Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia, The female urinary microbiota in relation to the reproductive tract microbiota, Gigabyte, 2020 https://doi.org/10.46471/gigabyte.9
Sample name | Sequencing amount | % of reads annotated to taxa | Archive accession number | |||
---|---|---|---|---|---|---|
#raw reads | #clean reads | #filtered reads | Genus | Species | ||
C001UR | 52506 | 11326 | 9347 | 100.00% | 75.51% | SAMEA5042945 |
C002UR | 55955 | 14529 | 5930 | 100.00% | 65.36% | SAMEA5042987 |
C003UR | 61367 | 21181 | 16831 | 100.00% | 91.06% | SAMEA5043040 |
C004UR | 54585 | 18506 | 3325 | 100.00% | 41.59% | SAMEA5042979 |
C005UR | 52177 | 22856 | 20683 | 100.00% | 92.62% | SAMEA5043003 |
C007UR | 50766 | 15468 | 8737 | 100.00% | 71.10% | SAMEA5043001 |
C008UR | 53748 | 14062 | 6169 | 100.00% | 64.05% | SAMEA5043004 |
C009UR | 53383 | 12247 | 11327 | 100.00% | 96.97% | SAMEA5043046 |
C011UR | 47814 | 13058 | 11292 | 100.00% | 66.76% | SAMEA5042941 |
C012UR | 55279 | 16923 | 7484 | 100.00% | 55.46% | SAMEA5042938 |
C014UR | 55713 | 15175 | 8818 | 100.00% | 64.31% | SAMEA5043060 |
C016UR | 73372 | 22054 | 17669 | 100.00% | 57.04% | SAMEA5043009 |
C018UR | 69142 | 26505 | 23581 | 100.00% | 12.12% | SAMEA5043006 |
C019UR | 72249 | 17868 | 14440 | 100.00% | 44.63% | SAMEA5043054 |
C020UR | 54574 | 19391 | 5452 | 100.00% | 63.83% | SAMEA5042942 |
C021UR | 58118 | 17294 | 12123 | 100.00% | 55.33% | SAMEA5042998 |
C023UR | 47476 | 18452 | 16795 | 100.00% | 16.09% | SAMEA5042947 |
C026UR | 46583 | 16741 | 3267 | 100.00% | 83.96% | SAMEA5042969 |
C028UR | 88245 | 26955 | 19268 | 100.00% | 19.93% | SAMEA5042984 |
C033UR | 90431 | 31998 | 26496 | 100.00% | 66.99% | SAMEA5043062 |
C035UR | 63773 | 27044 | 24115 | 100.00% | 97.31% | SAMEA5043037 |
C038UR | 55562 | 10165 | 9208 | 100.00% | 84.56% | SAMEA5042972 |
C039UR | 77957 | 18891 | 15748 | 100.00% | 33.38% | SAMEA5042963 |
C040UR | 58940 | 12555 | 5438 | 100.00% | 69.49% | SAMEA5043021 |
C041UR | 60028 | 15361 | 9366 | 100.00% | 78.38% | SAMEA5043000 |
C042UR | 74086 | 14402 | 11088 | 100.00% | 67.53% | SAMEA5042955 |
C043UR | 74146 | 23691 | 18730 | 100.00% | 60.19% | SAMEA5043032 |
C045UR | 61249 | 17801 | 10367 | 100.00% | 2.96% | SAMEA5043048 |
C047UR | 47742 | 11940 | 3506 | 100.00% | 54.25% | SAMEA5043024 |
C048UR | 35550 | 1100 | 816 | 100.00% | 62.75% | SAMEA5042931 |
C050UR | 51565 | 18902 | 290 | 100.00% | 72.76% | SAMEA5042936 |
