TABLE 2.
Occurrence of TRFs associated with E. coli O157:H7 suppression across all three experiments (August 2008, November 2008, and March 2009)a
| Parameter | Result for the following TRFs generated by MspI digestion of amplified 16S sequencesb |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| M89 | M96 | M99 | M118 | M142 | M156 | M202 | M299 | M488 | M492 | M508 | |
| Sum parameter A + parameter Bc | 6 | 5 | 5 | 8 | 7 | 6 | 5 | 9 | 5 | 5 | 5 |
| Sample timed | |||||||||||
| Early | 3 | 2, 3 | 2, 3 | 2 | 3 | 3 | 2, 3 | 1, 2, 3 | 3 | 2, 3 | |
| Late | 2 | 2 | 2 | 2 | 1, 2, 3 | 1, 2 | 2, 3 | 2 | 2, 3 | 1, 3 | |
| Abundance in bedding source: | |||||||||||
| 4 > 1, 2, 3e | 3 | 2 | 2 | 2, 3 | |||||||
| 3 > 1, 2, 4f | 2 | 2 | |||||||||
Livestock bedding samples from four distinct sources (fresh, in use, washed, recycled) were split into one nonheated (NH) and one heated (HT) sample, TRFs were recorded for higher fluorescence in nonheated than heat-treated samples (parameter A) and negative regression of the surviving numbers of CFU of E. coli O157:H7 over fluorescence strength or between nonheated samples of different levels of suppressiveness (parameter B).
TRFs of <300 nt were at an accuracy of ±1 nt; TRFs of >300 nt were binned at ±2 nt.
Frequency of occurrence of TRFs with both parameters A and B fulfilled in a total of 37 contexts.
Sampling times: early, 1 dpi; late, 15 dpi (experiment 1), 7 dpi (experiment 2), or 10 dpi (experiment 3). The numbers in the table body indicate the experiment(s) in which the TRFs were detected.
These comparisons among nonheated bedding samples 1 through 4 were conducted only in experiments 2 and 3; in experiment 1, the samples from the recycled source did not have significantly more CFU than those from the fresh source. The numbers in the table indicate the experiment(s) in which the TRFs were detected.
These comparisons among nonheated bedding samples 1 through 4 were conducted only in experiments 2 and 3. In experiment 2, samples from the washed source (bedding 3) did not have significantly fewer CFU of E. coli O157:H7 than those from the recycled bedding source 4. Also, in experiment 3, samples from the washed source (bedding 3) did not have significantly fewer CFU of E. coli O157:H7 than those from the in-use bedding source 2. The numbers in the table indicate the experiment(s) in which the noted TRFs were detected.