Classification of Microorganisms



The Taxonomic Scheme

Bacterial taxonomy is the rank-based classification of bacteria.

Learning Objectives

Outline the factors that play a role in the classification of bacterial taxonomy

Key Takeaways

Key Points

  • Bacterial species differ amongst each other based on several characteristics, allowing for their identification and classification.
  • Gram staining results are most commonly used as a classification tool.
  • In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today.

Key Terms

  • bacteria: A type, species, or strain of bacterium.
  • taxonomy: the academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Each group is given a rank and groups of a given rank can be aggregated to form a super group of higher rank and thus create a hierarchical classification.
  • Gram stain: Gram staining (or Gram’s method) is a method of differentiating bacterial species into two large groups (Gram-positive and Gram-negative).It is based on the chemical and physical properties of their cell walls. Primarily, it detects peptidoglycan, which is present in a thick layer in Gram positive bacteria. A Gram positive results in a purple/blue color while a Gram negative results in a pink/red color.

Taxonomic Systems

Bacterial taxonomy is the rank-based classification of bacteria. In the scientific classification established by Carl von Linné, each distinct species is assigned to a genus using a two-part binary name (for example, Homo sapiens). This distinct species is then in turn placed within a lower level of a hierarchy of ranks. These ranks range in ascending scale from family to suborder, and upward to order, subclass, class, division/phyla, kingdom and domain.

In the currently accepted scientific classification of Life, there are three domains of microorganisms: the Eukaryotes, Bacteria and Archaea, The different disciplines of study refer to them using differing terms to speak of aspects of these domains, however, though they follow similar principles. Thus botany, zoology, mycology, and microbiology use several different conventions when discussing these domains and their subdivisions. In zoology, for example, there are type specimens, whereas in microbiology there are type strains.

Historical Challenges of Classification

Despite there being little agreement on the major subgroups of the Bacteria, gram staining results were commonly used as a classification tool. As an example, Prokaryotes share many common features, such as lack of nuclear membrane, unicellularity, division by binary-fission and generally small size. Until the advent of molecular phylogeny the Kingdom Prokaryotae was divided into four divisions, a classification scheme still formally followed by Bergey’s manual of systematic bacteriology.The various species differ amongst each other based on several characteristics determined by gram staining, which allowed their identification and classification. Major groups of this system include: Gracilicutes (gram negative); Firmacutes (gram positive); Mollicutes (gram variable, e.g. Mycoplasma); and Mendocutes (uneven gram stain, “metlynogenic bacteria” now known as the Archaea).

Molecular Classification

In the Molecular era of classification, Carl Woese, who is regarded as the forerunner of the molecular phylogeny revolution, argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. However, a few biologists argue that the Archaea and Eukaryota arose from a group of bacteria. In any case, it is thought that viruses and archaea began relationships approximately two billion years ago, and that co-evolution may have been occurring between members of these groups. It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are “extreme environments” in archaeal terms, and organisms that live in cooler environments appeared only later. Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote’s only surviving meaning is “not a eukaryote”, limiting its value.

With improved methodologies it became clear that the methanogenic bacteria were profoundly different and were erroneously believed to be relics of ancient bacteria. Thus, though Woese identified three primary lines of descent the Archaebacteria, the Eubacteria and the Urkaryotes, the latter now represented by the nucleocytoplasmic component of the Eukaryotes. these lineages were formalised into the rank Domain (regio in Latin) which divided Life into 3 domains: the Eukaryota, the Archaea and the Bacteria. This scheme is still followed today.

In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today.

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Prokaryote phylogeny diagram: Phylogenetic tree showing the relationship between the archaea and other forms of life. Eukaryotes are colored red, archaea green and bacteria blue.

The Diagnostic Scheme

Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.

Learning Objectives

Outline the various types of diagnostic methods used to diagnose a microbial infection

Key Takeaways

Key Points

  • Diagnosis of infectious disease is nearly always initiated by medical history and physical examination.
  • Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype.
  • Diagnostic methods include: Microbial culture, microscopy, biochemical tests and molecular diagnostics.

Key Terms

  • Diagnosis: Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation.
  • infectious: Infectious diseases, also known as transmissible diseases or communicable diseases, comprise clinically evident illness (i.e., characteristic medical signs and/or symptoms of disease) resulting from the infection, presence, and growth of pathogenic biological agents in an individual host organism.
  • pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.

