BAC, Knight R, Mazmanian SK, Baranzini SE. Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. Proc Natl Acad Sci. 2017; 114(40):10713–8. https://doi.org/10.1073/pnas.1711235114.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks BW, Nam E, Org E, Kostem E, Norheim F, Hui ST, Pan C, Civelek M, Rau CD, Bennett BJ, Mehrabian M, Ursell LK, He A, Castellani LW, Zinker B, Kirby M, Drake TA, Drevon CA, Knight R, Gargalovic P, Kirchgessner T, Eskin E, Lusis AJ. Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab. 2013; 17(1):141–52. https://doi.org/10.1016/j.cmet.2012.12.007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet M-F, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK. Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease. Cell. 2016; 167(6):1469–8012. https://doi.org/10.1016/j.cell.2016.11.018.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sharon G, Cruz NJ, Kang D-W, Gandal MJ, Wang B, Kim Y-M, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. Human gut microbiota from autism spectrum disorder promote behavioral symptoms in mice. Cell. 2019; 177(6):1600–817. https://doi.org/10.1016/j.cell.2019.05.004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science. 2010; 328(5975):228–31. https://doi.org/10.1126/science.1179721.
Article
CAS
PubMed
PubMed Central
Google Scholar
Laudan L. A confutation of convergent realism. Philos Sci. 1981; 48(1):19–49. https://doi.org/10.1086/288975.
Article
Google Scholar
Griffiths P, Stotz K. Genetics and philosophy: an introduction. Cambridge: Cambridge University Press; 2013. https://doi.org/10.1017/CBO9780511744082.
Book
Google Scholar
Lloyd EA. Adaptationism and the logic of research questions: how to think clearly about evolutionary causes. Biol Theory. 2015; 10(4):343–62. https://doi.org/10.1007/s13752-015-0214-2.
Article
Google Scholar
Clarke E. The problem of biological individuality. Biol Theory. 2010; 5(4):312–25. https://doi.org/10.1162/BIOT\_a\_00068.
Article
Google Scholar
DiFrisco J. Kinds of biological individuals: sortals, projectibility, and selection. Br J Philos Sci. 2019; 70(3):845–75. https://doi.org/10.1093/bjps/axy006.
Article
Google Scholar
Godfrey-Smith P. In: Bouchard F, Huneman P, (eds).From groups to individuals: evolution and emerging individuality. Cambridge, MA: MIT Press; 2013, pp. 17–36.
Google Scholar
Moran NA, Sloan DB. The hologenome concept: helpful or hollow?PLOS Biol. 2015; 13(12):1–10. https://doi.org/10.1371/journal.pbio.1002311.
Article
CAS
Google Scholar
Douglas AE, Werren JH. Holes in the hologenome: why host-microbe symbioses are not holobionts. mBio. 2016; 7(2):02099–15. https://doi.org/10.1128/mBio.02099-15.
Article
Google Scholar
Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TCG, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR. Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems. 2016; 1(2):00028–16. https://doi.org/10.1128/mSystems.00028-16.
Article
Google Scholar
Lloyd EA, Wade MJ. Criteria for holobionts from community genetics. Biol Theory. 2019; 14(3):151–70. https://doi.org/10.1007/s13752-019-00322-w.
Article
Google Scholar
Gánti T. Chemoton theory: theoretical foundations of fluid machineries. New York: Kluwer Academic/Plenum Publishers; 2003.
Book
Google Scholar
Kaiser MI. Reductive explanation in the biological sciences. Cham: Springer; 2015. https://doi.org/10.1007/978-3-319-25310-7.
Book
Google Scholar
Kopac SM, Klassen JL. Can they make it on their own? Hosts, microbes, and the holobiont niche. Front Microbiol. 2016; 7:1647. https://doi.org/10.3389/fmicb.2016.01647.
Article
PubMed
PubMed Central
Google Scholar
The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486:207–14. https://doi.org/10.1038/nature11234.
Article
PubMed Central
CAS
Google Scholar
Hanage WP. Microbiology: microbiome science needs a healthy dose of scepticism. Nature. 2014; 412(7514):247–8. https://doi.org/10.1038/512247a.
Article
CAS
Google Scholar
Fischbach MA. Microbiome: focus on causation and mechanism. Cell. 2018; 174(4):785–90. https://doi.org/10.1016/j.cell.2018.07.038.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lynch KE, Parke EC, O’Malley MA. How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biol Philos. 2019; 34(6):62. https://doi.org/10.1007/s10539-019-9702-2.
Article
Google Scholar
Bourrat P, Griffiths PE. Multispecies individuals. Hist Philos Life Sci. 2018; 40(2):33. https://doi.org/10.1007/s40656-018-0194-1.
Article
PubMed
Google Scholar
Neville BA, Forster SC, Lawley TD. Commensal koch’s postulates: establishing causation in human microbiota research. Curr Opin Microbiol. 2018; 42:47–52. https://doi.org/10.1016/j.mib.2017.10.001.
Article
PubMed
Google Scholar
Ross LN, Woodward JF. Koch’s postulates: an interventionist perspective. Stud Hist Phil Sci Part C Stud Hist Phil Biol Biomed Sci. 2016; 59:35–46. https://doi.org/10.1016/j.shpsc.2016.06.001.
Article
Google Scholar
van Inwagen P, Sullivan M Zalta EN, (ed).Metaphysics. Metaphysics Research Lab, Stanford University; 2018. https://plato.stanford.edu/archives/spr2018/entries/metaphysics/.
O’Connor T, Wong HY. The metaphysics of emergence. Noûs. 2005; 39(4):658–78. https://doi.org/10.1111/j.0029-4624.2005.00543.x.
