1. Bacterial Classification (The second lecture)
Dr.Sahar Mahdi

2. Classification Systems
The classification of bacteria serves a variety of different functions. Because of this variety, bacteria may be grouped using many different typing schemes. The critical feature for all these classification systems is an organism identified by one individual is recognized as the same organism by another individual. At present the typing schemes used by clinicians and clinical microbiologists rely on phenotypic typing schemes. These schemes utilize the bacterial morphology and staining properties of the organism, as well as O2 growth requirements of the species combined with a variety of biochemical tests. Scientists interested in the evolution of microorganisms are more interested in taxonomic techniques that allow for the comparison of highly conserved genes among different species. As a result of these comparisons a phylogenetic tree can be developed that displays the degree of relatedness of different organisms.

3. Phenotypic classification systems
Gram stain and bacterial morphology: This method was Discovered by. Gram, H.C in 1884 it remains an important and useful technique to this day. It allows a large proportion of clinically important bacteria to be classified as either Gram positive or negative based on their morphology and differential staining properties. Slides are sequentially stained with crystal violet, iodine, then destained with alcohol and counter-stained with safranin. Gram positive bacteria stain blue-purple and Gram negative bacteria stain red. The difference between the two groups is believed to be due to a much larger peptidoglycan (cell wall) in Gram positives.

4. As a result the iodine and crystal violet precipitate in the cell wall and are not eluted by alcohol in contrast with the Gram negatives where the crystal violet is readily eluted from the bacteria. As a result bacteria can be distinguished based on their morphology and staining properties. Some bacteria such as mycobacteria (the cause of tuberculosis) are not stained due to the large lipid content of the peptidoglycan. Alternative staining techniques (acid fast stain) are therefore used for stained bacteria

5. Growth Requirements:
Microorganisms can be grouped on the basis of their need for oxygen to grow. Facultative anaerobic bacteria can grow in high oxygen or low oxygen content. In contrast, strictly anaerobic bacteria grow only in conditions where there is minimal or no oxygen present in the environment. Bacteria such as bacteroides found in the large bowel are examples of anaerobes. Strict aerobes only grow in the presence of significant quantities of oxygen. Pseudomonas aeruginosa, an opportunistic pathogen, is an example of a strict aerobe. Microaerophilic bacteria grow under conditions of reduced oxygen and sometimes also require increased levels of carbon dioxide. Neisseria species (e.g., the cause of gonorrhea) are examples of microaerophilic bacteria.

6. Biochemical reactions:
Clinical microbiology laboratories typically will identify a pathogen in a clinical sample, purify the microorganism by plating a single colony of the microorganism on a separate plate, and then perform a series of biochemical studies that will identify the bacterial species.
Serologic systems:
Selected antisera can be used to classify different bacterial species. This may be based on either carbohydrate or protein antigens from the bacterial cell wall or the capsular polysaccharide. (Group A streptococcal M proteins or O and H polysaccharide antigens of Salmonella)

7. Environmental Reservoirs:
When considering likely pathogens it is also important to know which of the different species are found in different locations. Environmental reservoirs are generally divided into those that are endogenous (i.e., on or within the human or animal body) and exogenous (somewhere in the environment). Requirement for oxygen like aerobic bacteria as Bacilli and Anaerobic bacteria, like Clostridium, also Facultative anaerobe like Staphylococci ,In addition sometime bacteria were Lactose fermenters as E. coli, Klebsiella and Non lactose fermenters as Salmonella, Shigella

8. Genotypic systems:
Universal Phylogenetic Tree((النشوء والتطور: depend of ribosomal RNA sequences. These sequences are highly conserved and undergo change at a slow, gradual and consistent rate. They are therefore useful for making comparisons among the different living organisms. Molecular subtyping: Sometimes it is necessary to determine whether strains from the same species are the same or different. For example, if there is an outbreak of infections that appear due to the same bacterial species, the hospital epidemiologist will want to know if all of the infections are due to the same strain. Clues can be obtained by examining the biochemical studies or the antibiotic susceptibility profile, but a more reliable method is by molecular analysis.

9. A microaerophile is a microorganism that requires oxygen to survive, but requires environments containing lower levels of oxygen than are present in the atmosphere (i.e. <21% O2; typically 2-10% O2).Many microaerophiles are also capnophiles, ( requiring high concentration of carbon dioxide )e.g. 10% CO2 in the case of Campylobacter spp.)

10. Linnaeus hierarchical sequences((تسلسل هرمي proceed this way
Old classification Domain Kingdom Phylum Class Order Family Genus Species New classification ex: Kingdom prokaryota division bacteria family Streptococcaceae genus Streptococcus species equi

11. Scientific nomenclature
Binomial nomenclature A binomen or a scientific name; more informally it is also called a Latin name. The first part of the name identifies the genus to which the species belongs; the second part identifies the species within the genus. For example, humans belong to the genus Homo and within this genus to the species Homo sapiens. The binomial names of species are usually typeset in italics; for example, Staphylococcus aureus . Generally, the binomial should be printed in a font style different from that used in the normal text; for example; Streptococcus . When handwritten, each part of a binomial name should be underlined; for example, Staphylococcus aureus . The first part of the binomial, the genus name, is always written with capital letter, the second name (species ) is written with small letter. ex: Pasteulla maltucida

12. .
The binomial name should generally be written in full. The exception to this is when several species from the same genus are being listed or discussed in the same paper or report, or the same species is mentioned repeatedly; in which case the genus is written in full when it is first used, but may then be abbreviated to an initial (and a period/full stop). For example, a list of members of the genus Canis might be written as "Canis lupus, C. aureus, C. simensis". In rare cases, this abbreviated form has spread to more general use; for example, the bacterium Escherichia coli is often referred to as just E. coli,
The abbreviation "sp." is used when the actual specific name cannot or need not be specified. The abbreviation "spp." (plural) indicates "several species". These abbreviations are not italicized (or underlined). 

13. ▀ Appearance ex: Streptococcus spp.
Most genus and species name are chosen to tell us something about the organism its:
▀ Appearance ex: Streptococcus spp.
▀ Source ex : Canis Spp.
▀ Characteristic property ex: Staphylococcus aureus
▀ The scientist associated with it ex : Shigella
For example : Escherishia coli is named for microbiologist Escherich and its habitat is the colon
Shigella is named for Japanes microbiologist Shiga
Staphylococcus aureus is named for the appearance and characteristics feature (staphyl means cluster) and (aureus means golden).
Also the species is used for :
▀ The infection like Bacillus anthracis & Mycobacterium tuberculosis
▀ The host ex: Streptococcus eque & Brucella ovis
▀ the locality like the name of town or country ex. Salmonella Dublin & S. London.

14. The characters used to classify bacteria:
Bergeys manual of determinative Bacteriology ► The characters used to classify bacteria fall into two groups A- Traditional 1-morphology 2-cultural characteristics 3- gram staining reaction 4- spore forming 5- flagellation 6- biochemical tests 7- antigenic properties 8- pathogenisity & toxin production

15. B- Genomic 1- present G+C (Guanine- Cytosine)
B- Genomic 1- present G+C (Guanine- Cytosine). 2- Sequences bases in DNA. 3- DNA Hybridization.