This document discusses the classification of microorganisms. It describes how Carl Linnaeus originated the formal system of taxonomy, which organizes and names living things in a hierarchical system of domains, kingdoms, phyla, classes, orders, families, genera and species. The three domains are Eubacteria, Archaea and Eukarya. Fungal classification is based on sexual reproduction structures like zygospores, ascospores and basidiospores. Protozoan classification groups them by motility and reproduction methods.

1. Classification ofClassification of
MicroorganismsMicroorganisms

2. TaxonomyTaxonomy
 Organizing, classifyingOrganizing, classifying
and naming living thingsand naming living things
 Formal system originatedFormal system originated
by Carl von Linné (1701-by Carl von Linné (1701-
1778)1778)
 Identifying and classifyingIdentifying and classifying
organisms according toorganisms according to
specificspecific criteriacriteria
 Each organism placedEach organism placed
into a classificationinto a classification
systemsystem

3. TaxonomyTaxonomy
 DomainDomain
 KKingdomingdom
 PPhylumhylum
 CClasslass
 OOrderrder
 FFamilyamily
 GGenusenus
 sspeciespecies

4. 3 Domains3 Domains
 EubacteriaEubacteria
 true bacteria, peptidoglycantrue bacteria, peptidoglycan
 ArchaeaArchaea
 odd bacteria that live in extremeodd bacteria that live in extreme
environments, high salt, heat, etc. (usuallyenvironments, high salt, heat, etc. (usually
called extremophiles)called extremophiles)
 EukaryaEukarya
 have a nucleus & organelles (humans,have a nucleus & organelles (humans,
animals, plants)animals, plants)

7. TaxonomyTaxonomy
 4 main kingdoms:4 main kingdoms:
 ProtistaProtista
 FungiFungi
 PlantaePlantae
 AnimaliaAnimalia
 AlgaeAlgae

8. Naming MicoorganismsNaming Micoorganisms
 Binomial (scientific) nomenclatureBinomial (scientific) nomenclature
 Gives each microbe 2 names:Gives each microbe 2 names:
 GenusGenus - noun, always capitalized- noun, always capitalized
 speciesspecies - adjective, lowercase- adjective, lowercase
 Both italicized or underlinedBoth italicized or underlined
 Staphylococcus aureus (S. aureus)Staphylococcus aureus (S. aureus)
 Bacillus subtilisBacillus subtilis (B. subtilis)(B. subtilis)
 Escherichia coliEscherichia coli (E. coli)(E. coli)

9. Evolution - living thingsEvolution - living things
change gradually overchange gradually over
millions of yearsmillions of years
 Changes favoring survival are retained and lessChanges favoring survival are retained and less
beneficial changes are lostbeneficial changes are lost
 All new species originate from preexistingAll new species originate from preexisting
speciesspecies
 Closely related organism have similar featuresClosely related organism have similar features
because they evolved from common ancestralbecause they evolved from common ancestral
formsforms
 Evolution usually progresses toward greaterEvolution usually progresses toward greater
complexitycomplexity

10. Insert figure 1.15
Woese-Fox System

11. ClassificationClassification
Systems in theSystems in the
ProcaryotaeProcaryotae

12. Classification SystemsClassification Systems
in the Procaryotaein the Procaryotae
1.1. Microscopic morphologyMicroscopic morphology
2.2. Macroscopic morphology – colonyMacroscopic morphology – colony
appearanceappearance
3.3. Physiological / biochemical characteristicsPhysiological / biochemical characteristics
4.4. Chemical analysisChemical analysis
5.5. Serological analysisSerological analysis
6.6. Genetic and molecular analysisGenetic and molecular analysis
• G + C base compositionG + C base composition
• DNA analysis using genetic probesDNA analysis using genetic probes
• Nucleic acid sequencing and rRNA analysisNucleic acid sequencing and rRNA analysis

13. Bacterial TaxonomyBacterial Taxonomy
Based onBased on BergeyBergey’’ss
ManualManual
 BergeyBergey’s Manual of Determinative’s Manual of Determinative
BacteriologyBacteriology – five volume resource– five volume resource
covering all known procaryotescovering all known procaryotes
 classification based on genetic information –classification based on genetic information –
phylogeneticphylogenetic
 two domains: Archaea and Bacteriatwo domains: Archaea and Bacteria
 five major subgroups with 25 different phylafive major subgroups with 25 different phyla

14. Major TaxonomicMajor Taxonomic
Groups of BacteriaGroups of Bacteria
 Vol 1A: Domain ArchaeaVol 1A: Domain Archaea
 primitive, adapted to extreme habitats andprimitive, adapted to extreme habitats and
modes of nutritionmodes of nutrition
 Vol 1B: Domain BacteriaVol 1B: Domain Bacteria
 Vol 2-5:Vol 2-5:
 Phylum ProteobacteriaPhylum Proteobacteria – Gram-negative cell– Gram-negative cell
wallswalls
 Phylum FirmicutesPhylum Firmicutes – mainly Gram-positive– mainly Gram-positive
with low G + C contentwith low G + C content
 Phylum ActinobacteriaPhylum Actinobacteria – Gram-positive with– Gram-positive with
high G + C contenthigh G + C content

