Important words and concepts from Chapter 9, Black, 1999 (1/26/2004):

by Stephen T. Abedon (abedon.1@osu.edu) for Micro 509 at the Ohio State University

 

 

Course-external links are in brackets

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Vocabulary words are found below

 

 

(1) Chapter title: An Introduction to Taxonomy: The Bacteria

(2) Taxonomy

(a)                    The science of organismal classification

(b)                    [taxonomy (Google Search)] [taxonomy on the web] [index]

(3) Classification

(a)                    Classification is the assignment of organisms (species) into an organized scheme of naming

(b)                    Ideally these schemes are based on evolutionary relationships (i.e., the more similar the name, the closer the evolutionary relationship)

(c)                    Thus, classification (and therefore the science of taxonomy) is concerned with

(i)                      The establishment of criteria for identifying organisms and assignment to groups (what belongs where)

(ii)                    The arrangement of organisms into groups of organisms (e.g., how large or inclusive groups should be; for example, at what level of diversity should a single species be split into two or more species?)

(iii)                   Consideration of how evolution resulted in the formation of these groups

(d)                    [classification of organisms (Google Search)] [index]

(4) Taxon (pl. taxa)

(a)                    A group or category of related organisms

(b)                    For example, at the lowest level, species is a taxonomic category as is genera and all the way on up to kingdom and domain

(c)                    These groups become increasingly inclusive as they become larger, going from species to kingdom or domain

(d)                    Two key characteristic of taxa are that

(i)                      Members of lower level taxa (e.g., species) are more similar to each other than are members of higher level taxa (e.g., kingdoms or domain)

(ii)                    Members of specific taxa are more similar to each other than any are to members of different specific taxa found at the same hierarchical level (e.g., humans are more similar to apes, i.e., comparison between species, than either is similar to, for example, Escherichia coli)

(iii)                   Thus, once you know that two individuals are members of the same taxon, you can infer certain similarities between the two organisms (e.g., all members of Family Enterobacteriaceae are facultatively anaerobic, Gram-negative rods)

(e)                    Note that taxa are dynamic, changing as our knowledge of organisms and evolutionary relationships change

(f)                     See Figure 9.2, Classification of a human, a dog, wolf, and a bacterium

(g)                    [taxon (Google Search)] [index]

(5) Binomial nomenclature

(a)                    Organisms are named using binomial nomenclature (viruses are exceptions)

(b)                    Binomial nomenclature employs the names of the two lower level taxa, genus and species, to name a species

(c)                    We've been through this, but conventions when using binomial nomenclature include:

(i)                      Genus comes before species (e.g., Escherichia coli)

(ii)                    Genus name is always capitalized (e.g., Escherichia)

(iii)                   Species name is never capitalized (e.g., coli)

(iv)                  Both names are always either italicized or underlined (e.g., Escherichia coli)

(v)                    The genus name may be used alone, but not the species name (i.e., saying or writing "Escherichia," alone is legitimate while saying or writing "coli" is not)

(vi)                  The genus name may be abbreviated but

·        It must be used first without abbreviation

·        If abbreviated it must be used with the species name (no E. all by itself)

·        It must be abbreviated unambiguously

·        If abbreviating as the first letter of the genus is unambiguous, then abbreviating as the first letter is what one does (e.g., Escherichia abbreviated as E. but only if no other genera considered also starts with E)

·        Genus abbreviations are only used in conjunction with the species name (i.e., E. coli)

(d)                    [binomial nomenclature (Google Search)] [index]

(6) Strain

(a)                    When considering microorganism species, a category (not usually considered a taxonomic one) found below the level of species is strain

(b)                    A strain in some ways is equivalent to a breed or a subspecies among plants or animals

(c)                    Two members of the same strain are more similar to each other than either is to an individual that is a member of a different strain, even if all three organisms are members of the same species

(d)                    See Figure 9.2, Classification of a human, a dog, wolf, and a bacterium

(7) Bacterial species

(a)                    "A bacterial species is defined by the similarities found among its members. Properties such as biochemical reactions, chemical composition, cellular structures, genetic characteristics, and immunological features are used in defining a bacterial species. Identifying a species and determining its limits presents the most challenging aspects of biological classification—for any type of organism."

