Taxonomy Identification and Classification

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.

Polymerase chain reaction is a method that uses primers to amplify specific sections of DNA. Signup and view all the answers

What is 'the dominant/most commonly used method for identifying unknown bacteria today'? What will it be replaced by?

Both B and C Signup and view all the answers

What is real-time PCR?

Measuring the DNA/RNA product as it develops to determine the amount of the organism present. Signup and view all the answers

What are restriction length polymorphisms?

Genetic differences shown by cutting DNA with restriction endonucleases and observing segment sizes. Signup and view all the answers

What is DNA sequencing?

The process used to determine the precise order of nucleotides within a DNA molecule. Signup and view all the answers

We can now sequence a whole genome in how many hours?

26 hours Signup and view all the answers

What is the significance of 'the clinician must make a tentative diagnosis before getting the laboratory results'?

Patients often cannot wait for lab results, so timely treatment is necessary. Signup and view all the answers

What are 6 practical steps that clinicians need to know regarding diagnostic medical microbiology?

<ol> <li>Proper sample size, 2. Correct specimen type, 3. Aseptic technique, 4. Timely transport, 5. Sample retrieval before antibiotics, 6. Understand normal flora.</li> </ol> Signup and view all the answers

List examples of areas where specimens are collected.

Saliva, sputum, blood, urine, catheter, nasopharynx, throat, skin, spinal tap, feces. Signup and view all the answers

How do you incubate swabs containing obligate anaerobes?

Using anaerobic chambers for transport to the lab. Signup and view all the answers

What tests are used to identify unknown causative agents of disease in a hospital microbiology lab?

Rapid assays, immunoassays, molecular testing, culture, and microscopy. Signup and view all the answers

Why are biochemical tests not generally used to identify unknown causative agents of disease in a hospital microbiology lab?

They are nonspecific and usually cannot be performed directly from mixed samples. Signup and view all the answers

Are ELISA tests quantifiable?

True Signup and view all the answers

In Linnaeus' time, how did they perceive classification?

They had a hierarchical system of living things. Signup and view all the answers

What is the order of classification from most specific to most general?

Species, genus, family, order, class, phylum, kingdom, domain. Signup and view all the answers

What's the acronym for memorizing the order of classification?

Domain, KING = Kingdom, Phillip = Phylum, Came = Class, Over = Order, For = Family, Good = Genus, Spaghetti = Species. Signup and view all the answers

What was the change of mindset that happened starting in the 70s? Who was essential in this?

The concept of evolutionary relationships radically changed, led by Karl Woese. Signup and view all the answers

What did Karl Woese try to figure out and how did he do so?

He aimed to understand prokaryotic evolution by studying conserved DNA, specifically ribosomal DNA. Signup and view all the answers

Describe the characteristics of ribosomal RNA and how Karl Woese worked with them.

Ribosomal RNA is homologous across domains and has a slow mutation rate; Woese sequenced the small subunit rRNA. Signup and view all the answers

What was the classification system from the 1960s?

Five kingdom classification. Signup and view all the answers

What did Woese come up with in the 1980s?

The three domain classification system. Signup and view all the answers

Describe the 3 domain classification system. What is its significance?

It divides life into Bacteria, Archaea, and Eukarya, emphasizing distinct evolutionary paths. Signup and view all the answers

What are the 4 reasons why the 3 domain classification system was revolutionary?

<ol> <li>Differentiates prokaryotes, 2. Shows Archaea closer to Eukarya, 3. Eliminates the kingdom idea, 4. Depicts us as 'little twigs' in a vast tree.</li> </ol> Signup and view all the answers

How would you measure how closely related two taxa are utilizing the 3 domain classification system?

By measuring the length of the lines on the phylogenetic tree. Signup and view all the answers

What does the endosymbiotic theory tell us?

Mitochondria are derived from bacteria related to E. coli; chloroplasts from cyanobacteria. Signup and view all the answers

What is the evidence for where chloroplasts came from?

Cyanophora paradoxa has a photosynthetic bacterium with peptidoglycan cell walls. Signup and view all the answers

What are examples of two different species associating together?

Lichens and corals + algae. Signup and view all the answers

Where are we now with classification?

We have a constantly updating phylogeny, predominantly reflecting bacteria. Signup and view all the answers

Describe the classification used in the medical/clinical world vs. the rest of the scientific world.

Clinical microbiologists use Bergey's classification; researchers use updated phylogeny. Signup and view all the answers

According to Bergey's Determinitive 9th edition, what are examples of gram negative bacteria that cause disease?

Spirochetes, Campylobacter, Alcaligenes, E. coli, Bacteroides, Rickettsia. Signup and view all the answers

According to Bergey's Determinitive 9th edition, what are examples of gram positive bacteria that cause disease?

Staphylococcus, Clostridium, Actinomyces, Mycobacterium, Nocardia. Signup and view all the answers

According to Bergey's Determinitive 9th edition, what are examples of cell wall-less eubacteria that cause disease?

Listeria, Mycoplasma. Signup and view all the answers

Compare the three kingdoms in terms of characteristics.

Archaea are more similar to Eukaryotes than to Bacteria, except for membrane lipid composition. Signup and view all the answers

Compare the number of species found between the three kingdoms.

Archaea have fewer known species compared to Bacteria and Eukarya. Signup and view all the answers

Define identification.

The determination of the identity of an unknown taxon. Signup and view all the answers

Define taxon.

A taxonomic category such as family, genus, species, or strain. Signup and view all the answers

Define classification.

