Systematized Classification of Microbes or Microorganisms

| Home | | Pharmaceutical Microbiology | | Pharmaceutical Microbiology |

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

After having studied the various aspects of characterization of microbes followed by the prelimi-nary discussions on certain important features related to their classification, one may now have an ex-plicit broader vision on the systematized classification.

Systematized Classification


After having studied the various aspects of characterization of microbes followed by the prelimi-nary discussions on certain important features related to their classification, one may now have an ex-plicit broader vision on the systematized classification. An extensive and intensive survey of literature would reveal that the microorganisms may be classified in a systematized manner under the following eight categories, namely:


(i) Natural classification,

(ii) Phyletic classification,

(iii) Linnean binomial scheme,

(iv) Phenotypic classification,

(v) Microscopic examination,

(vi) Cataloguing rRNA,

(vii) Computer-aided classification, and

(viii) Bacterial classification (Bergey’s Manual of Systematic Bacteriology).


The aforesaid eight categories in the systematized classification of microorganisms would now be dealt with individually in the sections that follows.


1. Natural Classification


The natural classification may be considered as one of the most desirable classification systems which is broadly based upon the anatomical characteristic features of the specific microorganisms. In actual practice, the natural classification predominantly helps to organize and arrange the wide spec-trum of organisms into various categories (or groups) whose members do share several characteristics, and reflects to the greatest extent the intricate and complex biological nature of organisms. In reality, a plethora of taxonomists have concertedly opined that a larger segment of the so called natural classifi-cation is importantly and essentially the one having the maximum informations incorporated into it or the emanated predicted values obtained thereof.


2. Phyletic* Classification


Phyletic classification usually refers to the evolutionary development of a species. Based upon the most spectacular and master piece publication of Darwin’s—On the Origin of Species (1859), microbiologists across the globe started making an attempt much to sincere and vigorous, so as to develop phyletic (or phylogenetic) classification systems. Interestingly, the present system serves exclusively as a supporting evidence on the evolutionary relationships in comparison to the general resemblance. It has offered an appreciable hindrance for bacteria and other microorganisms basically on account of the paucity of reliable and authentic fossil records. Nevertheless, the availability of most recent up to date copious volumes of genuine information(s) with reference to comparison of genetic material and gene products, for instance: DNA, RNA, proteins etc., mostly circumvent and overcome a large segment of these problems invariably encountered.


3. Linnean Binomial Scheme


The microorganisms are invariably classified according to the Linnean Binomial Scheme of various genus and species. The International Code of Nomenclature of Bacteria (ICNB) particularly specifies the scientific nomenclature (names) of all categories (taxa) solely based upon the following guidelines, namely:


(1) The ‘words’ used to refer to any taxonomic group are either to be drawn from Latin or are Latinized, if taken from other languages.


(2) Each distinct species is assigned a name comprising of two words viz., Salmonella typhi; Bacillus subtilis ; and the like. Here, the first word is the name of the genus and is always written with a capital letter, whereas the second word is a particular epithet (i.e., a descrip-tive word) which is not capitalized at all.


(3) A taxonomic sequence of taxonomic groups is usually employed to categorize the intimately related microorganisms at different stages of similarity. These categories or taxa are enu-merated as under:


Explanations: The terminologies, species or genus are invariably employed as in the case of other types of classification. A species may be defined as a single type of bacterium, whereas a genus essentially includes a cluster of species all of which predominantly possess substantial resemblance to one another to be considered intimately related; and, therefore, may be distinguished very conveniently from the respective bonafide members of the other genera. Importantly, the boundaries of certain gen-era are defined explicitly and sharply; whereas, the boundaries of species are relatively difficult and cumbersome to define precisely.


Example: The genus Bacillus can be evidently distinguished from the genus Escherichia as follows:

There are three terminologies that are used very commonly in ‘microbiology’ e.g., strain, clone, and a type species, which may be further expatiated as follows :

Strain: A stock, say of bacteria or protozoa from a specific source and maintained in successive cultures or animal inoculation.

Clone: It refers to the asexual progeny of a single cell.

A Type Species: It is a culture that is thoroughly studied and easily identifiable as a species. The ‘name’ of a type species mostly conveys the prevailing characteristic features of the group.


