TY - JOUR
T1 - The potential of metatranscriptomics for identifying screening targets for bacterial vaginosis
AU - Twin, Jimmy
AU - Bradshaw, Catriona
AU - Garland, Suzanne
AU - Fairley, Christopher Kit
AU - Fethers, Katherine A
AU - Tabrizi, Sepehr
PY - 2013
Y1 - 2013
N2 - 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.
Methodology/Principal Findings: 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,0.001, OR 23.3 (95 CI:2.9?190.7)) among the 90 women.
Conclusions/Significance: This study highlighted the potential of metatranscriptomics as a tool for characterising
metabolically active microbiota and identifying targets for further screening. Prevotella amnii was chosen as an example
target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a
high concentration by qPCR in 31 of cohort with BV, with an association with both oral and penile-vaginal sex.
AB - 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.
Methodology/Principal Findings: 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,0.001, OR 23.3 (95 CI:2.9?190.7)) among the 90 women.
Conclusions/Significance: This study highlighted the potential of metatranscriptomics as a tool for characterising
metabolically active microbiota and identifying targets for further screening. Prevotella amnii was chosen as an example
target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a
high concentration by qPCR in 31 of cohort with BV, with an association with both oral and penile-vaginal sex.
U2 - 10.1371/journal.pone.0076892
DO - 10.1371/journal.pone.0076892
M3 - Article
VL - 8
JO - PLoS ONE
JF - PLoS ONE
SN - 1932-6203
IS - 9
M1 - e76892
ER -