Bacteriology

  1. Bacterial Classification and Identification
    1. Taxonomy and Systematics
      1. Nomenclature
        1. Binomial Nomenclature
          1. Rules of Naming
            1. Type Strains
              1. Valid Publication
              2. Classification Hierarchy
                1. Domain
                  1. Phylum
                    1. Class
                      1. Order
                        1. Family
                          1. Genus
                            1. Species
                              1. Subspecies and Strains
                              2. Phylogeny
                                1. Molecular Phylogenetics
                                  1. Evolutionary Relationships
                                    1. Phylogenetic Trees
                                      1. Molecular Clocks
                                    2. Phenotypic Identification Methods
                                      1. Microscopic Morphology
                                        1. Cell Shape and Size
                                          1. Cell Arrangement
                                            1. Motility
                                            2. Staining Techniques
                                              1. Gram Stain
                                                1. Acid-Fast Stain
                                                  1. Spore Stain
                                                    1. Capsule Stain
                                                      1. Flagella Stain
                                                      2. Macroscopic Morphology (Colony Characteristics)
                                                        1. Colony Shape
                                                          1. Color and Pigmentation
                                                            1. Texture and Consistency
                                                              1. Elevation
                                                                1. Margin
                                                                  1. Size
                                                                  2. Biochemical Tests
                                                                    1. Enzyme Production Tests
                                                                      1. Catalase Test
                                                                        1. Oxidase Test
                                                                          1. Urease Test
                                                                            1. Coagulase Test
                                                                            2. Fermentation Tests
                                                                              1. Carbohydrate Fermentation
                                                                                1. Gas Production
                                                                                  1. Acid Production
                                                                                  2. IMViC Tests
                                                                                    1. Indole Test
                                                                                      1. Methyl Red Test
                                                                                        1. Voges-Proskauer Test
                                                                                          1. Citrate Utilization Test
                                                                                          2. Other Biochemical Tests
                                                                                            1. Nitrate Reduction
                                                                                              1. Hydrogen Sulfide Production
                                                                                                1. Motility Tests
                                                                                              2. Serological Methods
                                                                                                1. Serotyping
                                                                                                  1. Agglutination Tests
                                                                                                    1. ELISA
                                                                                                      1. Immunofluorescence
                                                                                                      2. Physiological Tests
                                                                                                        1. Growth Temperature Ranges
                                                                                                          1. Salt Tolerance
                                                                                                            1. pH Tolerance
                                                                                                              1. Antibiotic Susceptibility
                                                                                                            2. Genotypic Identification Methods
                                                                                                              1. DNA Base Composition (G+C Content)
                                                                                                                1. DNA Fingerprinting
                                                                                                                  1. Restriction Fragment Length Polymorphism (RFLP)
                                                                                                                    1. Pulsed-Field Gel Electrophoresis (PFGE)
                                                                                                                      1. Random Amplified Polymorphic DNA (RAPD)
                                                                                                                      2. Nucleic Acid Hybridization
                                                                                                                        1. DNA-DNA Hybridization
                                                                                                                          1. Fluorescent In Situ Hybridization (FISH)
                                                                                                                          2. Polymerase Chain Reaction (PCR)
                                                                                                                            1. Conventional PCR
                                                                                                                              1. Real-Time PCR (qPCR)
                                                                                                                                1. Multiplex PCR
                                                                                                                                2. Ribosomal RNA (rRNA) Sequencing
                                                                                                                                  1. 16S rRNA Gene Analysis
                                                                                                                                    1. 23S rRNA Gene Analysis
                                                                                                                                      1. Phylogenetic Tree Construction
                                                                                                                                      2. Whole Genome Sequencing
                                                                                                                                        1. Comparative Genomics
                                                                                                                                          1. Multilocus Sequence Typing (MLST)
                                                                                                                                          2. Mass Spectrometry
                                                                                                                                            1. MALDI-TOF MS

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                                                                                                                                        4. Bacterial Genetics

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                                                                                                                                        6. Host-Microbe Interactions