Supplemental Lecture (98/05/14 update) by Stephen T. Abedon (abedon.1@osu.edu)

  1. Chapter title: Eubacterial Classification
    1. A list of vocabulary words is found toward the end of this document
  2. Overview (of eubacterial classification)
    1. The following is quoted from Prescott et al., 1996 (p. 415, 439, 455, 491):
      1. (Gram-negative bacteria:)
        1. Volume 1 of Bergey's Manual describes 10 groups of gram-negative bacteria having general, medical, or industrial importance. Bacterial endosymbionts are also included in volume 1.
        2. The 10 sections are distinguished on the basis of a few major properties: general shape, the presence or absence of motility, mechanisms of motility (spirochetes), oxygen relationships, the absence of a cell wall (mycoplasmas), and the requirement for an intracellular existence (richettsias and chlamydiae).
        3. With the exception of the spirochetes (and possibly the mycoplasmas plus a few other groups), the gram-negative bacteria in volume 1 do not vary drastically in general shape or appearance. In contrast, they are very diverse in their metabolism and life-styles, which range from obligately intracellular parasitism to a free-living existence in soil and aquatic habitats.
        4. Many bacteria that specialize in predatory or parasitic modes of existence, such as Bdellovibrio, the rickettsias, and the chlamydiae, have relinquished some of their metabolic independence through the loss of metabolic pathways. They use the prey's or host's energy supply and/or cell constituents.
        5. Many gram-negative bacteria in volume 1 of Bergey's Manual are of considerable importance, either as disease agents or in terms of their effects on the habitat. Others, such as E. coli, are major experimental organisms studied in many laboratories.
      2. (Gram-positive bacteria:)
        1. Volume 2 of Bergey's Manual contains six sections covering all gram-positive bacteria except the actinomycetes. Bacteria are distributed among these sections on the basis of their shape, the ability to form endospores, acid fastness, oxygen relationships, the ability to temporarily form mycelia, and other properties.
        2. Peptidoglycan structure varies among different groups in ways that are often useful in identifying specific groups.
        3. The six endospore-forming genera are probably not closely related and are grouped together for convenience.
        4. Mycobacteria can form filaments, but unlike the actinomycetes, their filaments are easily fragmented into rods or coccoid elements. Actinomycete hyphae are more permanent.
        5. Although most gram-positive bacteria are harmless free-living saprophytes, species from all six sections of volume 2 of Bergey's Manual are major pathogens of humans, other animals, and plants. Other gram-positive bacteria are very important in the food and dairy industries.
      3. (Additional Gram-negatives plus cyanobacteria:)
        1. Volume 3 of Bergey's Manual contains eight sections, each describing a different group of gram-negative bacteria. Although few of these bacteria are of major medical or industrial significance, they are interesting biologically and often of considerable ecological importance.
        2. There are three major groups of photosynthetic procaryotes: the purple bacteria, the green bacteria, and the cyanobacteria. The cyanobacteria are placed in a separate section because they resemble eucaryotic phototrophs in that they possess photosystem II and carry out oxygenic photosynthesis. The purple and green bacteria use electron donors other than water and carry out anoxygenic photosynthesis.
        3. Chemolithotrophic bacteria obtain energy and electrons by oxidizing inorganic compounds rather than the organic nutrients employed by most bacteria. They often have substantial ecological impact because of their ability to oxidize many forms of inorganic nitrogen and sulfur.
        4. Bacteria do not always have simple, unsophisticated morphology but may produce prosthecae, stalks, buds, sheaths, or complex fruiting bodies.
        5. Gliding motility is widely distributed among bacteria and is very useful to organisms that digest insoluble nutrients or move over the surfaces of solid substrates.
        6. A group of bacteria is often placed in a particular section of volume 3 on the basis of a few carefully selected properties such as nutritional type even though it may share many characteristics (e.g., morphological traits) with organisms in different sections.
