title: Molecular probe technology detects bacteria without culture.
abstract: BACKGROUND
  Our ultimate goal is to detect the entire human microbiome, in health and in disease, in a single reaction tube, and employing only commercially available reagents. To that end, we adapted molecular inversion probes to detect bacteria using solely a massively multiplex molecular technology. This molecular probe technology does not require growth of the bacteria in culture. Rather, the molecular probe technology requires only a sequence of forty sequential bases unique to the genome of the bacterium of interest. In this communication, we report the first results of employing our molecular probes to detect bacteria in clinical samples.
  
  
  RESULTS
  While the assay on Affymetrix GenFlex Tag16K arrays allows the multiplexing of the detection of the bacteria in each clinical sample, one Affymetrix GenFlex Tag16K array must be used for each clinical sample. To multiplex the clinical samples, we introduce a second, independent assay for the molecular probes employing Sequencing by Oligonucleotide Ligation and Detection. By adding one unique oligonucleotide barcode for each clinical sample, we combine the samples after processing, but before sequencing, and sequence them together.
  
  
  CONCLUSIONS
  Overall, we have employed 192 molecular probes representing 40 bacteria to detect the bacteria in twenty-one vaginal swabs as assessed by the Affymetrix GenFlex Tag16K assay and fourteen of those by the Sequencing by Oligonucleotide Ligation and Detection assay. The correlations among the assays were excellent.
authors.affiliation: Departments of Biochemistry, Stanford University, Stanford, CA, USA. rhyman@stanford.edu
authors.forename: Richard W
authors.initials: RW
authors.lastname: Hyman
authors.forename: Robert P
authors.initials: RP
authors.lastname: St Onge
authors.forename: Hyunsung
authors.initials: H
authors.lastname: Kim
authors.forename: John S
authors.initials: JS
authors.lastname: Tamaresis
authors.forename: Molly
authors.initials: M
authors.lastname: Miranda
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Aparicio
authors.forename: Marilyn
authors.initials: M
authors.lastname: Fukushima
authors.forename: Nader
authors.initials: N
authors.lastname: Pourmand
authors.forename: Linda C
authors.initials: LC
authors.lastname: Giudice
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Davis
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D003198:Computer Simulation; D005260:Female; D006801:Humans; D008828:Microbiological Techniques / Q000379:methods*; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results; D014621:Vagina / Q000382:microbiology