MicroOrganism Identifier:微生物有效識別法以乳酸菌為例

Abstract

微生物的鑑定方法已經發展了數十年，但仍然需要繁鎖的操作步驟及費用才能完成鑑定工作。乳酸菌是一群多樣性很高的微生物，由於乳酸廣泛運用在食品工業上，非常需要一個可靠又正確的物種鑑定方法。因此本研究以乳酸菌為樣本來開發一個網頁工具來設計特殊的聚合酶連鎖反應引子，並藉由放大的聚合酶連鎖反應片段分析來完成微生物鑑定。我們先找出這些structural RNA在基因組上的位置。兩個相鄰structural RNA 之間的距離在不同的基因組上可能會不同。因此我們選出這些structural RNA pair來區分這些微生物基因組。structural RNA序列中的保守區域被我們用來設計聚合酶連鎖反應引子。最後我們也提出有效率的演算法找出最佳的引子組合來完成物種鑑定之工作。

The identifiable methods of microorganism have been developed for decades but still cannot get rid of the complex operation, long time waiting and expensive cost. The lactic acid bacteria (LAB) are one of the large and variable subgroup in microorganisms. Due to the prominent application of LAB in food industry, the correct and reliable species identification of LAB is an important issue. In this study, we use LAB as example to develop a web tool, which can design specific PCR primers for distinguishing microorganism by amplified fragment length analyses. We first annotated the structural RNAs in microorganism. The intergenic length between two neighboring structural RNAs may differ among microorganisms. We therefore can select several such neighboring structural RNA pairs which have various intergenic lengths. These structural RNA pairs can be used to distinguish the genomes of our interested microorganism. The conserved regions of the structural RNAs were used to design specific PCR primers. Finally, we proposed a heuristic algorithm that could effectively design as few suitable primers as possible to classify all the interested microorganisms.