      4. (Actinomycetes:)
        1. Volume 4 of Bergey's Manual contains aerobic, gram-positive bacteria---the actinomycetes---that form branching hyphae and asexual spores.
        2. The morphology and arrangement of spores, cell wall chemistry, and the types of sugars present in cell extracts are particularly important in actinomycete taxonomy and are used to divide these bacteria into different groups.
        3. Actinomycetes have considerable practical impact because they play a major role in mineralization of organic matter in the soil and are the primary source of most naturally synthesized antibiotics.
        4. Actinomycetes taxonomy is still developing. The classification of these organisms will probably change considerably in the future.
  3. Major eubacteria taxonomic categories
    1. Just how many eubacteria taxonomic categories there are, and what they are is by no means universally agreed upon.
    2. For example, Olson (1995) presents 15 distinct categories including:
      1. Aquifecales
      2. Chlorobium-Flavobacteria group
      3. Chlamydia-Planktomyces group
      4. Chloroflecales
      5. Cyanobacteria
      6. Fibrobacter group
      7. Firmicutes
      8. Flexistipes
      9. Leptospirillum group
      10. Proteobacteria (alpha Proteobacteria, beta Proteobacteria, delta & epsilon, gamma Proteobacteria)
      11. Spirochetes
      12. Synergistes
      13. Thermodesulfobacterium
      14. Thermotogales
      15. Thermus-Deinococcus group
    3. Woese (1987), on the other hand, presents the following list:
      1. Aquifex
      2. Chlamydiae
      3. Cyanobacteria
      4. Proteobacteria or purple photosynthetic bacteria and nonphotosynthetic relatives
      5. Spirochetes
      6. Thermotoga
      7. green nonsulfur bacteria and relatives
      8. Radio resistant micrococci and relatives
      9. Green sulfur bacteria
      10. Bacteroides, flavobacteria, and relatives
      11. Planctomyces and relatives
      12. Gram-positive eubacteria and mycoplasmas
    4. Prescott et al. (1996) presents this list:
      1. Planctomyces/Chlamydia group
      2. Cyanobacteria & chloroplasts
      3. Fibrobacteria
      4. Proteobacteria (alpha Proteobacteria, beta Proteobacteria, delta & epsilon, gamma Proteobacteria)
      5. Spirochetes
      6. Thermotogales
      7. Green Nonsulfur Bacteria
      8. Low G+C gram-positive bacteria
      9. Fusobacteria
      10. High G+C gram-positive bacteria
    5. As presented by Campbell, 1996 (makes no attempt at completeness ):
      1. Gram-positive bacteria
      2. Proteobacteria
      3. Chlamydias
      4. Spirochetes
      5. Cyanobacteria
    6. These five categories, plus the rickettsias, are presented in greater detail below, with the gram-positives presented constrasted with the gram-negatives, particularly as found in your binomials list.
    7. Finally I present a table summarizing our knowledge of the various bacteria on our list, plus introduce some of the diseases these bacteria are associated with.
  4. Gram-positive bacteria
    1. Gram-positive bacteria are the endospore formers.
    2. Gram-positive bacteria typically (though certainly not always) are the exotoxin releasers. This is because they are the exoenzyme employers.
    3. Chemoheterotrophs:
      1. Most species are chemoheterotrophic.
      2. There are, however, a few photosynthetic gram-positives.
  5. Proteobacteria
    1. The gram-negatives:
      1. The Proteobacteria are the gram-negatives, all of which are thought to have derived from an ancestral purple photosynthetic bacterium.
      2. Of those bacterial groups which are actively studied by humans, the Proteobacteria form the most diverse taxon.
    2. The Proteobacteria group includes:
      1. the alpha subdivision (which includes Agrobacterium spp., Brucella spp., Zea mays mitochondria, the purple non-sulfur bacteria, and the rickettsias)
      2. the beta subdivision (which includes Bordetella spp., Neisseria spp., and some Pseudomonas spp.)
      3. the gamma subdivision (which includes Family Enterobacteriaceae, Haemophilus spp., Legionella spp., Pasteurella spp., Vibrio spp., the purple sulfur bacteria, and some Pseudomonas spp.)
      4. the delta subdivision (which includes the Bdellovibrio)
