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Additional file 3 of Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

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posted on 13.05.2020, 03:40 by Shantelle Claassen-Weitz, Sugnet Gardner-Lubbe, Kilaza S. Mwaikono, Elloise du Toit, Heather J. Zar, Mark P. Nicol
Additional file 3. Bacterial composition of Zymobiomics-DNA (n = 8) compared to Zymobiomics-Primestore-high (n = 6) and Zymobiomics-STGG-high (n = 6). The two high biomass mock communities, Zymobiomics-Primestore-high and Zymobiomics-STGG-high, represent triplicate extractions using two extraction methods (blue filled circles: Kit-QS and red filled circles: Kit-ZB). Zymobiomics-DNA (darkgreen filled circles) were included to validate sequencing profiles generated using the two extraction methods. Unsupervised hierarchical clustering distances are based on Bray Curtis dissimilarity indices calculated at OTU-level. Differences between bacterial mock controls are shown at genus-level, with colour-codes representing phylum-level classification (Shades of blue: Proteobacteria, shades of red: Firmicutes). Genera with proportions < 1% in each of the specimens are grouped together as “Other” and shown in grey.


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