15. Diagnostic Scheme forDiagnostic Scheme for
Medical UseMedical Use
 Uses phenotypic qualities inUses phenotypic qualities in
identificationidentification
 restricted to bacterial disease agentsrestricted to bacterial disease agents
 divides based on cell wall structure, shape,divides based on cell wall structure, shape,
arrangement, and physiological traitsarrangement, and physiological traits

16. Species andSpecies and
SubspeciesSubspecies
 SpeciesSpecies
 collection of bacterial cells which share an overallcollection of bacterial cells which share an overall
similar pattern of traits in contrast to other bacteriasimilar pattern of traits in contrast to other bacteria
whose pattern differs significantlywhose pattern differs significantly
 StrainStrain oror varietyvariety
 culture derived from a single parent that differs inculture derived from a single parent that differs in
structure or metabolism from other cultures of thatstructure or metabolism from other cultures of that
species (biovars, morphovars)species (biovars, morphovars)
 TypeType
 subspecies that can show differences in antigenicsubspecies that can show differences in antigenic
makeup (serotype or serovar), susceptibility tomakeup (serotype or serovar), susceptibility to
bacterial viruses (phage type) and in pathogenicitybacterial viruses (phage type) and in pathogenicity
(pathotype)(pathotype)

17. Archaea: The OtherArchaea: The Other
ProcaryotesProcaryotes
 Constitute third Domain ArchaeaConstitute third Domain Archaea
 Seem more closely related to Domain Eukarya than toSeem more closely related to Domain Eukarya than to
bacteriabacteria
 Contain unique genetic sequences in their rRNAContain unique genetic sequences in their rRNA
 Have unique membrane lipids and cell wall constructionHave unique membrane lipids and cell wall construction
 Live in the most extreme habitats in nature,Live in the most extreme habitats in nature,
extremophilesextremophiles
 Adapted to heat, salt, acid pH, pressure andAdapted to heat, salt, acid pH, pressure and
atmosphereatmosphere
 Includes: methane producers, hyperthermophiles,Includes: methane producers, hyperthermophiles,
extreme halophiles, and sulfur reducersextreme halophiles, and sulfur reducers

18. EukaryotesEukaryotes

19. EukaryotesEukaryotes
 ProtistaProtista
 FungiFungi
 PlantaePlantae
 AnimaliaAnimalia
 AlgaeAlgae

20. Fungal ClassificationFungal Classification
 Sexual reproductionSexual reproduction
 Spores are formed following fusion of male andSpores are formed following fusion of male and
female strains and formation of sexual structurefemale strains and formation of sexual structure
 Sexual spores and spore-forming structuresSexual spores and spore-forming structures
are one basis for classificationare one basis for classification
 ZygosporesZygospores
 AscosporesAscospores
 BasidiosporesBasidiospores

24. Fungal ClassificationFungal Classification
 Subkingdom AmastigomycotaSubkingdom Amastigomycota
 Terrestrial inhabitants including those ofTerrestrial inhabitants including those of
medical importance:medical importance:
1.1. ZygomycotaZygomycota – zygospores; sporangiospores and– zygospores; sporangiospores and
some conidiasome conidia
2.2. AscomycotaAscomycota – ascospores; conidia– ascospores; conidia
3.3. BasidiomycotaBasidiomycota – basidiospores; conidia– basidiospores; conidia
4.4. DeuteromycotaDeuteromycota – majority are yeasts and molds;– majority are yeasts and molds;
no sexual spores known; conidiano sexual spores known; conidia

25. ProtozoanProtozoan
ClassificationClassification
 Difficult because of diversityDifficult because of diversity
 Simple grouping is based on method of motility,Simple grouping is based on method of motility,
reproduction, and life cyclereproduction, and life cycle
1.1. MastigophoraMastigophora – primarily flagellar motility, some– primarily flagellar motility, some
flagellar and amoeboid; sexual reproduction; cystflagellar and amoeboid; sexual reproduction; cyst
and trophozoiteand trophozoite
2.2. SarcodinaSarcodina – primarily ameba; asexual by fission;– primarily ameba; asexual by fission;
most are free-livingmost are free-living
3.3. CiliophoraCiliophora – cilia; trophozoites and cysts; most are– cilia; trophozoites and cysts; most are
free-living, harmlessfree-living, harmless
4.4. ApicomplexaApicomplexa – motility is absent except male– motility is absent except male
gametes; sexual and asexual reproduction; complexgametes; sexual and asexual reproduction; complex
life cycle – all parasiticlife cycle – all parasitic