      5. the epsilon subdivision (which include Helicobacter spp.).
    3. Facultatively anaerobic gram-negative rods
    4. Gram-negative , facultatively anaerobic bacilli are a very medically relevant group of bacteria .
    5. There are three families making up the bulk of facultative anaerobic gram-negative rods (39 of 46 genera):
      1. Enterobacteriaceae
      2. Vibrionaceae
      3. Pasteurellaceae
    6. Enterobacteriaceae:
      1. See section below.
    7. Family Pasteuellaceae includes the genera :
      1. Actinobacillus
      2. Haemophilus
      3. Pasteurella
    8. Family Vibrionaceae includes the genera :
      1. Aeromonas
      2. Enhydrobacter
      3. Phobacterium
      4. Plesiomonas
      5. Vibrio
  6. Enterobacteriaceae [enterics]
    1. The enterics:
      1. Members of family Enterobacteriaceae tend to inhabit the intestinal tracts of animals.
      2. Members of family Enterobacteriaceae are found in the intestines:
        1. some are found in nearly all members of a given species
        2. some in a smaller fraction
        3. some only during (and causing) a disease state
    2. Glucose fermenters:
      1. Enterics tend to be glucose fermenters .
      2. Some are fermenters of other carbohydrates .
      3. Lactose non-fermeters tend to be pathogenic.
    3. Additional characteristics:
      1. If motile they have peritrichous flagella .
      2. May have fimbriae which help them to adhere to mucous membranes .
    4. Family Enterobacteriaceae includes the genera:
      1. Citrobacter
      2. Enterobacter
      3. Erwinia
      4. Escherichia
      5. Klebsiella
      6. Proteus
      7. Providencia
      8. Salmonella
      9. Serratia
      10. Shigella
      11. Yersinia
  7. Gram staining characteristics, summary
    1. phylogenitic relationships vs. staining patterns:
      1. There exist some ambiguity both in the gram-staining characteristics of some organisms, and in the relationships of others based on staining characteristics.
      2. The former are typically gram-negatives which display some propensity to stain gram-positive.
      3. The latter results particularly because not all phylogenetically gram-positive organisms stain gram-positive. Exceptional are the Mycobacteria and the Mycoplasma which are acid-fast and gram-neative staining, respecitively.
      4. As follows I've grouped bacteria according to their phylogenetic relationships, indicating exceptional staining characteristics where appropriate.
    2. Examples of phylogenetically gram-positives:
      1. Bacillus anthracis
      2. Bacillus subtilis
      3. Clostridium botulinum
      4. Clostridium perfringens
      5. Clostridium tetani
      6. Corynebacterium diphtheriae
      7. Lactobacillus spp.
      8. Listeria monocytogenes
      9. Mycobacterium leprae*
      10. Mycobacterium tuberculosis*
      11. Mycoplasma pneumoniae**
      12. Staphylococcus aureus
      13. Streptococcus spp.
      14. *Genus Mycobacterium stain acid-fast but phylogentically are more closely related to the gram-positives than they are to the gram-negatives.
      15. **Genus Mycoplasma stain gram-negative but phylogentically are more closely related to the gram-positives than they are to the gram-negatives (it is their lack of a cell wall which leads to this confusing state).
    3. Acid fast bacteria include a number of types which stain neither gram-negative nor gram-positive. These include:
      1. Mycobacterium leprae
      2. Mycobacterium tuberculosis
    4. Mycoplasma:
      1. Mycoplasma pneumoniae stains gram-negative as a consequence of lacking a cell wall, but phylogenetically is a gram-positive.
      2. In other words, the cell wall-less state of Mycoplasma pneumoniae presumably is a derived character from the gram-positve cell-walled state possessed by its ancestors.
    5. Examples of phylogenetically gram-negatives:
      1. Bdellovibrio spp.
      2. Bordetella pertussis
      3. Borrelia burgdorferi
      4. Chlamydia trachomatis
      5. Escherichia coli
      6. Helicobacter pylori
      7. Haemophilus influenzae
      8. Klebsiella spp.
      9. Legionella spp.
      10. Neisseria gonorrhoeae
      11. Neisseria meningitidis
      12. Pasteurella pestis
      13. Proteus spp.
      14. Pseudomonas spp.
      15. Rickettsia prowazekii
      16. Rickettsia rickettsii
      17. Salmonella spp.
      18. Serratia marcescens
      19. Shigella spp.