C051UR | 58783 | 10403 | 8234 | 100.00% | 50.77% | SAMEA5042983 |
C053UR | 32311 | 1653 | 26 | 100.00% | 73.08% | SAMEA5043035 |
C055UR | 45054 | 13326 | 6184 | 100.00% | 56.40% | SAMEA5043016 |
C056UR | 69173 | 24652 | 8282 | 100.00% | 86.78% | SAMEA5043023 |
C057UR | 64417 | 27033 | 24444 | 100.00% | 98.11% | SAMEA5043059 |
C058UR | 42089 | 1415 | 912 | 100.00% | 4.28% | SAMEA5042935 |
C059UR | 53642 | 12618 | 577 | 100.00% | 74.70% | SAMEA5042930 |
C060UR | 73930 | 22110 | 19192 | 100.00% | 20.17% | SAMEA5043008 |
C062UR | 63220 | 19932 | 17112 | 100.00% | 79.58% | SAMEA5043012 |
C063UR | 44974 | 1201 | 790 | 100.00% | 53.42% | SAMEA5043039 |
C064UR | 63505 | 15051 | 7134 | 100.00% | 82.38% | SAMEA5042981 |
C065UR | 53884 | 15094 | 13794 | 100.00% | 52.97% | SAMEA5043027 |
C066UR | 63269 | 16157 | 12090 | 100.00% | 45.86% | SAMEA5042985 |
C067UR | 55812 | 19047 | 2481 | 100.00% | 86.86% | SAMEA5042986 |
C068UR | 54396 | 17456 | 15352 | 100.00% | 86.72% | SAMEA5042937 |
T000UR | 57607 | 11995 | 9166 | 100.00% | 37.51% | SAMEA5043045 |
T001UR | 47924 | 13474 | 2849 | 100.00% | 48.58% | SAMEA5043014 |
T002UR | 63839 | 18381 | 3623 | 100.00% | 49.71% | SAMEA5042975 |
T003UR | 70242 | 19166 | 5255 | 100.00% | 51.67% | SAMEA5042988 |
T004UR | 67280 | 20578 | 2947 | 100.00% | 57.24% | SAMEA5042943 |
T005UR | 52820 | 12868 | 4931 | 100.00% | 57.92% | SAMEA5043019 |
T006UR | 79409 | 19472 | 13710 | 100.00% | 19.58% | SAMEA5043017 |
T007UR | 34173 | 1403 | 797 | 100.00% | 50.06% | SAMEA5042999 |
T008UR | 30074 | 1346 | 1044 | 100.00% | 84.77% | SAMEA5043031 |
T009UR | 58440 | 10386 | 7936 | 100.00% | 81.92% | SAMEA5042950 |
T010UR | 65382 | 17191 | 9801 | 100.00% | 47.54% | SAMEA5042967 |
T011UR | 38550 | 1163 | 464 | 100.00% | 65.52% | SAMEA5043061 |
T012UR | 75848 | 21956 | 4605 | 100.00% | 52.62% | SAMEA5043049 |
T013UR | 26872 | 1383 | 203 | 100.00% | 74.38% | SAMEA5042996 |
T014UR | 23298 | 1741 | 518 | 100.00% | 93.44% | SAMEA5043042 |
T015UR | 40653 | 2052 | 1470 | 100.00% | 29.25% | SAMEA5042953 |
T016UR | 58448 | 16261 | 3993 | 100.00% | 58.75% | SAMEA5043053 |
T017UR | 58703 | 19270 | 1929 | 100.00% | 54.12% | SAMEA5042990 |
T018UR | 54726 | 12668 | 7152 | 100.00% | 17.18% | SAMEA5042970 |
T019UR | 67711 | 14153 | 1606 | 100.00% | 58.90% | SAMEA5042954 |
T020UR | 89936 | 22579 | 17919 | 100.00% | 68.74% | SAMEA5043052 |
T021UR | 66094 | 14761 | 5276 | 100.00% | 29.66% | SAMEA5042951 |
T022UR | 28712 | 803 | 422 | 100.00% | 74.88% | SAMEA5042940 |
