Table 3.

Gene markers of fecal-associated microbes detected in samples ($n=138$) from private household wells ($n=131$).

Host specificity	Microbea	Gene markerb	Number of positive wellsc	Number of positive samplesc	Concentration of positive samples (gene copies/L)
					Median	Range
Human-specific	Bacteroidales-like Hum M2	Glycosyl hydrolase family 92	7	8	4	$<1–\mathrm{1,050}$
	Human Bacteroides	16s rRNA (HF183/BacR287)	27	28	$<1$	$<1–34$
	Cryptosporidium hominis	18s rRNA	1	1	$<1$	$<1$
	Adenovirus A	hexon	1	1	1	1
	Rotavirus group A, G1 P[8]	NSP3	7	7	$<1$	$<1–3$
	Rotavirus group A, G1 P[8]	VP1	3	3	1	$<1–22$
	Any human marker	—	33	34	$<1$	$<1–\mathrm{1,050}$
Bovine- or ruminant-specific	Bacteroidales-like Cow M2	DHIG domain protein	2	2	472	29–915
	Bacteroidales-like Cow M3	HD super family hydrolase	4	4	174	3–49,818
	Ruminant Bacteroides	16s rRNA (Rum-2-Bac)	36	36	1	$<1–\mathrm{42,398}$
	Bovine polyomavirus	VP1	8	8	4	$<1–451$
	Bovine enterovirus	5’ non-coding region	1	1	2	2
	Rotavirus group A, G10 P[11]	NSP3	12	12	12	2–4,481
	Rotavirus group A, G10 P[11]	VP1	5	5	23	$<1–732$
	Any bovine or ruminant marker	—	44	44	3	$<1–\mathrm{49,818}$
No host specificity	Pepper mild mottle virus	replication-associated protein	13	14	14	2–3,811
	Cryptosporidium spp.	18s rRNA	2	2	$<1$	$<1–1$
	Cryptosporidium parvum	18s rRNA	13	13	$<1$	$<1-14$
	Giardia duodenalis group B	$\mathrm{\beta }\text{-}giardin$	2	2	$<1$	$<1$
	Campylobacter jejuni	mapA	1	1	$<1$	$<1$
	Salmonella spp.	invA	3	3	6	$<1–13$
	Salmonella spp.	ttr	5	5	10	5–59
	E. coli (pathogenic)	eae	1	1	4	4
	Shiga toxin producing bacteria	stx1	1	1	16	16
	Shiga toxin producing bacteria	stx2	1	1	1	1
	Rotavirus group C	VP6	3	3	50	45–1,301
	Any nonspecific marker	—	37	46	5	$<1–\mathrm{3,811}$
All	Any fecal marker	—	79	82	2	$<1–\mathrm{49,818}$

Note: —, Any of the gene markers within the specified group.

^aMicrobial markers analyzed but not detected: human adenovirus groups B, C, D, and F; human enterovirus; human norovirus genogroups I and II; human polyomavirus; Cryptosporidium bovis; bovine adenovirus; bovine coronavirus; and bovine viral diarrhea virus types 1 and 2.

^bPrimers, probes, and references for qPCR assays are reported in Table S1.

^cTotals are less than the sum of individual markers because some wells and samples were positive for more than one marker.