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Open Access Highly Accessed Research article

A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis

Katrine L Whiteson15*, David Hernandez1, Vladimir Lazarevic1, Nadia Gaia1, Laurent Farinelli2, Patrice François1, Paola Pilo3, Joachim Frey3 and Jacques Schrenzel14

Author Affiliations

1 Genomic Research Laboratory, Department of Internal Medicine, Service of Infectious Diseases, Geneva University Hospitals, Gabrielle-Perret-Gentil 4, CH-1211 Geneva 14, Switzerland

2 Fasteris SA, CH-1228 Plan-les-Ouates, Switzerland

3 Institute of Veterinary Bacteriology, University of Bern, Länggassstrasse 122, Postfach, CH-3001 Bern, Switzerland

4 Clinical Microbiology Laboratory, Department of Internal Medicine, Service of Infectious Diseases, Geneva University Hospitals, Gabrielle-Perret-Gentil 4, CH-1211 Geneva 14, Switzerland

5 Current address: Department of Biology, San Diego State University, San Diego, CA, USA

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BMC Genomics 2014, 15:169  doi:10.1186/1471-2164-15-169

Published: 1 March 2014

Abstract

Background

A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads.

Results

Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis of samples from cages with healthy parakeets suggested that the newly discovered bacterial species is not widespread in parakeet living quarters.

Conclusions

Classification of this organism in the current taxonomy system requires the formation of a new genus and species. We designate the new genus Basilea and the new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111 and GI 406042063).

Keywords:
Bacteria; Parakeet; High-throughput sequencing; Genome; Phylogenetic profile