T023UR | 27738 | 1338 | 385 | 100.00% | 30.65% | SAMEA5042961 |
T024UR | 19345 | 824 | 55 | 100.00% | 90.91% | SAMEA5042948 |
T025UR | 29739 | 1578 | 1214 | 100.00% | 76.85% | SAMEA5042995 |
T026UR | 79923 | 17606 | 6269 | 100.00% | 37.09% | SAMEA5042959 |
T027UR | 61145 | 10093 | 6169 | 100.00% | 59.51% | SAMEA5042949 |
T028UR | 71755 | 19529 | 16118 | 100.00% | 7.61% | SAMEA5042965 |
T029UR | 58776 | 11505 | 8300 | 100.00% | 6.04% | SAMEA5043018 |
T030UR | 57098 | 7000 | 5119 | 100.00% | 70.23% | SAMEA5042966 |
T031UR | 49283 | 16113 | 1636 | 100.00% | 38.63% | SAMEA5043063 |
T032UR | 46822 | 15041 | 1187 | 100.00% | 53.24% | SAMEA5042927 |
T033UR | 63044 | 14272 | 10097 | 100.00% | 80.89% | SAMEA5043043 |
T035UR | 50618 | 12403 | 1122 | 100.00% | 76.20% | SAMEA5043002 |
T036UR | 78781 | 22492 | 17075 | 100.00% | 84.36% | SAMEA5042982 |
T038UR | 73752 | 15237 | 11784 | 100.00% | 1.14% | SAMEA5043022 |
T039UR | 58904 | 22286 | 19836 | 100.00% | 95.82% | SAMEA5043015 |
T040UR | 77039 | 15332 | 8059 | 100.00% | 40.76% | SAMEA5043028 |
T041UR | 58382 | 13735 | 11893 | 100.00% | 97.26% | SAMEA5043056 |
T042UR | 53948 | 17112 | 1392 | 100.00% | 29.74% | SAMEA5043026 |
T043UR | 72662 | 15446 | 10584 | 100.00% | 16.18% | SAMEA5042956 |
T044UR | 59818 | 19779 | 724 | 100.00% | 73.48% | SAMEA5042993 |
T045UR | 63627 | 21438 | 19282 | 100.00% | 39.34% | SAMEA5043033 |
T046UR | 58142 | 20606 | 912 | 100.00% | 56.69% | SAMEA5042991 |
T047UR | 24190 | 736 | 26 | 100.00% | 73.08% | SAMEA5042978 |
T048UR | 10255 | 441 | 53 | 100.00% | 79.25% | SAMEA5043036 |
T049UR | 63640 | 22520 | 20236 | 100.00% | 98.73% | SAMEA5043010 |
T051UR | 22322 | 1066 | 101 | 100.00% | 77.23% | SAMEA5042997 |
T052UR | 57909 | 11757 | 6419 | 100.00% | 67.85% | SAMEA5043058 |
T053UR | 63637 | 24574 | 21178 | 100.00% | 99.17% | SAMEA5043034 |
T054UR | 59194 | 18986 | 17148 | 100.00% | 15.87% | SAMEA5042929 |
T055UR | 70744 | 14983 | 2724 | 100.00% | 84.07% | SAMEA5042962 |
T056UR | 58876 | 19486 | 846 | 100.00% | 65.84% | SAMEA5043051 |
T057UR | 53598 | 13889 | 12456 | 100.00% | 96.76% | SAMEA5042939 |
T058UR | 18302 | 739 | 45 | 100.00% | 64.44% | SAMEA5043044 |
T059UR | 59974 | 15542 | 12378 | 100.00% | 23.53% | SAMEA5042964 |
T060UR | 21736 | 500 | 203 | 100.00% | 89.16% | SAMEA5042946 |
T061UR | 33002 | 1153 | 503 | 100.00% | 56.46% | SAMEA5043011 |
T062UR | 64983 | 10519 | 6302 | 100.00% | 52.19% | SAMEA5042933 |
T063UR | 53347 | 12793 | 4023 | 100.00% | 40.00% | SAMEA5043041 |