      20. Treponema pallidum
      21. Vibrio cholerae
      22. Yersinia pestis
    6. Uncertain and ambiguous gram-stainers:
      1. Some organisms simply tend not to be well differentiated by gram staining, despite any known phylogenetic affiliation with the gram-negatives or gram-positives.
      2. These include:
        1. Rickettsia prowazekii
        2. Rickettsia rickettsii
        3. Treponema pallidum
  8. Chlamydias
    1. The chlamydias are all:
      1. small
      2. gram-negative
      3. peptidoglycan-less
      4. cocci
      5. that are obligate intracellular parasites
      6. of animals
    2. Chlamydias obtain all of their ATP directly from the cells they parasitize.
  9. Spirochetes
    1. The spirochetes are chemoheterotrophic bacteria whose cells are tightly coiled or resemble a stretched spring (see illustration ).
    2. Other characteristics:
      1. Spirochetes are actively motile .
      2. Spirochetes have gram-negative-like cell envelopes .
      3. Spirochetes can be free-living organisms.
    3. Spirochete pathogens:
      1. A number of pathogens are spirochetes including:
        1. Borrelia burgdorferi (Lyme disease)
        2. Leptospira spp. (leptospirosis)
        3. Treponema pallidum (syphilis)
  10. Cyanobacteria [blue-green algae]
    1. Free-living chloroplasts:
      1. Cyanobacteria are the taxon from which chloroplasts evolved.
      2. Cyanobacteria particularly have a "plant-like" photosynthetic apparatus which is capable of generating molecular oxygen (cyanobacteria were the world's original oxygen generators).
    2. Ecology:
      1. A majority of cyanobacteria are fresh water inhabitants.
      2. There exist a few species that live in salt waters.
      3. There also exist cyanobacteria which form symbiotic relationships with fungi to form lichens.
    3. Cell biology:
      1. Cyanobacteria lack flagella though some are capable of movement through gliding.
      2. Cyanobacteria have gram-negative-like cell envelopes .
    4. Multicellularity:
      1. Some cyanobacteria species exist in a truly, though primitive, multicellular form in which cellular differentiation occurs.
      2. Though not unique among bacteria, multicellularity is rare.
  11. A few additional bacteria [rickettsias, actinomycetes]
    1. The rickettsias have the following characteristics:
      1. small
      2. gram-negative
      3. pleomorphic bacilli and coccobacilli
      4. obligate intracellular parasites of eucaryotes
      5. transmitted with some exceptions by insects and ticks
    2. Actinomycetes:
      1. "An order of filamentous or rod-shaped bacteria tending strongly to the development of branches and true mycelium and lacking photosynthetic pigment." (Webster's, 1955)
      2. Included among these soil dwelling bacteria are the Streptomyces from which nearly a majority of known antibiotics have been derived.
  12. Bacteria binomials, summary
    1. Required memorization:
      1. The following list is a sample of mostly disease-causing bacteria.
      2. Information associated with these bacteria are located in the lecture on bacteria binomials.
      3. Micro 509 students are expected to memorize this list as well as all "larger font" information associated with these binomials and found in the lecture on bacteria binomials.
    2. The list of bacteria binomials includes:
      1. Bacillus anthracis
      2. Bacillus subtilis
      3. Bdellovibrio spp.
      4. Bordetella pertussis
      5. Borrelia burgdorferi
      6. Chlamydia trachomatis
      7. Clostridium botulinum
      8. Clostridium perfringens
      9. Clostridium tetani
      10. Corynebacterium diphtheriae
      11. Escherichia coli
      12. Helicobacter pylori
      13. Haemophilus influenzae
      14. Klebsiella spp.
      15. Lactobacillus spp.
      16. Legionella spp.
      17. Listeria monocytogenes
      18. Mycobacterium leprae
      19. Mycobacterium tuberculosis
      20. Mycoplasma pneumoniae
      21. Neisseria gonorrhoeae
      22. Neisseria meningitidis
      23. Pasteurella pestis
      24. Proteus spp.
      25. Pseudomonas spp.
      26. Rickettsia prowazekii
      27. Rickettsia rickettsii
      28. Salmonella spp.
      29. Serratia marcescens
      30. Shigella spp.
      31. Staphylococcus aureus
      32. Streptococcus spp.
      33. Treponema pallidum
      34. Vibrio cholerae
      35. Yersinia pestis
    3. Mini review:
      4.

