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    Microbiology Notes

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    superfr3shm
    I. Classification of organisms involves arranging them into taxonomic groups based on their similarities and evolutionary relationships. This helps identify unknown organisms and determine how to treat or study them. II. Organisms can be related through phenetics based on observable traits like morphology, metabolism, and motility, or phylogenetics based on genetic similarities and evolutionary descent from common ancestors. Phylogenetics is now more commonly used. III. Bergey's Manual is a reference for bacterial taxonomy that identifies organisms through tests of cell structure, metabolism, and genetics like 16S rRNA genes. It provides an organized key to classification.

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    Microbiology Notes

    Uploaded by

    superfr3shm
    88 views4 pages
    I. Classification of organisms involves arranging them into taxonomic groups based on their similarities and evolutionary relationships. This helps identify unknown organisms and determine how to treat or study them. II. Organisms can be related through phenetics based on observable traits like morphology, metabolism, and motility, or phylogenetics based on genetic similarities and evolutionary descent from common ancestors. Phylogenetics is now more commonly used. III. Bergey's Manual is a reference for bacterial taxonomy that identifies organisms through tests of cell structure, metabolism, and genetics like 16S rRNA genes. It provides an organized key to classification.

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    I. Classification of organisms involves arranging them into taxonomic groups based on their similarities and evolutionary relationships. This helps identify unknown organisms and determine how to treat or study them. II. Organisms can be related through phenetics based on observable traits like morphology, metabolism, and motility, or phylogenetics based on genetic similarities and evolutionary descent from common ancestors. Phylogenetics is now more commonly used. III. Bergey's Manual is a reference for bacterial taxonomy that identifies organisms through tests of cell structure, metabolism, and genetics like 16S rRNA genes. It provides an organized key to classification.

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    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    88 views4 pages

    Microbiology Notes

    Uploaded by

    superfr3shm
    I. Classification of organisms involves arranging them into taxonomic groups based on their similarities and evolutionary relationships. This helps identify unknown organisms and determine how to treat or study them. II. Organisms can be related through phenetics based on observable traits like morphology, metabolism, and motility, or phylogenetics based on genetic similarities and evolutionary descent from common ancestors. Phylogenetics is now more commonly used. III. Bergey's Manual is a reference for bacterial taxonomy that identifies organisms through tests of cell structure, metabolism, and genetics like 16S rRNA genes. It provides an organized key to classification.

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    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    of 4

    I.

    II.

    III.

    Classification of organisms
    a. Arrangement into groups
    b. Taxonomy
    i. Science of classification
    c. Systematics
    i. Science of systems of classification
    ii. Define the diff classes/ways to classify classes
    d. For:
    i. Treating organism
    ii. Guess abilities (when new in nature) based on name
    iii. Classifying new organisms, especially unknown ones on this planet
    1. Ex: bacteria in our bodies
    2. 80% unknown
    Relatidness
    a. Separate organisms (relationships)
    b. Phenetic (based on phenotype)
    i. Morphology
    1. Look alike
    2. Visual characteristics
    3. Ex: eukaryotes/prokaryotes: nucleus
    ii. Metabolism/biochemical
    1. Similar lifestyles
    2. Ex: plants/algae: photosynthesis, release oxygen, etc
    iii. Motility/physiology
    1. Move or not, method of movement
    c. Hard to distinguish bacteria by these above 3 phenetic tests
    i. Morphology 2 diff classes (round/long)
    ii. Metabolism/physiology time consuming, similar characteristics anyway
    d. => Group based on genetics and evolution (phylogenetics)
    i. More common
    ii. Similar/dissimilar DNA sequences
    iii. Common ancestors
    Bergeys Manual (bible for taxonomy)
    a. Of Systematic bacteriology
    i. More common
    ii. 9 volumes, 3rd or 4th edition
    b. Of Determinative Bacteriology
    i. Key - list how to identify organisms
    c. Identify organisms
    d. rDNA genes
    e. Phenetic rules
    i. Cell wall
    ii. Morphology
    iii. Metabolism/physiology

    IV.

