Table 3.
DESeq2 analysis of taxa differentially abundant between (A) randomized study arms at crossover and (B) between baseline and crossover (intention-to-treat analysis).
| (A) | Log2FCa | P adjb | Family | Genus | Species |
|---|---|---|---|---|---|
| COC arm versus Net-En arm | −10.557 | 0.0196 | Porphyromonadaceae | Tannerella | NA |
| −10.587 | 0.0196 | Spirochaetaceae | Treponema | vincentii | |
| −2.930 | 0.0269 | Prevotellaceae | Prevotella | amnii | |
| −22.839 | 5.92e–12 | Weeksellaceae | NA | NA | |
| −25.877 | 2.90e–15 | Prevotellaceae | Prevotella | denticola | |
| −26.790 | 3.22e–16 | Lachnospiraceae | Lachnoanaerobaculum | saburreum | |
| −26.891 | 3.22e–16 | Prevotellaceae | Prevotella | baroniae | |
| −3.933 | 0.0463 | Clostridiaceae | Clostridium | BVAB3_M_indolicus | |
| −7.012 | 0.0450 | Prevotellaceae | Prevotella | shahii | |
| −8.457 | 0.0300 | Prevotellaceae | Prevotella | oulorum | |
| −8.834 | 0.0087 | Atopobiaceae | Olsenella | NA | |
| 2.067 | 0.0321 | Lactobacillaceae | Lactobacillus | iners | |
| 3.374 | 0.0450 | Veillonellaceae | Veillonella | montpellieriensis | |
| 4.291 | 0.0071 | Lactobacillaceae | Lactobacillus | jensenii | |
| 5.046 | 0.0002 | Lactobacillaceae | Lactobacillus | johnsonii_gasseri_taiwanensis | |
| COC arm versus CCVR arm | −3.086 | 0.0468 | Prevotellaceae | Prevotella | amnii |
| −3.318 | 0.0331 | Enterobacteriaceae | NA | NA | |
| 3.875 | 0.0216 | Lactobacillaceae | Lactobacillus | johnsonii_gasseri_taiwanensis | |
| 4.242 | 0.0216 | Prevotellaceae | Prevotella | melaninogenica | |
| Net-En arm versus CCVR arm | −2.485 | 0.0159 | Prevotellaceae | Prevotella | disiens |
| −2.698 | 0.0114 | Gemellaceae | Gemella | asaccharolytica | |
| −3.288 | 0.0008 | Mycoplasmataceae | Mycoplasma | hominis | |
| −4.408 | 0.0008 | Lactobacillaceae | Lactobacillus | jensenii | |
| −4.614 | 0.0139 | Bifidobacteriaceae | Gardnerella | NA | |
| 10.862 | 0.0078 | Flavobacteriaceae | Bergeyella | NA | |
| 11.078 | 0.0064 | Lachnospiraceae | Lachnoanaerobaculum | saburreum | |
| 17.217 | 6.16e–07 | Prevotellaceae | Prevotella | baroniae | |
| 22.873 | 2.55e–12 | Prevotellaceae | Prevotella | nigrescens | |
| 24.071 | 1.53e–13 | Porphyromonadaceae | Tannerella | NA | |
| 24.324 | 9.47e–14 | Spirochaetaceae | Treponema | vincentii | |
| 24.588 | 4.90e–14 | Spirochaetaceae | Treponema | socranskii | |
| 25.338 | 2.23e–15 | Weeksellaceae | NA | NA | |
| 25.999 | 9.99e–18 | Prevotellaceae | Prevotella | oulorum | |
| 26.530 | 4.27e–16 | Actinomycetaceae | Actinomyces | NA | |
| 4.442 | 0.0334 | Spirochaetaceae | Treponema | NA | |
| 5.437 | 0.0060 | Veillonellaceae | Selenomonas | infelix | |
| (B)c,d | |||||
| COC arm | 1.941 | 0.0142 | Lactobacillaceae | Lactobacillus | iners |
| −11.005 | 0.0275 | Clostridiaceae | Clostridium | moniliforme | |
| −7.544 | 0.4809 | Clostridiaceae | Clostridium | perfringens | |
| Net-En arm | 1.446 | 0.3449 | Prevotellaceae | Prevotella | disiens |
| 2.002 | 0.1755 | Mycoplasmataceae | Mycoplasma | hominis | |
| 3.186 | 0.3449 | Campylobacteraceae | Campylobacter | NA | |
FC: fold change, CCVR: combined contraceptive vaginal ring (A: n = 32, B: n = 32 matched participants), COC: combined oral contraceptives (A: n = 35, B: n = 34 matched participants), Net-En (A: n = 28, B: n = 32 matched participants).
aPositive fold changes represent taxa more abundant in the first hormonal contraceptive arm.
bTaxa with an adjusted P < 0.05 after adjusting for condom use and antibiotic use included.
cPositive fold changes represent taxa more abundant at crossover.
dTaxa with an adjusted P < 0.5 included.
Source data are provided as a Source Data file.