Characterization of Microbes

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Chapter: Pharmaceutical Microbiology : Characterization, Classification and Taxonomy of Microbes

The microorganisms may be broadly characterized into the following categories, namely: (i) Morphological characteristics (ii) Chemical characteristics (iii) Cultural characteristics (iv) Metabolic characteristics (v) Antigenic characteristics (vi) Genetic characteristics (vii) Pathogenicity, and (viii) Ecological characteristics.



The microorganisms may be broadly characterized into the following categories, namely:


(i) Morphological characteristics


(ii) Chemical characteristics


(iii) Cultural characteristics


(iv) Metabolic characteristics


(v) Antigenic characteristics


(vi) Genetic characteristics


(vii) Pathogenicity, and


(viii) Ecological characteristics.


The aforesaid categories of characteristics shall now be treated individually in the sections that follow :


1. Morphological Characteristics


Morphology refers to the science of structure and form of organisms without any regard to their function. The morphological determinations invariably require the intensive studies of the individual cells of a pure culture. The microorganisms being of very small size are usually expressed in microm-eters (μm)*.


Interestingly, the morphological characteristic features are relatively easier to analyze and study, specifically in the eukaryotic microorganisms as well as the more complex prokaryotes. However, the morphological comparisons amongst the microbes play an important and vital role by virtue of the fact that their major structural features exclusively depend upon the prevailing expression of several genes. In fact, they are found to be fairly stable genetically, and hence fail to undergo drastic variation in response to the environmental alterations. Therefore, morphological similarity serves as an essential novel indicator with regard to phylogenetic **relationship.


However, the ‘morphological characteristics’ frequently employed in the classification and identification of certain microbial groups vis-a-vis their structural features are enumerated as under:

1 μm = 0.001 millimeter (mm) or 0.00004 inches. It may be carried out either with the help of a high-power microscope or an electron microscope (which provides magnification of thousands of diameters and enables to see more refined/detailed cellular structure(s).


2. Chemical Characteristics


Interestingly, one may observe a broad spectrum of organic compounds critically located in the microbial cells. These cells upon undergoing disintegration (broken apart) give rise to several different chemical entities that are methodically subjected to vigorous chemical analysis. Thus, each type of microorganism is observed to possess altogether specific and characteristic chemical composition. The presence of distinct qualitative and quantitative differences in composition does occur amongst the various prevailing microbial species.




(a) Gram-positive Microorganisms—they essentially possess in their cell walls an organic acid known as ‘teichoic acids’, and such compounds are not be seen in Gram-negative microorganisms.


(b) Gram-negative Microorganisms—they invariably contain ‘lipolysaccharide’ in their cell walls, and this is distinctly absent in Gram-positive bacteria.


Note. (1) Both algal and fungal cell walls are found to be entirely different in composition from those of microbes. 

(2) In viruses, the most prominent point of difference is solely based upon the type of nucleic acid they essentially possess, viz., RNA and DNA.


3. Cultural Characteristics

It has been amply established that each and every type of microorganism possesses specific as well as definitive growth-requirements.


Salient Features. The salient features of the important and vital cultural characteristics are as stated under:


(1) A plethora of microbes may be grown either on or in a cultural medium*.


(2) A few microorganisms could be cultivated (grown) in a medium comprising specifically organic chemical entities**, whereas some others require solely inorganic chemical enti-ties.


(3) Certain microbes do require complex natural materials*** only for their normal growth.


(4) Importantly, there are certain critical microbes that may be carefully and meticulously propogated only in a living host or living cells, and cannot be grown in an usual artificial laboratory medium.


Example: Rickettsias**** prominently require a definitive host in which they may grow conveniently and generously, for instance: (a) an arthroped*****; (b) a chick embryo (i.e., a fertilized chicken egg); and (c) a culture of mammalian tissue cells. In reality, the host being employed as an extremely complex specified and articulated ‘medium’ essentially required for such nutritionally demanding microorganisms.


(5) Specific physical parameters: Besides, certain highly critical and specific array of nutrients, each type of microorganism predominantly needs certain particular physical parameters for its natural and normal growth.


Examples :


(a) Microbes growing at high temperatures (e.g., Thermophilic bacteria): Some organisms do prefer to grow and thrive best at temperatures ranging between 40° and 70°C (104° and 158°F) ; and hence, fail to grow below 40°C e.g., Thermoactinomyces vulgaris; Thermus aquaticus; and Streptococcus thermophilus.


(b) Microbes growing at low temperatures : Certain microorganisms grow best in the cold en-vironmental conditions and simply cannot grow above 20°C e.g., Vibrio marinus strain MP-1 ; and Vibrio psychoerythrus.


(c) Pathogenic bacteria: A host of organisms that are solely responsible for causing diseases in humans do essentially require a temperature very close to that of the human body (i.e., 37°C or 98.4°F) e.g., Salmonella typhi; Vibrio cholerae; Mycobacterium tuberculosis; Clostridium tetani; Shigella dysenteriae; Treponema pallidum; Bordetella pertussis; Rickettsia rickettsii etc.