    f. Gram +/gram -, oxidase tests, etc


    g. Important
    i. Conduct tests in orderly fashion (decision tree), not every test
    h. Journal of systematics
    i. Publish and include genetic testing, rDNA, other analyses, description
    ii. -> put into literature
    iii. Vs GenBank
    1. Doesnt use real names
    2. Use what people submit
    Trees
    a. Show how organisms relate
    b. Whittaker Tree
    i. 1840/1850-1967
    ii. First tree
    iii. Animals, plants, fungi
    1. Common ancestor
    iv. Prostista
    v. Bacteria (monera)
    vi. 5 kingdom tree
    vii. Wrong (obsolete)
    1. 4 eukaryotes groups, bacteria are separate from archaea
    viii. Dr. shneegurt doesnt approve
    c. Current tree
    i. Tree base on ribosomal RNA genes
    ii. Started with: 5s
    iii. Now: 16s (bacteria/archaea), 18s (eukaryotes)
    1. Small subunit
    iv. 1500 bp long
    1. =>1500 characteristics!
    2. Ex: morphology round/rod; ferments glucose yes/no
    3. Each position along gene = characteristic
    v. Bacteria
    vi. Archaea and eukaryote (plants, animals, fungi, protists, algae)
    1. Same branch -> common ancestor
    2. Archaea more related to eukaryotes than w/ other prokaryotes (bacteria)
    vii. More diversity in bacteria and archaea than eukaryotes
    viii. Naming in bacteria
    1. Not by reproductive isolation?
    ix. Carl Woese
    1. 1990
    2. 2000 defending tree
    x. Problem in bacteria
    1. Two lineages
    a. Blue and green

    2. Binary fission
    3. Linear (vertical) inheritance
    a. Parent -> child
    4. However bacteria do horizontal gene transfer
    a. Evolution
    b. More important
    c. Making new organisms, evolutionary processes, mutation
    5. Doolittle
    a. Famous biologist
    b. Anti-darwinist
    c. Ex: lineages of genes
    i. Evolutionary processes and species that branch off
    ii. Gene transfer within a population
    1. Unnoticeable lateral gene transfer
    2. Doesnt make much difference (pretty equivalent)
    3. Transfer easy
    a. vs interchanging between two diff species
    6. rRNA
    a. ancient
    b. highly conserved regions
    i. similar among all organisms
    c. variable regions
    i. not important to function
    ii. diff between diff organisms
    d. all cellular organisms have
    e. Advantages
    i. make PCR primers for everything
    ii. make good trees (make sense)
    f. little/slow lateral transfer
    g. integrated early on
    i. => no/little lateral transfer
    7. Making into tree
    a. 16s rRNA sequences
    i. Experimental
    ii. Control (GenBank, ribosomal database project -RDP)
    b. Algorithms compare sequenes
    i. Alignment
    1. Program: Clustal W
    2. Packages: include all programs
    a. MEGA
    3. All sequences -> stack into positions
    4. E. coli gene as guide
    5. Compare
    a. Similarity match

    ii. Parsimony analysis


    1. Program PAUP
    2. Statistically treatment
    a. Ex: neighbor joining, maximum likelyhood
    3. Provides similarity matrix/distance map
    a. Ex: sequence ABC how similar they are to
    each other
    iii. Making tree
    1. Program Tree Plot, PAUP
    2. Root
    a. Common ancestor
    3. Outlier
    a. Ex: gram + tree, use gram as outlier
    b. Ex: bacteria tree, use archaea as outlier
    c. For comparison (depth in tree)
    d. Unrooted tree?
    iv. Tree
    1. Branching
    a. Common ancestor
    2. Branch lengths
    a. How long since diverge
    b. Phylogenetic
    c. Mutations
    d. Guess rate of mutation
    i. Jukes-Canter, Kimura 2
    3. Move slightly
    a. By changing sequences
    4. Determine how good branches are
    a. Add random sequence of bases (not on
    tree; not related) -> run tree -> see if
    branches end up same for everyone else
    b. Add diff unrelated sequences x a lot
    c. Bootstrap analysis/ Jackknife
    i. Statistical
    ii. Numbers on nodes- % branch
    support
    iii. Typically not less than 50% branch
    recorded
    V.

    Fig. building a cladogram


    a.

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