Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays

Study information

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

39569373

DOI Digital object identifier for electronic documents.

10.1016/j.isci.2024.111238

URI

https://pmc.ncbi.nlm.nih.gov/articles/PMC11576381/

Authors

Talukdar D, Sarkar M, Ahrodia T, Kumar S, De D, Nath S, Jana P, Verma J, Mehta O, Kothidar A, Yodhaanjali JR, Sharma K, Bakshi S, Singh U, Kshetrapal P, Wadhwa N, Thiruvengadam R, Nair GB, Bhatnagar S, Mukherjee S, Das B

Journal

iScience

Year

2024

Keywords:

Diagnostics, Medical science, Medicine, Microbiology, Microbiome, Reproductive medicine, Women’s health

Annually, in India, 13% of all newborns are preterm, accounting for 23.4% of preterm birth (PTB) globally. The composition and diversity of the vaginal microbiome have a notable degree of ethnic inequality. For understanding differences in vaginal microbiome composition and functions between adverse and normal pregnancy, we have collected, processed and sequenced 600 high vaginal swab (HVS) samples across the three trimesters of pregnancy from 140 women who delivered at term and 60 women who delivered PTB, adopting a targeted metagenomics approach. The microbial signatures in HVS samples showed Lactobacillus genera to be highly abundant in term birth (TB), while in early pregnancy the abundances of Gardnerella, Atopobium, and Sneathia were found to be high in PTB. We further extended our analysis, identified specific microbial genomic signatures, and developed a dipstick assay for rapid identification of PTB-associated microbiota in HVS samples in low-resource settings.

Experiment 1

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2024/11/26

Curator: Rahila

Revision editor(s): Rahila, Aleru Divine

Subjects

Location of subjects: India

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: Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae

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: Term birth (TB)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Preterm birth (PTB)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Samples collected during the first trimester of pregnancy (T1) from women who subsequently delivered preterm (PTB).

Group 0 sample size Number of subjects in the control (unexposed) group: 140

Group 1 sample size Number of subjects in the case (exposed) group: 60

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

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

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).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2.0

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Simpson Estimator of species richness and species evenness: more weight on species evenness: increased

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/11/26

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 7

Description: Differential abundance of the vaginal microbiome during the first trimester of pregnancy (T1) in women from India who delivered preterm (PTB) or at term (TB).

Abundance in Group 1: increased abundance in Preterm birth (PTB)

NCBI	Quality Control	Links
Lactobacillus iners
Pseudomonas sp.
Fannyhessea vaginae
Prevotella corporis
Sneathia sanguinegens

Revision editor(s): Aleru Divine

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/11/26

Curator: Rahila

Revision editor(s): Rahila

Source: Figure 7

Description: Differential abundance of the vaginal microbiome during the first trimester of pregnancy (T1) in women from India who delivered preterm (PTB) or at term (TB).

Abundance in Group 1: decreased abundance in Preterm birth (PTB)

NCBI	Quality Control	Links
Lactobacillus crispatus
Lactobacillus johnsonii

Revision editor(s): Rahila