Alterations of the vaginal microbiome in healthy pregnant women positive for group B Streptococcus colonization during the third trimester
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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
Shabayek S, Abdellah AM, Salah M, Ramadan M, Fahmy N
Journal
BMC microbiology
Year
2022
Keywords:
Group B Streptococcus, Healthy, Microbiome, Pregnant, Streptococcus agalactiae, Third trimester, Vagina
BACKGROUND: Streptococcus agalactiae or group B Streptococcus (GBS) asymptomatically colonizes the genitourinary tracts of up to 30% of pregnant women. Globally, GBS is an important cause of neonatal morbidity and mortality. GBS has recently been linked to adverse pregnancy outcomes. The potential interactions between GBS and the vaginal microbiome composition remain poorly understood. In addition, little is known about the vaginal microbiota of pregnant Egyptian women. RESULTS: Using V3-V4 16S rRNA next-generation sequencing, we examined the vaginal microbiome in GBS culture-positive pregnant women (22) and GBS culture-negative pregnant women (22) during the third trimester in Ismailia, Egypt. According to the alpha-diversity indices, the vaginal microbiome of pregnant GBS culture-positive women was significantly more diverse and less homogenous. The composition of the vaginal microbiome differed significantly based on beta-diversity between GBS culture-positive and culture-negative women. The phylum Firmicutes and the family Lactobacillaceae were significantly more abundant in GBS-negative colonizers. In contrast, the phyla Actinobacteria, Tenericutes, and Proteobacteria and the families Bifidobacteriaceae, Mycoplasmataceae, Streptococcaceae, Corynebacteriaceae, Staphylococcaceae, and Peptostreptococcaceae were significantly more abundant in GBS culture-positive colonizers. On the genus and species levels, Lactobacillus was the only genus detected with significantly higher relative abundance in GBS culture-negative status (88%), and L. iners was the significantly most abundant species. Conversely, GBS-positive carriers exhibited a significant decrease in Lactobacillus abundance (56%). In GBS-positive colonizers, the relative abundance of the genera Ureaplasma, Gardnerella, Streptococcus, Corynebacterium, Staphylococcus, and Peptostreptococcus and the species Peptostreptococcus anaerobius was significantly higher. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to the metabolism of cofactors and vitamins, phosphatidylinositol signaling system, peroxisome, host immune system pathways, and host endocrine system were exclusively enriched among GBS culture-positive microbial communities. However, lipid metabolism KEGG pathways, nucleotide metabolism, xenobiotics biodegradation and metabolism, genetic information processing pathways associated with translation, replication, and repair, and human diseases (Staphylococcus aureus infection) were exclusively enriched in GBS culture-negative communities. CONCLUSIONS: Understanding how perturbations of the vaginal microbiome contribute to pregnancy complications may result in the development of alternative, targeted prevention strategies to prevent maternal GBS colonization. We hypothesized associations between inferred microbial function and GBS status that would need to be confirmed in larger cohorts.
Experiment 1
Subjects
- Location of subjects
- Egypt
- 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 orifice Introitus,Introitus of vagina,Opening of vagina,Orifice of vagina,Ostium vaginae,Vagina opening,Vaginal introitus,Vaginal orifice,Vagina orifice,vagina orifice
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Streptococcal infection infection, streptococcal,infections, streptococcal,streptococcal infection,Streptococcal Infections,Streptococcus caused disease or disorder,Streptococcus disease or disorder,Streptococcus infectious disease,Streptococcal infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GBS culture-negative pregnant women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GBS culture-positive pregnant women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women whose culture status shows group B Streptococcus (GBS) to be Positive
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Within the previous six months
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: (Figs. 3 and 4 panels A, B, C, and D).
Description: Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing biomarker phylum (A), family (B), genus (C), and species (D) with significant differential abundance in GBS culture-negative and GBS culture-positive pregnant Egyptian women using SILVA database. FDR adjusted p values and LDA score > 2 was considered statistically significant. Not_Assigned refers to taxa that were challenging for biological interpretation
Abundance in Group 1: decreased abundance in GBS culture-positive pregnant women
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Lactobacillus iners | ||
| Lactobacillus iners AB-1 | ||
| Limosilactobacillus coleohominis |
Revision editor(s): Ayibatari
Signature 2
Source: (Figs. 3 and 4 panels A, B, C, and D).
Description: Linear discriminant analysis (LDA) effect size (LEfSe) biomarker analysis showing biomarker phylum (A), family (B), genus (C), and species (D) with significant differential abundance in GBS culture-negative and GBS culture-positive pregnant Egyptian women using SILVA database. FDR adjusted p values and LDA score > 2 was considered statistically significant. Not_Assigned refers to taxa that were challenging for biological interpretation
Abundance in Group 1: increased abundance in GBS culture-positive pregnant women
Revision editor(s): Ayibatari
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