Classification and Nomenclature

• Taxon is a group or "level" of classification that is hierarchical, with broad divisions divided into smaller divisions like Kingdom, Phylum, Class, Order, Family, Genus, and Species
• In microbiology, a species is a collection of microbial strains that share many properties and differ significantly from other groups of strains
• Species are identified by comparison with known "type strains," which are well-characterized pure cultures used as references for the identification of unknowns
• Species, strains, and types in microbiology:

  • Species: a collection of bacterial cells sharing an overall similar pattern of traits
  • Strain or variety: a culture derived from a single parent that differs in structure or metabolism from other cultures of that species
  • Type: a subspecies that can show differences in antigenic makeup, susceptibility to bacterial viruses, and in pathogenicity
• Scientific nomenclature in biology uses binomial nomenclature, with the genus and species name like Escherichia coli where Escherichia is the genus and coli is the species
• Classification methods in microbiology include morphology, differential staining, biochemical tests, serology, and genetic tests
• The Three-Domain System classifies organisms into Archaea, Bacteria, and Eukarya, with examples like methanogens and halophiles in Archaea, pathogenic bacteria in Bacteria, and fungi and algae in Eukarya
• Archaea are divided into two phyla: Crenarchaeota and Euryarchaeota, with different types of archaea in each
• Selected Bacteria Phyla - Gram-Negative:

  • Proteobacteria: very diverse, with all four modes of nutrition represented, and includes medically important genera like Escherichia and Pseudomonas
  • Chlamidiae: grow only in eukaryotic host cells
  • Spirochaetes: characterized by flexible, helical cells with a modified outer membrane and modified flagella, with important pathogenic genera like Treponema and Borrelia
• Selected Bacteria Phyla - Gram-Positive:

  • Firmicutes: low G+C content, include Bacilli and Clostridia
  • Actinobacteria: high G+C content, include genera like Actinomyces and Mycobacterium
• Structure of bacterial cells is used for classification, with criteria like morphology and arrangement into groups like Cocci, Rods / bacilli, Vibrios, Spirilla, and Spirochaetes
• Protists were originally classified under Kingdom Protista but have been broken up into different kingdoms
• The term Protist is used for eukaryotes that are not plants, animals, or fungi
• Stramenophila includes diatoms, brown algae, and water molds
• Alveolata includes dinoflagellates, ciliates, and apicomplexans
• Rhizaria includes Cercozoa, Foraminiferans, and Radiolarians
• Excavata includes parasites such as Giardia and Trichomonas, and free-living Euglena
• Unikonta includes Amoebozoa, Fungi, and Animals
• Protozoa is an informal term for amoebae, flagellates, ciliates, and apicomplexans
• Fungi are decomposers, heterotrophic, and absorb nutrients; most have chitin in cell walls
• Lichen is a symbiosis between fungi and green algae
• Mycorrhiza is a symbiosis between fungi and plant roots
• Fungi life cycle includes Chytrids, Zygomycetes, Glomeromycetes, Ascomycetes, and Basidiomycetes
• Archaeplastida includes red algae, green algae, and land plants
• Medically important groups include Bacteria and Eukaryotes