Table 3.

Microbe detection frequencies and concentrations in digester influent and effluent samples. For detection frequencies, n refers to the number of samples. Unless otherwise noted, concentrations are the minimum, maximum, and geometric mean of detected concentrations (i.e., nondetects have been excluded).

Microbe†	Detection frequency (n)		Concentration
	Influent	Effluent	Influent	Effluent
	% (no.)		copies wet g−1
Bacteroidales‐like CowM3	100 (118)	95 (119)	3.1 × 104–1.4 × 109, 6.5 × 106	1.9 × 104–2.8 × 107, 1.3 × 106
Bovine Bacteroides	99 (118)	97 (119)	2.4 × 103–1.5 × 108, 3.0 × 106	2.6 × 103–7.0 × 106, 5.0 × 105
Bovine polyomavirus	99 (118)	100 (119)	7.3 × 103–3.0 × 108, 9.2 × 105	6.4 × 103–7.1 × 107, 2.8 × 105
Bovine enterovirus	92 (118)	14 (118)	1.1 × 104–1.0 × 107, 2.6 × 105	1.4 × 104–1.6 × 105, 4.4 × 104
Clostridium perfringens	69 (118)	19 (119)	6.0 × 102–2.4 × 106, 2.2 × 104	2.4 × 103–3.8 × 105, 2.9 × 104
Campylobacter jejuni	65 (118)	19 (118)	8.8 × 102–2.4 × 105, 1.0 × 104	9.1 × 102–2.7 × 104, 3.6 × 103
Bovine coronavirus	59 (118)	0 (116)	9.1 × 103–5.6 × 109, 3.8 × 105	Not detected
Group A rotavirus	50 (118)	17 (119)	2.8 × 103–8.1 × 107, 1.1 × 105	8.7 × 103–7.2 × 106, 1.0 × 105
Salmonella spp.	29 (118)	3 (77)‡	3.7 × 102–1.9 × 105, 6.3 × 103	3.1 × 103–1.8 × 104, 7.6 × 103
Bovine adenovirus	8 (118)	1 (77)‡	2.9 × 103–2.6 × 104, 5.0 × 103	3.2 × 103 (n = 1)
Enterohemorrhagic Escherichia coli	4 (118)	0 (56)‡	1.4 × 103–8.5 × 104, 8.2 × 103	Not detected
Cryptosporidium parvum	0.8 (118)	0 (35)‡	4.4 × 103 (n = 1)	Not detected
Giardia lamblia	0.8 (118)	0 (35)‡	1.3 × 104 (n = 1)	Not detected

^†Group C rotavirus, bovine viral diarrhea virus 1 (BVDV1), bovine viral diarrhea virus 2 (BVDV2), Mycobacterium avium subsp. paratuberculosis, Staphylococcus spp., and Streptococcus spp. were never detected.

^‡Because these organisms were rare in influent, fewer effluent samples were analyzed for them.