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Table 2 Extraction and sequencing controls included in this study

From: Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

Control typeControl subtypeControl nameCompositionSourceDNA extraction performed in our laboratoryDNA extraction kitExtraction replicatesSequencing replicatesTotal included for equencing
Extraction controlsBacterial mock communitiesZymobiomics-Primestore-high900 μl of Zymobiomics-Cells suspended in 3600 μl PrimestoreZymo Research Corp., Irvine, CA, United States
&
Longhorn Vaccines & Diagnostics, Bethesda, MD, USA
Kit-QS
Kit-ZB
3 per DNA extraction kit6
  Zymobiomics-STGG-high900 μl of Zymobiomics-Cells suspended in 3600 μl STGGZymo Research Corp., Irvine, CA, United States & National Health Laboratory Services, Cape Town, South AfricaKit-QS
Kit-ZB
3 per DNA extraction kit6
  Zymobiomics-Primestore-low1-in-104 fold dilution of Zymobiomics-Primestore-highZymo Research Corp., Irvine, CA, United States & Longhorn Vaccines & Diagnostics, Bethesda, MD, USAKit-QS
Kit-ZB
3 per DNA extraction kit6
  Zymobiomics-STGG-low1-in-104 fold dilution of Zymobiomics-STGG-highZymo Research Corp., Irvine, CA, United States & National Health Laboratory Services, Cape Town, South AfricaKit-QS
Kit-ZB
3 per DNA extraction kit6
 NTCsPrimestoreStorage buffer PrimestoreLonghorn Vaccines & Diagnostics, Bethesda, MD, USAKit-QS
Kit-ZB
3 per DNA extraction kit6
  STGGStorage buffer STGGNational Health Laboratory Services, Cape Town, South AfricaKit-QS
Kit-ZB
3 per DNA extraction kit6
Sequencing controlsBacterial mock community DNABEI-DNA1-in-10 fold dilution of HM-783D in Milli-Q® ultrapure waterBEI Resources, NIAID, NIH as part of the Human Microbiome Project, Manassas, VA, USA & MilliporeSigma, Burlington, MA, USAxNot specified3
  Zymobiomics-DNA1-in-10 fold dilution of ZymoBIOMICS™ Microbial Community DNA Standard in Milli-Q® ultrapure waterZymo Research Corp., Irvine, CA, United States & MilliporeSigma, Burlington, MA, USAxNot specified8
 Technical repeatsWithin-run repeatsNP and IS specimens stored in PrimestoreCollected from infants enrolled in the DCHS [26]Kit-QS2 per specimen86
  Between-run repeatsNP and IS specimens stored in PrimestoreCollected from infants enrolled in the DCHS [26]Kit-QS2, 3 or 4 per specimen123
 NTCsPrimestoreStorage buffer PrimestoreLonghorn Vaccines & Diagnostics, Bethesda, MD, USAKit-QS35
  1. Zymobiomics-Cells ZymoBIOMICS™ Microbial Community Standard bacterial cells (Catalog No. D6300, Zymo Research Corp., Irvine, CA, United States), Kit-QS DSP Virus/Pathogen Mini Kit® using QIAsymphony® SP instrument (catalogue no. 937036, Qiagen GmbH, Hilden, Germany), Kit-ZB ZymoBIOMICS DNA Miniprep Kit (catalogue no. ZR D4300, Zymo Research Corp., Irvine, CA, United States), NTCs No template controls, Primestore PrimeStore® Molecular Transport medium (Longhorn Vaccines & Diagnostics Bethesda, MD, USA), STGG transport medium containing Skim-milk, Tryptone, Glucose and Glycerol, NP Nasopharyngeal swabs IS Induced sputum, DCHS Drakenstein Child Health Study