The coupling of taxonomy and function in microbiomes
- 683 Downloads
Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to (micro-ecological) function, and extracting useful measures from such comparisons (i.e. diversity, stability, or “health”). Although still unresolved, these problems are well studied in macro-ecology (the ecology of non-microbes) and are reiterated here as an historical precautionary for microbial ecologists. Beyond expected and unresolved terminological vagueness, we argue that assessments and comparisons of taxonomic and functional profiles in micro-ecology suffer from theoretically unresolvable arbitrariness and ambiguities. We divide these into problems of scale, individuation, and commensurability. We argue that there is no technically/theoretically “correct” scale, individuation, or comparison of taxonomy and function, but there are nonetheless better and worse methodologies for profiling.
KeywordsMicrobiome Taxonomy Function Ecology Metagenomics
We thank Adam Martiny and an anonymous reviewer for Biology and Philosophy for their very helpful comments. G.M.D. is supported by an NSERC Alexander Graham Bell Canada Graduate Scholarship. W.F.D. is supported by an NSERC Herzberg Medal Grant. M.G.I.L. is supported by an NSERC Discovery Grant.
- Bickle J (2016) Multiple realizability. In: Zalta EN (ed) The Stanford Encyclopedia of Philosophy (Spring). MIT Press, CambridgeGoogle Scholar
- Blaser MJ (2014) Missing microbes: How the overuse of antibiotics is fueling our modern plagues. Henry Holt, New YorkGoogle Scholar
- DeLaplante K, Picasso V (2011) The biodiversity-ecosystem function debate in ecology. In: DeLaplante K, Brown B, Peacock KA (eds) Philosophy of ecology. Elsevier, Oxford, pp 219–250Google Scholar
- Dietert R (2016) The human superorganism: how the microbiome is revolutionizing the pursuit of a healthy life. Dutton, New YorkGoogle Scholar
- Justus J (2011) A case study in concept determination: Ecological diversity. In: DeLaplante K, Brown B, Peacock KA (eds) Philosophy of ecology. Elsevier, OxfordGoogle Scholar
- Kuhn TS (1976) The structure of scientific revolutions (Chicago, 1962)Google Scholar
- May RM (1973) Stability and complexity of model ecosystems. Princeton University Press, PrincetonGoogle Scholar
- Mikkelson GM (1997) Methods and metaphors in community ecology: the problemof defining stability. Perspect Sci 5:481–498Google Scholar
- Odum EP (1953) Fundamentals of ecology. Saunders, PhiladelphiaGoogle Scholar
- Sarkar S (2007) From ecological diversity to biodiversity. In: Hull D, Ruse M (eds) Cambridge companion to the philosophy of biology. Cambridge University Press, CambridgeGoogle Scholar
- Sober E (1993) The nature of selection: evolutionary theory in philosophical focus. University of Chicago Press, ChicagoGoogle Scholar