Taxonomy and Classification Classification of Microbes

Taxonomy • Science of Classification of organisms • Hopes to show relationships among organisms • Is a way to provide universal identification of an organism • Why do we care things are related?

Q&A •

Pneumocystis jirovecii

was thought to be a protozoan until DNA analysis showed it is a fungus. Why does it matter whether an organism is classified as a protozoan or a fungus?

Phylogeny or Systematics • Shows evolutionary relationships and history among organisms • Some obtained from fossil record • Most bacteria use rRNA sequencing or some other sequence information • A goal is to identify all organisms by 2025

Hierarchy • Evolutionary relationships • Species are groups that interbreed (have productive sex) • How this goes • Species • Genus • Family • Order • Class • Division • Phylum • Kingdom (1969) • Domain (80’s)

The 5 Kingdoms based on nutrient procurement • Plantae – Multicellular photoautotrophs • Animalia – ingestive • Fungi – absorptive • Protozoa – Mostly singe celled • Prokaryotes • Which of these are microbes?

The 3 domains • Eukarya – Plants, animals fungi and protists • Bacteria – (with peptidoglycan) • Archaea – With unusual cell walls, and membreanes

The Three-Domain System Figure 10.1

The Three-Domain System Table 10.1

Endosymbiotic Theory Figures 10.2, 10.3

Table 10.2

Scientific Nomenclature • Binomial genus and specific epithet (species). Is used world wide • Is always underlined • Rules for naming are set by international committee’s – – – International Code of Zoological Momenclature International Code of Botanical Nomenclature Bacteriological Code and Bergey’s Manual

Scientific Binomial

Klebsiella pneumoniae

Scientific Names

Source of Genus Name

Honors Edwin Klebs

Source of Specific Epithet

The disease

Pfiesteria piscicida

Honors Lois Pfiester Disease in fish

Salmonella typhimurium Streptococcus pyogenes Penicillium chrysogenum

Honors Daniel Salmon Chains of cells (strepto-) Stupor (typh-) in mice (muri-) Forms pus (pyo-) Tuftlike (penicill-) Produces a yellow (chryso-) pigment

Trypanosoma cruzi

Corkscrew-like (trypano-, borer; soma-, body) Honors Oswaldo Cruz

Species Definition • Eukaryotic species: – A group of closely related organisms that breed among themselves • Prokaryotic species: – A population of cells with similar characteristics – – –

Clone: Strain:

Population of cells derived from a single cell Genetically different cells within a clone

Culture:

grown in the lab • Viral species: – Population of viruses with similar characteristics that occupies a particular ecological niche

Is it as easy to classify Microbes as it is Macrobes?

• How to classify • What do we have to look at?

Identifying Bacteria Applications, p. 283

Phylogenetic Relationships of Prokaryotes Figure 10.6

Of more than 2600 species identified so far • Only about 250 or 10% are pathogens

Classification and Identification • •

Classification

: Placing organisms in groups of related species. Lists of characteristics of known organisms.

Identification

organisms.

: Matching characteristics of an “unknown” organism to lists of known – Clinical lab identification

Bergey’s Manual of Systematic Bacteriology • Morphological characteristics • Presence of various enzymes • Serological tests • Phage typing • Fatty acid profiles • DNA finger printing • Sequence of ribosomal RNA • Is still very difficult

• Morphological characteristic s : Useful for identifying eukaryotes Identification Methods • • Differential staining: Gram staining, acid fast staining

Biochemical tests:

Determines presence of bacterial enzymes A dichotomous key Figure 10.8

A clinical microbiology lab report form

Figure 10.7

Identifying a Gram – Negative, Oxidase – Negative Rod Figure 10.8

•Unknown enteri inoculated into tube •After incubation the 15 tests are observed •A numerical score is assigned •The species is assigned •This may be of is the strain has changed somehow. More tests are required

• Design a rapid test for a

Staphylococcus aureus

. 10-14 Figure 6.10

Serology study of serum and its immune responce • Combine known antiserum + unknown bacterium • Slide agglutination • ELISA p288, 514 • • • Western blot p289 Southern Blot p292 DNA chip p293 Figure 10.10

• Strains with different antigens are called – Serotypes – Serovars – biovars

DNA Hybridization

Phage Typing Determining a strains suceptability to certain phage or bacterial viruses Figure 10.13

The Western Blot

Flow Cytometry • Uses differences in electrical conductivity between species • Fluorescence of some species • Cells selectively stained with antibody plus fluorescent dye Figure 18.12

A typical dichotomous key See appendix H in your lab book

• DNA base composition – Guanine + cytosine moles% (GC) • DNA fingerprinting – Electrophoresis of restriction enzyme digests • rRNA sequencing • Polymerase Chain Reaction (PCR) p251 Genetics Figure 10.14

Nucleic Acid Hybridization: DNA chip DNA Chip Technolog y Figure 10.17

Differentiate between classificaiton and identification Figure 10.5

FISH •

Fluorescent in situ hybridization

• Add DNA probe for

S. aureus

Figure 10.18

Differentiate between strain and species?

Classification of viruses?

• Not currently placed in Domains or Kingdoms • Why?

• Species are usually a population of viruses with similar characteristics that occupies a particular ecological niche.

Dichotomous keys are used for identification of organisms

Cladograms show phylogenetic relationships among organisms

Differential staining • Name examples

The gram stain

Using Bergies manual • Used to Identify bacteria not classify • Features that are used to differentiate various organism often have little to do with arranging the orgs in taxonomic groups

4 major groups • Domain Bacteria – Gram-negative Eubacteria that have cell walls.

Proteobacteria

–

Non proteobacteria

Gram negative bacteria – Gram positive Eubacteria that have cell walls • Domain archaeobacteria

Some groups by identificaiton • • • • • • •

Spirochetes

– Genus Borrelia, Leptospira, Treponema

Aerobic/microaerophilic, motikle, helical/vibroid gram negative bacteria

– Geneus Camphylobacter

Gram negative aerobic/microaerophilic rods and cocci

– Genus Agrobacterium, Alcaligenes, Pseudomonas

Facultatively anaerobic gram negative rods

– Genus Enterobater, Escherichia, Klebsiella, Serratia, Shigella, Yersinia, Eikenella

Gram positive Cocci

– Genus lactococcus, streptococcus, Staphylococcus

Endospore forming gram positive rods and cocci

– Genus bacillus, clostridium

Regular, nonsporing gram positive rods

– Genus Lactobacillus, listeria