臺灣博碩士論文加值系統

對於微生物的研究中，了解到龐大族群的細菌在生物分類上極其重要，未被發現的細菌可能存在著特殊基因及功能特性。本研究是以台灣的水域作為細菌樣本的採集來源，進行微生物的純化與篩選，進而予以鑑定、分類與命名。同時以Rapid Annotation using Subsystem Technology (RAST)、Kyoto Encyclopedia of Genes and Genomes (KEGG)與Clusters of Orthologous Groups (COG)等註解系統研究細菌的基因組。三株具有成為新分類群的菌株，分別為菌株CYK-10、KMS-5、ICH-3，以表現型、化學型與基因型進行分類研究，並與系統發育密切相關的模式菌株做比較，得到的實驗結果證明此三株菌株與密切相近的模式菌株皆有差別。確認菌株CYK-10為Rhodobacteraceae科的新屬新種之細菌，並將其命名為Prolixibaculum tardum，菌株KMS-5為Tabrizicola屬的新種細菌，命名為Tabrizicola oligotrophica，菌株ICH-3為Rubrivivax屬的新種細菌，命名為Rubrivivax albus。基因註解應用在細菌的分類是具有一定程度的指標性跟可行性的，但實驗中發現系統所註解的功能與實際的實驗結果存在差異性，對於具有矛盾的地方可做為往後實驗的探討，可用於往後改變實驗的參數或是更完善註解系統的完整性。

In the study of microorganisms, it is known that bacteria of a large group are extremely important in taxonomy, and undiscovered bacteria may have special genetic and functional characteristics. This study uses Taiwan's waters as a source of bacterial samples for microbial purification and screening, and then identifies, classifies and names them. At the same time, the genome of the bacteria was studied by an annotation system such as Rapid Annotation using Subsystem Technology (RAST), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG). Three strains with new taxonomic group, namely strains CYK-10(T), KMS-5(T) and ICH-3(T), were classified by phenotype, chemotaxonomicaltype and genotype, and compared with phylogenetic closely related strains. The experimental results obtained prove that the three strains are different from the closely related strains. Strain CYK-10(T) was as a new genus of the Rhodobacteraceae family and named as Prolixibaculum tardum. Strain KMS-5(T) was a new species of the genus Tabrizicola, named Tabrizicola oligotrophica. Strain ICH-3(T) was a new species of the genus Rubrivivax. Named Rubrivivax albus. The application of gene annotation in bacterial classification has certain indicators and feasibility, but in the experiment, it is found that the function of annotation is different from the actual experimental results, and the contradiction can be used to discuss later experiments. It can be used to change the parameters of the experiment later or to improve the integrity of the annotation system.

壹、 緒論 1
1. 前言 1
2. 研究動機 2
3. 研究目的 3
貳、 文獻回顧 4
1. 微生物分類學 4
2. 表現型分類 4
3. 化學型分類 5
3.1. 極性脂肪 6
3.2. 醌型 7
3.3. 多胺 9
3.4. 脂肪酸 9
4. 基因型分類 10
4.1. DNA G+C含量 10
4.2. DNA-DNA雜交 10
4.3. 16S rRNA基因序列比較 11
4.4. 平均核苷酸同源性 14
4.5. 系統發育樹 15
5. 新種(屬)細菌之分類標準 16
6. 基因註解 17
6.1. Rapid Annotation using Subsystem Technology 17
6.2. Kyoto Encyclopedia of Genes and Genomes 17
6.3. Clusters of Orthologous Groups 18
參、 材料與方法 20
1. 實驗流程與架構 20
2. 發現新種(屬)菌株之步驟 22
3. 樣品採集與分離純化 22
3.1. 菌株保存 23
3.2. SDS-PAGE電泳圖譜分析 24
3.3. 樣品製備處理 24
3.4. SDS-PAGE膠體製備 26
3.5. SDS-PAGE電泳分析 26
3.6. DNA 萃取 28
3.7. 16S rRNA基因定序 28
3.8. 16S rRNA親緣性比對 31
3.9. 系統發育樹建立 31
4. 新種(屬)菌株特徵 32
5. 形態學 (MORPHOLOGY) 33
5.1. 菌落描述 33
5.2. 菌體描述 34
5.3. 其他形態描述 40
6. 生理生化特性 44
6.1. 生長條件測試 44
6.2. 培養基生長測試 46
6.3. 氧氣需求 50
6.4. 光合作用測試 50
6.5. 生化代謝 52
6.6. 色素分析 53
6.7. 抗生素感受性 54
6.8. 水解試驗 58
6.9. Analytical Profile Index鑑定 65
6.10. 單一碳源利用測試 70
7. 化學型(CHEMOTYPE) 72
7.1. 極性脂肪分析 72
7.2. 脂肪酸分析 77
7.3. 多胺分析 79
7.4. 醌型分析 83
8. 基因型(GENOTYPE) 87
8.1. 16S rRNA基因定序 87
8.2. 全基因組定序 87
8.3. 序列登記 88
8.4. Overall genome relatedness index計算分析 88
8.5. 16S rRNA基因親緣性比對 88
8.6. 系統發育樹建立 88
9. 基因註解 92
肆、 結果與討論 94
1. 樣品採集 94
2. 菌株分離與純化 95
3. 初步鑑定 95
4. 分類與鑑定 98
4.1. 菌株CYK-10之分類鑑定 98
4.2. 菌株KMS-5之分類鑑定 116
4.3. 菌株ICH-3之分類鑑定 132
伍、 結論 179
陸、 參考資料 184