T064UR | 68122 | 23665 | 21094 | 100.00% | 79.99% | SAMEA5042934 |
T065UR | 51210 | 17070 | 1242 | 100.00% | 65.30% | SAMEA5042977 |
T066UR | 64589 | 26532 | 1911 | 100.00% | 56.04% | SAMEA5042968 |
T067UR | 67938 | 16248 | 4974 | 100.00% | 50.12% | SAMEA5043005 |
T068UR | 70192 | 28890 | 3698 | 100.00% | 40.37% | SAMEA5043013 |
T069UR | 60564 | 21236 | 17683 | 100.00% | 43.97% | SAMEA5042957 |
T070UR | 83453 | 20755 | 5034 | 100.00% | 44.18% | SAMEA5043038 |
T071UR | 80077 | 36770 | 29224 | 100.00% | 97.68% | SAMEA5043007 |
T072UR | 73469 | 29671 | 19787 | 100.00% | 87.68% | SAMEA5042992 |
T073UR | 73167 | 17577 | 3914 | 100.00% | 54.09% | SAMEA5042989 |
T074UR | 59084 | 23906 | 21347 | 100.00% | 89.11% | SAMEA5042973 |
T075UR | 60263 | 17726 | 15250 | 100.00% | 70.37% | SAMEA5042976 |
T076UR | 37428 | 809 | 514 | 100.00% | 63.42% | SAMEA5042960 |
T078UR | 76834 | 17034 | 4220 | 100.00% | 66.75% | SAMEA5042958 |
T080UR | 12172 | 609 | 61 | 100.00% | 52.46% | SAMEA5042932 |
T081UR | 63432 | 14841 | 6915 | 100.00% | 86.49% | SAMEA5043029 |
T082UR | 26941 | 693 | 609 | 100.00% | 2.96% | SAMEA5043047 |
T083UR | 69149 | 34307 | 30270 | 100.00% | 95.45% | SAMEA5043055 |
T084UR | 59304 | 25863 | 22866 | 100.00% | 89.34% | SAMEA5042928 |
T085UR | 65565 | 20426 | 1344 | 100.00% | 78.57% | SAMEA5043030 |
T086UR | 66605 | 23828 | 21243 | 100.00% | 95.16% | SAMEA5043025 |
T087UR | 62480 | 16656 | 6414 | 100.00% | 76.55% | SAMEA5043057 |
T088UR | 82733 | 32538 | 3794 | 100.00% | 71.09% | SAMEA5042994 |
T089UR | 110227 | 27223 | 11761 | 100.00% | 24.49% | SAMEA5042944 |
T090UR | 70526 | 29296 | 1917 | 100.00% | 71.62% | SAMEA5043020 |
T091UR | 27973 | 913 | 739 | 100.00% | 27.74% | SAMEA5042952 |
T092UR | 69694 | 10825 | 7894 | 100.00% | 55.26% | SAMEA5043050 |
T093UR | 58492 | 14656 | 7272 | 100.00% | 84.27% | SAMEA5042980 |
T094UR | 194564 | 59268 | 35224 | 100.00% | 37.26% | SAMEA5042971 |
T095UR | 42681 | 1009 | 560 | 100.00% | 45.00% | SAMEA5042974 |
Sample ID | Condition | Medium | 16S rRNA gene-PCR Identification | Accessions | Identity (%) | Supported by previous cultivation |
---|---|---|---|---|---|---|
S001U | Anaerobic, 37 °C | EG | Clostridium cochlearium | LR761333.1 | 99.26 | Meijer-Severs et al. [24] |
S001U | Anaerobic, 37 °C | 104 | Streptococcus sp. (S. tigurinus/S. mitis) | LR761334.1 | 99.72 | Hilt et al. [23] |
S003U | Anaerobic, 37 °C | BHI | Enterococcus faecalis | LR761335.1 | 99.91 | Hilt et al. [23], Guzmàn et al. [25], Fraimow et al. [26], |
