title: Novel microarray design strategy to study complex bacterial communities.
abstract: Assessing bacterial flora composition appears to be of increasing importance to fields as diverse as physiology, development, medicine, epidemiology, the environment, and the food industry. We report here the development and validation of an original microarray strategy that allows analysis of the phylogenic composition of complex bacterial mixtures. The microarray contains approximately 9,500 feature elements targeting 16S rRNA gene-specific regions. Probe design was performed by selecting oligonucleotide sequences specific to each node of the seven levels of the bacterial phylogenetic tree (domain, phylum, class, order, family, genus, and species). This approach, based on sequence information, allows analysis of the bacterial contents of complex bacterial mixtures to detect both known and unknown microorganisms. The presence of unknown organisms can be suspected and mapped on the phylogenetic tree, indicating where to refine analysis. Initial proof-of-concept experiments were performed on oral bacterial communities. Our results show that this hierarchical approach can reveal minor changes (<or=1%) in gingival flora content when samples collected in individuals from similar geographical origins are compared.
authors.affiliation: Genomic Research Laboratory, Infectious Diseases Service, University of Geneva Hospitals, Micheli-du-Crest 24, 1211 Geneva 14, Geneva, Switzerland. antoine.huyghe@genomic.ch
authors.forename: Antoine
authors.initials: A
authors.lastname: Huyghe
authors.forename: Patrice
authors.initials: P
authors.lastname: Francois
authors.forename: Yvan
authors.initials: Y
authors.lastname: Charbonnier
authors.forename: Manuela
authors.initials: M
authors.lastname: Tangomo-Bento
authors.forename: Eve-Julie
authors.initials: EJ
authors.lastname: Bonetti
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Paster
authors.forename: Ignacio
authors.initials: I
authors.lastname: Bolivar
authors.forename: Denise
authors.initials: D
authors.lastname: Baratti-Mayer
authors.forename: Didier
authors.initials: D
authors.lastname: Pittet
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D005881:Gingiva / Q000382:microbiology; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S