Amakata, D., Matsuo, Y., Shimono, K., Park, J. K., Yun, C. S., Matsuda, H., ... & Kawamukai, M. (2005). Mitsuaria chitosanitabida gen. nov., sp. nov., an aerobic, chitosanase-producing member of the ‘Betaproteobacteria’. International journal of systematic and evolutionary microbiology, 55(5), 1927-1932.

Angiuoli, S. V., Matalka, M., Gussman, A., Galens, K., Vangala, M., Riley, D. R., ... & Fricke, W. F. (2011). CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC bioinformatics, 12(1), 356.

Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., ... & Meyer, F. (2008). The RAST Server: rapid annotations using subsystems technology. BMC genomics, 9(1), 75.

Aziz, M. A., Cabral, J. D., Brooks, H. J., Moratti, S. C., & Hanton, L. R. (2012). Antimicrobial properties of a chitosan dextran-based hydrogel for surgical use. Antimicrobial agents and chemotherapy, 56(1), 280-287.

Bear, R., Rintoul, D., Snyder, B., Smith-Caldas, M., Herren, C., & Horne, E. (2016). Overview of Cellular Respiration. Principles of Biology. OpenStax CNX. Last modified May, 13.

Breakwell, D. P., Moyes, R. B., & Reynolds, J. (2009). Differential staining of bacteria: capsule stain. Current protocols in microbiology, 15(1), A-3I.

Brenner, D. J., Staley, J. T., & Krieg, N. R. (2005). Classification of procaryotic organisms and the concept of bacterial speciation. In Bergey’s Manual «of Systematic Bacteriology (pp. 27-32). Springer, Boston, MA.

Buck, J. D. (1982). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl. Environ. Microbiol., 44(4), 992-993.

Busse, H. J., Denner, E. B., & Lubitz, W. (1996). Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. Journal of biotechnology, 47(1), 3-38.

Busse, J., & Auling, G. (1988). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Systematic and Applied Microbiology, 11(1), 1-8.

Chien, A., Edgar, D. B., & Trela, J. M. (1976). Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. Journal of bacteriology, 127(3), 1550-1557.

Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D. R., da Costa, M. S., ... & Trujillo, M. E. (2018). Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. International journal of systematic and evolutionary microbiology, 68(1), 461-466.

Collins, M. D. (1994). Isoprenoid quinones. Chemical Methods in Prokaryotic Systematics, 265-309.

Colston, S. M., Fullmer, M. S., Beka, L., Lamy, B., Gogarten, J. P., & Graf, J. (2014). Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. MBio, 5(6), e02136-14.

Da Costa, M. S., Albuquerque, L., Nobre, M. F., & Wait, R. (2011). The identification of polar lipids in prokaryotes. In Methods in microbiology (Vol. 38, pp. 165-181). Academic Press.

Dance, D. A., Wuthiekanun, V., Naigowit, P., & White, N. J. (1989). Identification of Pseudomonas pseudomallei in clinical practice: use of simple screening tests and API 20NE. Journal of clinical pathology, 42(6), 645-648.

De Ley, J. (1968). Molecular biology and bacterial phylogeny. In Evolutionary biology (pp. 103-156). Springer, Boston, MA.