(b)                    A formal means of distinguishing bacterial species is by employing a dichotomous key to guide the selection of tests used to efficiently determine those bacterial properties most relevant to bacterial identification

(8) The five-kingdom system

(a)                    The five-kingdom system was first proposed in 1969 and is showing its age

(b)                    It posits the existence of five kingdoms (kingdom therefore being the highest/most inclusive taxonomic category in this system)

(c)                    The five kingdoms include:

(i)                      Plantae (the plants)

(ii)                    Fungi (the fungi)

(iii)                   Animalia (the animals)

(iv)                  Protista (the unicellular eucaryotes)

(v)                    Monera (the prokaryotes)

(d)                    Below we will walk through the five-kingdom kingdoms in which most microorganisms are found, before proposing alternatives to the five-kingdom system

(e)                    [five-kingdom system (MicroDude)] [index]

(9) Kingdom Monera

(a)                    Your text differentiates Monera into three categories (without assigning a taxonomic category to the distinctions)

(b)                    Included are the eubacteria, the cyanobacteria, and the archaeobacteria

(c)                    As we will see, these distinctions are more phenotypic than they are evolutionary (i.e., a cyanobacteria is a eubacteria, and neither is an archaeobacteria)

(d)                    That is,

(i)                      the eubacteria are our common, every-day bacteria, some of which are disease-causing; also the taxon from which mitochondria originated

(ii)                    the cyanobacteria are photosynthetic eubacteria, the taxon from which chloroplasts originated

(iii)                   the archaeobacteria are distinctive in their adaptation to extreme environments (e.g., very hot, salty, or acidic) though not all archaeobacteria live in extreme environments

(e)                    See Figure 9.6, Some typical monerans

(f)                      [kingdom Monera (Google Search)] [index]

(10) Kingdom Protista

(a)                    Protista, like Monera, consists mostly of unicellular organisms

(b)                    Distinctively, however, the members of kingdom Protista are all eucaryotic while the members of kingdom Monera are all prokaryotic

(c)                    Some members of protista are multicellular, however

(d)                    Kingdom protista represents a grab bag, essentially the place where species are classified when they are not classified as either fungi, animals, or plants (kingdom Protista is a paraphyletic taxon for those of you familiar with the term)

(e)                    Note that most members of protista are additionally more or less aquatic

(f)                      [protists (MicroDude)] [index]

(11) Kingdom Fungi

(a)                    Unlike protists, the eukaryotic fungi are typically non-aquatic species

(b)                    They additionally are nutrient absorbers plus have additional distinctive features

(c)                    There do exist unicellular fungi, which we call yeasts

(d)                    [fungi (MicroDude)] [index]

(12) The three-domain system

(a)                    Less than ten years after the creation of the five-kingdom system of classification, microbiologist Carl Woese was instrumental in establishing a new system of classification which a little over ten years later became the three-domain system

(b)                    This system was basically accepted by microbiologists during the late 1980s, early 1990s and is increasing the system of choice of non-microbiologist biologists

(c)                    It even made the headlines a few years back with the declaration that a "new" form or life had been discovered (a.k.a., archaeobacteria, which had been discovered years previously and had been shown to be a "different" form of cellular life in the late 1970s, but one member of which was DNA sequenced in full in the late 1990s supplying the genesis of the headlines; with a complete sequence we obtained unambiguous confirmation of just how different from bacteria and eucaryotes these beasts truly are) [completely sequenced Archaeal genomes]

(d)                    [universal tree (MicroDude)] [index]

(13) Domain

(a)                    The domain is a taxonomic category that, depending on point of view, is either above the level of kingdom (i.e., includes kingdoms within it) or supercedes the kingdom

(b)                    Regardless of viewpoint, the domain system contains three members

(i)                      Eukaryotes (domain Eukarya)

(ii)                    Eubacteria (domain Bacteria)

(iii)                   Archaebacteria (domain Archaea)

(c)                    A fourth domain or domain-like taxon, called the Urkaryotes, represents eukaryotes prior to their establishment of endosymbioses with eubacteria, i.e., mitochondria

(d)                    See Figure 9.11, A model of the major evolutionary lines of descent proposed after the discovery of archaeobacteria

(e)                    See Figure 9.13, The three-domain system of classification

