A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.
A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis.
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DOI：
10.1186/1471-2164-15-169
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发表时间：
2014-03-01
期刊：
影响因子：
4.4
通讯作者：
Schrenzel J
中科院分区：
文献类型：
--
作者：
Whiteson KL;Hernandez D;Lazarevic V;Gaia N;Farinelli L;François P;Pilo P;Frey J;Schrenzel J
在瑞士巴塞尔一家宠物店圈养的一只死亡长尾鹦鹉（Melopsittacus undulatus）的肺部发现了一种新的革兰氏阴性、非溶血性、非运动性杆状细菌。该生物体用化学分类学概况和通过短序列读数的组装获得的几乎完整的基因组序列来描述。基因组序列分析和呼吸醌，脂肪酸，极性脂质和生化表型的特点在这里。基因序列的比较显示，最相似的物种是Pelistega europaea，与16 S rDNA基因的BLAST同一性仅为93%，与rpoB基因的同一性为76%，并且与从长尾小鹦鹉中分离的生物DSM 24701（40%）的GC含量相似（~43%）。最接近的全基因组序列是博德特氏菌属的那些。和泰勒菌属（Taylorella spp.）来自Illumina-Solexa平台的高通量测序读段用Edena de novo组装器组装以形成包含约2 Mb基因组的195个重叠群。RAST的基因组注释、16 S rDNA（rrs）基因序列和rpoB基因的系统发育树构建以及ML Tree使用其他高度保守标记基因的系统发育放置均表明该细菌属于产碱菌科。对健康长尾小鹦鹉笼子样本的分析表明，新发现的细菌物种在长尾小鹦鹉生活区并不普遍。在目前的分类系统中，这种生物的分类需要形成一个新的属和种。我们命名为新属Basilea和新种psittacipulmonis。鹦鹉螺的模式菌株是DSM 24701（= CIP 110308 T，16 S rDNA基因序列Genbank登录号JX 412111和GI 406042063）。
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. 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. 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).
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