Lecture 2- Hl Nomenclature of bacteria & Classific PDF

Nomenclature of bacteria Introduction Nomenclature of bacteria refers to naming and bacteria and other organisms are named according to the binomial system, which was introduced by Carl Linnaeus (1674-1748). This means that a bacterium has a species name, which is composed of a genus name that tel...

Nomenclature of bacteria Introduction Nomenclature of bacteria refers to naming and bacteria and other organisms are named according to the binomial system, which was introduced by Carl Linnaeus (1674-1748). This means that a bacterium has a species name, which is composed of a genus name that tells you to which genus it belongs and a species epithet which, together with the genus name, is unique to the bacterium. An example of this is Moraxella bovis, where the genus name indicates that the bacterium belongs to the genus Moraxella and the species epithet indicates that the bacterium has been isolated from cattle. The genus name and the species epithet form together the scientific name of the species, which is always written in italics. Bacterial names are international and Latin or latinized Greek are used to form the name. If misunderstandings cannot occur, you can abbreviate the genus name after it has been written for the first time in a text, e.g. M. bovis. However, note that there are also bacteria called Mycoplasma bovis and Mycobacterium bovis. There are strict international rules for how bacteria should be named and these rules are published in a book named: "International Code of Nomenclature of Prokaryotes". In order to get a proposed name accepted, a scientific paper on the proposed species must be published and approved by an international taxonomy committee. Trivial name Trivial names are often used as a simplified way of naming a bacterial genus. A trivial name should neither be written with capital first letter nor in italic. Examples of trivial names are: lactobacilli, mycobacteria, salmonella, staphylococci and streptococci. The scientific names for these groups are: genus Lactobacillus (or Lactobacillus spp.), genus Mycobacterium (or Mycobacterium spp.), genus Salmonella (or Salmonella spp.), genus Staphylococcus (or Staphylococcus spp.), genus Streptococcus (or Streptococcus spp.), respectively. If you refer to a specific bacterial species, a trivial name referring to a complete genus should never be used. Subspecies, biovars and serovars Sometimes there is a need to divide bacterial species into subspecies, because they are too closely related to be regarded as different species, but too distantly related to be regarded as the same species. In this case a subspecies is introduced by adding a subspecies epithet and write subspecies (subsp. or ssp.) in front of it. An example of this is Streptococcus equi subsp. equi. When you divide a species into several subspecies, the original species always gets the same subspecies epithet as the species epithet. There is often a need to divide species and subspecies in different biovars (biological variants) or different strains, but this is not strictly regulated, which means that researchers themselves can name their strains or biovars. One type of biovar is serovar (serological variant), by which various surface antigens can be identified with specific antibodies. Contact tracing and epidemiology is based on identification of different variants of the same bacterial species. Serovar vs. serotype Serovar and serotype are synonyms and thus, interchangeable terms, but according to the Rules of the Bacteriological Code (1990 Revision), serovar is the preferred term. Serogroup is a group of bacteria containing a common antigen. A serogroup may contain several serotypes. Serogroup is not an official designation, but has been used to classify bacteria belonging to the genera Leptospira, Salmonella, Shigella and Streptococcus. Salmonella nomenclature A bacterial subspecies that occurs in several thousand different serovars is Salmonella enterica subsp. enterica. A common serovar is Dublin and if you you want to write the complete and correct name of the bacterium, it becomes Salmonella enterica subsp. enterica serovar Dublin. Please note that the name of the serovar is capitalized, but not italicized. If the name appears in several places in the text, you can write S. enterica subsp. enterica serovar Dublin. However, because even this abbreviated writing is rather lengthy, it has been agreed that it is acceptable to simply write Salmonella Dublin, except on the first occurrance in a text, where the name must be given in full. You can read more about naming of salmonellas on VetBact at Salmonella spp. and Salmonella enterica. Gram staining: A differential staining method.  