Questions and Answers
For what type of bacteria is the GC content test very informative?
Gram-positive bacteria
What is the best way to test the relationship between two taxa?
Nucleic acid hybridization
How can you use DNA hybridization to identify an unknown species?
Isolate a characteristic gene or segment of DNA specific for that species, tag it, and use it as a probe.
Tell me about PCR.
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What is 'the dominant/most commonly used method for identifying unknown bacteria today'? What will it be replaced by?
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What is real-time PCR?
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What are restriction length polymorphisms?
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What is DNA sequencing?
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We can now sequence a whole genome in how many hours?
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What is the significance of 'the clinician must make a tentative diagnosis before getting the laboratory results'?
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What are 6 practical steps that clinicians need to know regarding diagnostic medical microbiology?
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List examples of areas where specimens are collected.
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How do you incubate swabs containing obligate anaerobes?
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What tests are used to identify unknown causative agents of disease in a hospital microbiology lab?
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Why are biochemical tests not generally used to identify unknown causative agents of disease in a hospital microbiology lab?
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Are ELISA tests quantifiable?
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In Linnaeus' time, how did they perceive classification?
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What is the order of classification from most specific to most general?
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What's the acronym for memorizing the order of classification?
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What was the change of mindset that happened starting in the 70s? Who was essential in this?
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What did Karl Woese try to figure out and how did he do so?
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Describe the characteristics of ribosomal RNA and how Karl Woese worked with them.
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What was the classification system from the 1960s?
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What did Woese come up with in the 1980s?
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Describe the 3 domain classification system. What is its significance?
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What are the 4 reasons why the 3 domain classification system was revolutionary?
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How would you measure how closely related two taxa are utilizing the 3 domain classification system?
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What does the endosymbiotic theory tell us?
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What is the evidence for where chloroplasts came from?
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What are examples of two different species associating together?
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Where are we now with classification?
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Describe the classification used in the medical/clinical world vs. the rest of the scientific world.
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According to Bergey's Determinitive 9th edition, what are examples of gram negative bacteria that cause disease?
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According to Bergey's Determinitive 9th edition, what are examples of gram positive bacteria that cause disease?
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According to Bergey's Determinitive 9th edition, what are examples of cell wall-less eubacteria that cause disease?
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Compare the three kingdoms in terms of characteristics.
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Compare the number of species found between the three kingdoms.
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Define identification.
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Define taxon.
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Define classification.
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Compare and contrast classification and phylogeny.
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Define species.
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Define strain.
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Who came up with the binomial system for species names?
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What did Carl von Linne do?
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What was the first organism named by Carl von Linne?
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What are the 7 rules for species names? List one.
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Provide an example where the rule for species names may be troublesome.
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What two previous genera did they think E. coli was?
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What is an exception to the rule of using the first name of a species?
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Scientific names are universal.
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What is a character used for identification and classification in Eukaryotes?
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Provide examples of morphological features used in classification and identification.
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Provide examples of physiological and metabolic characteristics used in classification and identification.
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What is a character primarily used for identification and classification in bacteria/prokaryotes?
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Provide 3 examples that test biochemical characteristics/capabilities.
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What is currently the #1 source of information to identify unknown bacteria?
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What are the 3 different types of media? Describe them.
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What is an example of media that is selective and differential?
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What is used to look for bacteria in the blood?
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Identification of an unknown by a series of tests is a short procedure.
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List the series of tests done to identify an unknown bacteria.
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Why would a hospital microbiology lab never identify unknown bacteria with the proper series of tests?
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When is it appropriate to use the proper series of tests to identify unknown bacteria?
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Name the two early methods to miniaturize biochemical tests.
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What was the old school biochemical tests done on (hint: NOT miniaturized!)?
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Describe the API 20E system.
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Describe the enterotube.
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Most of the hospital microlabs have what current machine that does biochemical tests?
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How is the Vitek used for antibiotics?
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What is a method that is faster and more effective than biochemical tests?
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What are the different antigens on a bacterial cell?
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What are the three types of ways serology is used for identification?
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What are two different examples of serology tests in our everyday lives?
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Describe the role of serology in pregnancy tests.
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What was the old method for strep tests?
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Describe the role of serology in strep tests.
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What is the ELISA test?
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What is phage typing?
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Would you use phage typing to identify unknowns in healthcare?
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Serotyping and phage typing can be used to find relationships.
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What is a GC content test?
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The GC content test can tell you if two taxa are related AND if they are not related.
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What is a GC content test useful for? What is it not useful for?
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Study Notes
Identification and Classification in Taxonomy
- Identification involves determining the identity of an unknown taxon, which is a taxonomic category (e.g., family, genus, species).
- A taxon encompasses various taxonomic categories.
- Classification organizes taxa into systems based on measured characteristics and relationships between them.
- Phylogeny uses genetic and evolutionary relationships for classification.
Species and Strains
- A species is the fundamental unit of biology, comprising strains with a high degree of similarity among themselves and relative differences from others.
- Strains are groups of nearly genetically identical individuals derived from a single original cell or colony, differing in specific characteristics (e.g., capsule presence).
Binomial System and Naming Rules
- Carl von Linne, also known as Carolus Linnaeus, developed the binomial naming system for species.
- First species named by Linne was peppermint, classified as Mentha piperita.
- Species naming rules include binomial format, italicization, capitalized genus and lowercase specific epithet, use of Latin words, and adherence to international naming commissions.
Biochemical Characteristics in Identification
- Biochemical characteristics are more effective than morphology for identifying bacteria/prokaryotes.
- Common biochemical tests include catalase, carbohydrate fermentation, and urease tests, providing rapid identification of microbial characteristics.
Media Types for Classification Testing
- Selective media allows growth of specific bacteria while inhibiting others.