Dees, S. B., & Moss, C. W. (1975). Cellular fatty acids of Alcaligenes and Pseudomonas species isolated from clinical specimens. Journal of clinical microbiology, 1(5), 414-419.

Deutschbauer, A. M., Chivian, D., & Arkin, A. P. (2006). Genomics for environmental microbiology. Current opinion in biotechnology, 17(3), 229-235.

Drews, G. (2000). The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century. FEMS microbiology reviews, 24(3), 225-249.

Eliopoulos, G. M., & Huovinen, P. (2001). Resistance to trimethoprim-sulfamethoxazole. Clinical infectious diseases, 32(11), 1608-1614.

EZbiocloud. Help center COG Colors. Taken from 7 August 2019. The URL : https://help.ezbiocloud.net/cog-colors/

Fox, G. E., Pechman, K. R., & Woese, C. R. (1977). Comparative cataloging of 16S ribosomal ribonucleic acid: molecular approach to procaryotic systematics. International Journal of Systematic and Evolutionary Microbiology, 27(1), 44-57.

Fujie, K., Hu, H. Y., Tanaka, H., Urano, K., Saitou, K., & Katayama, A. (1998). Analysis of respiratory quinones in soil for characterization of microbiota. Soil science and plant nutrition, 44(3), 393-404.

Gest, H. (2004). The discovery of microorganisms by Robert Hooke and Antoni Van Leeuwenhoek, fellows of the Royal Society. Notes and records of the Royal Society of London, 58(2), 187-201.

Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P., & Tiedje, J. M. (2007). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. International journal of systematic and evolutionary microbiology, 57(1), 81-91.

Goodfellow, M., & O'Donnell, A. G. (1994). Chemical methods in prokaryotic systematics. Wiley.

Goss, W. A., Deitz, W. H., & Cook, T. M. (1965). Mechanism of action of nalidixic acid on Escherichia coli II. Inhibition of deoxyribonucleic acid synthesis. Journal of Bacteriology, 89(4), 1068-1074.

Hall, T. (2001). BioEdit version 5.0. 6. North Carolina State University, Department of Microbiology, Raleigh, North Carolina, 192.

Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., & Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry & biology, 5(10), R245-R249.

Henrichsen, J. (1972). Bacterial surface translocation: a survey and a classification. Bacteriological reviews, 36(4), 478.

Hiraishi, A., Yamanaka, Y., & Narihiro, T. (2000). Seasonal microbial community dynamics in a flowerpot-using personal composting system for disposal of household biowaste. The Journal of general and applied microbiology, 46(3), 133-146.

Hotta, K., YAMAMOTO, H., OKAMI, Y., & UMEZAWA, H. (1981). Resistance mechanisms of kanamycin-, neomycin-, and streptomycin-producing streptomycetes to aminoglycoside antibiotics. The Journal of antibiotics, 34(9), 1175-1182.

Hucker, G. J., & Conn, H. J. (1923). Methods of Gram staining.

Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017). Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Molecular biology and evolution, 34(8), 2115-2122.

Humble, M. W., King, A., & Phillips, I. (1977). API ZYM: a simple rapid system for the detection of bacterial enzymes. Journal of Clinical Pathology, 30(3), 275-277.

Johansson, B. G. (1972). Agarose gel electrophoresis. Scandinavian Journal of Clinical and Laboratory Investigation, 29(sup124), 7-19.

Jurtshuk Jr, P., Mueller, T. J., McQuitty, D. N., & Riley, W. H. (1978). The cytochrome oxidase reaction in Azotobacter vinelandii and other bacteria. In Functions of alternative terminal oxidases (pp. 99-121). Pergamon.

Kanehisa, M., Sato, Y., & Morishima, K. (2016). BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. Journal of molecular biology, 428(4), 726-731.

Katayama, A., Funasaka, K., & Fujie, K. (2001). Changes in the respiratory quinone profile of a soil treated with pesticides. Biology and fertility of soils, 33(6), 454-459.

Kearns, D. B. (2010). A field guide to bacterial swarming motility. Nature Reviews Microbiology, 8(9), 634.

Kim, M., Oh, H. S., Park, S. C., & Chun, J. (2014). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International journal of systematic and evolutionary microbiology, 64(2), 346-351.