An organization of taxa into a system based on measured characteristics. Signup and view all the answers

Compare and contrast classification and phylogeny.

Classification organizes taxa based on characteristics, while phylogeny uses genetic/evolutionary relationships. Signup and view all the answers

Define species.

The fundamental unit of biology; a group of strains that share a high degree of similarity. Signup and view all the answers

Define strain.

A group of individuals derived from one original cell/colony that are genetically identical. Signup and view all the answers

Who came up with the binomial system for species names?

Carl von Linne. Signup and view all the answers

What did Carl von Linne do?

Identified each species by genus name followed by a multi-word Latin description. Signup and view all the answers

What was the first organism named by Carl von Linne?

Plants, specifically peppermint Mentha piperita. Signup and view all the answers

What are the 7 rules for species names? List one.

Binomial (two words). Signup and view all the answers

Provide an example where the rule for species names may be troublesome.

Haemophilus influenzae is named despite not causing influenza. Signup and view all the answers

What two previous genera did they think E. coli was?

Bacterium and Bacillus. Signup and view all the answers

What is an exception to the rule of using the first name of a species?

If the earlier classification of the genus was wrong, it can be changed but not the original epithet. Signup and view all the answers

Scientific names are universal.

True Signup and view all the answers

What is a character used for identification and classification in Eukaryotes?

Morphology. Signup and view all the answers

Provide examples of morphological features used in classification and identification.

Cell shape, cell size, colonial morphology. Signup and view all the answers

Provide examples of physiological and metabolic characteristics used in classification and identification.

Carbon and nitrogen sources, energy sources, growth temperature optimum and range. Signup and view all the answers

What is a character primarily used for identification and classification in bacteria/prokaryotes?

Biochemical characteristics/capabilities. Signup and view all the answers

Provide 3 examples that test biochemical characteristics/capabilities.

<ol> <li>Catalase test, 2. Carbohydrate fermentation, 3. Urease test.</li> </ol> Signup and view all the answers

What is currently the #1 source of information to identify unknown bacteria?

Biochemical tests. Signup and view all the answers

What are the 3 different types of media? Describe them.

<ol> <li>Selective media, 2. Differential media, 3. Media to determine biochemical characteristics.</li> </ol> Signup and view all the answers

What is an example of media that is selective and differential?

MacConkey Agar. Signup and view all the answers

What is used to look for bacteria in the blood?

Blood culture bottles. Signup and view all the answers

Identification of an unknown by a series of tests is a short procedure.

False Signup and view all the answers

List the series of tests done to identify an unknown bacteria.

<ol> <li>Gram stain, 2. Shape, 3. Oxidase test, 4. Lactose fermentation, 5. Growth on citrate as sole carbon source, 6. Indole production.</li> </ol> Signup and view all the answers

Why would a hospital microbiology lab never identify unknown bacteria with the proper series of tests?

It would take too long. Signup and view all the answers

When is it appropriate to use the proper series of tests to identify unknown bacteria?

When trying to find out the characteristics of a newly found species. Signup and view all the answers

Name the two early methods to miniaturize biochemical tests.

<ol> <li>API 20E system, 2. Enterotube.</li> </ol> Signup and view all the answers

What was the old school biochemical tests done on (hint: NOT miniaturized!)?

Plates and tubes. Signup and view all the answers

Describe the API 20E system.

Used for rapid identification of Enterobacteriaceae species and other gram-negative bacteria. Signup and view all the answers

Describe the enterotube.

Media are in gels in compartments allowing for rapid inoculation and testing. Signup and view all the answers

Most of the hospital microlabs have what current machine that does biochemical tests?

Vitek. Signup and view all the answers

How is the Vitek used for antibiotics?

Vitek can determine the susceptibility of an isolated species to antibiotics. Signup and view all the answers

What is a method that is faster and more effective than biochemical tests?

Serology. Signup and view all the answers

What are the different antigens on a bacterial cell?

<ol> <li>H antigens, 2. K antigens, 3. O antigens.</li> </ol> Signup and view all the answers

What are the three types of ways serology is used for identification?

<ol> <li>Serological diagnosis of disease, 2. Identifying unknown microbe, 3. Positive identification with fluorescent dyes.</li> </ol> Signup and view all the answers

What are two different examples of serology tests in our everyday lives?

<ol> <li>ELISA pregnancy tests, 2. Strep test.</li> </ol> Signup and view all the answers

Describe the role of serology in pregnancy tests.

ELISA tests detect chorionic gonadotropin in urine. Signup and view all the answers

What was the old method for strep tests?

Inoculate a blood agar plate and look for beta hemolysis. Signup and view all the answers

Describe the role of serology in strep tests.

The strep test detects specific antibodies in minutes. Signup and view all the answers

What is the ELISA test?

A powerful immunologic method conducted on a 96-well plate. Signup and view all the answers

What is phage typing?

A method using specific bacteriophages to identify an unknown. Signup and view all the answers

Would you use phage typing to identify unknowns in healthcare?

No. Signup and view all the answers

Serotyping and phage typing can be used to find relationships.

False Signup and view all the answers

What is a GC content test?

Detects GC content (%) from DNA melting temperature. Signup and view all the answers

The GC content test can tell you if two taxa are related AND if they are not related.

False Signup and view all the answers

What is a GC content test useful for? What is it not useful for?

It is useful for showing that two taxa are NOT related, but not for showing relatedness. Signup and view all the answers

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.