- Differential media causes distinct appearances of species based on their biochemical capabilities.
- Media for biochemical characteristics assess specific metabolic activities of bacteria.
Rapid Identification Techniques
- Vitek system utilizes miniaturized biochemical tests for rapid identification of microbes, capable of reporting results in approximately 7 hours.
- The API 20E system and enterotube also provide methods for rapid identification, focusing on well-structured test environments.
Serology and Diagnostic Testing
- Serology uses specific antibodies to identify unknown microbes or diagnose diseases through color changes or clumping in tests.
- Examples include ELISA tests for pregnancy and rapid strep tests, which provide quick results based on antibody-antigen interactions.
Antigens and Their Role
- Bacterial cells possess various antigens—H antigens (flagella), K antigens (capsule carbohydrates), and O antigens (cell wall molecules)—that can be used for identification.
Relationships Among Bacteria
- GC content tests analyze the percentage of guanine and cytosine in DNA, useful for differentiating between high and low GC content organisms but not effective for specific unknown identifications.
- Nucleic acid hybridization provides the most accurate measurement of relationships between taxa, enabling identification of unknown species through specific DNA probes.
PCR in Identification
- Polymerase Chain Reaction (PCR) amplifies DNA, enabling detailed genetic analysis, widely used in identifying specific species based on unique DNA segments.
Summary of Testing Methods
- Series of tests utilized for identifying bacteria include gram staining, shape assessment, oxidase testing, and others, each dependent on previous results.
- Phage typing is a specific identification method using bacteriophages, primarily used in research rather than routine healthcare settings.
These structured notes cover crucial aspects of taxonomy identification and classification while providing context for their application in microbiological studies.### Polymerase Chain Reaction (PCR)
- PCR is a significant tool for DNA amplification using primers, enabling the detection of specific DNA segments among vast quantities.
- Takes 2-3 hours per sample for results.
- Assays are created to amplify unique genes of specific taxa; successful amplification indicates taxon presence.
- Kary Mullis received a Nobel Prize for his invention of PCR.
- Widely used for rapid identification and classification of unknown bacterial taxa from a single sample.
- Variants of PCR have been developed for diverse applications, such as diagnostic microbiology.
Current Methods for Identifying Bacteria
- The dominant method is biochemical testing (e.g., ViTek) for bacterial identification.
- This method is being phased out in favor of serology and DNA techniques like PCR.
- HIV can be identified via serology (antibodies) or PCR (viral RNA).
Real-Time PCR
- Measures DNA/RNA products during amplification for real-time quantification.
- Useful in assessing the extent of infections; earlier readings correlate to higher pathogen loads.
Restriction Length Polymorphisms (RFLPs)
- RFLPs reveal genetic differences by cutting DNA with restriction endonucleases at specific sequences.
- Different DNA segment sizes are analyzed via gel electrophoresis; smaller segments migrate faster.
- Unique patterns generated can serve as DNA fingerprints.
DNA Sequencing
- The gold standard for identifying bacterial species and relations is DNA sequencing.
- Automated sequencing has significantly increased throughput compared to manual techniques of the 90s.
- Nucleotide sequences are tagged with colored dyes for machine interpretation.
Classifications and Standards
- Whole genome sequencing can now be completed in 26 hours for around $6,500.
- Clinicians must often make preliminary diagnoses while waiting for lab results to expedite patient care.
Practical Steps in Diagnostic Microbiology
- Ensure adequate sample size for laboratory analysis.
- Collect the correct specimen type for testing.
- Utilize aseptic techniques to prevent contamination.
- Transport samples promptly to maintain viability.
- Retrieve samples before antibiotic administration to avoid loss of pathogens.
- Recognize that some diseases are caused by normal flora.
Specimen Collection Sites
- Common specimen types include saliva, sputum, blood, urine, and fecal matter.
- Swabbing techniques can be used on skin, throat, and nasopharyngeal areas.
Identification Tests in Clinical Labs
- Utilizes rapid assays (e.g., ELISA), molecular tests (e.g., PCR), cultures, and microscopy techniques for disease causative agents.
Limitations of Biochemical Tests
- Biochemical tests are not suitable for direct application on clinical samples due to the presence of diverse species (normal flora) diluting specificity.
Classification History
- Linnaeus established a hierarchical classification in the 1600s, which is now outdated.
- The current understanding has evolved to a three-domain system based on DNA sequencing, distinguishing bacteria, archaea, and eukarya.
Karl Woese's Contributions
- Woese pioneered the study of prokaryotic evolution through ribosomal RNA analysis.
- He highlighted that all living organisms share a lineage back to the earliest life forms, using conserved DNA.
Endosymbiotic Theory
- Mitochondria in eukaryotes derived from bacteria, while chloroplasts came from cyanobacteria.
- Evidence exists in organisms like Cyanophora paradoxa, supporting the theory of recent symbiotic relationships.
Current Classification Practices
- Medical classifications utilize Bergey's Determinative 9th edition, focusing on characteristics pertinent to human disease.
- Scientific classifications are increasingly based on genetic data for accurate evolutionary relationships.
Gram-positive and Negative Bacteria
- Key examples of gram-negative bacteria include spirochetes (Treponema), and facultatively anaerobic rods (Escherichia coli).
- Gram-positive examples include cocci (Staphylococcus) and endospore-forming rods (Clostridium).
Comparisons Among the Three Kingdoms
- Archaea share many characteristics with eukaryotes, emphasizing the complex relationship among these life forms.
- The number of species and their classification continues to reflect ongoing research and updates in phylogeny.
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Description
Explore key concepts in taxonomy with these flashcards focused on identification, taxa, and classification. Each card provides concise definitions to enhance your understanding of biological categorization. Perfect for students and enthusiasts in the field of biology.