title: A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.
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).
authors.affiliation: Genomic Research Laboratory, Department of Internal Medicine, Service of Infectious Diseases, Geneva University Hospitals, Gabrielle-Perret-Gentil 4, CH-1211 Geneva 14, Switzerland. katrinewhiteson@gmail.com.
authors.forename: Katrine L
authors.initials: KL
authors.lastname: Whiteson
authors.forename: David
authors.initials: D
authors.lastname: Hernandez
authors.forename: Vladimir
authors.initials: V
authors.lastname: Lazarevic
authors.forename: Nadia
authors.initials: N
authors.lastname: Gaia
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.forename: Patrice
authors.initials: P
authors.lastname: François
authors.forename: Paola
authors.initials: P
authors.lastname: Pilo
authors.forename: Joachim
authors.initials: J
authors.lastname: Frey
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
mesh_terms: D042401:Alcaligenaceae / Q000145:classification / Q000235:genetics*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics; D020451:Contig Mapping; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S