Ko, C. Y., Johnson, J. L., Barnett, L. B., McNair, H. M., & Vercellotti, J. R. (1977). A sensitive estimation of the percentage of guanine plus cytosine in deoxyribonucleic acid by high performance liquid chromatography. Analytical biochemistry, 80(1), 183-192.

Komagata, K., & Suzuki, K. I. (1988). 4 Lipid and cell-wall analysis in bacterial systematics. In Methods in microbiology(Vol. 19, pp. 161-207). Academic Press.

Konstantinidis, K. T., & Tiedje, J. M. (2007). Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Current opinion in microbiology, 10(5), 504-509.

Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution, 33(7), 1870-1874.

Kwon, K. K., Lee, H. S., Jung, H. B., Kang, J. H., & Kim, S. J. (2006). Yeosuana aromativorans gen. nov., sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae, isolated from estuarine sediment of the South Sea, Korea. International journal of systematic and evolutionary microbiology, 56(4), 727-732.

Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seeliger, H. P. R., & Clark, W. A. (1992). International code of nomenclature of bacteria: bacteriological code, 1990 revision. ASM Press.

Lee, I., Kim, Y. O., Park, S. C., & Chun, J. (2016). OrthoANI: an improved algorithm and software for calculating average nucleotide identity. International journal of systematic and evolutionary microbiology, 66(2), 1100-1103.

Lee, I., Chalita, M., Ha, S. M., Na, S. I., Yoon, S. H., & Chun, J. (2017). ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. International journal of systematic and evolutionary microbiology, 67(6), 2053-2057.

Li, W. J., Zhang, Y. Q., Schumann, P., Tian, X. P., Zhang, Y. Q., Xu, L. H., & Jiang, C. L. (2006). Sinococcus qinghaiensis gen. nov., sp. nov., a novel member of the order Bacillales from a saline soil in China. International journal of systematic and evolutionary microbiology, 56(6), 1189-1192.

Liang, K., Orata, F. D., Winkjer, N. S., Rowe, L. A., Tarr, C. L., & Boucher, Y. (2017). Complete Genome Sequence of Vibrio sp. Strain 2521-89, a Close Relative of Vibrio cholerae Isolated from Lake Water in New Mexico, USA. Genome Announc., 5(35), e00905-17.

Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P., & Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC bioinformatics, 14(1), 60.

Miller, L. T. (1982). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. Journal of Clinical Microbiology, 16(3), 584-586.

Minnikin, D. E., O'donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. Journal of Microbiological Methods, 2(5), 233-241.

Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C., & Kanehisa, M. (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic acids research, 35(suppl_2), W182-W185.

Moss, C. W. (1981). Gas-liquid chromatography as an analytical tool in microbiology. Journal of Chromatography A, 203, 337-347.

Moss, C. W. (1985). Uses of gas-liquid chromatography and high-pressure liquid chromatography in clinical microbiology. In Manual of Clinical Microbiology (pp. 1029-1036). American Society for Microbiology Washington, DC.

Na, S. I., Kim, Y. O., Yoon, S. H., Ha, S. M., Baek, I., & Chun, J. (2018). UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. journal of microbiology, 56(4), 280-285.

Nguyen, T. M., & Kim, J. (2017). A rapid and simple method for identifying bacterial polar lipid components in wet biomass. Journal of Microbiology, 55(8), 635-639.

Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T., ... & Vonstein, V. (2013). The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic acids research, 42(D1), D206-D214.

Park, M. H., & Igarashi, K. (2013). Polyamines and their metabolites as diagnostic markers of human diseases. Biomolecules & therapeutics, 21(1), 1.

Perry, S. F. (1998). Freeze-drying and cryopreservation of bacteria. Molecular biotechnology, 9(1), 59-64.

Rainey, F. A. (2011). How to describe new species of prokaryotes. In Methods in microbiology (Vol. 38, pp. 7-14). Academic Press.

Ramana, C. V., Sasikala, C., Arunasri, K., Kumar, P. A., Srinivas, T. N. R., Shivaji, S., ... & Imhoff, J. F. (2006). Rubrivivax benzoatilyticus sp. nov., an aromatic, hydrocarbon-degrading purple betaproteobacterium. International journal of systematic and evolutionary microbiology, 56(9), 2157-2164.

Rappé, M. S., & Giovannoni, S. J. (2003). The uncultured microbial majority. Annual Reviews in Microbiology, 57(1), 369-394.

