The potential of metatranscriptomics for identifying screening targets for bacterial vaginosis

The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. The sample from the BV patient underwent total RNA extraction, followed by physical subtractio...

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Bibliographic Details
Published in:PloS one 2013-09, Vol.8 (9), p.e76892-e76892
Main Authors: Twin, Jimmy, Bradshaw, Catriona S, Garland, Suzanne M, Fairley, Christopher K, Fethers, Katherine, Tabrizi, Sepehr N
Format: Article
Language:English
Subjects:
Adult
Bacteria
Bioinformatics
Deoxyribonucleic acid
DNA
E coli
Escherichia coli
Female
Gene expression
Gene Expression Profiling
Gene Library
Gene sequencing
Gynecology
Hospitals
Humans
Infectious diseases
Medical screening
Microbiota
Microorganisms
Obstetrics
Penis
Premature birth
Ribonucleic acid
RNA
RNA, Bacterial - analysis
RNA, Bacterial - genetics
rRNA 16S
Sexual Behavior
Studies
Subtraction
Target recognition
Taxonomy
Transcription
Vagina
Vaginosis
Vaginosis, Bacterial - diagnosis
Womens health
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Summary:The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. The sample from the BV patient underwent total RNA extraction, followed by physical subtraction of human rRNA and whole transcriptome amplification. The metatranscriptome was sequenced using Roche 454 titanium chemistry. The bioinformatics pipeline MG-RAST and desktop DNA analysis platforms were utilised to analyse results. Bacteria of the genus Prevotella (predominately P. amnii) constituted 36% of the 16S rRNA reads, followed by Megasphaera (19%), Leptotrichia/Sneathia (8%) and Fusobacterium (8%). Comparison of the abundances of several bacteria to quantitative PCR (qPCR) screening of extracted DNA revealed comparable relative abundances. This suggests a correlation between what was present and transcriptionally active in this sample: however distinct differences were seen when compared to the microbiome determined by 16S rRNA gene amplicon sequencing. To assess the presence of P. amnii in a larger pool of samples, 90 sexually active women were screened using qPCR. This bacterium was found to be strongly associated with BV (P
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0076892