Classification of Bacteria by DNA Genetic Marker and Its Theory

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This journal article is previously published as: Liu Huan. (2021). Classification of Bacteria by DNA Genetic Marker and Its Theory. Journal of Environment and Health Science (ISSN 2314-1628), 2021(02).https://doi.org/10.58473/JBS0002, which is converted into Journal of Biological Sciences (ISSN 2958-4035). Both Journals belong to the same publisher, Liu Huan. The previous journal article is closed to the public, but the previous reference is still valid.

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Latest revised on 25/11/2023.

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Article 1-2. Classification of Bacteria by DNA Genetic Marker and Its Theory/DNA遗传标记与细菌分类以及相关理论

Author: Liu Huan(1983 - ), Master of Science (First Class Honours,2009), The University of Auckland. ORCID: https://orcid.org/0000-0003-4881-8509

However, in addition to the experiment steps discussed for virus classification, a supplementary metabolomics test is advised for further classification of bacteria families, and the detailed methods is presented in other article this journal [5], resulting in more specific classification of bacteria families related to the incidence of pathological characters. In principal, the more enzyme species variation between pathogenic bacteria families, the higher pathogenicity against the epidemiological receptors due to the higher environmental adaptiveness of pathogen families. Consequently, this methodology is listed below:

Step 1. Each bacterium is isolated from bacteria samples, and cultivated separately in situ forming a bacterium stream. Then each bacterium stream is named as stream 1, stream 2,. , stream n.

Step 2. The cytoplasm sample is abstracted in each bacterium stream labeled for subsequent step 8, and the abstracting procedure and storage of isozyme is listed in page 47 of isozyme chapter [1]. Then the chromosome sample of each bacterium stream labeled is prepared for step 2.

Step 3. The molecular cytogenetic karyotype of each bacterium stream labeled is analyzed by fluorescence in situ hybridization (FISH) technique[2] using transmission electron microscopy;

Step 4. These bacterium streams are classified by multivariate cluster analysis and genetic distance analysis on the basis of molecular cytogenetic karyotype, preliminarily leading to different families of bacteria[3];

Step 5. The optima sampling units of each bacteria family, which can well represent the genetic diversity of each bacteria family, is examined and determined as pointed out by Liu et al.,(2015) [3] for further classification based on DNA molecular marker (SSR or AFLP);

Step 6. Classification of bacteria families is further conducted on the basis of DNA molecular marker, analyzed by multivariate cluster analysis of UPGMA (unweighted pair group method with arithmetic averages) and genetic distance analysis[3];

Step 7. Gene recombination and gene mutation rate is analyzed by the inconsistence  of classification between molecular cytogenetic karyotype and DNA molecular marker[3];

Step 8. Bacteria family ‘F’ is identified by cluster analysis and genetic distance analysis based on DNA molecular markers (genotype), which results in apparent incidence of pathological characters when exposure dose to bacteria family ‘F’ increases significantly (phenotype);

Step 9. Biochemical samples are abstracted from streams of Bacteria family ‘F,’ leading to various zymogram calculated as the average similarity coefficient across different isozyme families, which is listed [5]. A novel matrix of Matrix Xsum is designed for this classification across different bacteria bio-samples [7].

Step 10. Bacteria family ‘F’ is further classified into different sub-families by UPGMA (unweighted pair group method with arithmetic averages) method on the basis of the average similarity coefficient across different isozyme families between any two streams. The UPGMA calculation is listed in page 63 of isozyme chapter [1].

Step 11. Sub-Bacteria families, named as F1, F2 .... Fn, should be more specific in terms of correlation to the incidence of pathological characters.

Note: the above hypotheses and discussion about virus in other article [6] are also applicable on the bacteria ecosystem. This designed methods is also applicable on other more advanced creatures (such as plants), and step 3 to step 6 may be replaced by molecular structure biology method designed by my another article [8] to facilitate and improve the DNA classification, if it is necessary. The calculation of similarity coefficient between zymogram of different bacteria families is performed within one isozyme family[1]. However, this method is performed on the basis of unweighted average. Hence this article advises the steps of analyzing the zymograms with weighted average in future research:

1.If the electrophoresis pipe is the vertical one, then the horizontal bands in a pipe represent various enzyme species in an isozyme family. The bands at the same horizontal line between different pipes represent the same enzyme species, and the clearness of bands indicates activity of enzyme species (the more clearness, the higher activity of enzyme). Please note: the reproduction rate of microbial streams varies among different environmental cultivation conditions. Consequently, the density of microbial samples should be counted, ensuring the uniform concentration of microbial samples for the enzyme activity observation.