(d) Gaseous environment: It is equally important to have requisite gaseous environment for the substantial growth of the microorganisms.


Examples: (1) Aerobic Microbes: These are of two kinds, namely :


(i) Facultative Aerobes i.e., microbes that are able to live and grow preferably in an environ-ment devoid of oxygen, but has adapted so that it can live and grow in the presence of oxygen.


(ii) Obligate Aerobes i.e., microorganisms that can live and grow only in the presence of oxygen.


(2) Anaerobic Microbes: These microorganisms can live and grow in the absence of oxgyen, and are of two types, namely :


(i) Facultative Anaerobes i.e., microbes that can live and grow with or without oxgyen.


(ii) Obligatory Anaerobes i.e., microorganisms that can live and grow only in the absence of oxygen.


(e) Light (i.e., UV-Light): UV-Light provides a source of energy necessary for the growth of certain microbes e.g., cyanobacteria (blue green algae). Interestingly, some organisms may be indif-ferent to light or at times may even prove to be quite deleterious to their legitimate growth.


(f) Liquid Culture Medium: It has been observed that each and every type of microorganism invariably grows in an absolutely typical characteristic manner in various liquid culture medium with variant composition, such as:


(i) Sparse or abundant growth—as could be seen in a liquid medium.


(ii) Evenly distributed growth—as seen spread throughout the liquid medium.


(iii) Sedimented growth—as may be observed as a sediment usually at the bottom.


(iv) Thin-film growth—as could be seen on the surface of the liquid culture medium.


(v) Pellicle growth—as may be observed as a scum at the top.

Example: Salivary pellicle—The thin-layer of salivary proteins and glycoproteins that quickly adhere to the tooth surface after the tooth has been cleaned; this amorphous, bacteria-free layer may serve as an attachment medium for bacteria, which in turn form plaque.


(g) Solid Culture Medium: It has been amply demonstrated that microorganisms invariably grow on solid culture medium as colonies* which are markedly distinct, compact masses of cells evidently visible with a naked eye (macroscopically). In fact, the ensuing colonies are usually character-ized based upon, their particular shape, size, consistency, texture, colouration, compactness, and other several vital characteristic features.


4. Metabolic Characteristics


Metabolism refers to the sum of all physical and chemical changes that take place within an organism; all energy and material transformations that occur within living cells. It includes essentially the material changes (i.e., changes undergone by substances during all periods of life, for instance: growth, maturity, and senescence), and energy changes (i.e., all transformations of chemical energy of food stuffs to mechanical energy or heat). Metabolism involves two fundamental processes, namely: anabolism (viz., assimilation or building-up processes), and catabolism (viz., disintegration or tearing, down processes). Anabolism is the conversion of ingested substances into the constituents of protoplasm; Catabolism is the breakdown of substances into simpler substances, the end products usually being excreted.


The broad spectrum of these reactions gives rise to a plethora of excellent opportunities to char-acterize and differentiate categories of microorganisms.




(a) Absorption of Light: Certain microbes may derive energy via absorption of light.


(b) Oxidation: A few microorganisms may obtain energy through oxidation of a host of inor-ganic and organic compounds.


(c) Redistribution of Atoms: Some organisms engage actively in the redistribution of atoms within certain molecules thereby rendering the resulting molecules less stable.


(d) Synthesis of Cell Components: The microorganisms also vary a lot in the manner whereby they invariably synthesize their prevailing cell components in the course of their usual growth.


(e) Role of Enzymes: The wide variety of chemical reactions of an organism are duly catalyzed by certain proteineous substances termed as enzymes. Interestingly, the complement of en-zymes invariably owned by one specific type of organism, and the manners whereby such enzymes are meticulously modulated, may differ rather appreciably from that of other microbes.


5. Antigenic Characteristics


There are some chemical entities abundantly found in the microbial cells known as antigens. In fact, antigens refer to a protein or an oligosaccharide marker strategically located upon the surface of cells which critically identifies the cell as self or non-self; identifies the type of cell, e.g., skin, kidney; stimulates the production of antibodies, by B lymphocytes which will neutralize or destroy the cell, if necessary; and stimulates cytotoxic responses by granulocytes, monocytes, and lymphocytes.


It is, however, pertinent to state here that the very antigenic characterization of a microorgan-ism bears an immense practical significance. It has been duly observed that as soon as the ‘microbial cells’ enter the animal body, the latter quickly responds to their respective antigens due to the formation of particular blood serum proteins known as antibodies, which eventually get bound to the correspond-ing antigens. Obviously, the antibodies are extremely specific for the respective antigens which cat-egorically persuade their actual formation. Taking critical advantage of the vital fact that various types of microorganisms do significantly possess various types of antigens ; and, therefore, antibodies find their abundant utility and tremendous application as most vital tools for the precise as well as instant identification of specific types of microbes.


In other words, one may regard this antigen-antibody reaction very much similar to the ‘lock and key arrangement’. Therefore, keeping in view the extremely critical as well as highly specific nature of the said reaction, if one is able to decipher one segment of the ensuing system (antigen or antibody) one may most conveniently identify the other with great ease.


