Biotechnology and Microorganism Identification

Taxonomy: Organizing life into hierarchical groups (taxa).
*Key components:
1. Classification: Grouping organisms based on shared traits.
2. Phylogeny: Study of evolutionary history and relatedness.
3. Nomenclature: Standardized naming of organisms.

Levels: Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species.
Example:
* Escherichia coli belongs to:
Domain: Bacteria, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae, Genus: Escherichia, Species: coli.

- Firmicutes: "Tough skin," thick peptidoglycan with teichoic acids, low G+C content.
- Actinobacteria: Waxy coat on peptidoglycan, high G+C content.

- Gram-positive cocci: Includes Enterococcus, Streptococcus, and Staphylococcus.
- Mycoplasma: Lack a cell wall, making them resistant to beta-lactam antibiotics.

- Features: Thin peptidoglycan layer, outer membrane with lipopolysaccharides (LPS).
- Diversity: Includes cocci, bacilli, spiral forms, and varied metabolisms (heterotrophic, phototrophic, lithotrophic).

* A Gram-negative pathogen causing plague.
* Symptoms: Fever, nausea, bubo (lymphadenopathy), pneumonia, and sepsis.
* Diagnosis: Cultures confirmed Y. pestis. Treated with gentamycin, a protein synthesis inhibitor.
* Incidence: ~7 cases/year in the U.S.

1. Microscopic morphology: Size, shape, Gram reaction.
2. Macroscopic morphology: Colony size, shape, color.
3. Biochemical tests: Metabolic properties (e.g., lactose fermentation, H₂S production).
4. Antibody tests: Agglutination to detect specific strains.
5. Antimicrobial susceptibility: Determines resistance or sensitivity to antibiotics.

Based on DNA/RNA analysis:
- PCR: Amplifies specific DNA sequences.
- rRNA sequencing: Identifies evolutionary relationships.
- Whole-genome sequencing: Comprehensive genetic analysis.
- Hybridization: Detects specific DNA/RNA via probes.

1. PCR: Amplifies DNA for identification, variant detection, and transcript quantification (qPCR for measuring viral loads).
2. Sequencing: Determines DNA sequence (e.g., 6 trillion base pairs in one run).
3. Nucleic acid hybridization: Uses labeled probes to detect specific sequences (e.g., FISH).
4. Bioinformatics: Analyzes genomic, transcriptomic, and proteomic data to predict gene functions.

*Recombination: Editing DNA via cut and paste.
*Transgenesis: Introducing foreign DNA into cells.
*Cloning: Replicating cells or entire organisms.

1. Cell morphology: Shape, arrangement, Gram stain reaction.
2. Motility: Flagella presence and function.
3. Oxygen requirements: Aerobic, anaerobic, facultative.
4. Nutritional properties: Carbon/energy sources.
5. Pathogenicity: Virulence factors and disease-causing ability.

* Dichotomous keys: Stepwise tests (e.g., metabolic characteristics).
* ELISA: Detects antigens or antibodies; direct tests for microbes, indirect for host response.
* Flow cytometry: Uses fluorescence and light scattering to differentiate and sort cell types.

* Misdiagnosis of food poisoning delayed treatment.
* Importance of symptom recognition (e.g., bubo).
* Rapid identification and antibiotic treatment (gentamycin) can save lives.

A mass spectrometry technique identifying microorganisms by their molecular signatures.

Tools for detecting multiple DNA sequences simultaneously, often used in nucleic acid hybridization.