Systematic Bacteriology Course

Lesson 1 • Ecological Roles of Bacteria

Surveys bacteria in soil, water, host-associated, and extreme environments. Ecological context motivates the need for accurate species-level identification.

Lesson 2 • History and Scope of Bacteriology

Traces bacteriology from early microscopy to modern genomics. Establishes why systematic classification matters for research and applied microbiology.

Lesson 3 • Bacterial Growth and Reproduction

Covers binary fission, growth phases, and environmental growth factors. Understanding growth kinetics is prerequisite for culture-based identification methods.

Lesson 4 • Bacterial Metabolism Overview

Introduces energy-yielding pathways and nutritional categories. Metabolic diversity underpins ecological roles and identification strategies covered later.

Lesson 1 • Taxonomy, Nomenclature, and Classification

Defines taxonomy, systematics, and nomenclature as distinct disciplines. Provides the vocabulary used throughout all subsequent classification chapters.

Lesson 2 • Major Classification Systems

Compares phenetic, phylogenetic, and polyphasic classification approaches. Students understand which system applies in clinical, environmental, and industrial contexts.

Lesson 3 • The Prokaryotic Species Concept

Examines why the biological species concept fails for bacteria and what alternatives exist. Prepares students to evaluate species boundaries in later chapters.

Lesson 1 • Microscopy and Morphological Analysis

Covers light, phase-contrast, and electron microscopy techniques for bacterial morphology. Morphological data form the first tier of polyphasic identification.

Lesson 2 • Chemotaxonomic Markers

Covers fatty acid profiles, polar lipids, quinones, and cell wall chemotypes as taxonomic markers. Chemotaxonomy bridges phenotypic and genotypic classification.

Lesson 3 • Staining Techniques

Teaches Gram, endospore, capsule, and flagella staining protocols. Staining results provide rapid presumptive data that guide further testing.

Lesson 4 • Cultural and Biochemical Tests

Introduces colony morphology assessment and key biochemical assays. These tests generate phenotypic data matrices used in numerical taxonomy.

Lesson 1 • DNA-DNA Hybridization and ANI

Explains the gold-standard hybridisation method and its genomic surrogate, ANI. Students apply these metrics to make species-level delineation decisions.

Lesson 2 • Nucleic Acid Extraction and Quality

Covers cell lysis strategies, DNA purification, and quality assessment. High-quality nucleic acids are prerequisite for all downstream molecular analyses.

Lesson 3 • 16S rRNA Gene Analysis

Teaches amplification, sequencing, and phylogenetic interpretation of the 16S rRNA gene. This marker is the universal entry point for bacterial identification.

Lesson 4 • Multilocus Sequence Analysis

Extends single-gene analysis to multiple housekeeping loci for finer resolution. MLSA resolves closely related species that 16S rRNA cannot distinguish.

Lesson 1 • Tree Evaluation and Support

Teaches bootstrap resampling, posterior probabilities, and topology tests. Evaluating support values is essential for defensible taxonomic conclusions.

Lesson 2 • Substitution Models

Explains nucleotide and amino acid substitution models and model selection criteria. Choosing the correct model prevents systematic errors in tree topology.

Lesson 3 • Phylogenomic Approaches

Extends tree building to genome-scale datasets using core-genome and supertree methods. Phylogenomics resolves deep bacterial relationships unresolvable by single genes.

Lesson 4 • Tree-Building Methods

Compares neighbour-joining, maximum parsimony, maximum likelihood, and Bayesian methods. Students select the appropriate method based on dataset size and question.

Lesson 1 • Firmicutes and Actinobacteria

Examines low-GC Firmicutes and high-GC Actinobacteria, including spore-formers and mycelial forms. Both phyla contain major pathogens and biotechnologically valuable species.

Lesson 2 • Candidate Phyla and Uncultured Lineages

Introduces phyla known only from environmental sequences and their implications for the tree of life. Metagenomics has dramatically expanded known bacterial diversity.

Lesson 3 • Cyanobacteria and Photosynthetic Bacteria

Covers oxygenic and anoxygenic photosynthetic bacteria and their evolutionary significance. Cyanobacteria are the ancestors of chloroplasts and key environmental players.

Lesson 4 • Bacteroidetes, Chloroflexi, and Spirochaetes

Surveys three ecologically and medically distinct phyla with unique morphological traits. Spirochaetes illustrate how morphology alone can define a phylum.

Lesson 1 • Reclassification and Emended Descriptions

Covers procedures for reclassifying existing taxa and issuing emended descriptions. Reclassification is as rigorous as original description and follows the same standards.

Lesson 2 • Peer Review and Publication Process

Guides students through submitting taxonomic papers to specialised journals. Understanding reviewer expectations increases acceptance rates for novel taxon proposals.

Lesson 3 • Type Strain Designation and Deposition

Explains the rules for designating type strains and depositing them in culture collections. Proper deposition is a mandatory step for valid species publication.

Lesson 4 • Designing a Polyphasic Study

Outlines the workflow for collecting and integrating multiple data types for a novel isolate. A well-designed study prevents gaps that delay or invalidate formal publication.

Lesson 1 • Clinical Identification Workflows

Maps the path from patient sample to confirmed bacterial identification in a diagnostic lab. Systematic knowledge accelerates accurate diagnosis and appropriate treatment selection.

Lesson 2 • Emerging Pathogens and Novel Species

Examines how systematic bacteriology enables rapid characterisation of newly emerging pathogens. Early accurate identification is critical for outbreak containment and treatment development.

Lesson 3 • Industrial and Food Microbiology Applications

Applies systematic methods to quality control in fermentation, food safety, and pharmaceutical production. Accurate identification prevents product contamination and regulatory non-compliance.

Lesson 4 • Antimicrobial Resistance Surveillance

Integrates systematic identification with resistance profiling for surveillance programmes. Linking taxonomy to resistance genotypes informs public health interventions.