Taxonomy Identification and Classification
What happened between the period of 1974 to 1984 that allowed for Bergey's Manual to state that classification/relationship is just as important as identification?
- molecular biology - ability to read DNA sequence and figure out relationships between bacteria
Name the two early methods to miniaturize biochemical tests.
1. API 20E system 2. enterotube
What are two different examples of serology tests in our every day lives?
1. ELISA pregnancy tests for human chorionic gonadotropin 2. strep test
What was the name change of Bergey's manual from 1974 to 1984 and what was its significance?
1974: Bergey's manual of DETERMINATIVE bacteriology (emphasis on identification of unknowns) vs. 1984: Bergey's manual of SYSTEMATIC bacteriology (emphasis on relationship)
What happened to Bergey's Manual in 1994
2 different editions!! 1. Bergey's Manual of DETERMINATIVE Bacteriology 9th edition - used for identification ONLY - never updated since this one... 2. Bergey's Manual of SYSTEMATIC Bacteriology 2nd edition - 5 volumes! - very expensive...
We can now sequence a whole genome in ____ hours.
26 and it only costs $6,500!
Compare and contrast classification and phylogeny.
classification: an organization of taxa into a system based on measured characteristics (easily identifiable characteristics) vs. phylogeny: a scheme that uses genetic/evolutionary relationships to classify - we're leaning more towards this
What are the different antigens on a bacterial cell?
on the bacterial cell, there are many different proteins on different structures that can serve as antigens: 1. H antigens: proteins in the flagella that can serve as antigens 2. K antigens: molecules using carbohydrates in thh capsule that can serve as antigens 3. O antigens: a number of different molecules in the cell wall that can be used as antigens
How do the organelles of eukaryotes compare to prokaryotes?
organelles of eukaryotes are more like prokaryotes than they are like the cytoplasm of the cells they live in
What was the first organism named by Carl von Linne?
plants!! he studied plants!! (he first named peppermint Mentha piperita)
What was the old school biochemical tests done on (hint: NOT miniaturized!)?
plates and tubes
Define strain.
a group of individuals all derived from one original cell/colony that are or are nearly genetically identical - strains differ from one another in some important and discernible way (contain distinguishing characteristics, ex: capsule-forming)
What is the significance of "the clinician must make a tentative diagnosis before getting the laboratory results"
a lot of the time, the patient can't wait for the lab results to come back - you need to treat the patient asap with an initial diagnosis!
Define taxon.
a taxonomic category - ex: family, genus, species, strain, even individual, etc.
Define classification.
an organization of taxa into a system based on measured characteristics (relationship of taxa to each other) - a phylogeny is a scheme that uses genetic/evolutionary relationships to classify
Compare number of species found between the three kingdoms.
archaea: <200 species bacteria: 4500 species eukarya: 1.5 million species
Compare membrane lipids between the three kingdoms.
archaea: composed of branched carbon chains attached to glycerol by ether linkage - isoprene units bacteria: composed of straight carbon chains attached to glycerol by ester linkage - fatty acids eukarya: composed of straight carbon chain attached to glycerol by ester linkage - fatty acids
Compare rRNA loop between the three kingdoms.
archaea: lacking bacteria: present eukarya: present
Compare first amino acid in protein synthesis between the three kingdoms.
archaea: methionine bacteria: formylmethionine eukarya: methionine
Compare antibiotic sensitivity between the three kingdoms.
archaea: no bacteria: yes eukarya: no
Compare cell type between the three kingdoms.
archaea: prokaryotic bacteria: prokaryotic eukarya: eukaryotic
Compare cell wall between the three kingdoms.
archaea: varies in composition, contains no peptidoglycan bacteria: contains peptidoglycan eukarya: varies in composition, contains carbohydrates
What is currently the #1 source of information to identify unknown bacteria?
biochemical tests (ex: enzyme/capability tests)
How would you measure how closely related two taxa are utilizing the 3 domain classification system?
- level of genetic relationship on the tree has to do with the length of the line --> to figure out how closely related two taxa are, need to measure length of line
What are examples of two different species associating together?
