Categorization of Microfloral Communities

OTT Case 04-027 | US Patent 7,627,437

The present disclosure provides a method for assessing the phylogeny of populations in microbial communities. In an embodiment, the present disclosure provides a method of identifying one or more microbial communities involving providing a plurality of microbial profiles obtained from samples of microorganisms; identifying one or more consensus profiles from among the plurality of microbial profiles; and, assigning at least a subset of the plurality of microbial profiles to a consensus profile that defines a microbial community. The microbial profiles can be obtained by analysis of a variety of sample sources, including environmental samples, plant samples, animal subjects and human subjects. The samples can include symbiotic microorganisms, commensal microorganisms, pathogenic microorganisms, environmental microorganisms, and mixtures thereof in any combination.

Typically, the microbial profiles are provided by a culture-independent method. For example, the microbial profiles can be provided by preparing a nucleic acid sample including at least one molecular indicator of identity from at least one species of microorganism present in the sample of microorganisms. The molecular indicator of identity is then detected to provide a microbial profile. Typically, the molecular indicator of identity is polymorphic polynucleotide, such as a phylogenetically informative gene. One example of a molecular indicator of identity is an rRNA gene, for example the 16S rRNA gene. The molecular indicator of identity can be detected, for example, by determining the nucleotide sequence ("sequencing") the polymorphic polynucleotide, or a portion or subsequence thereof. In an embodiment, the molecular indicator of identity is detected by evaluating the sizes of terminal restriction fragments of the 16S rRNA gene. For example, the terminal restriction fragments of the 16S rRNA gene can be evaluated by T-RFLP (terminal restriction fragment length polymorphism) analysis.

In an embodiment, the disclosure provides a method for categorizing a vaginal microbiota community as normal. Such a method involves identifying one or more predominant species of microbiota in a vaginal sample, thereby producing a vaginal microbiota profile; and, categorizing the vaginal microbiota population as normal by assigning the vaginal microbiota profile to a category of normal vaginal microbiota. Most commonly, the predominant species of microbiota is a species of bacteria, or a combination of species of bacteria. Nonetheless, the predominant species of microbiota can also include species of yeast, species of fungi and species of viruses.