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Novel Microarray Design Strategy To Study Complex Bacterial Communities

Genomic Research Laboratory, Infectious Diseases Service, University of Geneva Hospitals, Geneva, Switzerland,¹ The Forsyth Institute, Boston, Massachusetts,² Institut für Angewandte Immunologie, Zuchwil, Switzerland,³ Reconstructive and Plastic Surgery, Faculty of Medicine, Geneva, Switzerland,⁴ Infection Control Program, Faculty of Medicine, Geneva, Switzerland⁵

Received 26 July 2007/ Accepted 10 January 2008

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 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 (1%) in gingival flora content when samples collected in individuals from similar geographical origins are compared.

Published ahead of print on 18 January 2008.