4. Phenotypic Classification

The spectacular and classical Adansonian approach of classifying microorganisms is exclusively based upon the phenotypic characteristic features found in them. In reality, such characteristics are overwhelmingly regarded as critical expressions of a plethora of genes i.e., the basic unit of heredity made of DNA, which essentially regulate and control the inherent cellular activities via enzymes. Interestingly, it has been now universally accepted that the phenotype ideally represents the reflection of the DNA base sequence. Therefore, the best practicable and suitable methodology ot distinguishing two individual organisms must be based upon the composition of their genetic material. Quite recently sufficient advancement and substantial progress has gained ground with regard to the genetic characterization of various microorganisms, such as:

(a) analysis of the base composition of DNA viz., to estimate the mole per cent of guanine and cytosine in DNA (% G + C), and

(b) determination of the extent of similarity existing between two DNA samples by causing hybridization either between DNA & DNA or DNA & KNA. The fundamental basis of this test is that the degree of hybridization would grossly serve as an indication of the degree of relationship existing between the two DNA samples (i.e., homology).

The DNA of microbes significantly contains four bases : adenine (A), guanine (G), thymine CD, and cytosine (C). and in a double-stranded DNA molecule usually, A pairs with T and G pairs with C. However, the relative percentage of guanine and cytosine may be expressed as follows:

which varies mostly with bacterial variants actually. Importantly, the composition of chromosomal DNA deems to be fixed property of each cell which is distinctly independent of age as well as other vital external influences.

Determination of % (G + C) of Chromosomal DNA: The various steps involved in the determination of % (G + C) of chromosomal DNA are as stated under:

(1) Extraction of DNA from the cells by causing rupture very carefully and meticulously.

(2) The resulting DNA is subject to purification to get rid of the non-chromosomal DNA.

(3) Subsequently, the base composition may be estimated by adopting either of the following two methodologies, namely:

(a) Subjecting the purified DNA to a gradually elevating temperature and determining the ultimate enhancement in hypochromicity*, and

(b) Centrifuging the resulting DNA in cesium chloride in density gradients.

Principle of Melting Point Method [i.e., Method 3(a)] : In an event when the double-stranded DNA is subject to enhancing temperature, the two DNA strands undergo separation at a characteristic temperature. The critical melting temperature solely depends on the actual (G + C) content of the DNA. It has been duly observed that higher the (G + C) content, higher shall be the melting point.


(4) Melting Point (Tm) : The particular mean temperature at which the thermal denaturation of DNA takes place is usually termed as the Melting Point (Tm). However, Tm may be determined by recording carefully the ‘observed change’ in the optical density of DNA solution at 260 nm in the course of heating period, as illustrated in Fig. 3.3.


From the ‘melting point curve’ (Fig. 3.3) the mole % (G + C) may be calculated by the help of the following expression:

 %(G + C) = Tm × 63.54/0.47.


(5) Density Gradient Centrifugation: The % (G + C) composition may also be calculated by estimating the relative rate of sedimentation in a cesium chloride solution. In actual practice, the DNA preparations on being subjected to ultracentrifugation in the presence of a heavy salt solution, shall emerge as a sediment at a specific region in the centrifuge tube where its density is equivalent to the density of the medium. Importantly, this method is particularly suitable for such DNA samples that are heterogeneous in nature, and hence could be sepa-rated simultaneously. It has been observed that the ensuing buoyant density is an extremely characteristic feature of each individual type of DNA; and hence is solely dependent on the

(G + C) values as shown in Fig. 3.4.


By the help of buoyant density, it is quite easy and convenient to arrive at the % (G + C) content precisely by employing the following empirical formula:

P = 1.660 + 0.00098 [% (G + C)] g . cm–3


(6) Chromatographic Method: Another alternative method of estimating % (G + C) is accom-plished by the controlled hydrolysis of DNA in the presence of acids, separating the nucleotides by ultracentrifugation, and ultimately assaying the nucleotides by chromatogra-phy. Though this method is apparently lengthy and tedious, yet is quite simple and gives reasonably accurate results.


5. Microscopic Examination


In general, microorganisms have been duly classified by microscopic examination based upon their shape, size, and various staining characteristics. It has been abundantly proved that the stained preparations have obviously provided much better and clear information ; however, the unstained preparations may also be employed for these investigations to a certain extent as well.