Richter, M., & Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences, 106(45), 19126-19131.

Schägger, H. (2006). Tricine–sds-page. Nature protocols, 1(1), 16.

Schleifer, K. H. (2009). Classification of Bacteria and Archaea: past, present and future. Systematic and applied microbiology, 32(8), 533-542.

Schlessinger, D. A. V. I. D. (1988). Failure of aminoglycoside antibiotics to kill anaerobic, low-pH, and resistant cultures. Clinical microbiology reviews, 1(1), 54-59.

SHIGI, Y., MATSUMOTO, Y., KAIZU, M., FUJISHITA, Y., & KOJO, H. (1984). Mechanism of action of the new orally active cephalosporin FK027. The Journal of antibiotics, 37(7), 790-796.

Smith, D. H., & Davis, B. D. (1967). Mode of action of novobiocin in Escherichia coli. Journal of bacteriology, 93(1), 71-79.

Stackebrandt, E., & GOEBEL, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International journal of systematic and evolutionary microbiology, 44(4), 846-849.

Stotz, E., Sidwell Jr, A. E., & Hogness, T. R. (1938). The role of the cytochromes in the action of" indophenol oxidase.". J. biol. Chem, 124, 733.

Taguchi, S., Maehara, A., Takase, K., Nakahara, M., Nakamura, H., & Doi, Y. (2001). Analysis of mutational effects of a polyhydroxybutyrate (PHB) polymerase on bacterial PHB accumulation using an in vivo assay system. FEMS microbiology letters, 198(1), 65-71.

Tamaoka, J., & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS microbiology letters, 25(1), 125-128.

Tatusov, R. L., Galperin, M. Y., Natale, D. A., & Koonin, E. V. (2000). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic acids research, 28(1), 33-36.

Tindall, B. J., Rosselló-Móra, R., Busse, H. J., Ludwig, W., & Kämpfer, P. (2010). Notes on the characterization of prokaryote strains for taxonomic purposes. International journal of systematic and evolutionary microbiology, 60(1), 249-266.

Tittsler, R. P., & Sandholzer, L. A. (1936). The use of semi-solid agar for the detection of bacterial motility. Journal of bacteriology, 31(6), 575.

Tringe, S. G., Von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K., Chang, H. W., ... & Bork, P. (2005). Comparative metagenomics of microbial communities. Science, 308(5721), 554-557.

Vartoukian, S. R., Palmer, R. M., & Wade, W. G. (2010). Strategies for culture of ‘unculturable’bacteria. FEMS microbiology letters, 309(1), 1-7.

Veys, A., Callewaert, W. A. L. T. E. R., Waelkens, E., & Van den Abbeele, K. A. R. E. L. (1989). Application of gas-liquid chromatography to the routine identification of nonfermenting gram-negative bacteria in clinical specimens. Journal of clinical microbiology, 27(7), 1538-1542.

Waksman, S. A. (1947). What is an antibiotic or an antibiotic substance?. Mycologia, 39(5), 565-569.

Warren, R. A. J. (1996). Microbial hydrolysis of polysaccharides. Annual review of microbiology, 50(1), 183-212.

Wehrli, W. (1983). Rifampin: mechanisms of action and resistance. Reviews of infectious diseases, 5(Supplement_3), S407-S411.

Willems, A., Gillis, M., & De Ley, J. (1991). Transfer of Rhodocyclus gelatinosus to Rubrivivax gelatinosus gen. nov., comb. nov., and phylogenetic relationships with Leptothrix, Sphaerotilus natans, Pseudomonas saccharophila, and Alcaligenes latus. International journal of systematic and evolutionary microbiology, 41(1), 65-73.

Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L., & Koonin, E. V. (2001). Genome trees constructed using five different approaches suggest new major bacterial clades. BMC evolutionary biology, 1(1), 8.

Yao, X. W., Zhou, M., Cao, Y. Y., Jiang, Y. Y., & Center, N. D. R. D. (2014). Recent progress of polyamines in microorganisms. Chinese Journal of Mycology, 9(2), 114-118.

Yarza, P., Richter, M., Peplies, J., Euzeby, J., Amann, R., Schleifer, K. H., ... & Rosselló-Móra, R. (2008). The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Systematic and applied microbiology, 31(4), 241-250.

