# Microbiology
#### Part I The Basics

* Introduction to Microbiology
Microbiology is the branch of biology which deals with the study of micro organisms. Micro organisms come in a wide variety of morphologies and can be found in any location on earth due to their highly robust and adaptable natures. Like other cells, micro organisms as a general rule obey the central dogma of microbiology and thus have DNA that code for the proteins that allow them to function. Some organisms, like viruses, do not use DNA though and employ unique strategies to proliferate by co opting the cellular machinery of host organisms.
Micro organisms can be found in every kingdom of life. The common example of micro organisms are bacteria which occupy their own Domain of life, Bacteria. Along side this Domain are the domains Archaea and Eukarya. Archaea is home to many microorganisms as well often referred to as protists. Protists are some of the most robust organisms on earth and can be found in extreme environments such as; geysers, ice lakes, and geothermal vents at the bottom of the ocean. Eukarya boasts a significant number of micro organisms as well, specifically in the kingdoms Animalia, with worms and other parasites, and Fungi.
** What is Microbiology?
Microbiology is the study of microscopic organisms, i.e. those we cannot readily observe with our naked eyes. To learn about Micro organisms we first had to discover how to observe them. (history of microscopy here).
Currently, microbiology is a massive field with endless numbers of industrial and clinical applications. Disease causing organisms are a subject of intense study and the identification of novel treatments for diseases has been a massive endeavor for the past century. However, not all micro organisms are bad and in many cases can be made extremely beneficial. Modern production of insulin for diabetic patients is accomplished through production by genetically modified Escherichia coli.
*** What are microbes?
*** What makes microbes different from other organisms?
** Why Study Microbiology?
*** Fields of microbiology
**** Medical microbiology
**** Environmental microbiology
**** Food microbiology
**** Microbiology as a basic science
*** Uses of microbiology
**** Biotechnology
**** Bio-remediation
**** Natural products (Bio-Pharmaceutics)
**** Synthetic biology
*** Medical microbiology
**** Pathology and the microbial basis of disease
**** Microbial nature of the human body
**** Virology
The branch of science which deals with the study of viruses
*** Summary
** History of Microbiology
*** Ancient History, what we knew before we knew what we didn't know
**** Ancient microbial foods
**** Ancient preservation techniques
**** The understanding of disease in a pre-microbial world
*** Conflict and Transition, the discovery of microbes and the debate surrounding spontaneous generation
**** Leeuwenhoek, microscopes, and animalcules
**** Hooke and Kircher, two alternate early microscopists
**** The theory of spontaneous generation and its detractors
**** Louis Pasture and the end of spontaneous generation
*** Pasture and Koch, the fathers of modern microbiology
**** Vaccination and pasteurization
**** The germ theory of disease
**** Koch's postulates
*** Summary
* A Tour of the Microbial World
** The Three Domains of Life
*** A historical perspective
*** Prokaryotes vs. eukaryotes
** Bacteria
*** What are bacteria?
*** Common bacterial characteristics
*** Classifying bacteria by cell wall
**** Gram Positive
**** Gram Negative
**** Acid Fast
**** Mycoplasma
**** Aside: use of the gram stain in microbiology and health today
*** Classifying bacteria by morphology
**** Cocci
**** Bacilli
**** Spirillum
**** Less common shapes
*** Classifying bacteria by metabolism
**** Energy source
**** Fermentation
**** Gas production/fixation
*** Classifying bacteria by genetics
** Archea
** Eukarya
* Structure and Function of Prokaryotic Cells
* The Chemistry of Life and Metabolism of Microbial Cells
* Nutrition and Growth
* Genetics and Gene Expression
* Viruses
Microbial Morphology and characteristics
* Bacteria
Bacteria are small, often no larger than a few micrometers, single celled organisms that have a wide range of living environments, morphologies, and food sources. Bacteria occupy the Domain Bacteria and are Prokaryotic organisms, meaning they lack specialized organelles and nucleus. Bacteria have cell walls composed of peptidoglycan, a sugar polymer that is cross-linked by amino acids. Alike other cells, bacteria also have cell membranes although certain species may have two membranes, referred to as gram negative. Bacterial species can also be motile and employ various means to accomplish this such as flagella.
Bacteria can, and often do, grow in just about any environment and have evolved to be able to adapt to rapid inputs of stress. The human GI tract, for example, is home to millions of bacteria and is constantly exposed to highly acid pHs and the release of antibiotic molecules. Many bacteria have evolved to inhabit this extreme environment and even to live along side us and provide much needed nutrients and even defense against invading micro organisms. this concept is referred to as the intestinal microbiota and carries over to almost every part of your body directly connected to your skin. In addition to assisting us with defense and digestion, bacteria are exceedingly important in the earth's nitrogen cycle and often associate with plants to fix nitrogen into the soil to fertilize it. Bacteria also act as decomposers, primary producers, and fulfill just about every single niche on earth.
Bacteria are by far the most numerous of all organisms on earth with a cell count that exceeds the number of all other living life forms as well as a biomass that is well in excess of the weight of every human being alive today. This immense mass of cells is helped by the rate at which bacteria reproduce. unlike Eukaryotic species bacteria replicate via a process known as binary fission wherein a single bacteria replicates its entire genome and then splits itself in half, effectively cloning itself. Due to this reproduction strategy, bacteria are capable of doubling their numbers exponentially. This is not to say though that bacteria are incapable of forms of mating. Certain species readily transfer genetic material between each other, such as in Helicobacter pylori which uses a specialized proteinc hannel known as the type 4 secretion system to move genetic material between cells in a process known as horizontal gene transfer. This amazing quality of bacteria to take up DNA is the basis of the transformation principle which allows us to genetically engineer bacteria for specific purposes in research, clinical practice, and industry.
Bacterial morphology
Bacteria can be classified by general morphology. Characteristic cell shape and size help to name and differentiate microorganisms. There are five types of bacterial cells: Cocci, Bacilli, Coccobacilli, Fusiform, and Spirilla. Cocci bacterium are spherical or oval shape. The cocci can occur in pairs (diplococci), chains (streptococci), and irregular clusters (staphylococci). The entire bacterial cell is very small, about the size of an eukaryotic mitochondria. The second type, bacilli, are rod shaped. Coccibacilli are very short rods that can easily be mistaken for cocci. Fusiform are rod-shaped bacteria that have tapered ends (like an American football). Spirilla are spiral shaped. If the spirilla is spiral shaped and the cell is more flexible it is called a spirochete.
bacteria structure