- lichens - choral + algae
True or false: identification of an known by a series of tests is a short procedure.
FALSE! each test is dependent on the results of the previous test and most results take 24+ hours to come about
What is real-time PCR?
- measuring of the product (DNA/RNA) as it develops to get an idea of how much of the organism is there - can tell the extent of the infection - in graph, patient that started to get a reading earlier than the other patient had more of the infectious agent in their body than the second one
Describe the enterotube.
- media are in gels in compartments - needle runs through - inoculate needle and pulls through all the gel compartments, so inoculation is rapid - color changes help identify unknowns
Provide some examples of morphological features used in classification and identification. (don't need to memorize, just know a few)
*some also apply to prokaryotes! - cell shape - cell size - colonial morphology (shapes and sizes of colonies) - ultrastructural characteristics - staining behavior - cilia and flagella - mechanism of motility - endospore shape and location - spore morphology and location - cellular inclusions - colony color
How did Bergey's Manual change between 1974 to 1984?
- 1 volume to 4 volumes - went from 19 parts to 33 sections - went from 249 genera to 367 genera - came clean and said that couldn't do classification/relationships in 1974, but in 1984, stated that classification/relationship is just as important as identification! - 1974: Bergey's manual of DETERMINATIVE bacteriology (emphasis on identification of unknowns) vs. 1984: Bergey's manual of SYSTEMATIC bacteriology (emphasis on relationship)
How can you use DNA hybridization to identify an unknown species?
- isolate a characteristic gene or segment of DNA that is specific for that species - tag that section with a dye or radioactive label - use that as a probe: take DNA from unknown, make it single stranded, add the "probe" (tagged specific section), and if the specific section with tag binds to unknown species' DNA, know that the unknown species is the specific taxa --> glow indicates positive identification
Describe the 3 domain classification system. What is its significance?
- 3 domains split into bacteria, archaea, and eukarya - shows prokaryotes (bacteria + archaea) as two different domains - shows that archaea and eukarya as more closely related to each other than either is related to bacteria --> radical because both archaea and bacteria are prokaryotes and seems to be the same - revolutionary because: 1. eliminates idea of kingdom (they're now just branches on a tree) 2. makes us very small in the eukaryotic branch - we're a "little twig in a big world" - level of genetic relationship on the tree has to do with the length of the line --> to figure out how closely related two taxa are, need to measure length of line
Elaborate on the evolution of Bergey's Manual.
- Bergey's Manual of Determinative Bacteriology went through 7 editions --> all for identification and classification - Bergey's Manual of Determinative Bacteriology 8th edition --> can't do classification, will only do identification - Bergey's Manual of SYSTEMATIC Bacteriology 1st edition --> both identification and classification ...then split... - Bergey's Manual of Determinative Bacteriology 9th edition --> only do identification - Bergey's Manual of SYSTEMATIC Bacteriology 2nd edition --> just classification - Bergey's Manual of Systematic of Archaea and Bacteria --> just classification
Describe the role of serology in pregnancy tests.
- ELISA pregnancy tests contain antibody specific for a particular antigen (chorionic gonadotropin) --> colored line indicates positive identification - women who are pregnant start producing chorionic gonadotropin (protein) almost immediately and is excreted in urine - chances for false positives and false negatives are low!
Describe the characteristics of ribosomal RNA and how Karl Woese worked with them.
- RNA composition of ribosomes is homologous (from the same ancestor) among Bacteria, Archaea, and Eukarya - the DNA sequence of ribosomal RNA goes back to the first life on earth + it mutates slowly - ribosome is made up of two subunits (one large and one small) --> large subunit was made up of large segment of DNA that codes for the ribosomal RNA and was too big for Woese to handle... --> small subunit had shorter segment of DNA that he was able to handle, so Woese worked with the DNA that codes for the rRNA of the small subunit of ribosomes
What did Karl Woese try to figure out and how did he do so?