      organism:

      stain1:

      shape2:

      O23:

      disease4:

      Bacillus anthracis

      p

      r

      f

      anthrax

      Bacillus subtilis

      p

      r

      a

      none

      Bdellovibrio spp.

      n

      cs

      a

      none

      Bordetella pertussis

      n

      cb

      a

      pertussis

      Borrelia burgdorferi

      n

      s

      m

      lyme disease

      Chlamydia trachomatis

      n

      c

      ?

      trachoma, etc.

      Chlostridium botulinum

      p

      r

      s

      botulism

      Chlostridium perfringens

      p

      r

      n

      gas gangrene, etc.

      Chlostridium tetani

      p

      r

      s

      tetanus

      Corynebacterium diphtheriae

      p

      pr

      f

      diphtheria

      Escherichia coli

      n

      r

      f

      traveler's diarrhea, etc.

      Helicobacter pylori

      n

      h

      m

      stomach ulcer

      Haemophilus influenzae

      n

      r

      f

      ear, lung infections, etc.

      Klebsiella spp.

      n

      r

      f

      pneumonia, etc.

      Lactobacillus spp.

      p

      r

      f/m

      none

      Legionella spp.

      n

      r

      a

      pnuemonia

      Listeria monocytogenes

      p

      r

      f

      damage to fetus

      Mycobacterium leprae

      a (p)

      r

      a

      leprosy

      Mycobacterium tuberculosis

      a (p)

      r

      a

      tuberculosis

      Mycoplasma pneumoniae

      n (p)

      p

      f

      walking pneumonia

      Neisseria gonorrhoeae

      n

      dc

      a

      gonorrhea

      Neisseria meningitidis

      n

      dc

      a

      bacterial meningitis

      Pasteurella pestis

      n

      r

      f

      plague

      Proteus spp.

      n

      r

      f

      wound infection, etc.

      Pseudomonas spp.

      n

      r

      a

      opportunist (many)

      Rickettsia prowazekii

      ? (n)

      p

      ?

      epidemic typhus

      Rickettsia rickettsii

      ? (n)

      p

      ?

      R.M.S. fever

      Salmonella spp.

      n

      r

      f

      salmonellosis, typhoid fever

      Serratia marcescens

      n

      r

      f

      nosocomial infections

      Shigella spp.

      n

      r

      f

      traveler's diarrhea, etc.

      Staphylococcus aureus

      p

      sc

      f

      TSS, etc.

      Streptococcus spp.

      p

      x

      f

      strep throat, etc.

      Treponema pallidum

      ? (n)

