Abstract
BackgroundA 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.ResultsGenome 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.ConclusionsClassification 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).
Highlights
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
Bacterium identification At necropsy, the post mortem examination of the parakeet revealed that the liver had a marbled surface and the spleen was swollen
Bacterial culture of the lung and liver revealed the presence of small Gram-negative, non-haemolytic, non-motile rods in the lung
Summary
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. Alcaligenaceae that was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) from a petshop in Basel, Switzerland. The bacterial family Alcaligenaceae includes genera that have been isolated from humans, animals and the environment. They are Gram-negative rods or coccobacilli that possess oxidase and catalase, growing well on complex media under aerobic or microaerobic conditions. There are nearly 25000 prokaryote genome projects registered in the NCBI database as of early 2014 [2], many of them human-associated. Filling out the tree of life is important for improving genome sequence annotation and creating good phylogenetic landmarks to analyze metagenomic data [3,4]
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