- Woese was concerned that we knew very little about the evolution of prokaryotes, so tried to figure out how we would be able to figure that out - came to the realization that every living thing has a line that goes back to the first living thing on the planet: DNA is the consistent molecule that goes from the first living thing on the planet to everything that is alive today --> so tried to read DNA and look for what DNA is the most conserved and essential to cell function (so wouldn't mutate at a fast rate) - so looked into ribosomal DNA which codes for ribosomal RNA - worked in 80s, so did not have ability to sequence large segments of DNA, so sequenced small sequences and put them together
Provide some examples of physiological and metabolic characteristics used in classification and identification. (don't need to memorize, just know a few)
- carbon and nitrogen sources - cell wall constituents - energy sources - fermentation products - general nutritional type - growth temperature optimum and range - luminescence - mechanisms of energy conversion - motility - osmotic tolerance - oxygen relationships - pH optimum and growth range - photosynthetic pigments - salt requirements and tolerance - secondary metabolites formed - sensitivity to metabolic inhibitors and antibiotics - storage inclusions
What is a GC content test?
- detects GC content (%) from DNA melting temperature - easy to perform, but can only tell you if two taxa are NOT related (there is a wide range in GC content of different species) - contains a spectrophotometer that has a temperature control in it --> slowly raise the temperature, and detect at what temperature the DNA melts (the relative absorbance will increase exponentially bc twice as many molecules as started with) - the higher the GC content of DNA, the more energy it takes to "melt" the DNA into two single strands (bc easier to break the two AT bonds than the three GC bonds) --> the higher the GC content, the higher the melting temperature - easy to get data, but doesn't tell you a whole lot..
Provide an example where abiding by the rule that states that we need to go by the first name of a species instead of another may be troublesome...
- discovered Haemophilus influenzae in someone who had the flu (caused by virus!) and thought that was the cause of the flu, so named it Haemophilus influenzae HOWEVER: -Haemophilus influenzae does not cause influenza but causes meningitis (so should change the name to Haemophilus meningititis) - the name was validly published so it may not be changed even though it is misleading
Define species.
- fundamental unit of biology - a group of strains that share a high degree of similarity and which are relatively different from other groups (this is fuzzy because high degree can be different for different groups)
In Linnaeus' time (1600s), how did they perceive classification?
- had a hierarchical concept/system of all living things in which taxa are related to each other at different levels
What is phage typing? List the steps used to carry out this test.
- highly specific method using specific bacteriophages to identify an unknown --> not commonly done in healthcare, but used in higher leveled studies, like research - uses viruses that are very specific for different species or strains of bacteria 1. petri dish contains a lawn of the species/strain you are trying to identify 2. different phages are applied to lawn 3. if virus is capable of attacking the particular unknown, will attack a cell and when it bursts, the viral particles will go to all the adjacent cells, which will produce many viruses, which will continue to infect the adjacent cells 4. grey area indicates that cells remain intact and clear area indicates that virus was able to attack and destroy the cell - apply a lot of different phages to each plate, and pattern helps identify which strain/species you have
Describe the classification used in the medical/clinical world vs. the rest of the scientific world.
- in the medical/clinical world, even though the updated phylogeny is what we should be using (bc reflects true evolutionary relationship based on DNA sequencing), clinical microbiologists utilize the major categories and groups of bacteria that cause human disease in Bergey's Determinitive 9th edition --> organizes bacteria based on easily identifiable characteristics - in the scientific world, researchers are up to date and use the updated phylogeny
Why are biochemical tests NOT used to identify unknown causative agents of disease in a hospital microbiology lab?
- mostly can't do biochemical tests directly from samples (ex: sputum or blood samples) because the biochemical tests are nonspecific and there would be too many species in the sample (normal flora)
What is the Elisa test?
- powerful immunologic method conducted on a 96-well credit card-shaped plate 1. wells on an ELISA plate have anti-ebola antibodies impregnated in the well surface 2. ebola antigen from patient serum is added to the plate and is captured by antibody on well 3. an enzyme-conjugated anti-Ebola antibody is added 4. if the ebola antigen is present, the conjugated antibody will be captured by the complex and adding the substrate would yield a colored product
What are the tests are used to identify unknown causative agents of disease in a hospital microbiology lab?
- rapid and immunoassays (ex: ELISA) - molecular testing (ex: PCR) - culture - microscopy (ex: antibody/DNA test w/ fluorescence)
List examples of areas where specimen are collected.
