The fur Gene as a New Phylogenetic Marker for Vibrionaceae Species Identification

Abstract

bMicrobial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family Vibrionaceae, where other molecular techniques allow better interspecies resolution. Although multilocus sequence analysis (MLSA) has been used successfully in the identification of Vibrio species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an in silico approach based on genomes from 103 Vibrionaceae strains, we demonstrate here the high resolution of the fur gene in the identification of Vibrionaceae species and its usefulness as a phylogenetic marker. The fur gene showed within-species similarity higher than 95%, and the relationships inferred from its use were in agreement with those observed for 16S rRNA analysis and MLSA. Furthermore, we developed a fur PCR sequencing-based method that allowed identification of Vibrio species. The discovery of the phylogenetic power of the fur gene and the development of a PCR method that can be used in amplification and sequencing of the gene are of general interest whether for use alone or together with the previously suggested loci in an MLSA.

Influence of Niche-Specific Nutrients on Secondary Metabolism in Vibrionaceae

“…Strains were selected based on their abilities to inhibit the growth of Vibrio anguillarum and were identified as Vibrionaceae based on their 16S rRNA gene sequences (17). Species affiliation of strains producing antibacterial extracts (see below), which had not been previously assigned to a species by multilocus sequence analysis, was carried out by analysis of the fur gene (29). The fur gene sequences were retrieved from whole-genome sequences (WGS) or sequencing of PCR products, obtained as described elsewhere (29).…”

“…Species affiliation of strains producing antibacterial extracts (see below), which had not been previously assigned to a species by multilocus sequence analysis, was carried out by analysis of the fur gene (29). The fur gene sequences were retrieved from whole-genome sequences (WGS) or sequencing of PCR products, obtained as described elsewhere (29).…”

Vibrio galatheae sp. nov., a member of the family Vibrionaceae isolated from a mussel

“…Based on the 16S rRNA T , sharing 98.5, 98.3, 98.2 and 97.8 % similarity, respectively. However, due to the low interspecies resolution that can be obtained in Vibrionaceae by using the 16S rRNA gene sequence (Sawabe et al, 2007), two phylogenetic trees based on complete sequences of the recently proposed Vibrionaceae phylogenetic marker fur gene (Machado & Gram, 2015) (Fig. 2) and on the concatenated sequences of five housekeeping genes (Fig.…”

“…3) were reconstructed. These phylogenetic trees were obtained as described above and elsewhere (Machado & Gram, 2015;Sawabe et al, 2013;Thompson et al, 2005). For the fur gene phylogenetic tree, gene sequences were obtained either by PCR-based gene amplification followed by sequencing as described previously (Machado & Gram, 2015), or from whole genome sequences as described above.…”

“…These phylogenetic trees were obtained as described above and elsewhere (Machado & Gram, 2015;Sawabe et al, 2013;Thompson et al, 2005). For the fur gene phylogenetic tree, gene sequences were obtained either by PCR-based gene amplification followed by sequencing as described previously (Machado & Gram, 2015), or from whole genome sequences as described above. For the multilocus sequence analysis, sequences of the 16S rRNA, DNA gyrase subunit B (gyrB), uridylate kinase (pyrH), recombinant protein RecA (recA) and DNA topoisomerase I (topA) genes were retrieved from the GenBank database or from whole genome sequences, as described above.…”