(f)                     See Table 9.3, Bacteria, archaea, and eukarya compared

(g)                    [universal tree (MicroDude)] [index]

(14) Domain Archaea

(a)                    Domain archaea is only minimally dealt with by your text in the chapters we will cover because

(i)                      these organisms are both less-well characterized than members of domain Bacteria

(ii)                    correlated with reason (i) (i.e., this latter is the reason for the former), the Archaea, unlike the Bacteria, do not cause human disease

(b)                    The Archaea are surprisingly diverse (perhaps not surprisingly, they show diversity on the order of that displayed by members of domain Bacteria)

(c)                    Typically they are distinguished by the environments in which they live as well as by their biochemical attributes

(d)                    For example,

(i)                      Methanogens live in anaerobic environments, breaking down organism molecules and giving rise to methane (i.e., swamp gas and cow farts) [methanogen home page]

(ii)                    Extreme halophiles live in highly saline environments such as inland seas as well as salt-preserved foods [halophilic microorganisms]

(iii)                   Extreme thermoacidophiles live in geothermally heated waters (e.g., hot springs) [thermophilic microorganisms]

(e)                    [domain Archaea (Google Search)] [domain Archaea] [Archaea: links] [introduction to Archaea] [triumph of the Archaea] [extremophiles] [index]

(15) Extremozymes

(a)                    These are the highly heat-stabilized enzymes employed by extremely thermophilic bacteria

(b)                    Such enzymes can be employed industrially, or even in down to earth applications such as cleaning clothing in high temperature washes (i.e., your washing machine on the hot cycle)

(c)                    [extremozymes (Google Search)] [scientists find jobs turning 'extremozymes' into industrial catalysts] [index]

(16) Viral classification

(a)                    Classification of viruses is not nearly as well developed as the classification of cellular organisms

(b)                    Today viruses tend to be classified by their chemical, morphological, and physiological attributes (e.g., genome = DNA vs. RNA, virion particle = enveloped vs. non-enveloped, and myriad details of their intracellular infection cycles)

(c)                    Binomial nomenclature is not employed to name viruses; instead viruses are named by their common names (e.g., Human Immunodeficiency Virus, a.k.a., HIV)

(d)                    [viral classification (Google Search)] [index]

(17) Dichotomous key

(a)                    A means of assigning an organism to a specific taxonomic category typically involves the use of specific criteria that may be posed as questions (e.g., what does the organism look like? etc.)

(b)                    Relevant criteria may be arranged as a dichotomous key

(c)                    In a dichotomous key questions are arranged hierarchically (just as taxonomic categories are) with more general questions (i.e., those arranging organisms into large categories) are asked first, with questions becoming more specific (better suited to arranging organisms into more specific taxa) asked subsequently

(d)                    In addition, questions are dichotomous, meaning that they each have two possible answers, with each answer distinguishing the organisms as well as the path to the next question

(e)                    See Figure 9.3, A dichotomous key for classifying typical U.S. coins

(f)                     See Figure 9.4, A dichotomous key for classifying major groups of bacteria

(g)                    [dichotomous key (Google Search)] [what is a dichotomous key] [index]

(18) Numerical taxonomy

(a)                    "Numerical taxonomy is based on the idea that increasing the number of characteristics of organisms that we observe increases the accuracy with which we can detect similarities among them. If the characteristics are genetically determined, the more characteristics two organisms share, the closer their evolutionary relationship."

(b)                    So, basically, numerical taxonomy involves taking a good, long look at the characteristics of two or more organisms, seeing how often these characteristics correspond, and, typically, using a computer to keep track of what you are doing

(c)                    That is, this is a dichotomous-tree-like device that is less easy to walk through manually so employs a computer to crunch the data

(d)                    ["Numerical taxonomy in the broad sense is the greatest advance in systematics since Darwin or perhaps since Linnaeus. It has stimulated several new areas of growth, including numerical phylogenetics, molecular taxonomy, morphometrics, and numerical identification. It has wide application outside systematic biology. Landmarks and trends are important aspects of numerical taxonomy. In microbiology, the program of numerical taxonomy has been successful, as indicated by the preponderance of papers describing numerical relationships in the International Journal of Systematic Bacteriology." Thirty Years of Numerical Taxonomy by P. H. A. Sneath, Syst. Biol. 44(3):281--298, 1995]

