Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth/Experiment 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/26

Curator: Joan Chuks

Revision editor(s): Joan Chuks, ChiomaBlessing, Victoria

Subjects

Location of subjects

Ireland

Host species Species from which microbiome was sampled. Contact us to have more species added.

Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Posterior fornix of vagina , External cervical os Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina,External os,External os of uterus,Ostium of uterus,Ostium uteri,External cervical os,external cervical os

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Spontaneous preterm birth Spontaneous preterm birth,spontaneous preterm birth

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Low-risk controls

Group 1 name Corresponds to the case (exposed) group for case-control studies

Risk Group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Pregnant women with either a history of previous spontaneous preterm birth (risk_PTB) or women with risk factors for preterm birth but who delivered full term (risk_FTB)

Group 0 sample size Number of subjects in the control (unexposed) group

14

Group 1 sample size Number of subjects in the case (exposed) group

35

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

Women currently on antibiotic treatment.

Lab analysis

Sequencing type

WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

raw counts

Statistical test

Linear Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.25

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Signature 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks

Source: Figure 2C

Description: Differentially abundant species within the Risk group.

Abundance in Group 1: increased abundance in Risk Group

NCBI	Quality Control	Links
Bifidobacterium breve

Revision editor(s): Joan Chuks

Signature 2

EditHistoryDelete

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks

Source: Figure 2C

Description: Differentially abundant species within the Risk group

Abundance in Group 1: decreased abundance in Risk Group

NCBI	Quality Control	Links
Caloramator mitchellensis
Mycobacterium sp. 852013-50091_SCH5140682
Stenotrophomonas maltophilia

Revision editor(s): Joan Chuks