Table 2. Relation between the percentages of 16S rRNA gene sequences obtained using the four different DNA extraction methods and the mixes P1, P2 and P3.
| MIX | Species | Cellnumber | % eachstrain | 16S copynumber | relative abundance not normalized | relative abundance normalized | ||||||
| P1 | MBio | MBioEz | Qia | QiaEz | MBio | MBioEz | Qia | QiaEz | ||||
| B. longum | 3,84E+09 | 10,71 | 4 | 2,99 | 57,36 | 3,39 | 23,47 | 1,07 | 43,68 | 1,35 | 20,54 | |
| B. coccoides+B. producta | 7,68E+09 | 21,42 | 1+ | 1,61 | 1 | 3,5 | 0,58 | 2,30 | 3,05 | 5,59 | 2,03 | |
| C. intestinalis | 3,84E+09 | 10,71 | 2* | 31,58 | 18,47 | 18,75 | 17,58 | 22,57 | 28,13 | 14,98 | 30,78 | |
| F. prausnitzii | 3,84E+09 | 10,71 | 1 | 47,14 | 4,62 | 42,04 | 3,61 | 67,38 | 14,07 | 67,19 | 12,64 | |
| E. coli | 3,84E+09 | 10,71 | 7 | 2,32 | 1,53 | 6,6 | 24,4 | 0,47 | 0,67 | 1,51 | 12,21 | |
| K. pneumoniae | 3,84E+09 | 10,71 | 8 | 3,45 | 2,6 | 11,37 | 4,18 | 0,62 | 0,99 | 2,27 | 1,83 | |
| P. copri | 3,84E+09 | 10,71 | 1* | 2,23 | 0,41 | 2,09 | 0,58 | 3,19 | 1,25 | 3,34 | 2,03 | |
| B. thetaiotaomicron | 3,84E+09 | 10,71 | 5 | 8,38 | 13,2 | 11,74 | 25,47 | 2,40 | 8,04 | 3,75 | 17,84 | |
| M. smithii | 1,30E+09 | 3,63 | 2 | 0,01 | 0,08 | 0 | 0,06 | 0,01 | 0,12 | 0,00 | 0,11 | |
| P2 | ||||||||||||
| B. longum | 3,84E+09 | 18,59 | 4 | 5,64 | 18,59 | 3,52 | 2,15 | 1,72 | 7,21 | 1,11 | 0,69 | |
| B. coccoides+B. producta | 7,68E+09 | 37,18 | 1+ | 2,86 | 2,43 | 9,06 | 6,35 | 3,49 | 3,77 | 11,42 | 8,17 | |
| C. intestinalis | 3,84E+09 | 18,59 | 2* | 27,11 | 33,14 | 32,12 | 35,76 | 16,56 | 25,72 | 20,25 | 23,01 | |
| F. prausnitzii | 3,84E+09 | 18,59 | 1 | 63,94 | 39,88 | 52,87 | 52,33 | 78,12 | 61,90 | 66,66 | 67,35 | |
| E. coli | 3,84E+07 | 0,19 | 7 | 0,08 | 3,21 | 0,63 | 0,8 | 0,01 | 0,71 | 0,11 | 0,15 | |
| K. pneumoniae | 3,84E+07 | 0,19 | 8 | 0,05 | 1,26 | 0,82 | 1,2 | 0,01 | 0,24 | 0,13 | 0,19 | |
| P. copri | 3,84E+07 | 0,19 | 1* | 0,03 | 0,12 | 0,1 | 0,17 | 0,04 | 0,19 | 0,13 | 0,22 | |
| B. thetaiotaomicron | 3,84E+07 | 0,19 | 5 | 0,19 | 0,84 | 0,75 | 0,86 | 0,05 | 0,26 | 0,19 | 0,22 | |
| M. smithii | 1,30E+09 | 6,29 | 2 | 0 | 0 | 0 | 0 | 0,00 | 0,00 | 0,00 | 0,00 | |
| P3 | ||||||||||||
| B. longum | 3,84E+07 | 0,23 | 4 | 0,1 | 0,2 | 0,05 | 0,29 | 0,09 | 0,26 | 0,05 | 0,42 | |
| B. coccoides+B. producta | 7,68E+07 | 0,46 | 1+ | 0 | 0 | 0,02 | 0,02 | 0,00 | 0,00 | 0,09 | 0,12 | |
| C. intestinalis | 3,84E+07 | 0,23 | 2* | 0,32 | 0,33 | 0,14 | 0,2 | 0,57 | 0,86 | 0,31 | 0,58 | |
| F. prausnitzii | 3,84E+07 | 0,23 | 1 | 0,35 | 0 | 0,29 | 0,08 | 1,24 | 0,00 | 1,27 | 0,47 | |
| E. coli | 3,84E+09 | 22,79 | 7 | 14,06 | 14,33 | 24,5 | 48,13 | 7,10 | 10,67 | 15,28 | 40,15 | |
| K. pneumoniae | 3,84E+09 | 22,79 | 8 | 27,77 | 17,97 | 36,86 | 9,24 | 12,28 | 11,70 | 20,12 | 6,74 | |
| P. copri | 3,84E+09 | 22,79 | 1* | 13,86 | 1,53 | 8,75 | 0,48 | 49,01 | 7,97 | 38,21 | 2,80 | |
| B. thetaiotaomicron | 3,84E+09 | 22,79 | 5 | 42,02 | 65,4 | 28,26 | 41,46 | 29,72 | 68,15 | 24,68 | 48,42 | |
| M. smithii | 1,30E+09 | 7,71 | 2 | 0 | 0,15 | 0 | 0,1 | 0,00 | 0,39 | 0,00 | 0,29 | |
The sequence of B. coccoides and B. producta were indistinguishable and were included in the same group.
*
Means that only draft genomes are available, thus the 16S copy number is probably underestimated.
+ Means that no sequenced genomes are available, thus the genera average 16S copy number was used.
The normalized relative abundance was calculated by division of the relative abundances of every species by their predicted 16S copy number. Results of each sample were normalized so that their sum is 100%.