Introduction
The Earth is home to upward of 1 trillion (1012) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome. We barely know 0.001%! It is impossible to arrive at a direct census starting from the "laboratory species" because they are only a fraction: most microorganisms do not tolerate artificial conditions and live only in nature. The 1 trillion ($10^2$) microbial species represent a still unknown universe compared, for example, to the approximately 100,000 species grown in the laboratory, and the 5-6 million species classified as animals, plants, fungi and others. All in all, the authors say, 99.999% of bacterial species have yet to be discovered.
It is estimated that there are 10 nonimillion ( $10^{31}$ ) of individual viruses on our planet. We could assign one to every star in the universe over 100 million times. Viruses belong to every aspect of the natural world, swarm in sea water, are transported into the atmosphere and nestle in tiny grains of earth. Generally considered non-living entities, these pathogens can replicate only with the help of a host, and are able to hijack organisms from any branch of the tree of life, including a multitude of human cells. However, in most cases, our species manages to live in this virus-filled world while remaining relatively "healthy". There are over 200 viruses known to cause disease in humans, and all of them are able to enter human cells. But it is almost certain that they are not born with this ability.
crispr cas9 (copia slide)
Another discovery involves the molecule that can be used to treat malaria, that comes from the Artemisia annua plant. After 6 months of usage the first resistant was found, so now it’s in use a combined therapy of drug and artemisinin.
In the twentieth century microbiology quickly developed into two distinct sectors: one application and one basic. From the point of view of application, significant developments have been made in medical microbiology and immunology, in agricultural microbiology, industrial microbiology and in microbiology of water. Advances in basic microbiology concerned bacterial taxonomy (identification of new etiologic agents and their classification), bacterial biochemistry, physiology, genetics, molecular biology, to the recent development of biotechnology. There are thousands of different types of microorganisms:
useful microorganisms for humans, like commensal microorganisms or microorganisms used by humans. Among them we remember the normal flora (Staphylococcus epidermidis e E. coli), in agriculture (bacteria capable of fixing atmospheric nitrogen), in the food industry for dairy products (Lactobacillus) bakery products (Saccharomyces cerevisiae) alcoholic beverages (Saccharomyces cerevisiae, Acetobacter), for methane production (methanogenic bacteria) and for biotechnology (antibiotics, human insulin, interferon, vaccines, transgenic plants and animals).
microorganisms that are infectious diseases agents, like Meningitis, Tuberculosis, Malaria, Papilloma virus, sexually trasmitted disease.
General Classification
Bacteria can be classified in base of:
Their shape
Cocci have a spherical shape and may be individual, in pairs (diplococcuss), chain (streptococcus), cluster (staphylococcus) or groups of eight cells in a cubic space (sarcine)
Bacilli have a rods shape and may be individual, in pairs (diplobacillus), chain (streptobacillus)
Spirilla have a spiral shape and are usually single
The temperature level they can grow at:
Cryophilic or psychrophilic bacteria develop around 15-20°C but can also multiply at 0 °J, in some cases, even at -7 °C. Their habitat is represented by the oceans and the Antarctic regions; they are also able to grow in chilled and frozen foods.
Mesophilic bacteria prefer temperature between 20-40°C. Human and animal pathogens are mesophilic and have adapted to the body temperature (37°C) even for fever (40°C). It is important to emphasize that mesophilic do not grow at refrigeration temperatures, and because the microorganism responsible for food alterations are mesophilic, the low temperatures for the preservation of foods are explained. Low temperatures generally slow the development of bacteria without killing them. Freezing does not kill most of the bacteria present in biological samples or in foods: when the temperatures return to the optimum, the microorganisms begin to multiply. The ability to withstand at very low temperatures is favoured by the presence of the capsule.
Thermophilic bacteria growth at temperatures above 40°C. The habitats from which such bacteria can be isolated include hot springs, tropical soils, water heating systems, and the warm currents of some oceans. The temperature range of this group has recently been raised to 90°C, as it has been shown that some bacteria have grown in a hot spring at that temperature. It is important to emphasize that the thermophilic bacterium proteins differ from the others because they are not denatured at high temperature. The thermostability of these proteins is intrinsic, depending on the composition and sequence of amino acids responsible for the appearance of strong bonds such as covalent disulfide bridges, and many hydrogen bonds and other weak bonds that stabilize the structure of proteins and enzymes.
Gram stain test that allows to divide the bacteria in Gram+ and Gram-. Gram staining differentiates bacteria by the chemical and physical properties of their cell walls. The bacteria are first stained with crystal-violet dye and then with an iodinated solution (Lugol's liquid); then washed with ethyl alcohol or acetone and counterstain with (safranin or fuchsine). The bacteria that lose the first stains are called Gram-, those who retain Gram+.
Their ability to live with or without oxygen:
Aerobic if they can survive and grow only in the presence of oxygen (the most common cause of clinical infection) or anaerobic bacteria that does not require oxygen to grow.
