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Using Cartesian Doubt To Build a Sequencing-Based View of Microbiology.

Authors
  • Tierney, Braden T1, 2, 3, 4
  • Szymanski, Erika5
  • Henriksen, James R6
  • Kostic, Aleksandar D2, 3, 4
  • Patel, Chirag J1
  • 1 Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
  • 2 Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, Massachusetts, USA.
  • 3 Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, Massachusetts, USA.
  • 4 Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA.
  • 5 Department of English, Colorado State University, Fort Collins, Colorado, USA.
  • 6 Mr. Fusion Inc., Fort Collins, Colorado, USA.
Type
Published Article
Journal
mSystems
Publication Date
Oct 26, 2021
Volume
6
Issue
5
Identifiers
DOI: 10.1128/mSystems.00574-21
PMID: 34636670
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

The technological leap of DNA sequencing generated a tension between modern metagenomics and historical microbiology. We are forcibly harmonizing the output of a modern tool with centuries of experimental knowledge derived from culture-based microbiology. As a thought experiment, we borrow the notion of Cartesian doubt from philosopher Rene Descartes, who used doubt to build a philosophical framework from his incorrigible statement that "I think therefore I am." We aim to cast away preconceived notions and conceptualize microorganisms through the lens of metagenomic sequencing alone. Specifically, we propose funding and building analysis and engineering methods that neither search for nor rely on the assumption of independent genomes bound by lipid barriers containing discrete functional roles and taxonomies. We propose that a view of microbial communities based in sequencing will engender novel insights into metagenomic structure and may capture functional biology not reflected within the current paradigm.

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