From molecules to dynamic biological communities

Daniel McDonald, Yoshiki Vázquez-Baeza, William A. Walters, J. Gregory Caporaso, Rob Knight

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.

Original languageEnglish (US)
Pages (from-to)241-259
Number of pages19
JournalBiology and Philosophy
Issue number2
StatePublished - Mar 2013


  • Microbial community analysis
  • Microbiome
  • Operational taxonomic units
  • Timeseries

ASJC Scopus subject areas

  • Philosophy
  • General Agricultural and Biological Sciences
  • History and Philosophy of Science


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