The Challenge of Diagnosis

Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation. Conclusions about the cause of the disease are based upon the likelihood that a patient came in contact with a particular agent, the presence of a microbe in a community, and other epidemiological considerations. Given sufficient effort, all known infectious agents can be specifically identified. The benefits of identification, however, are often greatly outweighed by the cost, as often there is no specific treatment, the cause is obvious, or the outcome of an infection is benign.

Primary and Opportunistic Pathogens

Among the almost infinite varieties of microorganisms, relatively few cause disease in otherwise healthy individuals. Infectious disease results from the interplay between those few pathogens and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen depends upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. Clinicians therefore classify infectious microorganisms or microbes according to the status of host defenses – either as primary pathogens or as opportunistic pathogens.

An Orderly Process

Diagnosis of infectious disease is nearly always initiated by taking a medical history and performing a physical examination. More detailed identification techniques involve the culture of infectious agents isolated from a patient. Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype. Other techniques, such as X-rays, CAT scans, PET scans or NMR, are used to produce images of internal abnormalities resulting from the growth of an infectious agent. The images are useful in detection of, for example, a bone abscess or a spongiform encephalopathy produced by a prion.

Diagnostic methods include microbial culture, microscopy, biochemical tests and molecular diagnostics:

  • Microbiological culture is a principal tool used to diagnose infectious disease. In a microbial culture, a growth medium is provided for a specific agent. A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium.
  • Microscopy may be carried out with simple instruments, such as the compound light microscope, or with instruments as complex as an electron microscope. Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. Microscopy is often also used in conjunction with biochemical staining techniques, and can be made exquisitely specific when used in combination with antibody based techniques.
  • Biochemical tests used in the identification of infectious agents include the detection of metabolic or enzymatic products characteristic of a particular infectious agent. Since bacteria ferment carbohydrates in patterns characteristic of their genus and species, the detection of fermentation products is commonly used in bacterial identification. Acids, alcohols and gases are usually detected in these tests when bacteria are grown in selective liquid or solid media.
  • Molecular diagnostics using technologies based upon the polymerase chain reaction ( PCR ) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids in order to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. Third, the essential tools for directing PCR, primers, are derived from the genomes of infectious agents, and with time those genomes will be known, if they are not already.

The Species Concept in Microbiology

The number of species of bacteria and archaea is surprisingly small, despite their early evolution, genetic, and ecological diversity.

Learning Objectives

Describe the concept of polyphasic species

Key Takeaways

Key Points

  • The differences in species concepts between the Bacteria and macro-organisms, the difficulties in growing/characterising in pure culture (a prerequisite to naming new species, vide supra), and extensive horizontal gene transfer blurring the distinction of species makes differentiation difficult.
  • The most commonly accepted definition is the polyphasic species definition, which takes into account both phenotypic and genetic differences.
  • A quicker diagnostic threshhold is to separate species as less than 70% DNA -DNA hybridization, which corresponds to less than 97% 16S DNA sequence identity.

Key Terms

  • bacteria: Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet.
  • species: In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring.
  • DNA hybridization: Hybridization is the process of establishing a non-covalent, sequence-specific interaction between two or more complementary strands of nucleic acids into a single complex, which in the case of two strands is referred to as a duplex. Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily.
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Biological classification: The hierarchy of biological classification’s eight major taxonomic ranks. A genus contains one or more species. Intermediate minor rankings are not shown.

Judging Species in an Asexual Context

Bacteria divide asexually and for the most part do not show regionalisms. In other words, “Everything is everywhere. ” Accordingly, the concept of species which works best for animals, becomes entirely a matter of judgement.

The approximately 5000 species of bacteria and archaea constitute a surprisingly small number, considering their relatively early evolution, genetic diversity, and ability to reside in all ecosystems on Earth. The reason for this numerical peculiarity lies in the differences in species concepts between the bacteria and macro-organisms and in the difficulties in growing and characterizing in pure culture (a prerequisite to naming new species, vide supra). In addition, the extensive amount of horizontal gene transfer among microorganisms results in the blurring of the distinctions between species among microorganisms.

The most commonly accepted definition is the polyphasic species definition,which takes into account both phenotypic and genetic differences. However, a quicker diagnostic ad hoc threshhold to separate species is less than 70% DNA-DNA hybridization, which corresponds to less than 97% 16S DNA sequence identity. It has been noted that if this were applied to animal classification the order of Primates would be considered a single species.

The International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM) is a peer-reviewed journal that acts as the official international forum for the publication of new prokaryotic taxa. If a species is published in a different peer review journal, the author can submit a request to IJSEM with the appropriate description. If the information is correct, the new species will be featured in the Validation List of IJSEM.