- saliva - sputum - blood - urine - catheter - nasopharynx - throat (tonsils) - skin (swab, scalpel) - spinal tap (csf) - feces
What are restriction length polymorphisms?
- show genetic differences - DNA is cut by restriction endonucleases (enzymes that look for a certain sequence along the DNA and cuts the DNA only if it finds that specific sequence) - after DNA is cut, you run it on a gel and observe the different sizes of DNA (smaller segments of DNA travel faster on gel than larger segments) - the more unrelated 2 taxa are, the more RFLPS (the pattern of segmented DNA travelling on the lanes of the gel) will be different - like a DNA fingerprint
Describe the beginning of Bergey's Manual.
- started in 1920something - publish new edition every 10 years w/ new information accumulated
Describe the role of serology in strep tests.
- strep test will tell you if you have strep in only a few minutes! - area on rod contain antibody specific for a particular antigen (strep)
Describe the API 20E system.
- used for rapid identification of Enterobacteriaceae species and other GRAM NEGATIVE bacteria in smaller SPACE and shorter TIME - plastic API strips have 20 small wells containing dehydrated media - tested bacterium is suspended in sterile saline, then added to each well, then strip is incubated for 16-24 hrs, and color reactions are noted as + or - - tests results can be entered into a computer program for identification
Where are we now with classification?
- we have a constantly updating PHYLOGENY that keeps refining + changing based on DNA sequencing of organisms - mostly dominated by bacteria, then archaea, then eukaryotes
What are the 7 rules for species names?
1. binomial (two words) 2. genus and specific epithet: Homo sapiens 3. always italicized or underlined 4. genus always captialized, specific epithet lower case 5. latin or latinized words (Escherichia coli honors Theodore Escherich, coli refers to the colon) 6. international commissions to protect names and maintain naming rules (if new species was described and validly published in a scientific journal, that's the name it needs to go by) 7. full name includes the initials of taxonomist who officially named the species (ex: Mentha piperita L., Sequoiadendron gigantea (Lindl.) Buchh.)
Provide 3 examples that test biochemical characteristics/capabilities.
1. catalase test: drop hydrogen peroxide on a colony and solution contains catalase, which splits H2O2 into water and oxygen which creates bubbles (so test is + if produce bubbles and - if does not produce bubbles) - ex: staph is catalase + and strep is catalase - 2. carbohydrate fermentation: tubes contain nutrients, a single carbohydrate, and an upside tube that can collect gas - inoculate and incubate the tubes, and if microbe can use and ferment sugar, it will produce acid and gas --> acid will turn pH indicator yellow and gas will form bubbles in upside down tube - 25+ different carbohydrate fermentation tests (we're only doing 4) 3. urease test: urea broth is used to detect the enzyme urease (an enzyme that splits urea) - some bacteria are able to break down urea, using urease, into ammonia and CO2, and media turns pink if urease is present - this tests if the microbe contains urease - several tests have been developed to look for specific enzymes and capabilities
According to the major categories and groups of bacteria that cause human disease in Bergey's Determinitive 9th edition, what are examples of gram positive bacteria with cell walls that cause disease?
1. cocci (staphylococcus) 2. endospore-forming rods and cocci (clostridium) 3. irregular non-sporing rods (actinomyces) 4. mycobacteria (mycobacterium) 5. actinomycetes (nocardia)
List the series of tests done to identify an unknown bacteria.
1. gram stain 2. shape 3. oxidase test 4. lactose fermentation 5. growth on citrate as sole carbon source 6. indole production
What does the endosymbiotic theory tell us?
1. mitochondria in eukaryotes came from bacteria related to e. coli 2. chloroplasts in photosynthetic organisms came from cyanobacteria
What are 6 practical steps that the clinicians need to know regarding diagnostic medical microbiology?