The size and shape of microbes invariably may provide sufficient valuable informations that may be gainfully utilized for the presumptive diagnostic identification, as depicted in the following Table 3.3:


6. Cataloguing rRNA


Since mid seventies, progressive comparative analysis of the 16 S rRNA sequences had gained a tremendous momentum which enabled its proper and legitimate usage to explore the prokaryotic phylogeny. The ribosomal RNA (i.e., rRNA) molecules are found to be of immense choice due to the following three cardinal reasons:


(a) They exhibit a constant function,

(b) They are universally present in all organisms, and

(c) They seem to have changed in sequence extremely slowly.


Salient Features. The various salient features in cataloguing rRNA are as enumerated under:


(1) 5S rRNA Molecule: Because of its relatively smaller size it has been taken as an accurate indicator of the phylogenetic relationship.


(2) 16S rRNA Molecule: It is sufficiently large ; and, therefore, quite easy to handle with a reasonably high degree of precision.


(3) 23S rRNA Molecule: Because of its relatively much larger size it is rather more difficult to characterize, and hence used in the comparative analysis.


(4) In the last two decades, the 16 S rRNA has been critically examined, explored, and extracted from a large cross-section of microorganisms and duly digested with ribonuclease T1. The resulting nucleotide are meticulously resolved by 2D-electrophoresis* technique, and sequenced appropriately.


(5) The advent of latest sophisticated instrument e.g., DNA-Probe** which may sequence nucleic acids have further aided in the phenomenon of sequencing of 16 S rRNA from microorganisms.


(6) The skilful comparison of rRNA catalogues predominantly designates genealogical rela-tionship existing amongst the wide range of microbes.


(7) The aforesaid genealogical relationship may be suitably quantified in terms of an associa-tion coefficient, designated as SAB, which proves to be a typical characteristic feature for a pair of microorganisms. The association coefficient SAB may be expressed as follows :

where, NAB = Number of residues existing in sequences common to two rRNA catalogues.

NA and NB = Total number of residues duly represented by oligomers of at least 6 nucleotides in catalogues A and B respectively.


(8) As to date, the rRNA sequences of more than 200 species of microbes and eukaryotes have been duly characterized and documented adequately.


(9) It has been observed that most of the microorganisms strategically give rise to a coherent but also a very large segment including the eubacteria. Importantly, the methanogens, halophiles, and thermoacidophiles do not necessarily fall within the domain of eubacteria***.


(10) The aforesaid kind of rRNA sequencing has in fact duly permitted the methodical and logi-cal characterization of archaeobacteria.


7. Computer Aided Classification


In the latest spectacular and astronomical growth in the field of computer technology, it has inducted a tremendous impetus and great help in the proper grouping of microorganisms, and eventually classifying them with an utmost accuracy and precision. One may come across a host of problems in comparing a relatively huge number of characteristic features as may be seen in the very instance of numerical taxonomy or the Adansonian approach under the perview of the general classification of microbes. In order to circumvent such difficulties and problems, the proper usage of computer-aided programmes and devices have been rightly pressed into service for determining the differentiating capacity of the tests and also for determining the overall similarity with the known organisms. As to date, the commendable extremely high speed and memory of computer conveniently allows it to accomodate very swiftly a host of possible species in the identification/classification phenomenon by judiciously comparing the characteristic properties of an ‘unknown microorganism’ with those stored duly in the computer. In fact, the advent of the utility of computer, definitely and grossly minimizes the probability of error in the identification/classification by virtue of either infrequent occurrence of a microorganism or the critical presence of a rather more frequent microbe with not-so similar or superfi-cial resemblance to other organisms. A good number of highly sophisticated, modern, and advanced computer softwares (systems) for microbiology have now been duly developed and put into practice across the world profusely. The ‘microbiological laboratories’ strategically attached to most modern hospitals and research and development (R & D) laboratories have gainfully commenced the utiliza-tion of the elaborated computer facilities in the handling/processing of ‘test samples’ to obtain most reliable, dependable, and reproducible results meant to be used in correct diagnosis and research activi-ties with certainly more confidence and fervour.


