TABLE 1

Impact of contamination (well to well and background) on NTC, low-biomass, and high-biomass sample typesa

Sample type
(no. of samples)b
LocationcExtraction
methodd
Well to wellBackground kit
composition (%)
Mean
prevalence
(%)e
RichnessComposition (%)MeanMedianMax
Avg no. of
total unique
reads
W2W%fMeanMedianMax
NTC
    61UCSDm_tube47.54204.124.640.0056.0095.36100.0100.0
    32Argonnem_tube53.131651.560.850.038.2399.1599.97100.0
    28Argonnem_plate10.7184.233.140.0075.1796.86100.0100.0
    116UCSDRobot95.691527.7963.7974.78100.036.2125.22100.0
Sink
    93UCSDm_tube15.05200.960.050.002.783.351.6898.73
    48Argonnem_tube50.001891.672.310.0059.3478.0883.8298.78
    46Argonnem_plate32.61166.6113.990.0098.7158.4662.67100.0
    187UCSDRobot67.381512.700.700.0815.610.930.2540.51
Source
    31UCSDm_tube61.29186.510.130.012.998.300.29100.0
    16Argonnem_tube87.502113.780.020.020.0711.540.4199.98
    16Argonnem_plate81.251716.792.370.0136.4013.130.3299.99
    64UCSDRobot70.311213.760.940.0450.677.320.16100.0
  • a Composition refers to the mean, median, or maximum frequency of sOTU contaminants that are due to well-to-well contamination or background kits.

  • b Refers to the total samples or well which had enough sequencing data for analysis.

  • c Location refers to the two laboratories which processed samples, either UCSD or Argonne.

  • d m_, manual (non-robotic-based extraction); Robot, robot-based DNA cleanup.

  • e Prevalence is calculated as the number of samples with any well-to-well contamination/total number of samples.

  • f W2W% is the percentage of total richness that is a result of well-to-well events, calculated as the number of unique well-to-well contaminants/total number of sOTUs (mean).