1. Ch 10
Classification
of Micro-
organisms

2. Student Learning Outcomes
Define taxonomy and phylogeny List some characteristics of 3 domains Differentiate among eukaryotic, prokaryotic, and viral species Explain scientific naming Differentiate between culture, clone, and strain Compare and contrast classification and identification. Explain the purpose of Bergey’s Manual. Describe how staining and biochemical tests are used to identify bacteria. Explain how serological tests can be used to identify an unknown bacterium. Describe how a newly discovered microbe can be classified by various genetic tests. For Dichotomous key application and explanation, see lab

3. Taxonomy vs. Phylogeny Taxonmoy: Science of classifying organisms.
Provides universal names for organisms.
Taxonomic categories: Taxon / Taxa
Phylogeny or Systematics: Based on evolutionary history of group of organisms.
Taxonomic hierarchy shows phylogenetic (evolutionary), relationships among organisms.
1969: Living organisms divided into five kingdoms.
1978: Two types of prokaryotic cells found. Prokaryotic relationships determined by rRNA sequencing. Domains!
Experts estimate that there are around 100 million species in the world. What percentage of these flora and fauna have we named in the 250 years since Carl Linnaeus devised a classification system to complete Adam's task? Remarkably, only 2 or 3 percent. So two blue-sky thinkers in San Francisco - Kevin Kelly and Stewart Brand - recently came up with a solution to this problem: the All-Species Inventory. The goal is to identify and name every living thing, all in a single human generation.
This effort will be organized by the newly created All-Species Foundation, which has already raised $1 million for the project. What the moon shot did for technology, the All-Species Inventory hopes to do for ecology.

4. The Three-Domain System
Foundation Fig 10.1
Eubacteria (virtuosos)
Archaea (weirdoes)
Eukarya (predators and thieves)

5. Level Above Kindom: The Three-Domain System
Carl
Woese
1978

6. Endosymbiotic Theory: Origin of Eukaryotes

7. Scientific Nomenclature
Common names
Vary with languages
Vary with geography
Binomial Nomenclature: __________+ _______________
Used worldwide
Examples: ?
Genus + specific epithet

8. Classification: Species Definition
Eukaryotic species: Interbreeding organisms
Prokaryotic species: A population of cells with similar characteristics (Bergey’s Manual of Systematic Bacteriology is standard reference on bacterial classification).
Culture: Bacteria grown in laboratory media
Clone: Population of cells derived from a single cell
Strain: Genetically different cells within a clone or species
Viral species: Population of viruses with similar characteristics occupying a particular ecological niche. Viruses not placed in kingdom or domain – why not?

9. Classification and Identification
Fig 10.8
Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.
Identification: Matching characteristics of an “unknown” to lists of known organisms.

10. David Hendricks Bergey, 1870 - 1937
David Hendricks Bergey, MD. Bergey, who matriculated as a student in the Laboratory of Hygiene in 1893, taught here from 1895 to His Manual of Determinative Bacteriology, first published in 1923, remains a classic text in bacteriology. Bergey also founded the Eastern Pennsylvania Chapter of the Society of American Bacteriologists, now one of the nation's most active branches. (American Society for Microbiology Archives)
Reviewer: Bruce E. Dunn, MD (Medical College of Wisconsin) Description: This book is a collection of brief descriptions of bacteria and detailed tables of differential characteristics of bacterial species described and cultured as of January Purpose: The purpose is to serve as a reference to aid in the identification of bacteria. Information is arranged strictly based on phenotypic characteristics of bacteria. In contrast to Bergey's Manual of Systematic Bacteriology, this determinative manual does not offer a natural classification of bacteria. Audience: Because of the concise organization of the descriptions and tables in the book, it should prove useful to students, diagnostic microbiologists, and researchers
Bergey's Manual of Determinative Bacteriology is a departure from past editions that attempted, usually inadequately, to combine systematic and determinative information. Systematic information will continue to be found in Bergey's Manual of Systematic Bacteriology, with the Determinative manual serving as a reference to aid in the identification of unknown bacteria.
The arrangement of the book is strictly phenotypic, with no attempt to offer a natural higher classification. The arrangement chosen is utilitarian and is intended to aid in the identification of bacteria. The bacteria are divided into 35 groups, which are comparable to the "Parts" in the eighth edition and the "Sections" in the Systematic volumes. These groups are not meant to be formal taxonomic ranks, but are a continuation of our tradition of dividing the bacteria into easily recognized phenotypic groups. We feel this arrangement is most useful for diagnostic purposes.
The book was compiled by abstracting the phenotypic information contained in the four volumes of Bergey's Manual of Systematic Bacteriology. Introductory material concerning identification and a key to the groups were added. The past decade has seen an explosion in the description of new taxa of bacteria. We have attempted to include as many of them as possible, but, in a manual of this type with its varied production schedule, not all of the new taxa could be included. For inclusion in this manual, we had to set a cut-off date of January, 1991, for valid publication. In some cases, we have been able to include more recent taxa and have taken their descriptions directly from the original publications.
David Hendricks Bergey,

11. Bergey’s Manual: Classifying and Identifying Prokaryotes
Bergey’s Manual of Determinative Bacteriology
Provides identification schemes for identifying eubacteria and archaebacteria
Morphology, differential staining, biochemical tests
Bergey’s Manual of Systematic Bacteriology
Provides phylogenetic information on eu- and archaebacteria
Based on rRNA sequencing

13. Clinical Lab Identification
Morphological characteristics only useful for identifying eukaryotes.
Numerical Rapid Identification
Differential stains:
____________
Biochemical tests: Determine presence of ____________
Determine presence of ____________ bacterial enzymes

14. Serological Testing - Serology
Involves reactions of microorganisms with specific _____________: Combine known anti-serum with unknown bacterium
Useful in determining the identity of species AND strains.
Slide agglutination serogrouping (SASG) test for serogrouping N. meningitidisisolatesFormalin-killed meningococcal suspensions should be used for SASG testing rather than saline suspensions of living organisms to maintain a safe working environment. 
A positive result is designated by a 3+ or 4+ (strong agglutination) within 1-2 minutes, except for serogroup B, which is considered positive with a rating of 2+ or greater.
A negative result is designated by a 0 (saline), +/-, 1+ or 2+ (weak agglutination).
Examples:
Slide agglutination
ELISA (see lab)
Western blot (see later)
Fig 10.10

15. Genetics The End DNA Fingerprinting
Nucleic Acid Amplification Tests use Polymerase chain reaction (PCR). Small amount of microbial DNA in a sample is amplified. The presence or identification of an organism is indicated by amplified DNA. (see lab)
Nucleic Acid Hybridization: ssDNA or RNA from related organisms will hydrogen-bond to form a ds molecule. Application: DNA chips
Ribotyping and rRNA sequencing
Whole Genome Sequencing (WGS)
Fig
The End
Fig 10.17