FurIOS: a web-based tool for identification of Vibrionaceae species using the fur gene

Henrique Machado, Joao Cardoso, Sonia Giubergia, Kristoffer Rapacki, Lone Gram

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Abstract

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
Original languageEnglish
Article number414
JournalBMC Microbiology
Volume8
Number of pages8
ISSN1471-2180
DOIs
Publication statusPublished - 2017

Bibliographical note

Copyright © 2017 Machado, Cardoso, Giubergia, Rapacki and Gram. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Keywords

  • Vibrionaceae
  • Vibrio
  • Photobacterium
  • Fur gene
  • Phylogeny
  • Identification

Cite this

Machado, Henrique ; Cardoso, Joao ; Giubergia, Sonia ; Rapacki, Kristoffer ; Gram, Lone. / FurIOS: a web-based tool for identification of Vibrionaceae species using the fur gene. In: BMC Microbiology. 2017 ; Vol. 8.
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FurIOS: a web-based tool for identification of Vibrionaceae species using the fur gene. / Machado, Henrique; Cardoso, Joao; Giubergia, Sonia; Rapacki, Kristoffer; Gram, Lone.

In: BMC Microbiology, Vol. 8, 414, 2017.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - FurIOS: a web-based tool for identification of Vibrionaceae species using the fur gene

AU - Machado, Henrique

AU - Cardoso, Joao

AU - Giubergia, Sonia

AU - Rapacki, Kristoffer

AU - Gram, Lone

N1 - Copyright © 2017 Machado, Cardoso, Giubergia, Rapacki and Gram. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

PY - 2017

Y1 - 2017

N2 - 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

AB - 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

KW - Vibrionaceae

KW - Vibrio

KW - Photobacterium

KW - Fur gene

KW - Phylogeny

KW - Identification

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DO - 10.3389/fmicb.2017.00414

M3 - Journal article

VL - 8

JO - B M C Microbiology

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