Classification and Nomenclature

Nomenclature is the set of rules and conventions that govern the names of taxa.

Learning Objectives

Recognize the factors involved with general classification and nomenclature used for microorganism classification

Key Takeaways

Key Points

  • The names ( nomenclature ) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria (Bacteriological Code).
  • Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype, while nomenclature is the application of formal rules for naming organisms.
  • Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter, with the exception of epithets for species and subspecies.

Key Terms

  • nomenclature: binomial nomenclature (also called binominal nomenclature or binary nomenclature) is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages. Such a name is called a binomial name (which may be shortened to just “binomial”), a binomen or a scientific name; more informally it is also called a Latin name.
  • prokaryotes: ( /proʊkæri.oʊts/, pro-kah-ree-otes or /proʊkæriəts/, pro-kah-ree-əts) a group of organisms whose cells lack a cell nucleus (karyon), or any other membrane-bound organelles. Most prokaryotes are unicellular organisms, although a few such as myxobacteria have multicellular stages in their life cycles.
  • Bacteriological code: The International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC) governs the scientific names for bacteria, including Archaea. It denotes the rules for naming taxa of bacteria, according to their relative rank. As such it is one of the Nomenclature Codes of biology.

Nomenclature is the set of rules and conventions which govern the names of taxa. It is the application of formal rules for naming organisms. Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype. Despite there being no official and complete classification of prokaryotes, the names (nomenclature) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria (Bacteriological Code), a book which contains general considerations, principles, rules, and various notes and advises in a similar fashion to the nomenclature codes of other groups.

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International Journal of Systematic and Evolutionary Microbiology (IJSEM): The IJSEM covers the naming of new bacteria and how they fit evolutionarily.

The taxa which have been correctly described are reviewed in Bergey’s manual of Systematic Bacteriology, which aims to aid in the identification of species and is considered the highest authority. An online version of the taxonomic outline of bacteria and archaea is available. Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter with the exception of epithets for species and subspecies. Despite it being common in zoology, tautonyms (e.g. Bison bison) are not acceptable and names of taxa used in zoology, botany or mycology cannot be reused for bacteria (Botany and Zoology do share names).

For bacteria, valid names must have a Latin or Neolatin name and can only use basic latin letters (w and j inclusive, see History of the Latin alphabet for these), consequently hyphens, accents and other letters are not accepted and should be translitterated correctly (e.g. ß=ss). Ancient Greek being written in the Greek alphabet, needs to be translitterated into the Latin alphabet.

Many species are named after people, either the discoverer or a famous person in the field of microbiology, for example Salmonella is after D.E. Salmon, who discovered it (albeit as “Bacillus typhi”). For the generic epithet, all names derived from people must be in the female nominative case, either by changing the ending to -a or to the diminutive -ella, depending on the name. For the specific epithet, the names can be converted into either adjectival form (adding -nus (m.), -na (f.), -num (n.) according to the gender of the genus name) or the genitive of the latinised name.

Many species (the specific epithet) are named after the place they are present or found (e.g. Borrelia burgdorferi). Their names are created by forming an adjective by joining the locality’s name with the ending -ensis (m. or f.) or ense (n.) in agreement with the gender of the genus name, unless a classical Latin adjective exists for the place. However, names of places should not be used as nouns in the genitive case.

For the Prokaryotes (Bacteria and Archaea) the rank kingdom is not used (although some authors refer to phyla as kingdoms). If a new or amended species is placed in new ranks, according to Rule 9 of the Bacteriological Code the name is formed by the addition of an appropriate suffix to the stem of the name of the type genus. For subclass and class the reccomendation from is generally followed, resulting in a neutral plural, however a few names do not follow this and instead keep into account Graeco-Latin grammar (e.g. the female plurals Thermotogae, Aquificae, and Chlamydiae, the male plurals Chloroflexi, Bacilli, and Deinococci, and the Greek plurals Spirochaetes, Gemmatimonadetes, and Chrysiogenetes).

Phyla are not covered by the Bacteriological Code, however, the scientific community generally follows the Ncbi and Lpsn taxonomy, where the name of the phylum is generally the plural of the type genus, with the exception of the Firmicutes, Cyanobacteria, and Proteobacteria, whose names do not stem from a genus name. The higher taxa proposed by Cavalier-Smith are generally disregarded by the molecular phylogeny community (vide supra).