      s

      m/n

      syphilis

      Vibrio cholerae

      n

      cr

      f

      cholera

      Yersinia pestis

      n

      r

      f

      plague

    4. 1gram staining: "n" = gram-negative, "p" = gram-positive, "a" = acid-fast positive, "?" = uncertain; in parentheses is actual phylogenetic classification if different from gram stain proficiency
    5. 2shape: "c" = cocci, "cb" = coccobacilli, "cr" = curved rod, "cs" = comma shaped (curved bacilli), "dc" = diplococci, "h" = helical, "p" = pleomorphic, "pr" = pleomorphic rod, "r" = rod (bacilli), "s" = spirochete, "sc" = staphylococci, "x" = ranges from diplococci to streptococci
    6. 3oxygen requirements: "a" = aerobic, "f" = facultatively anaerobic, "m" = microaerophile, "n" = anaerobe, "s" = strict anaerobe
    7. 4diseases: not all diseases caused by or synonymous names that you are responsible for are shown
  13. Vocabulary
    1. Bacteria binomials, summary
    2. Chlamydias
    3. Cyanobacteria
    4. Enterics
    5. Enterobacteriaceae
    6. Facultatively anaerobic gram negative rods
    7. Gram-positive bacteria
    8. Gram staining characteristics, summary
    9. Major eubacteria taxonomic categories
    10. Pasteurellaceae
    11. Proteobacteria
    12. Rickettsias
    13. Spirochetes
    14. Vibrionaceae
  14. Practice questions
    1. Use the following list as aid in answering some of the following questions: Genera: Acanthamoeba, Acinetobacter, Actinomyces, Actinomyces, Agrobacterium, Anisakids, Ascaris, Aspergillus, Azomonas, Azotobacter, Babesia, Bacillus, Bacteroides, Balantidium, Bdellovibrio, Bifidobacterium, Bordetella, Borrelia, Bradyrhizobium, Brucella, Campylobacter, Candida, Ceratocystis, Chlamydia, Chlorobium, Chloroflexus, Chromatium, Citrobacter, Clostridium, Corynebacterium, Coxiella, Cryphonectria, Cryptosporidium, Echinococcus, Etamoeba, Enterobacter, Enterobius, Enterococcus, Escherichia, Francisella, Fusobacterium, Gambierdiscus, Gardnerella, Gelidium, Giardia, Haloarcula, Halobacterium, Helicobacter, Haemophilus, Isospora, Klebsiella, Lactobacillus, Legionella, Leptospira, Listeria, Moraxella, Mucor, Mycobacterium, Mycoplasma, Naegleria, Neisseria, Necator, Nocardia, Nosema, Paragonimus, Pasteurella, Penicillium, Phytophthora, Pityrosporum, Plasmodium, Pneumocystis, Propionibacterium, Proteus, Pseudomonas, Rhizopus, Rickettsia, Rhizobium, Rhodopseudomonas, Saccharomyces, Salmonella, Schizosaccharomyces, Serratia, Shigella, Schistosoma, Staphylococcus, Stella, Streptococcus, Taenia, Thermus, Toxoplasmosis, Treponema, Trichinella, Trichomonas, Tripanosoma, Veillonella, Vibrio, Yersinia. Species: abortus, acnes, aerogenes, aeruginosa, albicans, americanus, anthracis, aquaticus, asteroides, aureus, botulinum, burgdorferi, brevis, brucei gambiense, brucei rhodesiense, burnetii, canis, carinii, cereus, cerevisiae, cholerae, choleraesuis, cloacae, coli, cruzi, difficile, diphtheriae, epidermis, exiguus, falciparum, fetus, flavus, fowleri, gondii, gonorrhoeae, granulosus, histolytica, infestans, influenzae, israelii, lacunata, lamblia, leprae, licheniformis, lumbricoides, marcescens, melitensis, meningitidis, microti, monocytogenes, multocida, mutans, nigricans, notatum, pallidium, parahaemolyticus, parasitica, perfringens, pertussis, pestis, pneumoniae, prowazekii, psittaci, pylori, pyogenes, rickettsii, rouxii, saginata, sanfransisco, solium, spiralis, subtilis, suis, tetani, thuringiensis, toxicus, trachomatis, tuberculosis, tularensis, tumefaciens, typhi, ulmi, vaginalis, vermicularis, westermani, xerosis.
    2. Why isn't Bordetella pertussis included among the facultatively anaerobic, gram-negative rods. [PEEK]
    3. List three general characteristics concerning morphology and biochemistry shared by members of family Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. [PEEK]
    4. Escherichia coli is a(n) (circle only one correct answer)? [PEEK]
      1. aerobe
      2. obligate anaerobe
      3. facultative anaerobe
      4. aerotolerant anaerobe
      5. microaerophile
      6. obligate aerobe
      7. all of the above
      8. none of the above
    5. Member family Enterobacteriaceae other than Escherichia coli. [PEEK]
    6. How do Chlamydias generate their ATP? [PEEK]
    7. What does the biochemistry of Cyanobacteria resemble? [PEEK]
    8. What do the rickettsias, the chlamydias, the bdelovibrios, and viruses all have in common? [PEEK]
    9. Name a facultatively anaerobic, gram positive bacterium. [PEEK]
    10. Besides being gram-positives and bacilli, what do all of the following have in common: Bacillus anthracis, Bacillus subtilis, Clostridium botulinum, Clostridium perfringens, Clostridium tetani. [PEEK]
