Table 1.
Composition of the mock community used to spike the samples of cold smoked salmon and concentration of each microorganism. Each concentration corresponded to an expected relative abundance calculated by the number of cells of each spiked microorganism multiplied for the genome size, as indicated in the GeneBank (https://www.ncbi.nlm.nih.gov/assembly), taking the value available or the mean * of the different values available for the same strain. The relative abundances were obtained by normalizing the resulting values to a sum of one.
| Taxon (Genome Size) | Number per Subsample (Cells/Virus Genome Copies) | Expected Relative Abundance | Feature |
|---|---|---|---|
| Bacteria | |||
| Bacteroides fragilis NCTC 9343/DSM 2151 (5,241,700 bp) | 5 × 107 | 0.065 | Gram − |
| Escherichia coli ATCC 25922 (5,166,282 * bp) | 5 × 107 | 0.064 | Gram − |
| Fusobacterium nucleatum subsp. nucleatum ATCC 25586/DSM 15,643 (2,177,300 * bp) | 5 × 107 | 0.027 | Gram − |
| Propionibacterium freudenreichii subsp. Freudenreichii DSM 20271 (2,649,166 bp) | 5 × 108 | 0.331 | Gram + |
| Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028S/DSM 19587 (4,964,097 bp) | 5 × 107 | 0.062 | Gram − |
| Staphylococcus aureus subsp. aureus NCTC 8325 (2,821,361 bp) | 5 × 108 | 0.352 | Gram + |
| Viruses | |||
| Bovine alphaherpesvirus 1 (135,098 *) | 2.41 × 109 | <0.001 | ds DNA |
| Border disease virus isolate Gifhorn (12,325 bp) | 6 × 106 | <0.001 | ssRNA |
| Bovine viral diarrhea virus type 1 isolate NADL (12,578 bp) | 3 × 105 | <0.001 | ssRNA |
| Eukaryota | |||
| Cryptosporidium parvum IOWA II isolate (9,102,324 bp) | 1 × 106 | 0.002 | |
| Saccharomyces cerevisiae S288C (12,157,105 bp) | 5 × 106 | 0.015 |