8. Bacterial Classification [Bergey’s Manual of Systematic Bacteriology]


Microorganisms represent an exceptionally large conglomerate of minute living body with enor-mous diversity having a procaryotic cellular organization. Several sincere intensive and extensive stud-ies were duly made with particular reference to their broad spectrum physical, structural, and functional characteristic qualities, but none of them could ever produce and evolve an overall satisfactory generally acceptable classification.


Chester (1899 and 1901) initiated and took active interest in the classification of bacteria, and subsequently published for the first time—‘The Manual of Determinative Bacteriology’. The said manual was painstakingly and meticulously revised, substantiated, and modified by David Hendrick’s Bergey (1923) and entitled as—‘Bergey’s Manual of Systematic Bacteriology’, later on commonly termed as ‘Bergey’s Manual’. In fact, Bergey’s Manual is being recognized as the ‘official compen-dium of all identified and classified bacteria, and serves as an indispensable and valuable guide to the microbiologists across the globe.


The latest edition of ‘Bergey’s Manual’—(1994) provides a more rational and emperical ap-proach for the classification of bacteria. Besides, it gives rise to an effective system of keys for establish-ing the precise genetic position of an unknown organism. Table 3.4 gives a comprehensive account of the classification of bacteria (Division II)* upto the generic level.


Table 3.4. Summary of Bacterial Classification [Bergey’s Manual — 1994]

Part-1: Phototrophic Bacteria

Order I : Rhodospirillales

Suborder I : Rhodospirillineae

Family I : Rhodospirillaceae

Genus I : Rhodospirillum

Genus II : Rhodopseudomonas

Genus III : Rhodopseudomonas

Family II : Chromatiaceae

Genus I : Chromatium

Genus II : Thiocystis

Genus III : Thiosarcina

Genus IV : Thiospirilum

Genus V : Thiocapsa

Genus VI : Lamprocystis

Genus VII : Thiodicatyon

Genus VIII : Thiopedia

Genus IX : Amoebobacter

Genus X : Ectothiorhodospira

Suborder : Chlorobineae

Family III : Chlorobiaceae

Genus I : Chlorobium

Genus II : Prosthecocloris

Genus III : Chloropseudomonas

Genus IV : Pelodictyon

Genus V : Clathrochloris

Incertae Sedis [Addenda]

Genus : Chlorochromatium

Genus : Cylindrogloea

Genus : Chlorobacterium

Part-2: Gliding Bacteria

Order I : Myxobacterales

Family I : Myxococcaceae

Genus I : Myxococcus

Family II : Archangiaceae

Genus I : Archangium

Family III : Cystobacteraceae

Genus I : Cystobacter 

Genus II : Melittangium

Genus III : Stigmatella

Family IV : Polyangiaceae

Genus I : Polyangium

Genus II : Nannocystis

Genus III : Chondromyces

Order II : Cytophagales

Family I : Cytophagaceae

Genus I : Cytophaga

Genus II : Flexibacter

Genus III : Herpetosiphon

Genus IV : Flexibacter

Genus V : Saprospira

Genus VI : Sporocytophaga

Family II : Beggiatoaceae

Genus I : Beggiatoa

Genus II : Vitreoscilla

Genus III : Thioploea

Family III : Simonsiellaceae

Genus I : Simonsiella

Genus II : Alysiella

Family IV : Leucotrichaceae

Genus I : Leucothrix

Genus II : Thiothrix

Incertae Sedis [Addenda]

Genus : Toxothrix

Familiae incertae sedis


Genus : Achromatium


Genus I : Pelonema

Genus II : Achronema

Genus III : Peloploca

Genus IV : Desmanthos

Part-3: Sheathed Bacteria

Genus : Sphaerotilus

Genus : Leptothrix

Genus : Streptothrix

Genus : Lieskeela

Genus : Phragmidiothrix

Genus : Crenothrix

Genus : Clonothrix

Part-4: Budding And/Or Appendaged Bacteria

Genus : Hyphomicrobium

Genus : Hyphomonas

Genus : Pedomicrobium

Genus : Caulobacter

Genus : Asticeacaulis

Genus : Ancalomicrobium

Genus : Prosthecomicrobium

Genus : Thiodendron

Genus : Pasteuria

Genus : Blastobacter

Genus : Seliberia

Genus : Gallionella

Genus : Nevskia

Genus : Planctomyces

Genus : Metallogenium

Genus : Caulococcus

Genus : Kusnezonia

Part-5: Spirochaetes

Order I : Spirochaetales

Family I : Spirochaetaceae

Genus I : Spirochaeta

Genus II : Cristispira

Genus III : Treponema

Genus IV : Borrelia

Genus V : Leptospira

Part-6: Spiral And Curved Bacteria

Family I : Spirillaceae

Genus I : Spirillum

Genus II : Campylobacter

Incertae Sedis [Addenda]