    11. Small, pleomorphic, gram-negative bacteria. [PEEK]
    12. Name 10 genera of facultatively anaerobic gram-negative rods. [PEEK]
    13. Aquatic bacteria which lack flagella, though are capable of movement by gliding, and can also exist in colonies suggesting a primitive form of multicellularity. (choose correct answer) [PEEK]
      1. Vibrionaceae
      2. Enterobacteriaceae
      3. cyanobacteria
      4. Proteobacteria
      5. spirochetes
      6. Bdellovibrio
    14. In terms of eubacteria types, what would you likely call a free-living ancestral chloroplast? [PEEK]
    15. Name nine genera of facultatively anaerobic, gram negative rods. [PEEK]
    16. Name a genera which stains gram-negative, though inconsistently, and is an obligately intracellular parasites. [PEEK]
    17. Name the genera of bacteria which lack cell walls. [PEEK]
    18. Given the lists above, give a binomial of an acid-fast microorganism? [PEEK]
    19. Given the lists above, give a binomial of a gram-positive bacilli? [PEEK]
    20. Circle 15 organisms which tend to consistently not stain gram positive. [PEEK] Bacillus anthracis, Bacillus subtilis, Bdellovibrio spp., Bordetella pertussis, Borrelia burgdorferi, Chlamydia trachomatis, Clostridium botulinum, Clostridium perfringens, Clostridium tetani, Corynebacterium diphtheriae, Escherichia coli, Gardnerella vaginalis, Helicobacter pylori, Haemophilus influenzae, Klebsiella spp., Lactobacillus spp., Legionella spp., Listeria monocytogenes, Mycobacterium leprae, Mycobacterium tuberculosis, Mycoplasma pneumoniae, Neisseria gonorrhoeae, Neisseria meningitidis, Pasteurella pestis, Proteus spp., Pseudomonas spp., Rickettsia prowazekii, Rickettsia rickettsii, Salmonella spp., Serratia marcescens, Shigella spp., Staphylococcus aureus, Streptococcus spp., Treponema pallidum, Vibrio cholerae, Yersinia pestis
    21. __________ does not stain gram-negatively. (choose one correct answer) [PEEK]
      1. Mycoplasma spp.
      2. Borrelia burgdorferi
      3. Escherichia coli
      4. Lactobacillus spp.
      5. Helicobacter pylori
      6. Salmonella spp.
      7. Proteus spp.
    22. The enterics consist of the genera Citrobacter, Erwinia, ____________________, Escherichia, Klebsiella, ______________________, Providencia, Salmonella, Serratia, ____________________, and Yersinia. Fill in the blanks. [PEEK]
    23. Which of the following phylogenetically (i.e., evolutionarily) gram-positive bacteria do not actually stain gram positive? Bacillus anthracis, Bacillus subtilis, Clostridium botulinum, Clostridium perfringens, Clostridium tetani, Corynebacterium diphtheriae, Lactobacillus spp., Listeria monocytogenes, Mycobacterium leprae, Mycobacterium tuberculosis, Mycoplasma pneumoniae, Staphylococcus aureus, or Streptococcus spp. [PEEK]
    24. Other than in terms of species name or diseases caused, describe two ways that members of genus Chlamydia differ from members of genus Richettsia. [PEEK]
    25. Give an example (i.e., the binomial) of a proteobacterium. [PEEK]
    26. Circle all members Enterobacteriaceae. (three misses = zero credit)[PEEK]
    27. Bacillus anthracis, Bacillus subtilis, Bdellovibrio spp., Bordetella pertussis, Borrelia burgdorferi, Chlamydia trachomatis, Clostridium botulinum, Clostridium perfringens, Clostridium tetani, Corynebacterium diphtheriae, Escherichia coli <==, Helicobacter pylori, Haemophilus influenzae, Klebsiella spp. <==, Lactobacillus spp., Legionella spp., Listeria monocytogenes, Mycobacterium leprae, Mycobacterium tuberculosis, Mycoplasma pneumoniae, Neisseria gonorrhoeae, Neisseria meningitidis, Pasteurella pestis <==(yes/no), Proteus spp. <==, Pseudomonas spp., Rickettsia prowazekii, Rickettsia rickettsii, Salmonella spp. <==, Serratia marcescens <==, Shigella spp. <==, Staphylococcus aureus, Streptococcus spp., Treponema pallidum, Vibrio cholerae, Yersinia pestis <==
    28. Distinguish Bacillus subtilis from Chlamydia spp. by listing four characteristics of each that are not shared with the other. [PEEK]
    29. What are the Gram-staining characteristics of each of the following: [PEEK]
      1. Clostridium tetani: positive / negative
      2. Corynebacterium diphtheriae: positive / negative
      3. Escherichia coli: positive / negative
      4. Helicobacter pylori: positive / negative
      5. Haemophilus influenzae: positive / negative
      6. Klebsiella spp.: positive / negative
      7. Lactobacillus spp.: positive / negative
      8. Legionella spp.: positive / negative
      9. Listeria monocytogenes: positive / negative