(e)                    [numerical taxonomy (Google Search)] [index]

(19) Genetic homology

(a)                    A homology is a similarity between two organisms that exists because the two organisms are closely evolutionarily related (that is, the feature in question existed in the common ancestor to the two organisms)

(b)                    The similarity of the DNA (or RNA) of organisms may be determined by a number of means including determinations of base composition, nucleotide sequence, or DNA hybridization rates

(c)                    Typically these means include very powerful ways by which organisms may be classified, either in terms of distinctions between organisms (i.e., the organisms may be classified as representing two or more species) or similarities (i.e., it may be concluded from evidence of genotypic similarity that the organisms are closely related, i.e., evolutionarily related); the latter similarities we would classify as a genetic homology

(d)                    The downside of genetic homology is that the acquisition of data often requires a laboratory and at least a little effort

(e)                    The upside is that genetic homology describes evolutionary relationships with only minimal interference from phenotype (which notoriously may be similar even without close evolutionary relationship)

(f)                      [genetic homology (Google Search)] [index]

(20) Base composition

(a)                    We know from Chargaff's rule that adenines (A's) and thymines (T's) are always present in DNA in equal proportions, and that the same is true for cytosines (C's) and guanines (G's)

(b)                    However, this says nothing about the relative proportions of A-T's to G-C's

(c)                    In fact, these vary from species to species, with more closely related species displaying more-similar ratios of A-T to G-C

(d)                    [base composition bias (Google Search)] [Chargaff's rule (MicroDude)] [index]

(21) DNA and RNA sequencing

(a)                    Genotype information at highest precision may be determined as DNA (or RNA) nucleotide-base sequences

(b)                    Very precise determination of base sequences can do wonders for establishing evolutionary relationships, but determining DNA or RNA sequence information is time consuming and relatively expensive, though becoming less so as time goes on

(c)                    RNA's are often sequenced either by converting the RNAs into DNA or by sequencing the DNA gene that gives rise to the RNA

(d)                    [DNA sequencing (MicroDude)] [cDNA (MicroDude)] [genomics grapevine (genomics is the study of organisms from genome sequence up, rather than from phenotype down) (Pharmaceutical Research and Manufacturers of America)] [index]

(22) DNA hybridization

(a)                    DNA hybridization takes advantage of the fact that heat will cause a DNA double helix to come apart into two strands of DNA (two individual molecules, not hydrogen bonded together)

(b)                    Allowing the DNA solution to cool will allow the DNA to reform (reanneal) into double helices again

(c)                    If the DNA from two different organisms is put together and treated thus, the total amount of reannealling accomplished will be dependent on how similar the organism's DNA sequences are (more similarity = more annealing), and in turn that will be dependent on how closely related to the two organisms are evolutionarily

(d)                    See Figure 9.18, DNA hybridization

(e)                    [DNA hybridization (Google Search)] [DNA hybridization] [DNA hybridization of apes – technical issues (science at its best and not quite its best)] [index]

(23) Distinguishing strains

(a)                    Very closely related organisms, i.e., members of the same species, are typically sufficiently similar that there exist additional methods that are able to distinguish the small differences seen between them

(b)                    These methods include:

(i)                      Protein profiling

(ii)                    Immunological reactions

(iii)                   Phage typing

(c)                    Note that these methods compare phenotypes and that, though useful (e.g., for determining clonality, i.e., clonal relationship, in the case of protein profiles), they are not as precise as genetic homologies in determining evolutionary relationships

(d)                    [methods of typing organisms] [index]

(24) Protein profile

(a)                    Various techniques exist for isolating (separating) and then visualizing the proteins from cells

(b)                    By distinguishing proteins in terms of their sizes and/or charges one can construct reproducible patterns that are typical of a given organism

(c)                    More-similar organisms display more-similar protein patterns

(d)                    See Figure 9.19, Separation of proteins

(e)                    [protein profile (Google Search)] [index]

(25) Immunological reactions

(a)                    The ability of antibodies to bind to and/or inactivate microorganisms can be employed to determine evolutionary relationships

(b)                    Two organisms that a single antibody (or antibody preparation) binds to are considered to be more likely closely related than a third organism to which the antibody preparation does not bind

