Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens.
Shantelle Claassen-WeitzSugnet Gardner-LubbeKilaza S MwaikonoElloise du ToitHeather J ZarMark P NicolPublished in: BMC microbiology (2020)
We provide insight into experimental design, quality control steps and "denoising" approaches for 16S rRNA gene high-throughput sequencing of low biomass specimens. We highlight the need for careful assessment of DNA extraction methods and storage buffers; sequence quality and reproducibility; and in silico identification of contaminant profiles in order to avoid spurious results.
Keyphrases
- quality control
- high throughput sequencing
- copy number
- genome wide
- wastewater treatment
- cystic fibrosis
- genome wide identification
- mycobacterium tuberculosis
- anaerobic digestion
- diabetic rats
- single molecule
- fine needle aspiration
- molecular docking
- cell free
- drug induced
- quality improvement
- dna methylation
- transcription factor
- nucleic acid
- molecular dynamics simulations
- amino acid