The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons
Table 5
Effect of extraction procedure and primer set on the comparative diversity indices of main bacterial genera in the ileum of pigs fed 200 mg g−1 or 3000 mg g−1 dietary ZnO1 (>0.1% of total sequence reads) ( per experimental group).
Extraction
Primer set
Database
Richness
Shannon
Evenness
200 mg g−1
3000 mg g−1
200 mg g−1
3000 mg g−1
200 mg g−1
3000 mg g−1
Procedure I
16.3 (±10.6)
19.9 (±9.9)
0.886 (±0.546)
1.241 (±0.602)
0.329 (±0.164)
0.424 (±0.148)
Procedure II
18.5 (±7.6)
27.1 (±11.0)
0.965 (±0.379)
1.144 (±0.351)
0.340 (±0.138)
0.353 (±0.095)
8f-534r
20.4 (±10.2)
23.0 (±13.5)
0.782 (±0.504)
1.019 (±0.443)
0.255 (±0.137)
0.343 (±0.106)
968f-1401r
14.5 (±7.1)
24.0 (±7.9)
1.068 (±0.386)
1.366 (±0.481)
0.414 (±0.120)
0.434 (±0.134)
Procedure I
8f-534r
18.6 (±11.4)
15.3 (±9.1)
0.750 (±0.578)
0.973 (±0.441)
0.250 (±0.150)
0.376 (±0.094)
968f-1401r
14.1 (±9.5)
24.6 (±8.7)
1.021 (±0.491)
1.508 (±0.632)
0.408 (±0.140)
0.472 (±0.177)
Procedure II
8f-534r
22.2 (±8.9)
30.8 (±12.9)
0.814 (±0.433)
1.064 (±0.452)
0.260 (±0.127)
0.309 (±0.109)
968f-1401r
14.8 (±3.5)
23.4 (±7.3)
1.115 (±0.247)
1.224 (±0.188)
0.420 (±0.098)
0.396 (±0.053)
Different superscripts within a row (highlighted in bold) are significantly different for the respective diversity index (; pairwise Mann-Whitney- Test).
