The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons
Table 4
Effect of extraction procedure and primer set on the relative distribution of main bacterial genera1 (>0.1% of total sequence reads) [% sequence reads].
Extraction
Primer set
Lactobacillus
Weissella
Leuconostoc
Streptococcus
Lactococcus
Aerococcus
I
8f-534r
70.4 (±7.8)
0.36 (±0.18)
n.d.
5.1 (±1.2)
0.31 (±0.14)
0.93 (±0.63)
968f-1401r
33.3 (±6.4)
3.0 (±1.1)
0.89 (±0.31)
5.3 (±1.7)
0.43
1.0 (±0.5)
II
8f-534r
59.1 (±8.7)
19.3 (±5.0)
4.6 (±1.1)
5.8 (±2.8)
1.9 (±0.5)
0.17
968f-1401r
14.2 (±5.5)
47.6 (±6.3)
18.8 (±2.8)
1.0 (±0.3)
0.34 (±0.06)
0.21 (±0.03)
Extraction
Primer set
Enterococcus
Sarcina
Clostridium
Lachnospira
Faecalibacterium
Veillonella
I
8f-534r
1.2 (±0.8)
13.9 (±7.4)
0.59 (±0.15)
0.72 (±0.16)
0.93
1.1 (±0.6)
968f-1401r
0.54
33.6 (±9.8)
1.7 (±0.5)
n.d.
n.d.
0.51 (±0.13)
II
8f-534r
0.28 (±0.05)
6.9 (±5.5)
0.25 (±0.07)
n.d.
n.d.
0.44 (±0.22)
968f-1401r
0.28
15.3 (±7.8)
0.51 (±0.14)
n.d.
n.d.
0.41 (±0.27)
Extraction
Primer set
Eubacterium
Peptostreptococcu
Ruminococcus
Dorea
Megasphaera
Klebsiella
I
8f-534r
0.20
0.31
0.43 (±0.24)
n.d.
1.1
11.0 (±10.3)
968f-1401r
1.8 (±1.2)
1.1 (±0.8)
n.d.
2.0 (±0.9)
n.d.
10.9 (±9.9)
II
8f-534r
n.d.
0.36 (±0.005)
n.d.
n.d.
n.d.
0.15 (±0.02)
968f-1401r
0.13 (±0.01)
0.72 (±0.21)
n.d.
n.d.
n.d.
0.14
Extraction
Primer set
Salmonella
Escherichia
Citrobacter
Enterobacter
Pantoea
Microbacterium
I
8f-534r
n.d.
0.47 (±0.22)
n.d.
n.d.
n.d.
1.2 (±0.3)
968f-1401r
0.19
0.93 (±0.80)
n.d.
0.51 (±0.28)
0.39 (±0.04)
10.3 (±3.2)
II
8f-534r
7.0 (±5.5)
0.15
0.26 (±0.14)
0.22
n.d.
0.17 (±0.03)
968f-1401r
n.d.
n.d.
0.31 (±0.05)
0.17
n.d.
1.0 (±0.2)
Extraction
Primer set
Actinomyces
Rhodococcus
Bacillus
Staphylococcus
Macrococcus
Kurthia
I
8f-534r
0.80 (±0.23)
0.63 (±0.18)
0.50 (±0.14)
0.25 (±0.06)
0.23 (±0.07)
0.31 (±0.06)
968f-1401r
0.31 (±0.09)
0.20
0.30 (±0.04)
2.7 (±1.1)
0.2 (±0.003)
n.d.
II
8f-534r
0.26 (±0.07)
0.14 (±0.03)
0.42 (±0.13)
n.d.
n.d.
n.d.
968f-1401r
0.33 (±0.18)
n.d.
0.13
0.17 (±0.02)
0.10
n.d.
n.d.: not detected.
1Different superscripts within a row are significantly different (; Tamhane Test).
