Fermentation (biochemistry) in the context of Humans

Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit the air, soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in mutualistic, commensal and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

Like all animals, humans carry vast numbers (approximately 10 to 10) of bacteria. Most are in the gut, though there are many on the skin. Most of the bacteria in and on the body are harmless or rendered so by the protective effects of the immune system, and many are beneficial, particularly the ones in the gut. However, several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, tuberculosis, tetanus and bubonic plague. The most common fatal bacterial diseases are respiratory infections. Antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. Bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector (biomining, bioleaching), as well as in biotechnology, and the manufacture of antibiotics and other chemicals.

Oxidative phosphorylation or electron transport-linked phosphorylation or terminal oxidation, is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine triphosphate (ATP). In eukaryotes, this takes place inside mitochondria. Almost all aerobic organisms carry out oxidative phosphorylation. This pathway is so pervasive because it releases more energy than fermentation.

In aerobic respiration, the energy stored in the chemical bonds of glucose is released by the cell in glycolysis and subsequently the citric acid cycle, producing carbon dioxide and the energetic electron donors NADH and FADH₂. Oxidative phosphorylation uses these molecules and O₂ to produce ATP, which is used throughout the cell whenever energy is needed. During oxidative phosphorylation, electrons are transferred from the electron donors to a series of electron acceptors in a series of redox reactions ending in oxygen, whose reaction releases half of the total energy.

A facultative anaerobic organism is an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation if oxygen is absent.

Some examples of facultatively anaerobic bacteria are Staphylococcus spp., Escherichia coli, Salmonella, Listeria spp., Shewanella oneidensis and Yersinia pestis. Certain eukaryotes are also facultative anaerobes, including pupfish, fungi such as Saccharomyces cerevisiae and many aquatic invertebrates such as nereid polychaetes.

Anaerobic digestion is a sequence of processes by which microorganisms break down biodegradable material in the absence of oxygen. The process is used for industrial or domestic purposes to manage waste or to produce fuels. Much of the fermentation used industrially to produce food and drink products, as well as home fermentation, uses anaerobic digestion.

Anaerobic digestion occurs naturally in some soils and in lake and oceanic basin sediments, where it is usually referred to as "anaerobic activity". This is the source of marsh gas methane as discovered by Alessandro Volta in 1776.

Effervescence is the escape of gas from an aqueous solution and the foaming or fizzing that results from that release. The word effervescence is derived from the Latin verb fervere (to boil), preceded by the adverb ex. It has the same linguistic root as the word fermentation .

Effervescence can also be observed when opening a bottle of champagne, beer or carbonated soft drink. The visible bubbles are produced by the escape from solution of the dissolved gas (which itself is not visible while dissolved in the liquid).

The process of fermentation in winemaking turns grape juice into an alcoholic beverage. During fermentation, yeasts transform sugars present in the juice into ethanol and carbon dioxide (as a by-product). In winemaking, the temperature and speed of fermentation are important considerations as well as the levels of oxygen present in the must at the start of the fermentation. The risk of stuck fermentation and the development of several wine faults can also occur during this stage, which can last anywhere from 5 to 14 days for primary fermentation and potentially another 5 to 10 days for a secondary fermentation. Fermentation may be done in stainless steel tanks, which is common with many white wines like Riesling, in an open wooden vat, inside a wine barrel and inside the wine bottle itself as in the production of many sparkling wines.

Polyhydroxyalkanoates or PHAs are polyesters produced in nature by numerous microorganisms, including through bacterial fermentation of sugars or lipids. When produced by bacteria they serve as both a source of energy and as a carbon store. More than 150 different monomers can be combined within this family to give materials with extremely different properties. These plastics are biodegradable and are used in the production of bioplastics.

They can be either thermoplastic or elastomeric materials, with melting points ranging from 40 to 180 °C.

Primary nutritional groups are groups of organisms, divided according to the sources of energy, carbon, and electrons needed for living, growth and reproduction. The sources of energy can be light or chemical compounds; the sources of carbon can be of organic or inorganic origin; the source of electron can be organic or inorganic.

The terms aerobic respiration, anaerobic respiration and fermentation (substrate-level phosphorylation) do not refer to primary nutritional groups, but simply reflect the different use of possible electron acceptors in particular organisms, such as O₂ in aerobic respiration, nitrate (NO
₃) or sulfate (SO
₄) in anaerobic respiration, or various metabolic intermediates in fermentation.

Dental plaque is a biofilm of microorganisms (mostly bacteria, but also fungi) that grows on surfaces within the mouth. It is a sticky colorless deposit at first, but when it forms tartar, it is often brown or pale yellow. It is commonly found between the teeth, on the front of teeth, behind teeth, on chewing surfaces, along the gumline (supragingival), or below the gumline cervical margins (subgingival). Dental plaque is also known as microbial plaque, oral biofilm, dental biofilm, dental plaque biofilm, and bacterial plaque biofilm. Bacterial plaque is one of the major causes for dental decay and gum disease. It has been observed that differences in the composition of dental plaque microbiota exist between men and women, particularly in the presence of periodontitis.

Progression and build-up of dental plaque can give rise to tooth decay, and periodontal problems. Hence it is important to disrupt the mass of bacteria and remove it. Tooth decay is the localized destruction of the tissues of the tooth by acid produced from the bacterial degradation of fermentable sugar. Periodontal problems you could develop are ones such as gingivitis and periodontitis. Plaque control and removal can be achieved with correct daily or twice-daily tooth brushing and use of interdental aids such as dental floss and interdental brushes.

Saccharomyces cerevisiae (/ˌsɛrəˈvɪsi.iː/) (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungal microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been originally isolated from the skin of grapes. It is one of the most intensively studied eukaryotic model organisms in molecular and cell biology, much like Escherichia coli as the model bacterium. It is the microorganism which causes many common types of fermentation. S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by budding.

Many proteins important in human biology were first discovered by studying their homologs in yeast; these proteins include cell cycle proteins, signaling proteins, and protein-processing enzymes. S. cerevisiae is currently the only yeast cell known to have Berkeley bodies present, which are involved in particular secretory pathways. Antibodies against S. cerevisiae are found in 60–70% of patients with Crohn's disease and 10–15% of patients with ulcerative colitis, and may be useful as part of a panel of serological markers in differentiating between inflammatory bowel diseases (e.g. between ulcerative colitis and Crohn's disease), their localization, and severity.

An aerobic treatment system (ATS), often called an aerobic septic system, is a small scale sewage treatment system similar to a septic tank system, but which uses an aerobic process for digestion rather than just the anaerobic process used in septic systems. These systems are commonly found in rural areas where public sewers are not available, and may be used for a single residence or for a small group of homes.

Unlike the traditional septic system, the aerobic treatment system produces a high quality secondary effluent, which can be sterilized and used for surface irrigation. This allows much greater flexibility in the placement of the leach field, as well as cutting the required size of the leach field by as much as half.