1. need to know how much of a sample the lab needs to work with the specimen 2. need to get the correct specimen (ex: sputum instead of saliva) 3. need to use aseptic technique (if you contaminate it, the lab needs to separate the contaminant from the true pathogen and may even mistake the contaminant for the pathogen) 4. need to transport specimen asap! (obligate anaerobes may die before they arrive at the lab and need alive specimen to conduct biochemical tests!) 5. need to retrieve the sample before administration of antibiotics (because may kill all the specimen before you retrieve it for lab tests, and it's important to identify what the disease was!) 6. some disease are caused by normal flora, and other disease are not (ex: salomonella typhae vs. candida albicans)
According to the major categories and groups of bacteria that cause human disease in Bergey's Determinitive 9th edition, what are examples of cell wall-less eubacteria (the mycopasmas or mollicutes) that cause disease?
1. regular non-sporing rods (listeria) 2. mycoplasmas (mycoplasma)
What are the 3 different types of media? Describe them.
1. selective media: prepared by the addition of specific substances to a culture medium that will permit growth of one group of bacteria while inhibiting the growth of some other group 2. differential media: medium itself on which the colonies grow will cause different species to look different based on their biochemical capabilities (the incorporation of certain chemicals into a medium may result in diagnostically useful growth or visible change in the medium after incubation) 3. media to determine biochemical characteristics: media used to test bacteria for particular metabolic activities, products, or requirements
What are the three types of ways serology is used for identification?
1. serological diagnosis of disease (see if patient has been exposed to disease bc if patient has been exposed to disease and immune system is functioning properlly, will develop antibodies against antigen of disease agent): blood sample is scanned for the presence of antibody using an antigen of known specificity --> color change or clumping indicates positive reaction (antibodies for known antigen is present, so patient either currently is infected with disease agent, or was exposed to it and developed antibodies for it) 2. identifying unknown microbe: unknown microbe (ex: bacteria) is mixed with serum containing antibodies of a known specificity --> color change or clumping indicates presence of the pathogen 3. positive identification with fluorescent dyes: get antibodies specific to a particular antigen of a cell and attach a fluorescent dye to that antibody, then look under microscope --> glow indicates positive identification
What are the 4 reasons why the 3 domain classification system was revolutionary?
1. shows prokaryotes (bacteria + archaea) as two different domains 2. shows that archaea and eukarya as more closely related to each other than either is related to bacteria --> radical because both archaea and bacteria are prokaryotes and seems to be the same 3. eliminates idea of kingdom (they're now just branches on a tree) 4. makes us very small in the eukaryotic branch - we're a "little twig in a big world"
According to the major categories and groups of bacteria that cause human disease in Bergey's Determinitive 9th edition, what are examples of gram negative bacteria with cell walls that cause disease?
1. spirochetes (treponema) 2. aerobic/microaerophillic, motile, helical/vibroid (campylobacter) 3. aerobic/microaerophillic rods and cocci (alcaligenes) 4. facultatively anaerobic rods (escherichia coli) 5. anaerobic, straight, curved, and helical rods (bacteroides) 6. rickettsiae and chlamydiae (rickettsia)
What is a character primarily used for identification and classification in bacteria/prokaryotes in general?
BIOCHEMICAL CHARACTERISTICS/CAPABILITIES are more informative than morphological characters in prokaryotes - a big source of information we use to IDENTIFY (not so much classify) unknowns
What is used to look for bacteria in the blood?
BLOOD CULTURE BOTTLES - incubated in a special incubator, both aerobically and anaerobically (bc there are anaerobes that can grow in the blood) - growth is detected by buildup of CO2, which causes an alarm to go off - blood sample is inoculated from patient into two bottles (blue cap bottle is incubated aerobically and orange cap bottle is incubated anaerobically) - tests for bacteremia or septicemia
What happened with the 8th edition of Bergey's Manual?
Bergey's Manual of Determinative Bacteriology (1974): - gave up with classification (up until this point, they were attempting to talk about how bacteria were related to each other) bc claimed that a means for hierarchy was impossible (just didn't have the data to figure out relationships), only committed to identification - 1 volume - divided into 19 parts, 249 genera
What is the most recent Bergey's Manual? Tell me about it!
Bergey's Manual of SYSTEMATICS of ARCHAEA and BACTERIA - published online - updated as more information comes out - just for classification, not identification - $1300 per year
Who came up with the binomial system for species names?
