title: FurIOS: A Web-Based Tool for Identification ofVibrionaceaeSpecies Using thefurGene.
abstract: Gene based methods for identification of species from theVibrionaceaefamily have been developed during the last decades to address the limitations of the commonly used 16S rRNA gene phylogeny. Recently, we found that theferric-uptake regulatorgene (fur) can be used as a single identification marker providing species discrimination, consistent with multi-locus sequencing analyses and whole genome phylogenies. To allow for broader and easy use of this marker, we have developed an online prediction service that allows the identification ofVibrionaceaespecies based on theirfur-sequence. The input is a DNA sequence that can be uploaded on the web service; the output is a table containing the strain identifier,e-value, and percentage of identity for each of the matches with rows colored in green for hits with high probability of being the same species. The service is available on the web at: http://www.cbs.dtu.dk/services/furIOS-1.0/. Thefur-sequences can be derived either from genome sequences or from PCR-amplification of the genomic region encoding thefurgene. We have used 191 strains identified asVibrionaceaebased on 16S rRNA gene sequence to test the PCR method and the web service on a large dataset. We were able to classify 171 of 191 strains at the species level and 20 strains remained unclassified. Furthermore, thefurphylogenetics and subsequentin silicoDNA-DNA hybridization demonstrated that two strains (ATCC 33789 and ZS-139) previously identified asVibrio splendidusare more closely related toV. tasmaniensisandV. cyclitrophicus, respectively. FurIOS is an easy-to-use online service that allows the identification of bacteria from theVibrionaceaefamily at the species level using thefurgene as a single marker. Its simplistic design and straightforward pipeline makes it suitable for any research environment, from academia to industry.
authors.affiliation: Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark.
authors.forename: Henrique
authors.initials: H
authors.lastname: Machado
authors.affiliation: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby Denmark.
authors.forename: João
authors.initials: J
authors.lastname: Cardoso
authors.affiliation: Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark.
authors.forename: Sonia
authors.initials: S
authors.lastname: Giubergia
authors.affiliation: Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby Denmark.
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Rapacki
authors.affiliation: Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby Denmark.
authors.forename: Lone
authors.initials: L
authors.lastname: Gram
keywords: Photobacterium; Vibrio; Vibrionaceae; fur gene; identification; phylogeny