Journal article
FurIOS: a web-based tool for identification of Vibrionaceae species using the fur gene
Department of Systems Biology, Technical University of Denmark1
Bacterial Ecophysiology and Biotechnology, Department of Systems Biology, Technical University of Denmark2
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark3
iLoop, Translational Management, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark4
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark5
Department of Bio and Health Informatics, Technical University of Denmark6
Genomic Epidemiology, Department of Bio and Health Informatics, Technical University of Denmark7
Department of Biotechnology and Biomedicine, Technical University of Denmark8
Bacterial Ecophysiology and Biotechnology, Section for Microbial and Chemical Ecology, Department of Biotechnology and Biomedicine, Technical University of Denmark9
Gene based methods for identification of species from the Vibrionaceae family have been developed during the last decades to address the limitations of the commonly used 16S rRNA gene phylogeny. Recently, we found that the ferric-uptake regulator gene (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 of Vibrionaceae species based on their fur-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/. The fur-sequences can be derived either from genome sequences or from PCR-amplification of the genomic region encoding the fur gene. We have used 191 strains identified as Vibrionaceae based 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, the fur phylogenetics and subsequent in silico DNA-DNA hybridization demonstrated that two strains (ATCC 33789 and ZS-139) previously identified as Vibrio splendidus are more closely related to V. tasmaniensis and V. cyclitrophicus, respectively.
FurIOS is an easy-to-use online service that allows the identification of bacteria from the Vibrionaceae family at the species level using the fur gene as a single marker. Its simplistic design and straightforward pipeline makes it suitable for any research environment, from academia to industry. Introduction
Language: | English |
---|---|
Publisher: | Frontiers Media S.A. |
Year: | 2017 |
Pages: | 414 |
ISSN: | 1664302x and 14712180 |
Types: | Journal article |
DOI: | 10.3389/fmicb.2017.00414 |
ORCIDs: | Cardoso, Joao , Giubergia, Sonia and Gram, Lone |