Carl von Linne aka carollus linaeus (latin version)
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
What is the evidence for where chloroplasts came from? What is its significance?
EVIDENCE: - Cyanophora paradoxa is a protozoan with a photosynthetic organelle/bacterium (red alga that resembles a cyanobacteria) living inside its cell - the "chloroplasts" still have peptidoglycan cell walls (only found in bacteria!!) --> suggestion that it was a recent association between a eukaryote and photosynthetic bacterium (so recent that the bacterium that now serves as chloroplast did not lose its peptidoglycan cell wall yet) SIGNIFICANCE: - this and many examples of organisms whose cells contain living cells of other species supports the endosymbiotic theory that chloroplasts and mitochondria are derived from once free living bacteria
True or false: the GC content test can tell you if two taxa are related AND if they are not related.
FALSE: a GC content test can ONLY tell you if two taxa are NOT related! - bc if related, GC content will be close BUT two taxa that aren't related may also have close GC content - if GC content is different, we know for sure that the taxa are NOT closely related to each other
True or false: serotyping and phage typing can be used to find relationship.
FALSE: serotyping and phage typing can ONLY be used for SPECIFIC identification and NOT for relationships.
What is DNA sequencing?
GOLD STANDARD FOR DNA: DNA sequencing - closely related species have similar DNA sequences - now DNA sequencing is automated to process much DNA in a short time (used to be very time consuming and required careful technique in the 90s) - different nucleotides are tagged with different colored dyes, and machine will read the color for nucleotdies in the sequence (in powerpoint, every colored peak indicated the present of that nucleotide) - there are many variations of method and target
For what type of bacteria is the GC content test very informative (in terms of relationships)?
GRAM + BACTERIA!! - gram + bacteria is distinctly divided into a high GC content group and a low GC content group --> ex: staph and strep are in the low GC content group, and mycobacteria and streptomyces are in the high GC content group
Why would a hospital microbiology lab never identify unknown bacteria with the proper series of tests?
IT WOULD TAKE TOO LONG!! - each test takes a day! - patient would be dead by the time they figured out what he/she had!!
What is a character used for identification and classification in Eukaryotes? How about in regards to Prokaryotes?
MORPHOLOGY - can utilize bone structure and characteristics passed on through evolution (easily observable characteristics) to identify and classify eukaryotes (even single-celled eukaryotes!!) --> ex of morphological features that are helpful in identifying and classifying eukaryotes: mosquito: length of wings, amount of ornaments, length of antennae, shape of wings - for prokaryotes, morphology isn't helpful in identification and classification bc not a lot to go by
What is an example of media that is selective and differential?
MacConkey Agar: - selects for gram - - different species look different on MacConkey agar
Would you use phage typing to identify unknowns in healthcare?
NO, it's used moreso in research
What is the best way to test relationship between two taxa? Describe it.
NUCLEIC ACID HYBRIDIZATION - the more 2 taxa are related, the more alike their DNA and the more likely their DNA will hybridize procedure: 1. make DNA of known species single stranded 2. make DNA of other species you want to use to compare single stranded as well 3. suspend both in solution and detect how many single strands of DNA from the two different species hybridized with each other --> high hybridization (lots of double stranded DNA) indicates a high degree of similarity, low hybridization (little double stranded DNA) indicates low degree of similarity, and no hybridization indicates no similarity between the two species
What is a method that is faster and more effective than biochemical tests (and may eventually replace it)?
SEROLOGY! (refers to blood serum and has to do with specific antibodies to specific microbial antigens) - the use of the specific antibody-antigen reaction to identify unknown molecules, viruses, and cells - antibodies are produced by vertebrates in specific response to foreign chemicals/molecules (antigens) steps to developing antibodies: - antigens are injected into rabbit - rabbit develops antibodies (molecules that are specific to and will react to the antigen) - we purify the antibodies - use those antibodies in diagnostic tests
True or false: scientific names are universal.
TRUE!! scientific names are universal, whereas common names are not universal
How is the vitek used for antibiotics?