    30. Name a species of bacteria whose Gram-staining is in some way different from that expected given the evolutionary classification of the organism, and explain how this staining characteristic deviates from expectations. [PEEK]
  15. Practice question answers
    1. Binomial list (above)
    2. It's an aerobe, not a facultative anaerobe.
    3. They are all gram-negative, facultatively anaerobic, bacilli (press here for more information).
    4. iii, facultative anaerobe
    5. See Enterobacteriaceae.
    6. they don't, they obtain their ATP directly from their hosts cytoplasm.
    7. plants (or chloroplasts) due to chloroplasts having evolved from cyanobacteria.
    8. they're all obligate intracellular parasites.
    9. Bacillus anthracis, Corynebacterium diphtheriae, Lactobacillus spp., Listeria monocytogenes, Staphylococcus aureus, Streptococcus spp.
    10. They are all endospore formers; they are all found in soil.
    11. Rickettsia spp.; Francisella tularensis is also correct.
    12. Citrobacter, Enterobacter, Erwinia, Escherichia, Klebsiella, Proteus, Salmonella, Serratia, Shigella, Yersinia, Haemophilus, Vibrio, Pasteurella, Providencia, etc.
    13. Cyanobacteria
    14. a cyanobacteria
    15. Actinobacillus, Aeromonas, Citrobacter, EnhydrobacterEnterobacter, Erwinia, Escherichia, Haemophilus, Klebsiella, Phobacterium, Plesiomonas, Proteus, Providencia, Salmonella, Serratia, Shigella, Vibrio, Yersinia
    16. Rickettsia.
    17. Mycoplasma.
    18. Mycobacterium spp. such as Mycobacterium tuberculosis
    19. Bacillus spp. such as Bacillus subtilis, or Clostridium such as Clostridium perfringens.
    20. (i) Bdellovibrio spp., (ii) Bordetella pertussis, (iii) Borrelia burgdorferi, (iv) Chlamydia trachomatis, (v) Escherichia coli, (vi) Helicobacter pylori, (vii) Haemophilus influenzae, (viii) Klebsiella spp., (ix) Legionella spp., (x) Mycobacterium spp., (xi) Mycoplasma pneumoniae, (xii) Neisseria gonorrhoeae, (xiii) Neisseria meningitidis, (xiv) Pasteurella pestis, (xv) Proteus spp., (xvi) Pseudomonas spp., (xvii) Rickettsia prowazekii, (xviii) Rickettsia rickettsii, (xix) Salmonella spp., (xx) Serratia marcescens, (xxi) Shigella spp., (xxii) Vibrio cholerae, (xxiii) Yersinia pestis.
    21. iv, Lactobacillus spp.
    22. Enterobacter, Proteus, Shigella
    23. Mycobacterium leprae, Mycobacterium tuberculosis, Mycoplasma pneumoniae
    24. Members of genus Chlamydia lack peptidoglycan, are monomorphic cocci, consistently stain gram-negative, and utilize their host's ATP. Members of genus Richettsia have peptidoglycan, are pleomorphic cocci or rods, inconsistently stain gram-negative, are able to make their own ATP, and typically are acquired via arthropod vectors.
    25. Any gram-negative will do.
    26. Escherichia coli <==, Klebsiella spp. <==, Proteus spp. <==, Salmonella spp. <==, Serratia marcescens <==, Shigella spp. <==, Yersinia pestis <==
    27. Bacillus subtilis: aerobic, rod, spore-former, gram-positive, soil bacterium, not pathogenic; Chlamydia spp.: gram-negative, cocci, peptidoglycan-less, cannot synthesize own ATP, obligate intracellular parasite, pathogen of animals
    28. (a) positive, (b) positive, (c) negative, (d) negative, (e) negative, (f) negative, (g) positive, (h) negative, (i) positive
    29. Mycobacterium tuberculosis and Mycobacterium leprae = both are phylogenetically gram positive but both do not stain gram positive, only acid fast; Mycoplasma pneumoniae = phylogenetically gram positive by stains gram negative due to lacking a cell wall; Treponema pallidum, Rickettsia prowazekii, and Rickettsia rickettsia = are all phylogenetically gram-negative but all stain gram variable
  16. References
    1. Black, J.G. (1996). Microbiology. Principles and Applications. Third Edition. Prentice Hall. Upper Saddle River, New Jersey. pp. 246-266.
    2. Campbell, N.A. (1996). Biology. Fourth Edition. Benjamin/Cummings Pub. Co. Menlo Park, CA. p. 498-499.
    3. Olson, G.J. (1995). Eubacteria. in The Tree of Life. http://phylogeny.arizona.edu/tree/eubacteria/eubacteria.html
    4. Postlethwait, J.H., Hopson, J.L. (1995). The Nature of Life. Third Edition. McGraw Hill, Inc. p. 455.
    5. Prescott, L.M., Harley, J.P., Klein, D.A. (1996). Microbiology. Third Edition. Wm. C. Brown Pub. Dubuque, Iowa. pp. 415-476, 416-437,491-502.
    6. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 589-609.
    7. Tortora, G.J., Funke, B.R., Case, C.L. (1995). Microbiology. An Introduction. Fifth Edition. The Benjamin/Cummings Publishing, Co., Inc., Redwood City, CA, pp. 273-294.
    8. Woese, D.J. (1987). Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eucarya. Microbiological Reviews 51:221-227.