TABLE 3.

Results from Bifidobacterium species-specific PCR assays using different animal fecal DNA extracts

Animal type (n)aNo. of samples detected with Bifidobacterium sp.- and group-specific primerb
BiADOBiANGBiBIFBiBREBiCATBiDENBiGALBiINFBiLON
Alpaca (2)1--------
Beef cattle (14)----11---
Canadian goose (20)----22---
Chicken (29)1-22--3--
Coyote (11)1---11---
Dairy cattle (14)4--1281--
Deer (17)1---222--
Domestic cat (10)--2-5----
Domestic dog (15)--1-2----
Goat (4)----22---
Guinea pig (1)-----1---
Hog, feral (1)-----1---
Horse (16)----234--
Human (19)7-4-41--1
Pig (43)13112222015722
Pigeon (4)--1------
Possum (2)-----1---
Prairie dog (2)-----1---
Rabbit (4)-121111--
Septic (9)113-111--
Sheep (8)31--252-2
Squirrel (4)-----1---
Turkey (10)-1-------
  • a n, number of fecal samples tested for that animal type. The results do not include assays against armadillo (n = 1), bobcat (n = 1), dove (n = 1), ferret (n = 1), fox (n = 1), hedgehog (n = 1), llama (n = 1), peacock (n = 1), raccoon (n = 1), and vulture (n = 1) fecal DNA extracts produced since these did not produce PCR signals with any of the species-specific assays.

  • b BiADO, BiANG, BiBIF, BiBRE, BiCAT, BiDEN, BiGAL, BiINF, and BiLON refer to PCR assays targeting B. adolescentis, B. angulatum, B. bifidum, B. breve, B. catenulatum group, B. dentium, B. gallicum, B. infantis, and B. longum, respectively. -, no amplification product was visualized for any of the samples from a given animal type using that primer. The total numbers of amplification products for all 269 fecal samples using the indicated group- or genus-specific marker were as follows (percent positive): BiADO, 32 (11.9%); BiANG, 15 (5.6%); BiBIF, 37 (13.8%); BiBRE, 6 (2.2%); BiCAT, 47 (17.4%); BiDEN, 47 (17.4%); BiGAL, 21 (7.8%); BiINF, 2 (0.74%); and BiLON, 5 (1.9%).