Brady Carrie, Cleenwerck Ilse, Venter Stephanus, Vancanneyt Marc, Swings Jean, Coutinho Teresa
Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa.
Syst Appl Microbiol. 2008 Dec;31(6-8):447-60. doi: 10.1016/j.syapm.2008.09.004. Epub 2008 Nov 12.
Species belonging to the genus of Pantoea are commonly isolated from plants, humans and the natural environment. The species of the genus are phenotypically closely related, making rapid identification of Pantoea strains to the species level difficult. Multilocus sequence analysis (MLSA) was evaluated as a means for rapid classification and identification of Pantoea strains. Four housekeeping genes, gyrB, rpoB, atpD and infB, were sequenced for strains assigned to the genus. Included in the study were (1) reference strains from the seven currently recognized species of Pantoea, (2) strains belonging to Brenner DNA groups II, IV and V, previously isolated from clinical samples and difficult to identify because of high phenotypic similarity to P. agglomerans or P. ananatis and (3) isolates from diseased Eucalyptus, maize and onion, assigned to the genus on the basis of phenotypic tests. Phylogenetic trees were constructed from the sequences of the four housekeeping genes. The "core"Pantoea species formed a cluster separate from the "Japanese" species which formed a tight cluster that included the genus Tatumella when the tree was based on concatenated sequences of the four genes. The MLSA data further suggested the existence of ten potential novel species, phylogenetically related to the currently recognized Pantoea species and the possible inclusion of Pectobacterium cypripedii in the genus Pantoea. When compared with DNA-DNA hybridization data, a good congruence was observed between both methods, with gyrB sequence data being the most consistent. In conclusion, MLSA of partial nucleotide sequences of the genes gyrB, rpoB, atpD and infB can be used for classification, identification and phylogenetic analyses of Pantoea strains.
泛菌属的物种通常从植物、人类和自然环境中分离得到。该属的物种在表型上密切相关，因此很难将泛菌菌株快速鉴定到种水平。多基因座序列分析（MLSA）被评估为一种快速分类和鉴定泛菌菌株的方法。对归入该属的菌株进行了四个管家基因（gyrB、rpoB、atpD和infB）的测序。该研究包括：（1）来自目前公认的泛菌属七个物种的参考菌株；（2）属于布伦纳DNA组II、IV和V的菌株，这些菌株先前从临床样本中分离得到，由于与成团泛菌或菠萝泛菌表型高度相似而难以鉴定；（3）从患病的桉树、玉米和洋葱中分离得到的菌株，这些菌株根据表型测试归入该属。根据四个管家基因的序列构建了系统发育树。当基于四个基因的串联序列构建系统发育树时，“核心”泛菌物种形成了一个与“日本”物种分开的簇，“日本”物种形成了一个紧密的簇，该簇在包含塔图姆菌属时。MLSA数据进一步表明存在十个潜在的新物种，它们在系统发育上与目前公认的泛菌属物种相关，并且可能将兰科果胶杆菌纳入泛菌属。与DNA-DNA杂交数据相比，两种方法之间观察到良好的一致性，其中gyrB序列数据最为一致。总之，gyrB、rpoB、atpD和infB基因部分核苷酸序列的MLSA可用于泛菌菌株的分类、鉴定和系统发育分析。
