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

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).