Rapid, Inexpensive Measurement of Synthetic Bacterial Community Composition by Sanger Sequencing of Amplicon Mixtures

Nathan Cermak; Manoshi Sen Datta; Arolyn Conwill

doi:10.1016/j.isci.2020.100915

Rapid, Inexpensive Measurement of Synthetic Bacterial Community Composition by Sanger Sequencing of Amplicon Mixtures

iScience. 2020 Mar 27;23(3):100915. doi: 10.1016/j.isci.2020.100915. Epub 2020 Feb 14.

Authors

Nathan Cermak¹, Manoshi Sen Datta², Arolyn Conwill³

Affiliations

¹ Fremont, CA, USA, 94555.
² Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel. Electronic address: mdatta8788@gmail.com.
³ Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Abstract

Synthetic bacterial communities are powerful tools for studying microbial ecology and evolution, as they enable rapid iteration between controlled laboratory experiments and theoretical modeling. However, their utility is hampered by the lack of fast, inexpensive, and accurate methods for quantifying bacterial community composition. Although next-generation amplicon sequencing can be very accurate, high costs (>$30 per sample) and turnaround times (>1 month) limit the nature and pace of experiments. Here, we quantify amplicon composition in synthetic bacterial communities through Sanger sequencing. We PCR amplify a universal marker gene, then we sequence this amplicon mixture in a single Sanger sequencing reaction. We then fit the "mixed" electropherogram with contributions from each community member as a linear combination of time-warped single-strain electropherograms, allowing us to estimate the fractional amplicon abundance of each strain within the community. This approach can provide results within one day and costs ∼$5 per sample.

Keywords: Bioinformatics; Microbial Genetics; Microbiology; Sequence Analysis.