Zhang, W., Du, P., Zheng, H., Yu, W., Wan, L., & Chen, C. (2014). Whole-genome sequence comparison as a method for improving bacterial species definition. The Journal of general and applied microbiology, 60(2), 75-78.

Zhong-Hua, H. H. Y. T. (2002). Bacterial quinone profile for the study of microbial community structure in environmental samples [J]. Microbiology, 4.

Zottig, X., Meddeb-Mouelhi, F., & Beauregard, M. (2016). Development of a high-throughput liquid state assay for lipase activity using natural substrates and rhodamine B. Analytical biochemistry, 496, 25-29.

萬滔(2018)。基於麥氏比濁原理的細菌濁度分析儀校準方法探討。 計量與測試技術， 45(7)，117-119。

王玲燕、李元(2002)。微生物胞外多糖生物合成研究進展。藥物生物技術， 9(6)，369-373。

王效義、暢瑞馥(2003)。高效液相色譜法(HPLC)在微生物分析鑒定中的應用。微生物學免疫學進展， 31(3)，56-61。

龍雯、陳存社(2006)。16S rRNA 測序在細菌鑒定中的應用。北京工商大學學報 (自然科學版)， 24(5)，10-12。

湯偉、劉敏、張燚、陳瀅、莫娟(2014)。紫外分光光度法測定產氫顆粒污泥中聚-β-羥基丁酸酯的含量。理化檢驗-化學分冊， 50(8)，954。

張冬梅、 阿穎利、宋靜(2012)。青黴素的抗菌作用機制及合理使用分析。 求醫問藥: 下半月刊，10(8)，149-149。

李婷(2015)。鏈黴菌產生的(4S/R)-4，5-雙氫-4-羥基格爾德黴素及其他新次級代謝產物的發現與探索。Doctoral dissertation，北京協和醫學院。

楊瑾、勵建榮、顧青(2006)。乳酸菌代謝工程的研究與應用。食品研究與開發，27(10)，149-153。
谷海瀛(2006)。形態學檢查方法的標準化及其在細菌鑒定中的作用。Doctoral dissertation。

連淑華、李珮玲、葉美伶、王德原(2011)。九十九年抗生素製劑之品質監測。食品藥物研究年報，(2)，261-269。

陳玉珊(2015)。從龜山島海底熱泉分離出一株高溫菌Thermoanaerobacterium saccharolyticum NTOU1之基因序列分析草稿。國立臺灣海洋大學海洋生物研究所碩士論文，基隆市。

郭雅萍(2019)。分離自淡水環境中的新屬新種擬桿菌和變形菌之分類學研究。國立高雄科技大學海洋生物技術系碩士論文，高雄市。

陳威廷(2004)。纖維素水解菌之培養策略與纖維素水解酵素之鑑定。成功大學化學工程學系學位元論文，1-76。

黃淑芬、郜晨、劉麗輝、譚志遠、彭桂香(2018)。植物內生固氮菌系統發育進化新進展。微生物學通報，45(1)，181-190。

惠文彥、張和平(2016)。基因組分析方法在微生物分類學中的應用。微生物學通報、43(5)、1136-1142。

隋新華(2015)。原核生物進化與系統分類學實驗教程。北京科學出版社 1。

黃至昶、黃憲達(2009)。建立基因體計畫的計算流程:序列重組、基因註解與重建代謝路徑 (Doctoral dissertation)。

賀紀正、張麗梅、沈菊培、朱永官(2008)。宏基因組學 (Metagenomics) 的研究現狀和發展趨勢 (Doctoral dissertation)。

劉麗萍(2016)。分離自台灣淡水與海水的新屬新種菌株之鑑定與特性分析。國立高雄海洋科技大學水產食品科學研究所碩士論文、高雄市。

鄧小晨、胡承、汪復進、賴志河、李慶孝(2008)。微生物學。新文京開發出版有限公司。

戴寄帆、王雪娟、王中原、劉丹英(1986)。用 KOH 試驗鑒別革蘭氏陰、陽性菌。臨床檢驗雜誌、 (2)、 11。

魏林陽、徐金晶、吳紅軍(2007)。水產品中氯黴素殘留的氣質聯用法檢測。光譜實驗室、 24(2)、201-205。

魏培蓮(2002)。微生物胞外多糖研究進展。浙江科技學院學報、 14(2)、 8-12。