Microbiology History and Scientists with their Discoveries Robert Hooke (1635-1703) In the 1660’s modified the basic design of the microscope and developed a compound microscope that was six inches long and had two convex lenses which very much resembles the design of the modern microscope. He observed specimens of various things under the microscope such as the leaves, thin specimens of cork, hair of peacock, seaweed, wood, sponges, etc. He described the repetitive rectangular box-like structures as “cell” Antony van Leeuwenhoek (1632-1723) He was a self-made scientist and explores in Delft, Holland. He was not the first person to observe microscopic forms but probably the first one to report it. Antony Van Leeuwenhoek is known as the Father of Microscopy He made 419 lenses and more than 250 microscopes. The highest magnification at which he observed was 200-300 times. He observed a variety of things like blood, leaves, scrapings from his teeth, and many more. In a series of his letters written to the British Royal Society he carefully recorded his observations and descriptions. In one of his letters, he described the tiny creatures as ‘animalcules’. He also described the shapes of bacteria in these letters. In 1683 he published a sketch of the principle shape of bacteria, rods, cocci, and spiral-shaped. Francesco Redi (1626-1697) He was an Italian physician and opposed the theory of abiogenesis. He performed a 3 jar experiment to disprove abiogenesis. He placed pieces of rotten meat in 3 jars. He covered one jar with parchment paper, the other with fine mesh or gauze, and the third jar was left open.  The jar left uncovered showed maggots and attracted flies, whereas the jars covered did not show maggots or flies in the jar but eggs were laid on the parchment paper and the gauze. Experiment by Redi could not completely prove that microbial life does not originate spontaneously but it proved that entry of flies and eggs in the jars can lead to the formation of life and life cannot be created spontaneously. John Needham (1713-1781) He was a strong proponent of abiogenesis or spontaneous generation. He conducted an experiment in which he boiled the meat broth in a corked flask and upon standing for a few days he observed growth in the flask. He concluded that this was due to spontaneous generation. This result was due to insufficient boiling of the broth and hence it failed to kill the heat- resistant spores in the broth. Lazzaro Spallanzani (1729-1799) He repeated the experiment of John Needham but arrived at an opposite end. He boiled the meat infusion for a longer period and sealed the flask in the flame. Upon keeping the flask for a few days he did not find any growth in the flask. He examined the meat broth from various flasks. He argued that prolonged boiling destroyed the heat-resistant spores, and to prove this he opened the sealed flask and exposed it to air. Within a short time, the opened flask showed growth in the broth. Louis Pasteur (1822-1895) He is the father of Medical Microbiology. To disprove the theory of spontaneous generation Louis Pasteur in 1862 designed a special flask with a long neck called ‘Swan necked Flask’ or ‘S-shaped flask. He placed the nutrient medium and boiled it to ensure sterilization. Though the flask was kept open no growth was seen in the medium due to the long neck. Later when the neck of the flask was cut open, the nutrient broth was exposed to air soon microbial growth was seen in the nutrient medium. He was also the first person to use gun cotton for filtration. In 1877 Louis Pasteur discovered the anaerobic bacteria during his study on butyric acid fermentation. He also solved the problem of the souring of wine due to the presence of bacteria in France. He proposed boiling the fruit juice to kill contaminants. This process is known as ‘Pasteurisation’. He discovered microorganisms called ‘Yeast’ which are responsible for the conversion of sugar into alcohol. He discovered the principle of active immunization in 1880. Pasteur also prepared an attenuated rabies vaccine and tried it on a young boy which protected him from rabies. John Tyndall (1820-1893) In 1877 the final blow to the spontaneous generation was given by physicist John Tyndall. While studying optical properties he observed that the air containing germs and dust particles was visible while the air that does not have dust particles and germs is invisible. He also designed a chamber to prove that germs are carried by dust.  The chamber contained a rack of test tubes filled with sterile nutrient broth. The inner parts of the chamber were coated with glycerol to trap the dust particles containing germs. This system was allowed to stand for several days and no growth was seen in the test tubes. This could have been due to dust-free air. When dust containing air was introduced into the chamber microbial growth appeared in a brief period. Tyndall also concluded that some bacteria exist in two phases- thermolabile and thermostable. His observations stated that the thermolabile forms can be destroyed by significant boiling while thermostable forms are resistant to heat. This confirmed the presence of endospore in certain bacteria. He also developed a method of fractional sterilization known as Tyndallisation. What is the Difference Between Tyndallization and Pasteurization? Tyndallization is heating of things at 100 C for three consecutive days with incubation period in between while pasteurization is heating of especially milk