Vitek has cards (just like the ones for identification of unknown species) that have antibiotics in them, and Vitek can provide information with what antibiotic the isolated species is susceptible to in only 7 hrs
Most of the hospital microlabs have what current machine that does biochemical tests?
Vitek: - a computerized miniaturized biochemical test the size of a large microwave - utilizes credit card-sized cards that contain wells that contain the different biochemical tests - straw on one end is attached to saline solution of unkown - vacuum on straw fills all the wells with the culture (inoculum) - incubate card and get different reactions - Vitek contains spectrophotometer checks every test and when has positive identification, will show it on report - can get 100% of identification of microbes within 7 hours --> very accurate and very rapid!
What was the classification system from the 1960s?
five kingdom classification
Compare the three kingdoms.
for most characteristics, archaea are more similar to eukaryotes than they are to bacteria (except for membrane lipid characteristics)
How does Les Mis have to do with taxonomy? LOLLLLLL I LOVE DR COLOSI :')
identification of unknowns: Jean vau Jean asks who am I figuring out relationships: Jean vau Jean is figuring out his relationship with others throughout les mis
What did Carl von Linne do?
identified each species by genus name followed by a multi word Latin description
What is an exception to the rule that states that we need to go by the first name of a species instead of another?
if the earlier classification of the GENUS was wrong, we CAN change it, but CANNOT change the original EPITHET
What was the old method for strep tests?
inoculate a blood agar plate and look for beta hemolysis
Tell me about PCR!
polymerase chain reaction: one of the most powerful tools developed in the past century that uses primers to amplify (make multiple copies) of specific sections of DNA, "finding needle in haystack" (using primers to copy a specific segment out of a haystack of DNA) - take 2-3 hrs per sample - assays have been developed to amplify unique genes of specific taxa, if the DNA gets amplified, the taxon is detected - gave Kary Mullis the nobel prize for inventing PCR method - increasingly used for identification and classification of unknowns (in short period of time, able to identify all 67 unknown taxa of bacteria) FROM A SINGLE SAMPLE --> will become the primary tool for identifying unknowns in our career - variations for many purposes exist (ex: diagnostic microbiology)
What two previous genus did they think E. coli was? What was the original name and what did they end up naming it?
previously suspected genuses: Bacterium and Bacillus original name: Bacterium coli finalized name: Escherichia coli (to honor Theodore Escherich)
What is the gold standard for DNA?
sequencing DNA!
What is the order of classification from most specific to most general?
species (Canis familiaris) genus (canis) family (canidae) order (carnivore, primate) class (mammalia) phylum (chordata) kingdom (animal, fungi plantae) domain (eukarya vs. bacteria vs. archaea)
What was the change of mindset (revolution) that happened starting in the 70s? Who was essential in this?
the concept of the relationship of organisms on the planet to each other radically changed - Karl Woese was an essential figure
Define identification.
the determination of the identity of an unknown taxon - a taxon is a taxonomic category (family, genus, species, strain, even individual)
What is Bergey's manual?
the reference work that you would refer to learn about a taxon of prokaryotes
What did Woese come up with? (according to colosi, this was a "revolution")
the three domain classification in the 1980s - comparisons of DNA sequence of ribosomal RNA and more recently genome comparisons has led to fundamental change in concepts of relationships of life on earth - 3 domain classification system blows up the idea of kingdom and makes us very small - we're a "little twig in a big world"
How do you incubate swabs containing obligate anaerobes?
there are anaerobic chambers for swabs containing obligate anaerobes that need to be transported to a lab!
What is the dominant/most commonly used method for identifying unknown bacteria today? What will it be replaced by?
today's dominant/most commonly used method: biochemical tests! - ex: ViTek will be replaced by: serology, DNA techniques - ex: PCR --> HIV can be identified by antibodies (serology) or by RNA of virus (PCR)
What is a GC content test useful for? What is it not useful for?
useful for: identifying relationships between different organisms/species not useful for: identification of unknown (bc multiple species/strains can have the same GC content)
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
Are ELISA tests quantifiable?
yes! you can measure the extent to which the enzyme catalyzes the substrate via spectrophotometer!