Fig. 2: Limit of detection, sample exclusion, and microbial biomass estimation for FMP101 dataset.

a Application of KatharoSeq formula to calculate limit of detection of microbiota plates using the Bacillus/Paracoccus mock community (1150 reads at 90%). b Limit of detection based on cell counts of Bacillus/Paracoccus mock community (~16 cells into extraction at 90%). c Model fit of the log(sequencing read counts) of positive extraction controls vs. the log cell counts of those positive extraction controls (empirically determined using plate counts. The linear regression of the line is indicative of the quality of method to estimate microbial biomass from sequencing read counts. Confidence intervals of 95% are displayed as dotted lines. This method is similar to a qPCR curve where the log (Ct) would be equivalent to the log(read counts). This equation is then used to estimate the number of “microbial density” of the existing samples which is then further normalized by the volume of the DNA extraction, biomass of material going into the extraction and finally normalized to at estimated microbial cells per gram of tissue. d Community analysis comparison and validation of compositionality of controls of two sets of mock community controls (section 1 = Bacillus/Paracoccus mock community; section 2 = zymo mock community). Putative contaminant g__Geobacillus identified (present in 93% of negatives and higher relative abundance as compared to positives and samples). e Number of samples successful across the four body sites collected from the broad fish microbiota dataset. QC quality control, g__ refers to a genus of bacteria, HM mock homemade mock or human made mixture of bacteria to use as a control whereas zymo mock = mock microbial community created by a company “Zymo”.