Bacterial Taxonomy and basic Nomenclature

 Bacterias are every where, The air we breathe, the food we eat, the surfaces we touch, and especially all the natural wonders around us. If you were to scoop up about a tablespoon of soil or a small cup of ocean water, scientists predict that you would be holding as many as one million bacterial species in your hand.
   We’re unable to grow the vast majority of bacterial species in the lab in order to study them more closely. Of all these bacterial species, thousands cover the human body, some transiently stopping by, others taking up permanent residence. However, just a fraction, a few hundred or so, can cause disease in humans. With so many different types of bacteria out there,

How bacteria are named?

The science of classifying living beings is called taxonomy, and we’ve been doing it ever since Swedish botanist Carl von LinnĂ©, also called Linnaeus, established a system for classification using taxonomic categories in the 1700s. He wanted to minimize chaos as new species were discovered, and provide a structure for defining and recognizing any newly discovered species.
  In the case of bacteria, we use a binomial or two-name, system of nomenclature. The scientific name for any bacteria is always the name of the genus first, which is capitalized, followed by the species name, which begins with a lowercase letter. Both should be italicized.

  The names of the genus and species have a wide variety of origins.
• Sometimes they were named after the microbiologist that discovered them.
• In other cases, the name might be related to how the microbe looks, or the disease it causes.

How bacteria got sorted into their respective categories in the first place.
  When it comes to classifying bacteria, it may seem a daunting or even impossible task. However, scientists have developed a system to observe test, and then categorize bacteria into logical relationships.
There are three main types of classification:
- Phenotypic,
- Analytic, and
- Genotypic.

1). Phenotypic characterization meaning the set of observable characteristics of bacteria. Those are size, shape, and staining characteristics. Before we had the advanced technology we have now, scientists relied on observing microscopic and macroscopic morphologies of bacteria. i.e, using Gram staining, a method developed by Hans Christian Gram in 1884, we can determine if bacteria are Gram-positive or Gram-negative, and thus how much peptidoglycan their cell wall contains.

Gram-positive organisms have a thick peptidoglycan wall, retaining lots of crystal violet stain when using this method, and thus appearing a purple blue under a microscope.
Gram-negative organisms have a much thinner peptidoglycan   layer which does not hold the blue dye. Even just separating bacteria into Gram-positive versus Gram-negative can tell us a lot about how they might behave.
  Certain microbes have unique staining characteristics, such as the genus Mycobacterium, which can be detected by an acid-fast stain.

  Another example involves identifying the shape of individual organisms under a microscope, which will be either rods, cocci, curved or spiral. Zooming out a bit, scientists also look at how bacteria grow on agar in the lab. They look at the colonies of bacteria that grow, taking note of the size, shape, color, and even smell.
   For instance, streptococci colonies tend to be smaller in relation to most other types of bacteria, and Serratia marcescens typically appear red when grown at 22 degrees Celsius.
   We can test for hemolytic properties on blood agar, identifying if the bacteria produce toxic byproducts capable of destroying red blood cells. i.e, Streptococcus pyogenes, the causative agent of strep throat, is a gram-positive bacterium that forms long cocci chains and grows as small, white, hemolytic colonies on blood agar plates. Since it is likely for multiple species to appear similar in these types of tests, these phenotypic characterization methods serve only as a starting point for further investigation.

Next, there are tests to determine what biochemical properties the bacteria have, like the ability to ferment specific carbohydrates, what carbon sources they can use for growth, and the presence or absence of different enzymes, like lipases, proteases, or nucleases. All of these observations combined can identify with reasonable precision a species of bacteria. These techniques have also been used to subdivide groups of organisms beyond the species level, down to a specific strain.

Doing this by looking at the genetic makeup of the organism, especially in the case of an outbreak, is called biotyping. Many bacteria also possess antigens, which might be a toxin or other substance that triggers an immune response in the body. Grouping bacteria based on these antigens is called serotyping.

Using serotyping, scientists can work backwards using antibodies to detect which antigens are present, thus allowing them to narrow down the bacterial possibilities. Serotyping is a powerful tool for classification, especially for those species that are difficult to grow, those that are difficult to test biochemically, or those that need to be identified rapidly, such as during an outbreak.

  Scientists can also look at which antibiotics bacteria are susceptible to, which is called analyzing their antibiogram patterns. Finally, using phage typing, scientists can assess which bacteriophages bacteria might be susceptible to.

2) Analytic classification.

  Analytic classification methods include
- Whole cell lipid analysis,
- Cell wall fatty-acid analysis,
- Whole cell protein analysis via 
  mass spectroscopy, and
- The presence of cellular enzymes via multilocus enzyme electrophoresis.

  Analytic classification can be a bit labor-intensive, requiring expensive machines and specialized training. For these reasons, analytic classification is typically done in special laboratories.

3). Genotypic Classification

Finally, the most precise method for classifying bacteria is through genotypic classification. Put simply, this means using bacterial DNA to determine what species or family bacteria might belong to.

  In the early days, scientists used the ratio of guanine to cytosine to classify bacteria. As technology has progressed, so has our ability to quickly and accurately identify bacteria using DNA. Using DNA-DNA hybridization, scientists measure the degree of genetic similarity among bacterial isolates. Taking this a step further, scientists can extract DNA from an organism and expose it to species-specific molecular probes.

  If the nucleic acid probe binds to the DNA, then you know you’ve properly identified the organism. We can also use nucleic acid sequence analysis to compare unknown bacteria with already known sequences that are unique to a genus, species or subspecies. Additionally, some bacteria carry plasmids, which are small circular DNA strands that replicate independently of the chromosome.

  Genetic makeup of bacteria can vary drastically between species, their ribosomal genes are remarkably well conserved. Scientists routinely use 16S ribosomal RNA sequences to establish taxonomic relationships between prokaryotic strains.
  That’s why in situations such as an outbreak or epidemiological investigation, scientists can use plasmid analysis or ribotyping to quickly identify bacteria.

Bacterial classification

  Bacterial clasification into families, genera, and species changes all the time, evolving as we learn more about these microscopic creatures. Generally speaking, however, our classification system is a robust starting point. Using all of these techniques we discussed, we can organize bacteria into categories and predict their pathogenic capabilities.

  Some of these categories for medically important bacteria.
a). Aerobic, gram-positive cocci, which can be further subdivided into catalase-positive cocci, which includes the Staphylococcus group of bacteria, and catalase-negative cocci, which includes the Enterococcus and Streptococcus groups.
2). Aerobic, gram-positive rods, which can be grouped into actinomycetes with cell wall mycolic acids, actinomycetes with no cell wall mycolic acids, and miscellaneous gram-positive rods. Then, aerobic gram-negative rods, cocci, and curved rods, which include a wide variety of pathogenic organisms. Additionally, there are anaerobic gram-positive and gram-negative bacteria, which are further grouped by shape: cocci or rods.