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Revolutionary Application of Genomic Sequencing Platform Provides Powerful Insight Into Bacterial Guests

May 24, 2011

NEW YORK, May 24, 2011 /PRNewswire/ — A revolutionary way of using a
next generation sequencing platform enables us to identify and describe whole
populations of bacteria in areas of the body such as the genital tract
according to an article in the newly released June issue of leading journal,
Systems Biology in Reproductive Medicine.

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:

http://informahealthcare.com/doi/full/10.3109/19396368.2011.565111

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.

Additional information is available by visiting:
http://www.informahealthcare.com/sbirm

For further information and/or interviews with the lead author or editor,
please contact: kirstin.stocker@informa.com

SOURCE Informa Healthcare


Source: newswire



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