Abstract
Commentary: How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches.
Highlights
Reviewed by: Renate Lux, University of California, Los Angeles, United States Lisa Stinson, University of Western Australia, Australia
The recent article by Galazzo et al (2020) compared two popular approaches for quantitative microbiome profiling (QMP), cellbased flow cytometry (Vandeputte et al, 2017), and quantitative PCR applied for DNA extracts (Jian et al, 2020) using a mock mix of bacterial cells and fecal samples. They included a variant of flow cytometry-based QMP, where dead or damaged cells were removed by propidium monoazide (PMA) pre-treatment before sequencing to study how removing extracellular DNA (on average approximately 40% of the total DNA in the fecal samples (Galazzo et al, 2020)), captured in standard next-generation sequencing (NGS) but otherwise excluded in flow-cytometry counting, affected the comparisons
The authors found that total bacterial loads quantified by quantitative PCR (qPCR) and flow cytometry were highly correlated when performed in the mock mix
Summary
Reviewed by: Renate Lux, University of California, Los Angeles, United States Lisa Stinson, University of Western Australia, Australia. The Effect of Different Quantitative Microbiome Profiling Approaches by Galazzo, G., van Best, N., Benedikter, B.J., Janssen, K., Bervoets, L., Driessen, C., et al (2020). The Effect of Different Quantitative Microbiome Profiling Approaches.
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