Profiling bacterial communities in low biomass samples: pitfalls and considerations
Lisa F Stinson A C , Jeffrey A Keelan B and Matthew S Payne B
+ Author Affiliations
- Author Affiliations
A School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
B Division of Obstetrics and Gynaecology, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, WA, Australia
C Tel: +61 6488 3200, Fax: +61 6488 7086, Email: lisa.stinson@uwa.edu.au
Microbiology Australia 40(4) 181-185 https://doi.org/10.1071/MA19053
Published: 14 November 2019
Abstract
Bacterial 16S rRNA gene sequencing studies are popular across many fields of biology. This technique has allowed us to study bacterial communities like never before, leading to significant insights into microbial ecology and host– microbe interactions. However, 16S rRNA gene-based workflows are vulnerable to confounding and bias at every step. Many studies are plagued by entrenched methodological errors, producing data riddled with experimental artefacts. These issues are amplified in the study of low bacterial biomass samples, such as forensic and ancient samples, blood, meconium, ice and the built environment. It is, therefore, necessary to define the pitfalls of low biomass 16S rRNA gene-based work flows and to identify methods that may allow more accurate characterisation of bacterial communities in such samples.
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