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Unit 6: Microbial Identification and Classification - Coggle Diagram
Unit 6: Microbial Identification and Classification
Classification of Unicellular Microbes
Classification
Arranging organisms into similar/related groups and defining what set of features defines a group/taxa
Based on phenotype
Based on whether two organisms can breed and produce viable offspring
Difficult to apply to prokaryotes
Better option: DNA sequencing
Ribosomal RNA
Nomenclature
System of assigning names
Numbers
Identification
Process of characterizing a microbe to determine where it belongs
Microbial identification
Microscopic morphology
Helps determine size, shape, staining characteristics
Hard to distinguish different strains
Culture characteristics
Colony morphology gives clues to the organisms
Metabolic capabilities
Biochemical tests
Catalase test, color changes
Dichotomous key (flowchart)
Serology
Use of antisera (antibodies) from animals to diagnose a particular pathogen
Fatty acid analysis
Methyl esters (FAME)
Distinguishing strain differences
Biochemical typing
Identify bacterial species and distinguish strains: group of strains - biovar/biotype
Serological typing
Proteins and carbohydrates that vary among strains can be used as markers (antiserums needed)
Molecular typing
Differences in DNA structure distinguish phenotypically identical strains
Multi-locus sequence typing (MLST)
Looking for small changes in sequences
Phage typing
Relies on differences in bacterial strain susceptibility to bacteriophages
Antibiograms
Helps distinguish bacterial strains by looking at antibiotic susceptibility patterns on a disc
16S rRNA-based methods of microbial identification
Uses
Identify an organism's taxonomic group
Calculate relatedness between groups
Describe new species, and those that have never been successfully cultured
Bacterial DNA is extracted, run through PCR, sequence PCR product and analyse the sequence by comparison
Can detect microorganisms that can't be cultured or it is difficult
Advanced diagnostic tools
MALDI-TOF-MS
Protein profile is compared to database containing unique fingerprints specific to oragnism
Laser beam breaks molecule into ions, which travel at different speeds --> protein profile is created
Specimen type: culture
Real-time PCR/qPCR
Less than 3 hours to get results
Requires prior sequence knowledge
Uses fluorescent dyes and reporters that allow for real-time monitoring of amplification
Amplification curve depicts the rate at which DNA is amplified at each cycle
1) Non-specific fluorescent dyes - interact with any DNA
2) Sequence-specific DNA probes - bind to complimentary DNA sequence of a known target
Specimen type: Nucleic acid
Can identify multiple pathogens
Whole-genome sequencing
Target sample is made into smaller fragments --> PCR --> sequence is generated (reads) --> data analysis
Illumina MiSeq
Sequencing by synthesis: primers add fluorescently tagged nucleotides to DNA strands attached to flow cell
Specimen type: Nucleic acid
Costly, requires strong laboratory infrastructure