Abstract
The Vaginal Microbiome: Disease, Genetics and the Environment
Highlights
Data deposited into NCBI after that date have instructions to Hold Until Publication (HUP)
Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms
Because of the nature of this organ, and the fact that it is continuously colonized by bacteria from birth to death, it is virtually certain that this rich environment evolved in concert with its microbial flora
Summary
The 16S rDNA post-sequencing analysis pipeline is designed to filter the reads based on quality, to trim the barcode (Multiplex Identifier) and PCR amplification primer sequences, and to assign taxonomy to the high quality reads obtained. 80% of the reads are retained after the application of these quality control metrics These high quality reads are assigned taxonomy using the RDP Classifier (1) with a minimum bootstrap confidence of 80%. Sequences are assembled using Velvet (2), Newbler (Roche Diagnostics) or other appropriate assembler Sequences of these bacterial clones will meet or exceed ‘Standard Draft’ quality as defined in Chain et al (3). We have compared the complete genome sequences from a panel of Gardnerella vaginalis (4), Lactobacillus sp., Sneathia, and other isolates (in preparation), taken from our samples
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