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
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Course-external links are
in brackets Click [index] to access site index Click here to access
texts website Vocabulary
words
are found below |
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(1) Chapter title: An Introduction to
Taxonomy: The Bacteria
(a)
The science of organismal classification
(b)
[taxonomy (Google Search)] [taxonomy on the web]
[index]
(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]
(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]
(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]
(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
(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 classificationfor
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
(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]
(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]
(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]
(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]
(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]
(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]
(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.,
(e)
[domain Archaea (Google Search)]
[domain Archaea] [Archaea: links] [introduction to Archaea]
[triumph of the Archaea]
[extremophiles] [index]
(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]
(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]
(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
(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]
(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]
(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]
(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]
(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]
(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]
(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:
(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]
(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]
(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]
(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]
(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
(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]
(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)]
[Bergeys 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 |
|
|
|
||||
|
urinary tract infections,
burns, and wounds |
||||
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pneumonia and other
respiratory infections |
|||
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gonorrhea;
meningitis & nasopharylngeal infections by other species |
||||
|
opportunistic infections
of colon and other sites |
||||
|
bacillary dysentery |
||||
|
typhoid fever,
enteritis, and food poisoning |
||||
|
respiratory and urinary
tract infections |
||||
|
opportunistic infections |
||||
|
opportunistic infections |
||||
|
urinary tract infections,
especially nosocomial |
||||
|
|
|
|||
|
respiratory infections, meningitis, conjunctivitis |
||||
|
|
||||
|
|
various infections from
fecal contamination |
|||
|
skin abscesses,
opportunistic infections such as toxic shock syndrome |
||||
|
[pyogenes] |
strep throat and
other infections, puerperal fever = childbirth fever |
|||
|
[luteus] |
|
|||
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(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)
(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
(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
(d)
Base composition
(e)
Bergey's Manual
(g)
Chlamydiae
(h)
Classification
(i)
Dichotomous key
(m)
Domain
(n)
Domain Archaea
(o)
Endospore-forming Gram-positive rods and cocci
(p)
Extremozymes
(q)
Facultatively anaerobic Gram-negative rods
(s)
Genetic homology
(t)
Gram-negative aerobic rods and cocci
(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