S003U | Anaerobic, 37 °C | 104 | Lactobacillus crispatus | LR761337.1 | 99.82 | Hilt et al. [23] |
S003U | Anaerobic, 37 °C | 104 | Propionibacterium granulosum | LR761336.1 | 99.02 | Ormerod et al. [27] |
S008U | Anaerobic, 37 °C | 104, BHI, EG | Streptococcus agalactiae | LR761340.1, LR761339.1, LR761338.1 | 99.65, 99.35, 99.52 | Hilt et al. [23] |
Phenotype | Bray-Curtis | Unweighted-UniFrac | Weighted-UniFrac | ||||||
---|---|---|---|---|---|---|---|---|---|
R2 | P value | Fdr | R2 | P value | Fdr | R2 | P value | Fdr | |
Age | 0.018 | 0.005 | 0.049 | 0.010 | 0.178 | 0.541 | 0.019 | 0.026 | 0.419 |
Age-2 groups | 0.013 | 0.050 | 0.236 | 0.011 | 0.116 | 0.429 | 0.016 | 0.042 | 0.452 |
Age-3 groups | 0.032 | 0.026 | 0.150 | 0.025 | 0.228 | 0.577 | 0.030 | 0.135 | 0.539 |
Pulses | 0.015 | 0.019 | 0.131 | 0.010 | 0.159 | 0.505 | 0.015 | 0.072 | 0.456 |
Frequent colds | 0.011 | 0.080 | 0.270 | 0.011 | 0.108 | 0.429 | 0.021 | 0.017 | 0.419 |
Antibiotics | 0.014 | 0.036 | 0.194 | 0.012 | 0.108 | 0.429 | 0.007 | 0.525 | 0.782 |
Constipation | 0.011 | 0.114 | 0.325 | 0.014 | 0.039 | 0.400 | 0.018 | 0.033 | 0.419 |
Surgical history | 0.018 | 0.005 | 0.049 | 0.018 | 0.006 | 0.172 | 0.034 | 0.001 | 0.091 |
Abdominal surgical history | 0.010 | 0.187 | 0.418 | 0.007 | 0.466 | 0.755 | 0.019 | 0.030 | 0.419 |
Menstrual cycle | 0.009 | 0.200 | 0.421 | 0.018 | 0.005 | 0.172 | 0.015 | 0.065 | 0.455 |
Menstrual phase (lower) | 0.018 | 0.260 | 0.468 | 0.024 | 0.048 | 0.408 | 0.020 | 0.207 | 0.623 |
Menstrual phase (upper) | 0.018 | 0.006 | 0.056 | 0.018 | 0.009 | 0.172 | 0.014 | 0.096 | 0.456 |
Contraception | 0.044 | 0.010 | 0.086 | 0.038 | 0.098 | 0.429 | 0.029 | 0.470 | 0.782 |
Vaginal deliveries | 0.018 | 0.003 | 0.049 | 0.016 | 0.014 | 0.172 | 0.016 | 0.051 | 0.455 |
Abortion | 0.028 | 0.004 | 0.049 | 0.014 | 0.239 | 0.585 | 0.016 | 0.198 | 0.623 |
Multipara / nullipara | 0.019 | 0.003 | 0.049 | 0.017 | 0.014 | 0.172 | 0.013 | 0.091 | 0.456 |
Infertility due to endometriosis | 0.045 | 0.000 | 0.008 | 0.029 | 0.013 | 0.172 | 0.019 | 0.181 | 0.599 |
Endometriosis | 0.014 | 0.022 | 0.141 | 0.011 | 0.095 | 0.429 | 0.005 | 0.644 | 0.857 |
Pelvic adhesiolysis | 0.008 | 0.346 | 0.572 | 0.013 | 0.042 | 0.400 | 0.006 | 0.489 | 0.782 |
Anemia | 0.016 | 0.012 | 0.090 | 0.008 | 0.354 | 0.740 | 0.006 | 0.511 | 0.782 |
Hysteromyoma | 0.018 | 0.003 | 0.049 | 0.012 | 0.057 | 0.429 | 0.021 | 0.014 | 0.419 |