TABLE 5.
Summary of the presence of a given species in the different sample categoriesa
| Identification | Presence (%)
|
||||
|---|---|---|---|---|---|
| Raw milk | Fodder | Green crop | Milking equipment | Overall | |
| Bacillus barbaricus | 1.2 | 0.3 | |||
| Bacillus cereus group | 2.3 | 0.6 | |||
| Bacillus circulans | 2.3 | 1.4 | 0.9 | ||
| Bacillus farraginisb | 8.6 | 16.3 | 2.9 | 6.9 | |
| Bacillus flexus | 1.2 | 0.3 | |||
| Bacillus fordiib | 1.2 | 2.0 | 5.8 | 2.2 | |
| Bacillus fortisb | 2.0 | 0.7 | 0.7 | ||
| Bacillus licheniformis | 22.3 | 5.5 | 9.3 | 11.6 | 12.2 |
| Bacillus oleronius | 1.2 | 4.3 | 1.4 | ||
| Bacillus pallidus | 15.1 | 15.2 | 11.6 | 22.5 | 16.1 |
| Bacillus smithii | 1.2 | 2.7 | 4.7 | 7.2 | 4.0 |
| Bacillus sphaericus | 0.7 | 0.2 | |||
| Bacillus sporothermodurans | 5.9 | 2.3 | 2.0 | ||
| Bacillus subtilis group | 1.2 | 25.4 | 4.7 | 2.9 | 8.5 |
| Bacillus thermoamylovorans | 0.4 | 4.7 | 2.9 | 2.0 | |
| Bacillus sp.c | 0.4 | 0.1 | |||
| Bacillus sp. nov. B | 3.0 | 3.9 | 1.7 | ||
| Bacillus sp. nov. C | 6.0 | 1.4 | 1.9 | ||
| Bacillus sp. nov. D | 0.6 | 1.2 | 0.4 | ||
| Bacillus sp. nov. E | 0.7 | 0.2 | |||
| Bacillus sp. nov. K | 4.7 | 1.2 | |||
| Aneurinibacillus aneurinilyticus | 0.4 | 1.4 | 0.5 | ||
| Aneurinibacillus thermoaerophilus | 1.2 | 2.0 | 0.8 | ||
| Brevibacillus agri | 4.8 | 2.0 | 11.6 | 7.2 | 6.4 |
| Brevibacillus borstelensis | 7.2 | 2.3 | 2.4 | ||
| Brevibacillus brevis | 0.7 | 0.2 | |||
| Brevibacillus spp. | 4.8 | 1.2 | 4.7 | 5.8 | 4.1 |
| Brevibacillus sp. nov. H | 2.7 | 0.7 | |||
| Geobacillus spp. | 5.9 | 11.6 | 4.4 | ||
| Paenibacillus lactisb | 4.2 | 2.9 | 1.8 | ||
| Paenibacillus thiaminolyticus | 2.2 | 0.5 | |||
| Paenibacillus sp.d | 2.9 | 0.7 | |||
| Paenibacillus sp. nov. G | 1.2 | 4.7 | 1.5 | ||
| Paenibacillus sp. nov. I | 1.4 | 0.4 | |||
| Paenibacillus sp. nov. J | 3.0 | 2.0 | 1.2 | ||
| Paenibacillus sp. nov. L | 0.6 | 0.2 | |||
| Paenibacillus sp. nov. M | 2.4 | 0.6 | |||
| Paenibacillus sp. nov. N | 0.4 | 0.1 | |||
| Virgibacillus proomii | 3.6 | 0.9 | |||
| Virgibacillus sp. nov. A | 0.8 | 0.2 | |||
| Virgibacillus sp. nov. F | 5.4 | 1.4 | |||
| Ureibacillus thermosphaericus | 6.6 | 0.7 | 1.8 | ||
| No identificatione | 4.2 | 3.9 | 4.7 | 9.4 | 5.5 |
All FAME, ARDRA, and 16S rRNA gene sequence data were considered.
P. lactis, B. farraginis, B. fortis, and B. fordii were described as new species following their isolation in this study (36, 38).
Strain R-6685 could not be attributed to the three new species B. farraginis, B. fortis, and B. fordii (38) and is therefore designated as Bacillus sp.
Four strains (R-6440, R-6441, R-6449, and R-6461) clustered together with P. lactis isolates in FAME but are reported as Paenibacillus sp. because a taxonomic study excluded them from P. lactis (36).
Strains which held a single position in the FAME clustering of a given sample category and were not further analyzed or strains which clustered together with B. sporothermodurans strains in FAME but reacted negatively in a PCR with the primers described by Scheldeman et al. (37).