AI Article Synopsis
- Synthetic bacterial communities are valuable for microbial ecology studies but face challenges due to high costs and long turnaround times of existing sequencing methods.
- The authors present a method using Sanger sequencing to quickly and affordably quantify bacterial community composition by amplifying a universal marker gene.
- Their technique provides results in about one day at a cost of approximately $5 per sample, significantly enhancing the feasibility of iterative experiments in microbial research.
Article 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.
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|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7047173 | PMC |
| http://dx.doi.org/10.1016/j.isci.2020.100915 | DOI Listing |
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