NEW YORK, May 24, 2011 /PRNewswire/ -- A revolutionary way of using a next generation sequencing platform enables
The new strategy for using the Illumina Genome Analyzer sequencing platform provides scientists with a cost-effective and clear picture of life inside the genital tract, with potential applications in diagnosis and epidemiology, which will lead to an unprecedentedly clearer understanding of how the microflora in our bodies affect a range of issues, including pregnancy miscarriages.
"In an obstetrical context, many millions of bacteria and other organisms populate the lower genital tract (LGT)," explains Dr David Miller, Ph.D. Reader in Molecular Andrology, Division of Reproduction and Early Development, University of Leeds Institute of Genetics, Health and Therapeutics and author of the preface on the article for Systems Biology in Reproductive Medicine.
"Although cervical mucus maintains a sterile environment above, perturbations of the vaginal microflora can permit pathological species to gain a foothold and compromise upper genital tract sterility, causing the potential for problems conceiving, miscarriage and other health issues for women and unborn children."
"This new strategy provides us with a usable method of obtaining a clear picture of what lives in the LGT at a reasonable cost," says Dr Miller.
Chlamydia is the main etiological factor responsible for the rise in sexually transmitted disease among the young and infection with this and many other pathological organisms - such as Candida and Gardnerella - provoke immune responses that can lead to inflammatory and frequently permanent damage.
"Recurrent miscarriage and pre-term labor have long been thought to have a bacteriological component in the form of pathogens or 'bad' bacteria," explains Dr Miller. "However, our knowledge of the composition and diversity of the healthy LGT's microflora and how it might help protect this special environment from potentially invasive pathogens is still rather poor. This new way of examining flora within the body will provide an enlightening view of the patient's LGT as well as ultimately giving us signposts to treatments."
One of the key messages to come out of this paper is that although the Illumina sequencing platform ordinarily uses the manufacturer's primers for initiating sequencing, this is not a requirement of their technology. By designing primers specially targeted at 3 different highly conserved sequences in bacterial 16S ribosomal sequences, the sequencing strategy in this paper can assemble much longer sequences for individual DNA molecules on the Illumina platform than heretofore possible.
The Illumina sequencing platform provides an extraordinarily large number of sequences compared to several other platforms but ordinarily is more limited in the lengths of the DNA that it can sequence.
"The article describes a new strategy for using the Illumina system that can overcome the length limitations of individual sequences by demonstrating how to couple together multiple sequences in order to obtain much longer sequences - and a more complete picture - from individual DNA molecules," says the author Professor Jeffrey Ram, Department of Physiology, Wayne State University School of Medicine.
"When fully implemented, the strategy should enable more complete descriptions at lower cost than other analyses of genital tract bacteria, with potential applications in diagnosis and epidemiology of the genital tract," explains Professor Ram.
"A better, more accurate understanding of our microscopic guests will lead, in turn, to better, more accurate treatment of patients."
The full article from Systems Biology in Reproductive Medicine, titled, "Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform" by Ram et al is available to all by free access at: http://informahealthcare.com/doi/full/10.3109/19396368.2011.555598
The preface to the full article can also be freely accessed at:
About Systems Biology in Reproductive Medicine
Published by Informa Healthcare as part of the company's unrivalled stable of leading scientific and healthcare journals, Systems Biology in Reproductive Medicine publishes research involving human and animal gametes, stem cells, developmental biology and toxicology, and clinical care in reproductive medicine.
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