Table 3.
List of pathogens identified in SPF and non-SPF mice
| Superkingdom | Species ID | Species | Number positive mice (non-SPF set A) | Number positive mice (non-SPF set B) | Number positive mice (non-SPF total) | Number positive mice (SPF total) |
|---|---|---|---|---|---|---|
| Bacteria | 32025 | Helicobacter hepaticus | 27 | 15 | 42 | 0 |
| Bacteria | 76936 | Helicobacter typhlonius | 27 | 15 | 42 | 0 |
| Endo- and ectoparasites | 545931 | Entamoeba muris | 6 | 6 | 12 | 0 |
| Endo- and ectoparasites | 5726 | Tritrichomonas muris | 4 | 12 | 16 | 0 |
| Virus | 28875 | Murine Norovirus | 1 | 0 | 1 | 0 |
| Bacteria | 83560 | Chlamydia muridarum | 0 | 5 | 5 | 0 |
| Bacteria | 1280 | Staphylococcus aureus | 0 | 2 | 2 | 0 |
| Bacteria | 1314 | Streptococcus pyogenes | 0 | 4 | 4 | 0 |
| Bacteria | 758 | Pasteurella pneumotropica | 0 | 7 | 7 | 0 |
| Bacteria | 67825 | Citrobacter rodentium | 0 | 1 | 1 | 0 |
| endo- and ectoparasites | 1046713 | Myocoptes musculinus | 0 | 7 | 7 | 0 |
| endo- and ectoparasites | 39710 | Spironucleus muris | 0 | 2 | 2 | 0 |
| pinworm nematode | 451377 | Aspiculuris tetraptera | 0 | 4 | 4 | 0 |
| pinworm nematode | 412127 | Syphacia obvelata | 0 | 1 | 1 | 0 |
List of the pathogenic species identified by mNGS and number of positive mice for each species. Each different line represents one pathogen species identified in the course of the study. For each species there are columns that describe a short taxonomy (superkingdom, species ID, species); the last four columns indicate the number of non-SPF mice of set A (non-SPF set A), non SPF-mice of set B (non-SPF set B) non-SPF mice all sets (non-SPF total), which were found positive for at least one pathogen. No pathogens were detected in SPF mice (SPF total). All data were confirmed by PCR and sequencing