Table 4.

Number of raw reads per sample and the percentage of reads that can be assigned to a specific higher taxonomic group of microorganisms.

Sampling Site	Sample Type	Number of Raw Reads	Microbial Reads (%)	Bacterial Reads (%)	Viral Reads (%)	Fungal Reads (%)	Protozoan Reads (%)
Jedilnica before therapy	Nitrocellulose filter	5,978,569	80.2	75.9	0.00095	0.00184	0.00314
Jedilnica before therapy	Collection liquid	6,950,426	36.7	31.2	0.00099	0.00302	0.00119
Jedilnica before therapy	Collection liquid duplicate	4,666,878	86.9	85.3	0.00024	0.30500	0.10400
Jedilnica after therapy	Nitrocellulose filter	2,323,706	84.2	79.9	0.00039	0.00435	0.00409
Jedilnica after therapy	Collection liquid	6,293,127	8.35	0.8	3.3	0.00663	0.00923
Jedilnica after therapy	Collection liquid duplicate	13,148,700	71.7	17.3	50.7	0.42200	0.00294
Spalnica before therapy	Nitrocellulose filter	5,665,593	94.7	94.3	0.00005	0.04660	0.00007
Spalnica before therapy	Collection liquid	4,509,290	17.5	14.0	0.01510	0.03830	0.01590
Spalnica before therapy	Collection liquid duplicate	27,049,966	41.9	36.2	0.01910	0.46200	0.02200
Spalnica after therapy	Nitrocellulose filter	5,707,536	83.4	72.5	7.7	1.1	0.00137
Spalnica after therapy	Collection liquid	3,274,666	50.9	0.09	45.8	0.00083	0.00018
Spalnica after therapy	Collection liquid duplicate	6,049,608	54.2	28.7	25.0	0.02690	0.00063
Telovadnica before therapy	Nitrocellulose filter	7,298,271	80.4	78.9	0.00058	0.00174	0.0037
Telovadnica before therapy	Collection liquid	117,357	27.7	26.7	0.00682	0.08180	0.00170
Telovadnica before therapy	Collection liquid duplicate	8,019,772	71.3	68.2	0.03170	0.03250	0.00168
Telovadnica after therapy	Nitrocellulose filter	8,963,828	76.0	31.5	39.9	0.02200	0.00167
Telovadnica after therapy	Collection liquid	8,976,140	4.07	0.771	2.5	0.00136	0.00031
Telovadnica after therapy	Collection liquid duplicate	8,947,973	52.1	51.2	0.00834	0.1	0.00750