(c)                    [immunological reactions (Google Search)] [index]

(26) Phage typing

(a)                    Bacteriophages, like antibodies, bind to cells, a requirement for their infecting a cell

(b)                    Additionally, phages are not able to infect some cells even given adsorption (i.e., restriction endonucleases can prevent phage replication)

(c)                    Different strains of organisms with different surface receptors or restriction systems or prophages will support the growth of different types of phages

(d)                    The phage type (or typing) pattern thus may be employed to distinguish strains

(e)                    [phage typing (Google Search)] [phage typing] [phage intro] [bacteriophage ecology group] [a diagnostic phage typing set for identification of enterobacteria] [index]

(27) Other methods

(a)                    Distinguishing members of Eubacteria is often accomplished using differential staining and various biochemical tests

(b)                    These methods are what we are exploring in our microbiology laboratories

(c)                    See Table 9.4, Criteria for classifying bacteria for an overview of the various methods discussed above

(d)                    Note that Table 9.5 gives a good overview of biochemical methods and what they mean

(28) Type strain

(a)                    In classifying an organism, it is helpful to have some standard to compare it to

(b)                    Such standards for a given strain are termed type strains

(c)                    Often the type strain is the first example of a species or strain

(d)                    Type strains are kept preserved by the American Type Culture Collection (ATCC)

(e)                    [ATCC (Google Search)] [ATCC search engine] [ATCC description] [index]

(29) Bergey's Manual

(a)                    Methods for distinguishing and identifying bacteria are assembled into Bergey's Manual of Determinative Bacteriology

(b)                    "It is important to remember that, in their current state, both Bergey's Manuals do not present an accurate picture of evolutionary relationships among bacteria. Rather, they are practical groupings of bacteria that make it easy to identify them. We do not yet have enough information to draw a complete evolutionary tree for bacteria." However, see the three-domain system and Figure 9.13

(c)                    Below is from Bergey's Manual and in turn represents a modified Table 9.13

(d)                    See Table 9.13, Characteristics and medically important members of selected sections of bacteria defined in Bergey's Manual of Systematic Bacteriology

(e)                    Note that all of the following are members of domain Bacteria

(f)                      Keep in mind that these groupings are phenotypic and do not necessarily imply close evolutionary relationships (i.e., are not above-the-genus-level taxonomic categories)

(g)                    [Bergey's Manual (Google Search)] [Bergey’s Manual trust] [list of bacterial  names with standing in nomenclature] [bacterial taxonomy (this site  needs to be linked individually with the organisms below)] [index]

(h)                    Note that below contains a serious chunk of memorization. In particular, you will be held responsible for Table 9.6 with the exception of the following genera: Brucella, Francisella, Leptospira, Providencia, Morganella, Calymmatobacterium, Eikenella, Streptobacillus, Fusobacterium, Veillonella, Rochalimaea, Coxiella, Bartonella, Ureaplasma, Peptococcus, Peptostreptococcus, Erysipelothrix, Propionibacterium, Eubacterium, Actinonmyces, Nocardia, and Dermatophilus [all of the previous genera are linked to Google Search]

 

Genera

Species

Category

Disease

 

Treponema

pallidum

spirochete

syphilis

X

Borrelia

burgdorferi

spirochete

Lyme disease

X

Campylobacter

 

Aerobic, motile, helical, Gram-negative

[campylobacteriosis]

X

Helicobacter

pylori

Aerobic, motile, helical, Gram-negative

peptic ulcer disease

X

Pseudomonas

aeruginosa

Gram-negative aerobic rods and cocci

urinary tract infections, burns, and wounds

X

Legionella

 

Gram-negative aerobic rods and cocci

pneumonia and other respiratory infections

X

Neisseria

gonorrhoeae

Gram-negative aerobic rods and cocci

gonorrhea; meningitis & nasopharylngeal infections by other species

X

Moraxella

lacunata

Gram-negative aerobic rods and cocci

conjunctivitis

X

Bordetella

pertussis

Gram-negative aerobic rods and cocci

whooping cough (pertussis)

X

Escherichia

coli

Facultatively anaerobic Gram-negative rods

opportunistic infections of colon and other sites

X

Shigella

[dysenteriae, sonnei]

