Introduction To Microbiology PDF

# Introduction to Microbiology ## What is Microbiology? - **logy** = science of or the study of - **Micro** = small - **Bios** = Life - The science or study of small life - The study of living things not visible to the naked eye ## The Importance of Microbiology - Many microbes are beneficial -...

# Introduction to Microbiology ## What is Microbiology? - **logy** = science of or the study of - **Micro** = small - **Bios** = Life - The science or study of small life - The study of living things not visible to the naked eye ## The Importance of Microbiology - Many microbes are beneficial - **Beneficial tasks microorganisms can perform**: - Recycling of essential elements (decomposition of organic matter) - Production of antibiotics - Source of other nutrients (Vitamins, etc.) - Vitamin K is synthesized by certain intestinal bacteria *(Lactobacillus, Bifidobacterium, Bacillus)* - Thousands of bacteria inhabit human skin - Provide protection from pathogenic microorganisms - **Microbiologists can play a major role in many scientific fields:** - Medicine - Diagnostic Laboratories, Medical research - Environmental science - Food and drink production - Food production (yoghurt, pickles, cheese...etc) - Fundamental research - All areas - Agriculture - Study of beneficial and harmful microorganisms - Pharmaceutical industry - Productions of nutrients and other beneficial products - Genetic engineering - Gene engineering for better life ## Microbial Taxonomy - **Taxonomy:** An area of biologic science that includes three distinct but highly interrelated disciplines: - Classification - Nomenclature (naming) - Identification of organisms - **Classification:** A method for organizing microorganisms into groups or taxa based on similar morphologic, physiologic, and genetic traits ## Classification Hierarchy - **Domains:** - Bacteria - Archaea - Eukarya _(Used to be in one domain: prokaryotes)_ - **Kingdom:** (contains similar divisions or phyla; most inclusive taxa) - **Phylum:** (contains similar classes) - **Class:** (contains similar orders ) - **Order:** (contains similar families) - **Family:** (contains similar genera) - **Genus:** (contains similar species) - **Species:** Two-part name (binomial) - The first part of a binomial is the genus to which the species belongs - The second part is called the specific name or specific epithet ## Species - **Neisseria gonorrhoeae:** - Causes the sexually transmitted disease gonorrhea - **Helicobacter pylori:** - Causes gastritis and ulcers - **Neisseria meningitidis:** - Causes meningitis - **Escherichia coli strains:** - Causes food poisoning. - Urinary tract infections. ## Classification Hierarchy - **Family:** - Formed by adding the suffix -aceae to the root name of genera - Streptococcus' family: Streptococcaceae - **Genus** (genera): - Contains different species that have several important features in common - *Pseudomonas aeruginosa* - *Pseudomonas fluorescens* - Each species within a genus differs sufficiently to be classified as an individual species. ## Classification Hierarchy - **Species:** - Species - abbreviated as sp. (singular), or spp. (plural) - A collection of bacterial strains that share common physiologic and genetic features and differ notably from other microbial species - **Taxonomic subgroups below species:** - Subspecies - Biotype, Serotype, or Genotype - Organisms with similar antigens are collectively referred to as a serogroup - Groups below Subspecies - Share specific but relatively different characteristics ## Pseudomonas aeruginosa vs Pseudomonas fluorescens - Two pictures of different agar plates with bacterial growth are present. - One is labeled **Pseudomonas aeruginosa** and the other is labeled **Pseudomonas fluorescens** - A phylogenetic tree is also present showing the relationship between both species and other species of Pseudomonas. ## Microbial Taxonomy - **Taxonomy:** An area of biologic science that includes three distinct but highly interrelated disciplines: - Classification - Nomenclature (naming) - Identification of organisms ## Nomenclature - Naming of microorganisms according to established rules and guidelines of the International Code of Nomenclature of Bacteria *(ICNB)* or the Bacteriological Code *(BC)* - Provides the accepted labels by which organisms are universally recognized - Genus and species are the groups commonly used by microbiologists - Each organism has a scientific name (label) consisting of two parts: - The genus - The first letter is always capitalized - The species - The first letter is always lowercase *Streptococcus pneumoniae* - Abbreviated: *S. pneumoniae* ## Microbial Taxonomy - **Taxonomy:** An area of biologic science that includes three distinct but highly interrelated disciplines: - Classification - Nomenclature (naming) - Identification of organisms ## Microbial Identification - **Microbial identification:** The process by which a microorganism's key features are described - **Identification Methods:** - **Phenotype-based methods:** - Study observable characteristics and features of microorganisms - **Genotype-based methods:** - Study the organism's genetic makeup, including the nature of the organism's genes and constituent nucleic acids ## Microbial Identification | Criteria | Characteristics | |---|---| | **Phenotypic** | **Characteristics** | | Macroscopic morphology | The microbial growth patterns on artificial media as are observed when inspected with the unaided eye. Examples include the size, texture, and pigmentation of bacterial colonies. | | Microscopic morphology | The size, shape, intracellular inclusions, cellular appendages, and arrangement of cells when observed with the aid of microscopic magnification. | | Staining characteristics | The ability of an organism to reproducibly stain a particular color with the application of specific dyes and reagents. Staining is used in conjunction with microscopic morphology for bacterial identification. For example, the Gram stain for bacteria is a critical criterion for differential identification. | | Environmental requirements | The ability of an organism to grow at various temperatures, in the presence of oxygen and other gases, at various pH levels, or in the presence of other ions and salts, such as NaCl. | | Nutritional requirements | The ability of an organism to utilize various carbon and nitrogen sources as nutritional substrates when grown under specific environmental conditions. | | Resistance profiles | The exhibition of a characteristic inherent resistance to specific antibiotics, heavy metals, or toxins. | | Antigenic properties | The profiles of microorganisms established by various serologic and immunologic methods to determine relatedness among various microbial groups. | | Subcellular properties | Molecular constituents of the cell that are typical of a particular taxon, or organism group, as established by various analytic methods. Some examples include cell wall components, components of the cell membrane, and enzymatic content of the microbial cell. | | Chemotaxonomic properties | The chemical constituents of the cell, such as the structure of teichoic acids, fatty acid analysis, and protein profiles, as determined by analytical methods. | ## Microbial Identification | Criteria | Characteristics | |---|---| | **Genotypic** | **Characteristics** | | Deoxyribonucleic acid (DNA) base composition ratio | DNA comprises four bases (guanine, cytosine, adenine, and thymine). The extent to which the DNA from two organisms is made up of cytosine and guanine (I.e., G + C content) relative to their total base content can be used as an indicator of relatedness or lack thereof. For example, an organism with a G + C content of 50% is not closely related to an organism with a G + C content of 25%. | | Nucleic acid (DNA and ribonucleic acid [RNA] base sequence characteristics, including those determined by hybridization assays | The order of bases along a strand of DNA or RNA is known as the base sequence. The extent to which sequences are homologous (similar) between two microorganisms can be determined directly or indirectly by various molecular methods. The degree of similarity in the sequences may be a measure of the degree of organism relatedness, specifically, the ribosomal RNA (rRNA) sequences that remain stable in comparison to the genome as a whole. |