2.The whole environmental conditions (such as temperature) are simulated in situ from T1 to Tn (T1,T2,……,Tn). Within the environmental range [T1, Tn], the range of [T2, Ta] is the environmental range triggering the gene expression of enzyme species A, and the range of [T3, Tb] is the environmental range triggering the gene expression of enzyme species B,… etc. Consequently, the weight of enzyme species A is the ratio of range [T2,Ta] to the total range [T1, Tn], and the weight of enzyme species B is the ratio of range [T2, Tb] to the total range [T1,Tn],… etc. Then the similarity coefficient in one isozyme family between zymogram of different bacteria sub-families is calculated as: similarity coefficient = 2*∑(enzyme i * weight i) /

{∑(enzyme j * weight j) + ∑(enzyme k * weight k)}. In this equation, enzyme j is the enzyme species in bacteria sub-family 1 and weight j is the weight of enzyme species j; enzyme k is the enzyme species in bacteria sub-family 2 and weight k is the weight of enzyme species k; enzyme i is the common (or same) enzyme species between sub-family 1 and sub-family 2.

3.In principle, the gene expression of enzyme species A should start at the environmental condition T2 with increasing activity along the environmental gradient, and the activity should decrease after the peak value until gene expression ceases at environmental condition Ta, which can be observed by the ‘smooth’ comparison of one bacteria sub-family’ zymograms between different bacteria cultivation conditions. However, the comparison of zymograms between different sub-families should be conducted at the same environmental cultivation condition.

This is the revised materials in book “Proceedings for Degree of Postgraduate Diploma in Environmental Science (3rd Edition).” published in 2016. Firstly Revised on 03/01/2021; Secondly Revised on 05/02/2021; Thirdly Revised on 04/01/2022. This journal article is previously published as: Liu Huan. (2021). Article 1-2. Classification of Bacteria by DNA Genetic Marker and Its Theory. Journal of Environment and Health Science (ISSN 2314-1628), 2021(02)., which is converted into Journal of Biological Sciences (ISSN 2958-4035). Both Journals belong to the same publisher, Liu Huan. The previous journal article is closed to the public, but the previous reference is still valid.  Latest revised on 29/05/2023; 25/11/2023.

References:

[1]. 周延清, 张改娜与杨清香, 生物遗传标记与应用, 2008, 化学工业出版社.

[2]. 刘焕, 张洪初与唐秋盛, 保护遗传学方法在生物多样性监测和评价领域的应用研究.  科技视界, 2014(8).

[3]. Liu, H, Ouyang T. L, Tian Chengqing (2015). Review of Evolutionary Ecology Study and Its Application on Biodiversity Monitoring and Assessment. Science & Technology Vision (6) 2015.

[4]. 郑成木, 植物分子标记原理与方法, 2003, 湖南科学技术出版社.

[5].  Liu Huan. Metabolomics (1) --- The Systematic Chemistry Fingerprints Between Genotype and Phenotype and its Application on the Conservation Genetics. Journal of Environment and Health Science. Feb. 2021. https://doi.org/10.58473/JBS0005

[6]. Liu Huan. Classification of Virus by DNA Genetic Marker and Its Theory. Journal of Environment and Health Science. Feb. 2021. https://doi.org/10.58473/JBS0001

[7]. Liu Huan. Metabolomics and Application on The Specificity of Host-Invasion Interaction. Journal of Environment and Health Science. Feb. 2021. https://doi.org/10.58473/JBS0006

[8]. Liu Huan. (2022). Article 19. Essay: Structural Molecular Biology. Journal of Environment and Health Science (ISSN 2314-1628), 2022(08). https://doi.org/10.58473/JBS0021