以貼序法找出牙周病患之口腔環境基因體樣本可能含有的毒力因子分析

Analysis on Potential Virulence Factor Contained in the Metagenome Sample of a Periodontitis Patient by Map Reads to Reference Method

陳立倫(Chen, Li Lun)

指導教授 ： 唐傳義

國立清華大學/電機資訊學院/資訊工程學系/碩士(2015年)

摘要

隨著人們對低成本基因序列檢測的需求與日俱增，推動了高通量測序的發展，而次世代定序( Next Generation Sequencing, NGS)是目前最新且高通量的定序方法。由於次世代定序可在短時間內產生大量的序列資訊，使得可以透過計算機的運算實現對總體基因體學(Metagenomics)的大量研究。本論文藉由次世代定序中的邊合成邊測序方法(Sequencing by synthesis )得到的人體口腔環境總體基因(Whole genome)樣本，探討牙周病病患口腔中的微生物群落，可能含有的毒力因子(Virulence factor)。本論文使用的分析方法為貼序法(Map Reads to Reference)，其中參考序列是由美國能源部勞倫斯利福摩爾國家實驗室(Lawrence Livermore National Laboratory, LLNL)的所建立的毒力因子整合資料庫MvirDB內的資訊組成，而分析結果也找出了數個樣本中可能含有的毒力因子。

關鍵字

總體基因 ； 毒力因子 ； 牙周病

並列摘要

With increasing demand for low-cost sequencing of genome, Next Generation Sequencing (NGS), was developed. NGS features in high throughput property, which means it can produce huge amount of sequences in short time period. This advantage on sequencing had improved the research about metagenomics by utilizing algorithms and computers. In this thesis, we analyzed human oral whole genome produced by Illumina sequencing machine, in order to find potential virulence factors in oral microbiome of periodontitis sufferer. We use Map Reads to Reference method to analyze the sample with reference sequence formed by the elements in MvirDB established by Lawrence Livermore National Laboratory (LLNL), which is in fact an integration database of several virulence database. The result shows that different type of virulence factors were found in 8 samples, and each of them benefits pathogens in its own ways.

並列關鍵字

metagenomics ； virulence factor ； periodontitis

參考文獻

[2] A.M. Richards, Y. Abu Kwaik, and R.J. Lamont, "Code blue: Acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity". Molecular Oral Microbiology Volume 30, Issue 1, pages 2–15, February 2015.

[3] W. J. Loesche, S. A. Syed, and J. Stoll, "Trypsin-Like Activity in Subgingival Plaque A Diagnostic Marker for Spirochetes and Periodontal Disease?". Journal of Periodontology. April 1987, Vol. 58, No. 4, Pages 266-273 , DOI 10.1902/jop.1987.58.4.266.

[4] E. STACKEBRANDT, B. M. GOEBEL, "Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology". Int J Syst Evol Microbiol, October 1994, 44: 846-849.

[5] Ulrike Edwards, Till Rogall, Helmut Blöcker1, Monica Emde and Erik C. Böttger, "Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA ". Nucl. Acids Res., 1989, 17(19):7843-7853.

[6] Alan S Cross, "What is a virulence factor?". Crit Care. 2008, 12(6): 196.