either at 63 C for 30 minutes or 72 C for 15-20 seconds followed by cooling quickly and sealing. Robert Koch (1843-1910) A German bacteriologist is known for the isolation of microorganisms causing Anthrax and Tuberculosis. He also developed solid media for culturing bacteria and various techniques to isolate bacteria. He developed the streak plate technique to isolate bacteria. The postulates given by Koch proved as guidelines to identify the causative agent of an infectious disease. Joseph Lister (1827-1912) He is the father of antiseptic surgery. He developed antiseptic surgical procedures. He used carbolic acid for antiseptic surgical procedures. This reduced the rate of wound infections. He was the first person to isolate bacteria (Bacillus lactis) in pure form in a liquid culture form. Paul Ehrlich (1854-1915) He discovered a synthetic drug, arsenic chemotherapeutic derivative ‘Salvarsan’ known as ‘Magic bullet’. The drug was effective against Syphilis. Hans Christian Gram (1853-1938) He developed the most important staining method in 1884 to visualize bacteria known as Gram Staining. Based on the differences in the peptidoglycan content in the cell wall of bacteria, they acquire different colors. Bacteria are differentiated into Gram-Positive (Violet) and Gram-negative (Pink) by the staining procedure. It is the basic staining procedure used to identify bacteria. Alexander Fleming (1881-1955) In 1928 discovered the antibiotic Penicillin which has been extensively used since then.  He discovered that this was effective against several Gram-positive bacteria which caused diseases like gonorrhea, scarlet fever, and many more. Edward Jenner (1749-1823) The concept of vaccination was invented by this British physician. He successfully developed a vaccine against smallpox and today smallpox has been eradicated from society. Dr Jenner performing his first vaccination on James Phipps, a boy of age 8, on 14 May 1796. Painting by Ernest Board (early 20th century). Elie Metchnikoff (1845-1916) In 1892 Elie Metchnikoff discovered the process of phagocytosis and the phagocytes. This was an important discovery in the clinical microbiology sector. Frederick Griffith (1877-1941) He performed experiments to identify the transforming principle in organisms. He showed that bacteria can transform the genetic material through the process of transformation. Rosalind Franklin (1920-1958) She was the first person to perform X-Ray crystallography for identifying the structure of DNA. The major clues for the structure of DNA were discovered by her. James Dewey Watson (1928) and Francis Harry Compton Crick (1916-2004) They published a brief paper describing the structure of DNA in 1953. They described that the genetic material – DNA has a double helix structure. In 1990, Watson was appointed as the head of the Human Genome Project at the National Institutes of Health, a position he held until April 10, 1992. Kary Mullis (1944-2019) He discovered a method to amplify the DNA and develop multiple copies by using the process of PCR (Polymerase Chain Reaction). This process is widely used and can be performed over a short period.  Human use of Microorganisms Microbes are an integral and essential part of the web of life. They carry out a variety of important ecological functions, from recycling organic matter to aiding in the carbon and nitrogen cycles. This article will discuss their importance to both nature and human industry and society as well as their applications in some key industries. Humans and microbes: A brief history Disease caused by pathogenic microorganisms has been a major killer throughout history. Our species continued survival has been a source of fascination for people all the way back to prehistory. Over the millennia, physicians and scientists have struggled to better understand disease has led to many treatments, some sadly not as effective as others. The domestication of animals for food sources also brought additional problems, with pathogens jumping from animal to human hosts. Humans have had an intimate relationship with microbes throughout history, using them for many important purposes. The food industry especially has long used microbes, and over the last couple of centuries they have been utilized in the life sciences and medical industries, the energy industry, waste treatment, and many more industries besides. Microbiology, the study of microbes, has existed since the early 17 th century with the invention of the microscope. Earlier works such as the theory of contagious diseases in the 16th century, proposed by Girolamo Fracastoro, paved the way for the field. Modern studies have further revealed details aboutthe structure and uses of microorganisms such as viruses, bacteria, fungi, and plasmodia. Thousands of industrially important products are derived from microbes including actinomycetes, bacteria, and fungi. More products created by microbiologists are entering the market every year. Microorganisms in nature Microorganisms play an intrinsic role in almost every natural cycle. Found in most environments, from aquatic to land, air, inside