Obligate anaerobic bacteria are microorganisms that can only live in the absence of oxygen. Intestinal bacteria are a type of anaerobic bacteria defined oxygen- intolerant bacteria, in fact, if they encounter oxygen, they stop not only to multiply but die in a very short time.
Facultative anaerobic bacteria are microorganisms that can also survive in the absence of oxygen without being affected, but they growth better in the presence of this element. Microaerophilic bacteria can multiply in the presence of air (about 20% oxygen), but unlike the facultative anaerobic bacteria better with very low oxygen concentration (2-18%).
Nutrition (autotrophic and heterotrophic). Autotrophic bacteria are organisms that, like green plants, can synthesize their cellular constituents using simple inorganic substances.
The photosynthetic bacteria use light energy to produce useful chemical energy for vital processes.
The chemoautotrophic bacteria use inorganic compounds for energy and to synthesize their cellular constituents. The difference from photosynthesis is that chemosynthesis can also occur in the absence of light.
Heterotrophic bacteria, such as animals, are organisms that can only metabolize compounds already synthesized by other organisms. Most bacteria belong to this group. These bacteria can be further divided in saprophytic bacteria from parasites.
Saprophytic bacteria get food from plant and animal decomposition.
The parasitic bacteria, however, use the metabolism of other animals to obtain the food (internal bacteria) without ever causing obvious damage (see also symbiosis)
For biochemical characteristics like luminescence. Luminescence is the generic term that defines the emission of light by molecules without specifying the cause at its origin. The most famous form of luminescence is that resulting from the absorption of light (photo-luminescence), of which fluorescence is the most common example. Less commonly known is chemiluminescence. Chemiluminescence represents luminescence resulting from an exergonic chemical process, leading to a product in an electronically excited state, which decays by emitting photons. In chemiluminescence, bioluminescence is always caused by a chemical process but occurs in living organisms and is catalysed by enzymes. Bioluminescence is widely used in research to reveal microorganisms. If you apply an antibiotic and if the antibiotic is going to work, for example, after 24-28 hours, this is the answer. So it's very easy because the characteristic is the emission of not the light, but the photons. If you're using fluorescence molecules, you can't apply this type of technology, because the fluorescence doesn't have concentration. If you want to see how the cells, the metastatic cells, they move within the mouse, and where and which order they're going to be located, you can use this system. And see if a specific treatment is going to work because it's going to kill the patient or this case, the mouse, using a limited number of mice. And then you can also look at the 3D reconstruction of the animals. You can clearly visualize in which order, because this is an image that gives you an idea of just the surface of the animals. But there is a specific software in the machine that gives you a 3D image of the animals, and you can clearly visualize in which order your cells are going to rise.
Prokaryotic cell structure
One of the most important parts in the prokaryotic cells is the cell wall: it is made by peptidoglycan, and sometimes we have another structure that is the capsule of polysaccharide. The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. When it’s present, the capsule is a factor of virulence and is a way to hide from phagocytosis. C3B is one of the proteins that belong to the complex and that bind to the bacteria to opsonize it, but this is not possible if a capsule is present. The capsule enables the cell to attach to surfaces in its environment and escape phagocytosis. Some prokaryotes have flagella (for locomotion), pili (to exchange genetic material during a type of reproduction called conjugation), or fimbriae (to attach to a host cell).
For the cytoplasmatic membrane, there is a double phospholipidic layer, and we have got some proteins that can cross this layer, and they are very important because they allow some nutrients to be exchanged from the internal and external part of the bacteria. Going back to the cell wall, we say that the cell wall is made by peptidoglycan, also called murine.
It's formed with two polymers, some amino acids and two sugars (NAG: N-acetylglucosamine, and NAM: N-acetylmuramic acid). These two molecules are linked together with a $\beta$-1,4-glycosidic bridge and can be broken by the lysozyme. Then some peptides form a lateral chain: L-alanine, glutamic acid and then two different peptides based on the Gram +(L-Lysine) or Gram - (L-diaminopimeric). The peptides give a rigid structure to the prokaryotic cell, strengthened by the presence of bridges between lateral chains. This bridge is created by transferase, losing the last peptide. In Gram + the bridge is made of 5 peptides (pentapeptide bridge) while in the Gram - the bridge is direct (3rd aminoacid linked to the 4th of another branch). Transferase is also the target of some antibiotics, like penicillin.
The cell wall of Gram + is characterized by several layers of peptidoglycan, with filaments of lipoteichoic and teichoic acids. In Gram - bacteria, between the inner cell and peptidoglycan there’s a periplasmic space, while outside the peptidoglycan there’s an outer membrane (double layer of phospholipids) where the lipopolysaccharides are linked. LPS are made of three parts:
antigen O, differs for the number of saccharides in different bacteria and differentiates the LPS
lipid A, endotoxin that makes the LPS harmful, also presents an acid chain that contributes to avoid cleavage by the complement system
polysaccharide core, made of KDO (not present in human cells).