Facultatively anaerobic Gram-negative rods

bacillary dysentery

X

Salmonella

typhimurium

Facultatively anaerobic Gram-negative rods

typhoid fever, enteritis, and food poisoning

X

Klebsiella

pneumoniae

Facultatively anaerobic Gram-negative rods

respiratory and urinary tract infections

X

Enterobacter

aerogenes

Facultatively anaerobic Gram-negative rods

opportunistic infections

X

Serratia

marcescens

Facultatively anaerobic Gram-negative rods

opportunistic infections

X

Proteus

vulgaris

Facultatively anaerobic Gram-negative rods

urinary tract infections, especially nosocomial

X

Yersinia

pestis

Facultatively anaerobic Gram-negative rods

plague

X

Vibrio

cholerae

Facultatively anaerobic Gram-negative rods

cholera

X

Pasteurella

 

Facultatively anaerobic Gram-negative rods

 

X

Haemophilus

 influenzae

Facultatively anaerobic Gram-negative rods

respiratory infections, meningitis, conjunctivitis

X

Gardnerella

 

Facultatively anaerobic Gram-negative rods

vaginitis

X

Bacteroides

 

Anaerobic Gram-negative rod

various infections from fecal contamination

X

Rickettsia

[prowazekii, rickettsii]

Rickettsia and Chlamydiae

typhus, Rocky Mountain spotted fever

X

Chlamydia

[trachomatis]

Rickettsia and Chlamydiae

trachoma, nongonococcal urethritis

X

Mycoplasma

pneumoniae

Mycoplasmas

walking pneumonia

X

Staphylococcus

aureus

Gram-positive cocci

skin abscesses, opportunistic infections such as toxic shock syndrome

X

Streptococcus

[pyogenes]

Gram-positive cocci

strep throat and other infections, puerperal fever = childbirth fever

X

[Micrococcus]

[luteus]

Gram-positive cocci

 

X

Bacillus

anthracis

Endospore-forming Gram-positive rods and cocci

anthrax

X

Clostridium

[botulinum, difficile, tetani, perfringens]

Endospore-forming Gram-positive rods and cocci

botulism, tetanus, gas gangrene

X

Corynebacterium

diphtheriae

Irregular nonsporing Gram-positive rods

diphtheria

X

Mycobacterium

[tuberculosis, leprae,  paratuberculosis]

Mycobacteria

tuberculosis, leprosy (Hanson's disease)

X

Streptomyces

 

Streptomyces

 

X

 

(30)  Spirochetes

(a)                    Gram-negative, helical, move by axial filaments

(b)                    [spiral forms] [index]

(31)  Aerobic, motile, helical, Gram-negative bacteria

(a)                    Additional characteristics:

(i)                      Move by flagella (i.e., as opposed to axial filaments)

(ii)                    Helical or comma-shaped

(b)                   

(c)                    [Helicobacter pylori is the causative agent of gastric and duodenal ulcers.  Over 50% of the world is infected with H. pylori.  It has also been implicated to play a role in stomach cancer.  This bacterium lives deep in the mucous layer of the stomach but does not invade the gastric mucosa… Campylobacter is the most common bacterial cause of diarrheal disease in humans in North America.  The most typical form of transmission is food-borne, through chicken products.  The bacterium is a gram-negative, spiral-shaped rod that is flagellated on both ends to enable it to move through the thick viscid mucosa of the jejunum, allowing it to invade the instestinal epithelial cells.]

(d)                    [spiral forms] [index]

(32)  Gram-negative aerobic rods and cocci

(a)                    Additional characteristics:

(i)                      Some are obligate parasites

(33)  Facultatively anaerobic Gram-negative rods

(a)                    Additional characteristics:

(i)                      Many can be distinguished by their characteristic fermentation reactions

(b)                    [the E. coli index (The University of Birmingham)] [frequently asked questions about plague] [index]

(34)  Anaerobic Gram-negative rods

(35)  Rickettsia and Chlamydiae

(a)                    Additional characteristics:

(i)                      Intracellular parasites

(b)                    [Rickettia literature] [index]

(36)  Mycoplasmas

(a)                    Additional characteristics:

(i)                      Lack cell walls

(ii)                    Extremely small

(37)  Gram-positive cocci

(a)                    Additional characteristics:

