New directions in biology: Metagenomics and microbiology
John Dupré and Maureen O'Malley (University of Sydney)
This project was funded by the Arts and Humanities Research Council from 2006-2008.
Metagenomics is the large-scale study of the DNA of naturally existing microbial communities rather than ‘artificial’ lab cultures. It can involve the shotgun sequencing of all the genomes in these communities, but is most likely to be about screening and sequencing large segments of DNA extracted from wide-ranging environmental samples. Metagenomics does more, however, than merely provide microbiologists with lots of interesting DNA sequence data. It takes a non-traditional focus on the genomic resource of a dynamic microbial community, rather than on individual strains of microbes or individual genes and their functions. A community genomics perspectives examines how horizontal transfer allows otherwise distantly related organisms to share these resources. Moreover, metagenomics analyses microbial communities as systems that have functional properties that go beyond those of individual genes or individual microbes (or even single-taxon populations). Metabolic cascades, for example, can be distributed over different members of multi-taxa syntrophic communities. It could be said, therefore, that metagenomics studies something like a metaorganism, and that understanding such an entity also requires a systems-biologic approach. The project examines all these aspects of metagenomics. In the process of situating metagenomics within microbiology more generally, I have also indulged in broader historical work on microbial biogeography, as well as more general reflections on the nature of living things (see publications below).
One of the major success stories in metagenomics involves the discovery in marine bacteria of totally unexpected genes and proteins called proteorhodopsins, which are involved in previously undetected processes of photobiology. The torrent of research (biophysical, biochemical, physiological, phylogenetic) that finding has initiated provides a remarkable illustration of the power of metagenomic approaches. This case study has been the focus of some of my recent work on metagenomics. These efforts connect with the project on microbial rhodopsins, and my ongoing collaborations with several life scientists on prokaryote phylogeny and its implications for the . A further ramification has been a philosophical and historical project on (funded by the British Academy). This sideline, which connects with work I am doing on eukaryote microbiology, has produced has produced a special issue on the history and philosophy of cell research in Studies in History and Philosophy of the Biological and Biomedical Sciences (2010, Volume 41, issue 3).
O'Malley, M.A., and Stotz, K. (2011). Intervention, integration and translation in obesity research: Genetic, developmental and metaorganismal approaches. Philosophy, Ethics, and Humanities in Medicine, 6(2)O'Malley, M.A. (2010). What microbes can do: A sensory guide to microbiology (essay review of John L. Ingraham's March of the Microbes: Sighting the Unseen, 2010, Belknap). Biological Theory, 5 (2): 182-186.O'Malley, M.A. (2010). The first eukaryote cell: An unfinished history of contestation. Studies in the History and Philosophy of Biological and Biomedical Sciences (special issue on the history and philosophy of cell research), 41 (3): 212-224.
Dupré, J., and O'Malley, M.A. Varieties of living things: Life at the intersection of lineage and metabolism. Philosophy & Theory in Biology, 1, 2009.
O'Malley, M.A. What did Darwin say about microbes, and how did microbiology respond? Trends in Microbiology, 17 (8), 2009: 341-347.
O'Malley, M.A., and Dupré, J. 'Philosophical themes in metagenomics', in D. Marco (ed.), Metagenomics: Theory, methods and applications. Hethersett, Norwich: Horizon Scientific Press, 2009.
O'Malley, M.A. Review of Microcosm: E.coli and the New Science of Life, by Zimmer, C. (part of a review symposium, 'Life through a microbial lens', with Susan Spath, Jesse Zaneveld, Rob Knight and Carl Zimmer), Metascience, 18 (2), 2009: 186-194.
Dupré, J., and O'Malley, M.A. 'A metagenomic world view': Comment on 'Metagenomic metaphors: New images of the human from "translational" research', by Eric T. Juengst. In M. Drenthen et al. (eds.), New Visions of Nature. Springer, 2009.
O'Malley, M.A. 'Everything is everywhere: but the environment selects': Ubiquitous distribution and ecological determinism in microbial biogeography. Studies in History and Philosophy of Biological and Biomedical Sciences, 39 (3), 2008: 314-325.
O'Malley, M.A. 'Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case'. History and Philosophy of the Life Sciences, 29 (3), 2008: 335-358 (Preprint available). [This is one of a group of three papers (plus an introduction by C. Kenneth Waters) on exploratory experimentation in recent molecular life sciences. The other papers are by Richard Burian and Kevin Elliott.
O'Malley, M. A. The nineteenth-century roots of 'Everything is everywhere'. em>Nature Reviews Microbiology, 5, 2007: 647-651.
Dupré, J., and O’Malley, M. A. 'Metagenomics and biological ontology'. Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4), 2007: 834-846.
O'Malley, M. A., and Dupré, J. 'Size doesn't matter: Towards a more inclusive philosophy of biology'. Biology and Philosophy, 22 (2), 2007: 155-191.
O’Malley, M. A., and Dupré, J. 'Introduction: Towards a philosophy of microbiology'. Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4), 2007: 775-779.
Workshop on ‘Philosophical and Social Dimensions of Microbiology’, July 2007.