MOTIVATION: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial 'black-box', the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. RESULTS: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called 'PhylArray', designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.
MOTIVATION: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial 'black-box', the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. RESULTS: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called 'PhylArray', designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.
Authors: Tom O Delmont; Patrick Robe; Sébastien Cecillon; Ian M Clark; Florentin Constancias; Pascal Simonet; Penny R Hirsch; Timothy M Vogel Journal: Appl Environ Microbiol Date: 2010-12-23 Impact factor: 4.792
Authors: William Tottey; Jeremie Denonfoux; Faouzi Jaziri; Nicolas Parisot; Mohiedine Missaoui; David Hill; Guillaume Borrel; Eric Peyretaillade; Monique Alric; Hugh M B Harris; Ian B Jeffery; Marcus J Claesson; Paul W O'Toole; Pierre Peyret; Jean-François Brugère Journal: PLoS One Date: 2013-05-17 Impact factor: 3.240
Authors: Jérémie Denonfoux; Nicolas Parisot; Eric Dugat-Bony; Corinne Biderre-Petit; Delphine Boucher; Diego P Morgavi; Denis Le Paslier; Eric Peyretaillade; Pierre Peyret Journal: DNA Res Date: 2013-01-30 Impact factor: 4.458
Authors: Faouzi Jaziri; Eric Peyretaillade; Mohieddine Missaoui; Nicolas Parisot; Sébastien Cipière; Jérémie Denonfoux; Antoine Mahul; Pierre Peyret; David R C Hill Journal: ScientificWorldJournal Date: 2014-01-06
Authors: Faouzi Jaziri; Nicolas Parisot; Anis Abid; Jérémie Denonfoux; Céline Ribière; Cyrielle Gasc; Delphine Boucher; Jean-François Brugère; Antoine Mahul; David R C Hill; Eric Peyretaillade; Pierre Peyret Journal: Database (Oxford) Date: 2014-04-26 Impact factor: 3.451