A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing

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)
Bacteria	32025	Helicobacter hepaticus	27	15	42
Bacteria	76936	Helicobacter typhlonius	27	15	42
Endo- and ectoparasites	545931	Entamoeba muris	6	6	12
Endo- and ectoparasites	5726	Tritrichomonas muris	4	12	16
Virus	28875	Murine Norovirus	1	0	1
Bacteria	83560	Chlamydia muridarum	0	5	5
Bacteria	1280	Staphylococcus aureus	0	2	2
Bacteria	1314	Streptococcus pyogenes	0	4	4
Bacteria	758	Pasteurella pneumotropica	0	7	7
Bacteria	67825	Citrobacter rodentium	0	1	1
endo- and ectoparasites	1046713	Myocoptes musculinus	0	7	7
endo- and ectoparasites	39710	Spironucleus muris	0	2	2
pinworm nematode	451377	Aspiculuris tetraptera	0	4	4
pinworm nematode	412127	Syphacia obvelata	0	1	1

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

ISSN: 2524-4671