Defintion of “species” in microbiology:
• Classic definition: A collection of microbial strains that share many properties and differ significantly from other groups of strains •There are several collections of type strains, including the American Type Culture Collection (ATCC)
Classification Systems
• Classification systems continue to evolve and will change as new information is discovered
– emerging technology increases the knowledge base of organisms
– virus particle structure
• isometric, helical, pleomorphic???
– presence or absence of viral envelope
4. Nomenclature
• Organisms must have a Latin suffix • Name is italicized or underlined • All organisms have a binomial name – 1st part of the binomial name is genus • 1st letter capitalized – 2nd part or the binomial name is the species epithet
– Linnaeus placed all microorganism in one genus he named Chaos
Classification Systems: a short history
• in 1866, Ernst Haeckel 海克尔） （海克尔）divided animals, plants, and microorganisms into 3 kingdoms
Microbial Taxonomy
Zhijiang Zhou 2009.10.05
Outline
• • • • • Taxonomy Levels of Classification Classification Systems: a short history Nomenclature Useful Properties in Microbial Classification • Microbial Phylogeny
rRNA作为进化的指征 rRNA作为进化的指征
16S rRNA相对分子质量大小适中，便于序列分 相对分子质量大小适中， 相对分子质量大小适中 析； – 16S rRNA: ancient conserved sequences of about 1500kb 16S rRNA普遍存在于真核生物和原核生物中 普遍存在于真核生物和原核生物中 真核生物中其同源分子是18SrRNA）。 ）。 （真核生物中其同源分子是
– identification
• characterizing organisms
– classification
• arranging into similar groups
– nomenclature
• naming organisms
Taxonomy
organizing larger organisms d on morphology is often quite simple:
3. Classification Systems: a short history
• in 1750, Carl Linnaeus devised the first classification system, placing plants and animals in separate systems
Nomenclature
• Species name – include both genus and species epithet（种号） （种号） • Lactococcus lactis – Genus name is capitalized and may be abbreviated • L. lactis – Species name is never abbreviated – A genus name may be used alone to indicate a genus group; a species name is never used alone – eg: Bacillus subtilis B. subtilis
verses
feathers
verses
fur
fins legs with microorganisms, it is not as simple
Classification technologies
• used to characterize and ID Microorganisms
– microscopic examination – culture characteristics – biochemical testing – nucleic acid analysis – combination of the above is most accurate
Defintion of “species” in microbiology:
• type
– Biovars: Strains that differ in biochemical or physiological differences – Morphovars: Strains that vary in morphology – Serovars: Stains that vary in their antigenic properties
Defintion of “species” in microbiology:
• Strain:
– A population of microbes descended from a single individual or pure culture – Different strains represent genetic variability within a species
– – – – – Animalia Plantae Fungi Protista（原生生物）： include algae and protozoa （原生生物）： Monera（原核生物） （原核生物）
Classification Systems: a short history
• in 1970, Carl Woese, by analyzing RNA, developed the 3 domain classification system
Classification of Viruses
• Viruses are not included in the 3 Domain classification system • Viruses are not composed of cells
– the ecological niche of a virus is the host cell – viruses may be more related to their host than to other viruses
16S rRNA as a biomarker gene
• Carl Woese: 1928• Comparison of the DNA sequences of a specific gene can offer evolutionary and taxonomical insights in the microbial world. • Ideal molecule: Universally distributed. Functionally homologous. Evolving at a suitable rate. Suitable size: 500-2000 bp. No lateral gene transfer.
– Animalia – Plantae – Protista（原生生物） （原生生物）
Haeckel’s Tree of Life
Classification Systems: a short history
• in 1969, Robert Whittaker（魏塔科） created （魏塔科） a 5 Kingdom classification system, using obvious morphological differences
Classification of Viruses
• Though not included in the 3 domain system, classification of virus is currently based on
– genome structure
• single, double, DNA, RNA???
– archaebacteria – bacteria – eucarya
• This system is currently favored by microbiologists.
rRNA作为进化的指征 rRNA作为进化的指征
• rRNA参与生物蛋白质的合成过程，其功能是任何 参与生物蛋白质的合成过程， 参与生物蛋白质的合成过程 生物都必不可少的， 生物都必不可少的，而且在生物进化的漫长历程 其功能保持不变； 中，其功能保持不变； • 在16S rRNA分子中，即含有高度保守的序列区 分子中， 分子中 又有中度保守和高度变化的序列区域， 域，又有中度保守和高度变化的序列区域，因而 它适用于进化距离不同的各类生物亲缘关系的研 究；