Mock Community DNA Preparation

A single aliquot of the mock community was used throughout the sequencing effort analyzed in this study. This mock community represented 21 strains distributed among members of the Bacteria (n = 20) and Archaea (n = 1). Among the 20 bacterial sequences, there were 6 phyla, 10 classes, 12 orders, and 18 families and genera. The aliquot of mock community DNA was prepared by mixing genomic DNA from Acinetobacter baumanii (NC_009085), Actinomyces odontolyticus (DS264586), Bacillus cereus (AE017194), Bacteroides vulgatus (NC_009614), Clostridium beijerinckii (NC_009617), Deinococcus radiodurans (NC_001263), Enterococcus faecalis (NC_004668), Escherichia coli (NC_000913), Helicobacter pylori (NC_000915), Lactobacillus gasseri (NC_008530), Listeria monocytogenes (NC_003210), Neisseria meningitidis (NC_003112), Propionibacterium acnes (NC_006085), Pseudomonas aeruginosa (NC_002516), Rhodobacter sphaeroides (NC_007493, NC_007494), Staphylococcus aureus (NC_007793), Staphylococcus epidermidis (NC_004461), Streptococcus agalactiae (NC_004116), Streptococcus mutans (NC_004350), Streptococcus pneumoniae (NC_003028), and Methanobrevibacter smithii (NC_009515). Given the low homology between the three PCR primer pairs and the M. smithii 16S rRNA gene sequence, these sequences were rarely observed and have been omitted from the analysis of this study. The proportions of genomic DNAs added were calculated to have an equal number of 16S rRNA genes represented for each species; however, the original investigators did not verify the final relative abundances.

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Schloss P.D., Gevers D, & Westcott S.L. (2011). Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies. PLoS ONE, 6(12), e27310.

Publication 2011

16s rrna Acinetobacter Actinomyces odontolyticus Archaea Bacillus cereus Bacterial Bacteroides vulgatus Clostridium beijerinckii Deinococcus radiodurans Dnas Enterococcus faecalis Escherichia coli Gene Genomic Helicobacter pylori Lactobacillus gasseri Listeria monocytogenes Methanobrevibacter Neisseria meningitidis Primer Propionibacterium acnes Pseudomonas aeruginosa Rhodobacter sphaeroides Rrna genes Staphylococcus aureus Staphylococcus epidermidis Strains Streptococcus agalactiae Streptococcus mutans Streptococcus pneumoniae

Corresponding Organization :

Other organizations : University of Michigan–Ann Arbor, Michigan United, Broad Institute

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Variable analysis

independent variables

The aliquot of mock community DNA was prepared by mixing genomic DNA from 21 different strains (20 bacterial and 1 archaeal)

dependent variables

Not explicitly mentioned

control variables

A single aliquot of the mock community was used throughout the sequencing effort analyzed in this study
The proportions of genomic DNAs added were calculated to have an equal number of 16S rRNA genes represented for each species

controls

Positive control: The 21 strains of the mock community DNA, which was used as the input throughout the sequencing effort
Negative control: Not explicitly mentioned

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