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Various Factors contributing to Bacterial Classification
Bacteria a part of the microbial flora is omnipresent either being beneficial or harmful or harmless to other living forms like plants, animals and humans. With over millions of bacteria present in the planet, it is not an easy job to identify, isolate and study a particular species or particular bacteria as such. But thanks to the microbiologists who categorized bacteria based on basic and important factors making all the bacteria fall under any one of the categories and thus making the process of isolation and identification much easier.

Bacteria are classified based on various factors like shape (morphology), Cell wall structure, Respiration (metabolism), type of nutritional source, characteristic and environmental factor.

Bacteria are of different shapes and are classified based on their morphology into Bacillus, Coccus, spiral, comma shaped and flagellated.
Bacilli: Rod shaped bacteria. Diplobacilli (2 cells), tetrad (4 cells), palisade (two cells arranged parallel) or sterptobacilli (chain arrangement).
Coccus: Spherical shaped bacteria which is further classified as monococcus (a cell), diplococci (2 cells), streptococci (cells arranged like chain) and cells in bunch (Staphylcocci).
Spiral: Spiral shaped bacteria sub divided into spirilla and spirochetes.
Comma shaped: Vibrio cholera is an example of comma shaped bacterium.
Flagellated: Some bacteria have flagella projecting from the cell membrane which is used for mobility and are classified under the group flagellated bacterium. Atrichous (no flagella), monotrichous (uni flagella), amphitrichous (bi flagella) and polytrichous (more flagella).

Cell wall structure
Gram’s staining is the procedure introduced by a Danish scientist, Cristian Gram in the year 1884 which is used till date to differentiate the bacteria based on their cell wall structure. The cell wall of bacteria is composed of peptidoglycans and lipopolysachharide and the varying amount of these two components is used to classify the bacteria by Gram staining into Gram positive and Gram Negative bacteria. Gram staining procedure involves step by step treatment of the cells with dyes.
1. Smear bacteria on a slide
2. Add Drops of Crystal violet dye to the smeared slide
3. Add a mordant solution
4. Wash with ethanol
5. Add Safranin dye and once the slide is ready observe under microscope
Gram positive bacteria appears violet as it retains the violet dye which is related to the thick layer composed of peptidoglycans and Gram negative bacteria appears pink as the treatment with ethanol washes off the violet dye by disrupting the external lipopolysaccharide layer and hence the secondly added red dye is retained. Gram negative bacteria have thin walls.

Respiration of bacteria is generally seen as a metabolic process which involves production of energy by breaking down the sugar molecule. Some bacteria require oxygen for this metabolic process and are called as aerobes and bacteria which do not require oxygen for this metabolic process are classified as anaerobes. There is another category called as facultative anaerobes which metabolize either way (both in the presence and absence of oxygen).

Nutritional Source
Like herbivores, carnivores and omnivores in animals and humans bacteria are also classified based on the type of energy source utilized by them for survival. Accordingly they are grouped as, photoautotrophs, chemoautotrophs, heterotrophs, symbiotic, saprophytes and parasites.

Bacteria thrive by being either harmless or harmful or beneficial to the other life forms. Accordingly they are classified as beneficial and pathogenic bacteria. There are many bacteria being isolated and identified in the area of biodegradation and are considered as beneficial microbes for its potential to degrade the waste and can also be called environmental friendly. Another example for the beneficial bacteria is the bacterial flora present in the gut which helps in proper degradation of the food molecules thus enhancing the absorption and hence is considered as beneficial. The bacteria classified as pathogens are known to cause infections and disease in the host organism.

All bacteria do not survive in common environmental condition. Different bacteria survives different environmental conditions and based on this factor bacteria are classified as Mesophiles, neutrophiles, extremophiles, acidophiles, alkaliphiles, thermophiles, psychroplhiles, halophiles and osmophiles.

Spore Formation
Different species of bacteria under unfavorable conditions form spores and remains dormant and revert back to active vegetative state under favorable environmental conditions and based on this bacteria is classified as spore forming and non-spore forming bacteria.

All the factors used to classify the bacteria acts as an important tool in identification of a bacterium and ensures better understanding while studying different species of bacteria.
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The bacterial classification serves a diversity of functions. Due to this diversity, bacteria may be classified based on many different typing methods. The significant characteristic of all these classification systems is that a life form recognized by a scientist, clinician or an epidemiologist is recognized as the same life form by another. In the recent years, the typing modes utilized by the clinical microbiologists and clinicians are based on phenotypic typing. These typing methods involve staining properties, bacterial morphology or the oxygen requirements of the organism along with an array of biochemical analysis. In addition to that, the modes of pathogen transmission, the organism’s natural reservoir and the vectors of transmission are also of huge importance.

The clinical microbiology labs characterize or identify the bacteria by means of a series of biochemical analysis. The procedure involves isolating and purifying the pathogen that is present in the clinical sample followed by performing various biochemical tests that indicates the bacterial species.

Bacteria can be classified on the basis of serology that is by means of particular selected antiserum. This is due to the protein or carbohydrate moiety on the cell wall or the polysaccharide capsule of the bacteria that acts as an antigen (for example H and O polysaccharide antigens of the bacterial species salmonella).

While analysing the probable pathogen of the disease it is also essential to know the environmental reservoirs of the probable organism. The environmental or natural reservoirs are normally categorized into those that are endogenous (present on or inside the human body) and exogenous (present in the environment somewhere). The possible source of the infection also plays a key role while considering the probable cause of the infection for differential diagnosis. For instance, the skin rashes appearing in a hiker who had the multiple tick bites in the past is more probable to be borrelia, the agent which causes the Lyme disease.
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Researchers who are engaged in studying the evolution of bacteria are more concerned with the taxonomic classification schemes that allow them to compare the genes that are highly conserved between diverse species. A phylogenetic tree is based upon these comparisons and presents the extent of relatedness among various organisms. Among the novel application of this taxonomic classification is the identification and characterization of pathogens that are non cultivable in the laboratory.

The universal phylogenetic tree was initially developed by American microbiologist Carl Richard Woese consisting of three main divisions namely Archaea, Bacteria and Eucarya for all the living organisms. The basis of the classification was the comparison of the 16s rRNA (ribosomal RNA) sequences. The rRNA sequence comparison between various organisms is very useful since these sequences are efficiently conserved and have a gradual, slow and consistent change rate.

Scientists utilize the phylogenetic trees for a variety of purposes including, studying the features of the extinct species and ancestral lineages, testing of the evolutionary hypothesis and to classify the organisms. Utilizing phylogenies as a base for the classification is relatively a new advance in biology. The key advantages of the phylogenetic classification in comparison to the Linnaean system are that, it provides the information about the evolutionary history and it does not rank the organisms artificially into kingdoms, orders and so on.

Molecular subtyping is essential to verify whether the two strains of bacteria are from the same species or different species. PFGE (Pulsed Field Gel Electrophoresis) is the mainly utilized molecular technique in this analysis. Chromosomal DNA is digested with the aid of a restriction enzyme that creates comparatively infrequent cuts in the DNA and as a consequence produces DNA fragments of different sizes in different strains. The DNA fragments obtained from the different strains are then compared by running them on a gel.
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