Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ng S, Chen M, Kundu S, Wang X, Zhou Z, Zheng Z, Qing W, Sheng H, Wang Y, He Y, Bennett PR, MacIntyre DA, Zhou H
Journal
NPJ biofilms and microbiomes
Year
2021
Vaginal microbiota-host interactions are linked to preterm birth (PTB), which continues to be the primary cause of global childhood mortality. Due to population size, the majority of PTB occurs in Asia, yet there have been few studies of the pregnancy vaginal microbiota in Asian populations. Here, we characterized the vaginal microbiome of 2689 pregnant Chinese women using metataxonomics and in a subset (n = 819), the relationship between vaginal microbiota composition, sialidase activity and leukocyte presence and pregnancy outcomes. Vaginal microbiota were most frequently dominated by Lactobacillus crispatus or L. iners, with the latter associated with vaginal leukocyte presence. Women with high sialidase activity were enriched for bacterial vaginosis-associated genera including Gardnerella, Atopobium and Prevotella. Vaginal microbiota composition, high sialidase activity and/or leukocyte presence was not associated with PTB risk suggesting underlying differences in the vaginal microbiota and/or host immune responses of Chinese women, possibly accounting for low PTB rates in this population.
Experiment 1
Subjects
- Location of subjects
- China
- 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 Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Birth measurement Birth measurement,birth measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low vaginal sialidase activity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High vaginal sialidase activity
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with high sialidase activity had significantly higher prevalence of Lactobacillus species depleted microbiota.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 783
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Within 30 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)?
- Yes
- 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
- Richness Number of species
- increased
Signature 1
Source: FIG 2 (C)
Description: LDA showing effect size of differentially abundant taxa associated with microbiota of women with high (red) sialidase activity.
Abundance in Group 1: increased abundance in High vaginal sialidase activity
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (C)
Description: LDA showing effect size of differentially abundant taxa associated with microbiota of women with low (green) sialidase activity.
Abundance in Group 1: decreased abundance in High vaginal sialidase activity
Revision editor(s): Rahila
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Leukocyte low (grades I-II)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Leukocyte high (grades III-IV)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vaginal microbiota of women with Leukocyte high (grades III-IV)
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 3 (C)
Description: LDA analysis in vaginal microbiota of women with leukocyte high (grades III-IV, red).
Abundance in Group 1: increased abundance in Leukocyte high (grades III-IV)
Revision editor(s): Rahila
Signature 2
Source: FIG 3 (C)
Description: LDA analysis in vaginal microbiota of women with leukocyte low (grades I-II, green).
Abundance in Group 1: decreased abundance in Leukocyte high (grades III-IV)
Revision editor(s): Rahila
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