(i)                      Non-spore forming

(ii)                    Pyogenic (pus-forming)

(38)  Endospore-forming Gram-positive rods and cocci

(a)                    Additional characteristics:

(i)                      Aerobic to strictly anaerobic

(b)                    [endospore stain of genus Bacillus] [endospore stain of Clostridium tetani] [index]

(39)  Irregular nonsporing Gram-positive rods

(a)                    Additional characteristics:

(i)                      Pleomorphic or club-shaped

(40)  Mycobacteria

(a)                    Additional characteristics:

(i)                      Gram-positive (evolutionary relationship)

(ii)                    Acid fast (staining characteristic)

(b)                    [acid-fast cell wall] [index]

(41)  Streptomyces

(a)                    Additional characteristics:

(i)                      Gram-positive

(ii)                    Filamentous [image, filamentous bacterium]

(iii)                   Antibiotic producer

(b)                    [Streptomyces, Streptomyces and antibiotics (Google Search)] [index]

(42) More binomials (not responsible for & not all are bacteria)

(a)                    Bacillus cereus [pronounce] [characteristics] [Bacillus cereus (Google Search)]

(b)                    Bacillus subtilis [pronounce] [characteristics] [Bacillus subtilis (Google Search)]

(c)                    Balantidium coli (an amoeba) [pronounce] [characteristics] [Balantidium coli (Google Search)]

(d)                    Bdellovibrio bacteriovorus [pronounce] [characteristics] [Bdellovibrio bacteriovorus (Google Search)]

(e)                    Corynebacterium xerosis [pronounce] [characteristics] [Corynebacterium xerosis (Google Search)]

(f)                      Mycobacterium tuberculosis [pronounce] [characteristics] [Mycobacterium tuberculosis (Google Search)]

(g)                    Neisseria meningitidis [pronounce] [characteristics] [Neisseria meningitidis (Google Search)]

(h)                    Rickettsia rickettsii [pronounce] [characteristics] [Rickettsia rickettsii (Google Search)]

(i)                      Saccharomyces cerevisiae (a yeast) [pronounce] [characteristics] [Saccharomyces cerevisiae (Google Search)]

(j)                      Shigella dysenteriae [pronounce] [characteristics] [Shigella dysenteriae (Google Search)]

(k)                    Shigella sonnei [pronounce] [characteristics] [Shigella sonnei (Google Search)]

(l)                      Staphylococcus epidermidis [pronounce] [characteristics] [Staphylococcus epidermidis (Google Search)]

(m)                  Streptococcus mutans [pronounce] [characteristics] [Streptococcus mutans (Google Search)]

(n)                    Toxoplasma gondii (protozoa) [pronounce] [characteristics] [Toxoplasma gondii (Google Search)]

(43) Vocabulary [index]

(a)                    Aerobic, motile, helical, Gram-negative bacteria

(b)                    Anaerobic Gram-negative rods

(c)                    Bacterial species

(d)                    Base composition

(e)                    Bergey's Manual

(f)                      Binomial nomenclature

(g)                    Chlamydiae

(h)                    Classification

(i)                      Dichotomous key

(j)                      Distinguishing strains

(k)                    DNA and RNA sequencing

(l)                      DNA hybridization

(m)                  Domain

(n)                    Domain Archaea

(o)                    Endospore-forming Gram-positive rods and cocci

(p)                    Extremozymes

(q)                    Facultatively anaerobic Gram-negative rods

(r)                     Five-kingdom system

(s)                     Genetic homology

(t)                      Gram-negative aerobic rods and cocci

(u)                    Gram-positive cocci

(v)                    Immunological reactions

(w)                  Irregular nonsporing Gram-positive rods

(x)                    Kingdom Fungi

(y)                    Kingdom Monera

(z)                     Kingdom Protista

(aa)                 More binomials

(bb)                Mycobacteria

(cc)                 Mycoplasmas

(dd)                Numerical taxonomy

(ee)                 Other methods

(ff)                    Phage typing

(gg)                 Protein profile

(hh)                 Rickettsia

(ii)                     Spirochetes

(jj)                    Strain

(kk)                Streptomyces

(ll)                     taxa

(mm)             Taxon

(nn)                 Taxonomy

(oo)                Three-domain system

(pp)                Type strain

(qq)                Viral classification