the human body, and even in extreme environments such as hydrothermal vents and volcanoes, microorganisms are an essential part of the web of life. Microbes help to break down organic matter from plants, animals, and other microbes. They are involved with the nitrogen and carbon cycles. Microorganisms help to generate oxygen and carbon dioxide, as well as fix atmospheric nitrogen into useable forms for multiple organisms. They also help animals ingest food by being part of the gut microbiome. Some species of microbe are symbiotic in nature. It is estimated that the total number of bacteria and archaea on Earth is in the region of 10 30. Microbes and drug discovery Microorganisms cause numerous diseases in humans, plants, animals, and there are even strains of microbe (such as bacteriophages) that are pathogenic to other microorganisms. Early advances in the field of medicine that utilized microbes include the discovery of penicillin and the development of antibiotics in the early part of the 20th century and the discovery of an effective vaccineagainst smallpox in the 19th century. Microbes are used in numerous drug discovery studies today. In 1991, half the pharmaceuticals on the market were either natural products or derivatives. In 1997, 42% of the top-selling pharmaceuticals were obtained from natural sources. Today, hundreds of thousands of secondary metabolites have been identified, and these are used widely in the pharmaceutical industry. Antivirals, antibiotics, and antifungals are commonly used in healthcare settings across the world. Resistance to drugs has grown in recent decades, most notably antibiotic resistance. This presents several challenges in drug discovery, but new designer drugs are entering the market that is allowing clinicians to treat and cure deadly diseases that are becoming increasingly hard to tackle via existing means. Mechanisms of Bacterial Action in Cancer Treatment Live strains of Streptococci and Clostridia were the first strains to be used for trials in cancer treatment. A variety of techniques can be used on bacteria in order to achieve tumor therapy. Bacteria belonging to the genus of Pseudomonas, Caulobacter, Listeria, Proteus, Bifidobacteria, and Salmonellae among many others have been shown to have the capability to destroy tumors through different mechanisms. Some of the mechanisms involve the use of their bacterial toxicity, producing immunotherapy constituents, producing enzymes, producing biofilms, producing bacteriocins, capability to carry out RNA interference as well as prodrug cleavage. These bacterial species have also been tested for their therapeutic effect in cancer in animal models; however, more work has to be done so that the trials can be carried out in humans with different malignancies. Microbes in the food industry The history of microbe use in the food industry stretches back to antiquity. Many food products including bread, yogurt, cheese, kombucha, preserves and preserved meats, and alcoholic beverages take advantage of microbes and their chemical reactions. Microbes also play a vital role in the gut as part of the microbiome, which has spurred techniques to improve the design ofmicrobiome-friendly foods. Techniques to prevent contamination by pathogenic bacteria improve food safety, design, quality, and shelf-life. Antimicrobial food packaging is a relativelyrecently developed technology in the food industry. Research into microbes and safeguarding against their danger to human health is of paramount importance to the multi-billion-dollar food industry. Waste treatment and environmental remediation Microbes break down and feed on human waste. They have been used in sewage and wastewater treatment for the last couple of centuries, with ever- more sophisticated applications improving sanitation and health for billions worldwide. Both aerobic and anaerobic bacteria are commonly utilized by thewaste industry. Research over the past few decades has also provided microbial applications for cleaning up pollution and disposing of plastic waste, two of the most critical issues facing modern society. Microbial systems that help to reduce carbonemissions have also been explored extensively. Microbes and agriculture Agriculture takes advantage of the natural cycles and behavior of both plants and animals. Microbes have played a vital role in the history of farming and agriculture. They are a major source of concern for farmers and agricultural scientists due to common diseases such as black rot, bacterial soft rot, bacterial leaf spot, blight, and numerous fungal and viral infections that affect crops worldwide. Numerous treatments and remediation strategies have been developed over the years. A recent important development in the field of agriculture has been genetic modification. Genetic modification techniques use microbes to amplify beneficial genes. The rise of genetic modification, whilst controversial, offers the possibility of disease-resistant crops and strains that show a more robust response to climate change. Microbes are intrinsically linked with the future of sustainable agriculture.