Genome Technology Center

Use of Molecular Probes with Barcodes to Identify Microbes


Richard W. Hyman
Robert St.Onge

For more than a century, if you wanted to determine what bacteria were in any given ecological niche, you passed a sterile swab or solution across the niche and, then, passed the swab or solution across an agar plate and incubated the plate. You could use multiple agar plates, varying the nutrients in the plate, and incubating the plates under aerobic or anaerobic conditions and at various temperatures. This method is simple, elegant, and inexpensive. However, it is now well understood that the vast lion's share of the earth's bacteria have not yet been grown in culture and do not form colonies on agar plates. These statements are particularly true of the bacteria living in or on human beings. The Human Microbiome Project is employing DNA sequencing, and other genome-based technology, to reveal the plethora of microbes living in, on, with, or symbiotically with humans. DNA sequencing is too expensive and cumbersome to apply as a routine or diagnostic method.

Therefore, we are proposing an independent method to identify microbes. Our method neither requires nor needs growth of the microbes. Rather, molecular probe technology is a nucleic acid-based technology. We emphasize the use of currently available reagents: particularly commercially available oligonucleotides and a commercially available array. Because of our ongoing interest in the bacteria that inhabit the human vagina, our current focus is on that ecological niche."

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