#### Part II Microbial Diversity

* Taxonomy and Phylogeny
* Bacteria
* Archea
* Fungi
* Protozoa
* Unicellular Algae
* Viruses
* Actinomycetes

#### Part III Medical Microbiology

Medical Microbiology is the field of study primarily concerned with the identification, characterization, and neutralization of diseases caused by micro organisms.
The following fields are related to Medical Microbiology: Immunology Bacteriology
Bacteriology is the study of organisms that exists within the Domain Bacteria Virology Mycology Pharmacology

#### Part V Food and Industrial Microbiology

Industrial Microbiology
Introduction-
Use of microbes in industrial or large scale productions is known as industrial microbiology. Mostly the bacteria and fungi are used in industrial applications. Bacteria have the property of rapid reproduction, as they divide rapidly leading to an exponential increase in population. By using bacteria we can transform substrates into more useful or valuable products.
Modern Industrial Microbiology has evolved in demand to develop cheap and faster substitute of chemical reactions. In earlier years of industrial development the transformation reactions are carried out by several steps of lengthy and delicate chemical reactions. They are very hard to control, depend on various other factors, sometimes require harsh conditions like high temperature, high pressure, use of alkali and acids and use of costly transition metals as catalyst. Often, performing a single transformation requires many steps of chemical reaction. By using industrial microbiology we can transform substrates without such harsh conditions more easily than ever.
Microbes are also used to produce antibiotics, vitamins, amino acids, organic acids, alcohols, and also as food called single cell proteins (SCP).
In industrial microbiology we use the native properties of microbes to grow in various environmental conditions (can use various materials as their carbon/energy source). The yeast sacchromyces spp. for example, can grow in both in presence or absence of oxygen. When it grows in presence of oxygen it breaks glucose into CO$_2$ and water and yields energy for growth. while growing in anaerobic conditions it produces ethyl alcohol and CO$_2$ and just survives with little growth. This property was identified earlier in the development of humankind and thus humans started production of various alcoholic beverages.

##### List of Products

* Ethanol
* Acetic acid
* Lactic acid
* Vitamins
* Amino acids
* Enzymes
* Some insecticides
* Lipids
* Coloring compounds
* Polysaccharides (gum)
Most important use of microbes is as enzyme producers. In the beginnings of microbiology it was discovered that something within the yeast is responsible for the conversion of sugar into alcohol. This biological compound was known as an enzyme ( en= within, zyme= yeast)
Nowadays the following industrially important enzymes are produced by microbes:
* Amylases (to degrade starch)
* Proteases (to degrade proteins)
* Lipases (to degrade lipids)
* Pectinases (clarification of wine and fruit juices)
* Cellulases (to convert cellulose into glucose)
* Proteases and lipases are used as additives in modern detergents.
Microbes naturally produce enzymes in order to utilize the food sources present around them. For example, various fungi and bacteria growing on fruit-based substrates produce pectinases and cellulases to degrade the materials present on the cell wall of fruit cells.