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).

From: Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial

(A)	Log2FC^a	P adj^b	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.

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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).

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