Genus : Bdellovibrio

Genus : Microcyclus

Genus : Pelosigma

Genus : Brachyarcus

Part-7: Gram-Negative Aerobic Rods And Cocci

Family I : Pseudomonadaceae

Genus I : Pseudomonas

Genus II : Xanthomonas

Genus III : Zoogloea

Genus IV : Gluconobacter

Family II : Azotobacteraceae

Genus I : Azotobacter

Genus II : Azomonas

Genus III : Beijerinckia

Genus IV : Derxia

Family III : Rhizobiaceae

Genus I : Rhizobium

Genus II : Agrobacterium

Family IV : Methylomonadaceae

Genus I : Methylomonas

Genus II : Methylococcus

Family V : Halobacteriaceae

Genus I : Halobacterium

Genus II : Halococcus

Incertae Sedis [Addenda]

Genus : Alcaligenes

Genus : Acetobacter

Genus : Brucella

Genus : Bordetella

Genus : Francisella

Genus : Thermus

Part-8: Gram-Negative Facultatively Anaerobic Rods

Family I : Enterobacteriaceae

Genus I : Escherichia

Genus II : Edwardsiella

Genus III : Citrobacter

Genus IV : Salmonella

Genus V : Shigella

Genus VI : Klebsiella

Genus VII : Enterobacter

Genus VIII : Hafnia

Genus IX : Serratia

Genus X : Proteus

Genus XI : Yersinia

Genus XII : Erwinia

Family II : Vibrionaceae

Genus I : Vibrio

Genus II : Acromonas

Genus III : Plesiomonas

Genus IV : Photobacterium

Genus V : Lucibacterium

Incertae Sedis [Addenda]

Genus : Chromobacterium

Genus : Zymomonas

Genus : Flavobacterium

Genus : Haemophilus

Genus : Pasteurella

Genus : Actinobacillus

Genus : Cardiobacterium

Genus : Streptobacillus

Genus : Calymmatobacterium

Part-9: Gram-Negative Anaerobic Bacteria

Family I : Bacteriodaceae

Genus I : Bacteroides

Genus II : Fusobacterium

Genus III : Leptotrichia

Incertae Sedis [Addenda]

Genus : Desulfovibrio

Genus : Butyrivibrio

Genus : Succinivibrio

Genus : Succinimonas

Genus : Lachnospira

Genus : Selenomonas

Part-10: Gram-Negative Cocci And Coccobacilli

Family I : Neisseriaceae

Genus I : Neisseria

Genus II : Branhamella

Genus III : Moraxella

Genus IV : Acinetobacter

Incertae Sedis [Addenda]