Article
Google Scholar
El-Hani CN, Emmeche C. On some theoretical grounds for an organism-centered biology: property emergence, supervenience, and downward causation. Theory Biosci. 2000; 119(3):234–75. https://doi.org/10.1007/s12064-000-0018-0.
Article
Google Scholar
Malaterre C. Making sense of downward causation in manipulationism: illustrations from cancer research. Hist Philos Life Sci. 2011; 33(4):537–61.
PubMed
Google Scholar
Mossio M, Bich L, Moreno A. Emergence, closure and inter-level causation in biological systems. Erkenntnis. 2013; 78(2):153–78. https://doi.org/10.1007/s10670-013-9507-7.
Article
Google Scholar
Green S. Cancer beyond genetics: on the practical implications of downward causation In: Brooks DS, DiFrisco J, Wimsatt WC, editors. Levels of Organization in the Biological Sciences. Cambridge, MA: MIT Press: 2020.
Google Scholar
WHO Constitution. https://www.who.int/about/who-we-are/constitution. Accessed 07 Apr 2020.
Lemon KP, Armitage GC, Relman DA, Fischbach MA. Microbiota-targeted therapies: an ecological perspective. Sci Transl Med. 2012; 4(137):137–51375. https://doi.org/10.1126/scitranslmed.3004183.
Article
CAS
Google Scholar
Inkpen SA. Philosophy of biology: health, ecology and the microbiome. eLife. 2019; 8:47626. https://doi.org/10.7554/eLife.47626.
Article
Google Scholar
Kouhsari E, Abbasian S, Sedighi M, Yaseri HF, Nazari S, Bialvaei AZ, Dahim P, Mirzaei EZ, Rahbar M. Clostridium difficile infection: a review. Rev Med Microbiol. 2018; 29(3):103–9. https://doi.org/10.1097/MRM.0000000000000135.
Article
Google Scholar
Abt MC, McKenney PT, Pamer EG. Clostridium difficile colitis: pathogenesis and host defence. Nat Rev Microbiol. 2016; 14(10):609–20. https://doi.org/10.1038/nrmicro.2016.108.
Article
CAS
PubMed
PubMed Central
Google Scholar
andCho Young-Seok CHH. Fecal microbiota transplantation: current applications, effectiveness, and future perspectives. Clin Endosc. 2016; 49(3):257–65. https://doi.org/10.5946/ce.2015.117.
Article
Google Scholar
de Groot PF, Frissen MN, de Clercq NC, Nieuwdorp M. Fecal microbiota transplantation in metabolic syndrome: history, present and future. Gut Microbes. 2017; 8(3):253–67. https://doi.org/10.1080/19490976.2017.1293224.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wilson BC, Vatanen T, Cutfield WS, O’Sullivan JM. The super-donor phenomenon in fecal microbiota transplantation. Front Cell Infect Microbiol. 2019; 9:2. https://doi.org/10.3389/fcimb.2019.00002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lawley TD, Walker AW. Intestinal colonization resistance. Immunology. 2013; 138(1):1–11. https://doi.org/10.1111/j.1365-2567.2012.03616.x.
Article
CAS
PubMed
Google Scholar
Litvak Y, Bäumler AJ. The founder hypothesis: a basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens. PLOS Pathog. 2019; 15(2):1–6. https://doi.org/10.1371/journal.ppat.1007563.
Article
CAS
Google Scholar
Buffie CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol. 2013; 13(11):790–801. https://doi.org/10.1038/nri3535.
Article
CAS
PubMed
PubMed Central
Google Scholar
Borody TJ, Khoruts A. Fecal microbiota transplantation and emerging applications. Nat Rev Gastroenterol Hepatol. 2012; 9(2):88–96. https://doi.org/10.1038/nrgastro.2011.244.
Article
CAS
Google Scholar
Wang S, Xu M, Wang W, Cao X, Piao M, Khan S, Yan F, Cao H, Wang B. Systematic review: adverse events of fecal microbiota transplantation. PLOS ONE. 2016; 11(8):1–24. https://doi.org/10.1371/journal.pone.0161174.
Google Scholar
Zhang Z, Tang H, Chen P, Xie H, Tao Y. Demystifying the manipulation of host immunity, metabolism, and extraintestinal tumors by the gut microbiome. Sig Transduct Target Ther. 2019; 4(1):41. https://doi.org/10.1038/s41392-019-0074-5.
Article
Google Scholar
Suárez J, Triviño V. A metaphysical approach to holobiont individuality: holobionts as emergent individuals. Quaderns Filos. 2019; VI(1):59–76. https://doi.org/10.7203/qfia.6.1.14825.
Article
Google Scholar
Hull D. In: Keller EF, Lloyd EA, (eds).Keywords in evolutionary biology. Cambridge, MA: Harvard University Press; 1992, pp. 180–7.
Google Scholar
Lloyd E Zalta EN, (ed).Units and levels of selection. Metaphysics Research Lab, Stanford University; 2020. https://plato.stanford.edu/archives/spr2020/entries/selectionunits/.
Zhou X, Bent SJ, Schneider MG, Davis CC, Islam MR, Forney LJ. Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology. 2004; 150(Pt 8):2565–73. https://doi.org/10.1099/mic.0.26905-0.
Article
CAS
PubMed
Google Scholar
Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, Foster JA, Forney LJ. Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J. 2007; 1(2):121–33. https://doi.org/10.1038/ismej.2007.12.
Article
CAS
PubMed
Google Scholar
Skillings D. Holobionts and the ecology of organisms: multi-species communities or integrated individuals?Biol Philos. 2016; 31(6):875–92. https://doi.org/10.1007/s10539-016-9544-0.
Article
Google Scholar
Meincke AS, Dupré J, (eds.)Biological identity. Perspectives from Metaphysics and the Philosophy of Biology. London: Routledge; 2020.
Book
Google Scholar