Example: Identification of typhoid organism : The typhoid bacterium antibody when duly mixed with a suspension of unknown bacterial cells, and consequently a positive reaction takes place, one may safely infer that the bacterial cells are definitely those of the typhoid organism. In turn, if there is no definite reaction taking place, one may draw a conclusion that these ensuing bacterial cells are not of the typhoid bacterium but may belong to certain other bacterial species.


6. Genetic Characteristics


It has been duly established that the double-stranded chromosomal DNA of each individual type of microbe essentially inherits some typical characteristic features which remain not only constant and absolutely specific for that microorganism, but also quite beneficial for its methodical classification as well.


However, there are two predominant criteria invariably employed for determining the ‘genetic characteristics’ of microbes, namely:


(a) DNA base composition, and


(b) Sequence of nucleotide bases in DNA.


These two aspects shall now be treated individually in the sections that follows:


6.1. DNA Base Composition


Importantly, one may evidently observe that the double-stranded DNA molecule is essentially comprised of base pairs, such as: adenine-thymine, and guanine-cytosine. However, the entire gross aggregate of the actual nucleotide bases present in the DNA, the relevant percentage articulately consti-tuted by guanine plus cytosine is known as the mole % G + C value (or more concisedly as mole % G + C). Such values usually vary from 23 to 75 for various organisms.


Table 3.1. Records the DNA base composition of certain typical microbial species.


In other words, in a double-stranded DNA, one may observe that A pairs with T, and G pairs with C; and thus, the (G + C)/(A + T) ratio or G + C content i.e., the per cent of G + C in DNA, actually reflects the base sequence which in turn critically varies with the prevailing sequence changes as given below:


Chemical methods—are used frequently to ascertain the G + C content after due hydrolysis of DNA and separation of its bases.


Physical methods—are employed more often and conveniently e.g., the melting temperature (Tm) of DNA.


6.2. Sequence of Nucleotide Bases in DNA


Based on intensive and extensive studies it has been duly revealed that the sequence of nucleotide bases in DNA is not only absolutely extraordinary for each type of organism, but also designates the most fundamental of all the characteristic features of a microorganism. As a result of this unique genetic characteristic feature it commands an immense significance for the legitimate classification of microbes.


Besides, there are two cardinal factors, namely : chromosomal DNA, and plasmid DNA that may occasionally show their very presence in the microbial cells.


Plasmids represent an altogether diverse category of extra-chromosomal genetic elements. In fact, these are circular double-stranded DNA molecules critically present intracellularly and symbiotically in most microorganisms. They invariably reproduce inside the bacterial cell but are not quite essential to its viability. In addition, plasmids are responsible for carrying out the autonomous replication within the bacterial cells, and their presence would ably impart highly specific characteristic features upon the cells that essentially contain them, such as:

·        Capability of producing toxins

·        Render resistance to different range of ‘antibiotics’

·        Make use of ‘uncommon chemical entities’ as nutrients

·        Ability to produce enzymes that specifically produce certain antibiotics

·        Ability of the cell to detoxify harmful materials, and

·        Production of bacteriocins*.


7. Pathogenicity


Pathogenicity refers to the particular state of producing or being able to produce pathological changes and diseases. Therefore, the ability to cause pathogenicity of certain microorganisms is defi-nitely an unique noticeable characteristic feature that has virtually given a tremendous boost to the earlier researches carried out with the microbes. It has been observed that comparatively a few microbial variants actually produce disease, some microorganisms prove to be pathogenic for plants and animals, and lastly certain microbes may bring about specific disease in other microbes.




(a) Bdellovibrio: A parasite that invades bacteria by forming a hole in the cell wall. It usually lives and reproduces inside the cell.


(b) Bacteriophage: A virus that infects bacteria. Bacteriophages are widely distributed in na-ture, having been isolated from faeces, sewage, and polluted surface waters. They are re-garded as bacterial viruses, the phage particle consisting of a head composed of either RNA or DNA and a tail by which it attaches the host cells.


8. Ecological Characteristics


Exhaustive and meticulous studies have provided a substantial evidence that the habitat (i.e., a microbe’s or an animal’s or plant’s natural environment) of a microorganism is extremely vital and important in the precise and definitive characterization of that particular organism.




(a) Microbes in Buccal Cavity: The population of the microorganisms present in the buccal cavity (or oral cavity) distinctly differs from that of the gastrointestinal tract (GIT).


(b) Marine Microorganisms: Invariably the microorganisms located specifically in the marine environments differ predominantly from those found in the fresh water and terrestrial envi-ronments.


(c) Distribution in Nature: Quite often one may observe that certain microorganisms are abun-dantly and widely distributed in nature, whereas others, may be significantly restricted to a specific environment.


Besides, a number of vital factors, such as : life-cycle patterns, the nature of symbiotic** rela-tionships, the capability for causing disease in a specific host, and preferential habitats e.g., pH, O2, temperature, osmotic concentration, do represent other befitting examples of taxonomically important ecological characteristic features.


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