Genus : Paracoccus

Genus : Lampropedia

Part-11: Gram-Negative Anaerobic Cocci

Family I : Veillonellaceae

Genus I : Acidaminococcus

Genus II : Veillonella

Genus III : Megasphaera

Part-12: Gram-Negative Chemolithotrophic Bacteria

Family 1 : Nitrobacteraceae

Genus I : Nitrobacter

Genus II : Nitrospina

Genus III : Nitrococcus

Genus IV : Nitrosomonas

Genus V : Nitrospira

Genus VI : Nitrosococcus

Genus VII : Nitrosolobus

Organisms Metabolizing Sulphur

Genus I : Thiobacillus

Genus II : Sulfolobus

Genus III : Thiobacterium

Genus IV : Macromonas

Genus V : Thiovulum

Genus VI : Thiospira

Family II : Siderocapsaceae

Genus I : Siderocapsa

Genus II : Naumanniella

Genus III : Ochrobium

Genus IV : Siderococcus

Part-13: Methane Producing Bacteria

Family I : Methanobacteriaceae

Genus I : Methanobacterium

Genus II : Methanosarcina

Genus III : Methanococcus

Part-14: Gram Positive Cocci

Family I : Micrococcaceae

Genus I : Micrococcus

Genus II : Staphylococcus

Genus III : Planococcus

Family II : Streptococcaceae

Genus I : Streptococcus

Genus II : Leuconostoc

Genus III : Pediococcus

Genus IV : Acrococcus

Genus V : Gemella

Family III : Peptococcaceae

Genus I : Peptococcus

Genus II : Peptostreptococcus

Genus III : Ruminococcus

Genus IV : Sarcina

Part-15: Endospore Forming Rods and Cocci

Family I : Bacillaceae

Genus I : Bacillus

Genus II : Sporolactobacillus

Genus III : Clostridium

Genus IV : Desulfotomaculum

Genus V : Sporosarcina

Incertae Sedis [Addenda]

Genus : Oscillospira

Part-16: Gram-Positive Asporogenous Rod-Shaped Bacteria

Family I : Lactobacillaceae

Genus I : Lactobacillus

Incertae Sedis [Addenda]

Genus : Listeria

Genus : Erysipelothrix

Genus : Caryophanon

Part-17: Actinomycetes And Related Organisms

Coryneform Group of Bacteria

Genus I : Corynebacterium

Genus II : Arthrobacter

Incertae Sedis [Addenda]

Genus A : Brevibacterium

Genus B : Microbacterium

Genus III : Cellulomonas

Genus IV : Kurthia

Family I : Propionibacteriaceae

Genus I : Propionibacterium

Genus II : Eubacterium

Order I : Actinomycetales

Family I : Actinomycetaceae

Genus I : Actinomyces

Genus II : Arachnia

Genus III : Bifidobacterium

Genus IV : Bacterionema

Genus V : Rothia

Family II : Mycobacteriaceae

Genus I : Mycobacterium

Family III : Frankiaceae

Genus I : Frankia

Family IV : Actinoplanaceae

Genus I : Actinoplanes

Genus II : Spirillospora

Genus III : Streptosporangium

Genus IV : Amorphosphorangium

Genus V : Ampullariella

Genus VI : Pilimelia 

Genus VII : Planomonospora

Genus VIII : Planobispora

Genus IX : Dactylosporangium

Genus X : Kitastoa

Family V : Dermatophillaceae

Genus I : Dermatophilus

Genus II : Geodermatophilus

Family VI : Nocardiaceae

Genus I : Nocardia

Genus II : Pseudonocardia

Family VII : Streptomycetaceae

Genus I : Streptomyces

Genus II : Streptoverticilium

Genus III : Sporichthya

Genus IV : Microellobosporia

Family VIII : Micromonosporaceae

Genus I : Micromonospora

Genus II : Thermoactinomyces

Genus III : Actinobifida

Genus IV : Thermonospora

Genus V : Microbispora

Gebus VI : Micropolyspora

Part-18: Rickettsias

Order I : Rickettsiales

Family : Rickettsiaceae

Tribe I : Rickettsieae

Genus I : Rickettsia

Genus II : Rochalimaea

Genus III : Coxiella

Tribe II : Ehrlichieae

Genus IV : Ehrlichia

Genus V : Cowdria

Genus VI : Neorickettsia

Tribe III : Wolbachieae

Genus VII : Wolbachia

Genus VIII : Symbiotes

Genus IX : Blattabacterium

Genus X : Rickettsiella

Family : Bartonellaceae

Genus I : Bartonella

Genus II : Grahamella

Family : Anaplasmataceae

Genus I : Anaplasma

Genus II : Paranaplasma

Genus III : Aegyptionella

Genus IV : Haemobartonella

Genus V : Eperythrozoon

Order II : Chlamydiales

Family I : Chlamydiaceae

Genus I : Chlamydia

Part-19 : Mycoplasmas

Class Mollicutes

Order I : Mycoplasmatales

Family I : Mycoplasmataceae

Genus I : Mycoplasma

Family II : Acholeplasmataceae

Genus I : Acholeplasma

Incertae Sedis [Addenda]

Genus : Thermoplasma

Incertae Sedis [Addenda]

Genus : Spiroplasma 

Contact Us, Privacy Policy, Terms and Compliant, DMCA Policy and Compliant

TH 2019 - 2025; Developed by Therithal info.