Gut flora in the context of Pathogenic bacterium

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.

Flora (pl.: floras or florae) is all the plant life present in a particular region or time, generally the naturally occurring (indigenous) native plants. The corresponding term for animals is fauna, and for fungi, it is funga. Sometimes bacteria and fungi are also referred to as flora as in the terms gut flora or skin flora for purposes of specificity.

A herbivore is an animal anatomically and physiologically evolved to feed on plants, especially upon vascular tissues such as foliage, fruits or seeds, as the main component of its diet. These more broadly also encompass animals that eat non-vascular autotrophs such as mosses, algae and lichens, but do not include those feeding on decomposed plant matters (i.e. detritivores) or macrofungi (i.e. fungivores).

As a result of their plant-based diet, herbivorous animals typically have mouth structures (jaws or mouthparts) well adapted to mechanically break down plant materials, and their digestive systems have special enzymes (e.g. amylase and cellulase) to digest polysaccharides. Grazing herbivores such as horses and cattles have wide flat-crowned teeth that are better adapted for grinding grass, tree bark and other tougher lignin-containing materials, and many of them evolved rumination or cecotropic behaviors to better extract nutrients from plants. A large percentage of herbivores also have mutualistic gut flora made up of bacteria and protozoans that help to degrade the cellulose in plants, whose heavily cross-linking polymer structure makes it far more difficult to digest than the protein- and fat-rich animal tissues that carnivores eat.

Pathogenic bacteria are bacteria that can cause disease. This article focuses on the bacteria that are pathogenic to humans. Most species of bacteria are harmless and many are beneficial but others can cause infectious diseases. The number of these pathogenic species in humans is estimated to be fewer than a hundred. By contrast, several thousand species are considered part of the gut flora, with a few hundred species present in each individual human's digestive tract.

The body is continually exposed to many species of bacteria, including beneficial commensals, which grow on the skin and mucous membranes, and saprophytes, which grow mainly in the soil and in decaying matter. The blood and tissue fluids contain nutrients sufficient to sustain the growth of many bacteria. The body has defence mechanisms that enable it to resist microbial invasion of its tissues and give it a natural immunity or innate resistance against many microorganisms.

Ulcerative colitis (UC) is one of the two types of inflammatory bowel disease (IBD), with the other type being Crohn's disease. It is a long-term condition that results in inflammation and ulcers of the colon and rectum. The primary symptoms of active disease are abdominal pain and diarrhea mixed with blood (hematochezia). Weight loss, fever, and anemia may also occur. Often, symptoms come on slowly and can range from mild to severe. Symptoms typically occur intermittently with periods of no symptoms between flares. Complications may include abnormal dilation of the colon (megacolon), inflammation of the eye, joints, or liver, and colon cancer.

The cause of UC is unknown. Theories involve immune system dysfunction, genetics, changes in the normal gut bacteria, and environmental factors. Rates tend to be higher in the developed world with some proposing this to be the result of less exposure to intestinal infections, or to a Western diet and lifestyle. The removal of the appendix at an early age may be protective. Diagnosis is typically by colonoscopy, a type of endoscopy, with tissue biopsies.

The lactose operon (lac operon) is an operon required for the transport and metabolism of lactose in E. coli and many other enteric bacteria. Although glucose is the preferred carbon source for most enteric bacteria, the lac operon allows for the effective digestion of lactose when glucose is not available through the activity of β-galactosidase. Gene regulation of the lac operon was the first genetic regulatory mechanism to be understood clearly, so it has become a foremost example of prokaryotic gene regulation. It is often discussed in introductory molecular and cellular biology classes for this reason. This lactose metabolism system was used by François Jacob and Jacques Monod to determine how a biological cell knows which enzyme to synthesize. Their work on the lac operon won them the Nobel Prize in Physiology in 1965.

Most bacterial cells including E. coli lack introns in their genome. They also lack a nuclear membrane. Hence the gene regulation by lac operon occurs at the transcriptional level, by controlling transcription of DNA.

Lactobacillus is a genus of gram-positive within the Lactobacillaceae family, aerotolerant anaerobes or microaerophilic, rod-shaped, non-spore-forming bacteria. Until 2020, the genus Lactobacillus comprised over 260 phylogenetically, ecologically, and metabolically diverse species; a taxonomic revision of the genus assigned lactobacilli to 25 genera (see § Taxonomy below).

Lactobacillus species constitute a significant component of the human and animal microbiota at a number of body sites, such as the digestive system and the female genital system. In women of European ancestry, Lactobacillus species are normally a major part of the vaginal microbiota. Lactobacillus forms biofilms in the vaginal and gut microbiota, allowing them to persist in harsh environmental conditions and maintain ample populations. Lactobacillus exhibits a mutualistic relationship with the human body, as it protects the host against potential invasions by pathogens, and in turn, the host provides a source of nutrients. Lactobacilli are among the most common probiotic found in food such as yogurt, and the bacteria are diverse in their application in maintaining human well-being, by helping to treat diarrhea, vaginal infections, and skin disorders such as eczema.

In medicine, the hygiene hypothesis states that early childhood exposure to particular microorganisms (such as the gut flora and helminth parasites) protects against allergies by properly tuning the immune system. In particular, a lack of such exposure is thought to lead to poor immune tolerance. The time period for exposure begins before birth and ends at school age.

While early versions of the hypothesis referred to microorganism exposure in general, later versions apply to a specific set of microbes that have co-evolved with humans. The updates have been given various names, including the microbiome depletion hypothesis, the microflora hypothesis, and the "old friends" hypothesis. There is a significant amount of evidence supporting the idea that lack of exposure to these microbes is linked to allergies or other conditions, although it is still rejected by many scientists.

Phage therapy, viral phage therapy, or phagotherapy is the therapeutic use of bacteriophages for the treatment of pathogenic bacterial infections. This therapeutic approach emerged at the beginning of the 20th century but was progressively replaced by the use of antibiotics in most parts of the world after the Second World War. Bacteriophages, known as phages, are a form of virus that attach to bacterial cells and inject their genome into the cell. The bacteria's production of the viral genome interferes with its ability to function, halting the bacterial infection. The bacterial cell causing the infection is unable to reproduce and instead produces additional phages. Phages are very selective in the strains of bacteria they are effective against.

Advantages include reduced side effects and reduced risk of the bacterium developing resistance, since bacteriophages are much more specific than antibiotics. They are typically harmless not only to the host organism but also to other beneficial bacteria, such as the gut microbiota, reducing the chances of opportunistic infections. They have a high therapeutic index; that is, phage therapy would be expected to give rise to few side effects, even at higher-than-therapeutic levels. Because phages replicate in vivo (in cells of living organism), a smaller effective dose can be used.

Candida albicans is an opportunistic pathogenic yeast that is a common member of the human gut flora. It can also survive outside the human body. It is detected in the gastrointestinal tract and mouth in 40–60% of healthy adults. It is usually a commensal organism, but it can become pathogenic in immunocompromised individuals under a variety of conditions. It is one of the few species of the genus Candida that cause the human infection candidiasis, which results from an overgrowth of the fungus. Candidiasis is, for example, often observed in HIV-infected patients.C. albicans is the most common fungal species isolated from biofilms either formed on (permanent) implanted medical devices or on human tissue. C. albicans, C. tropicalis, C. parapsilosis, and C. glabrata are together responsible for 50–90% of all cases of candidiasis in humans. A mortality rate of 40% has been reported for patients with systemic candidiasis due to C. albicans. By one estimate, invasive candidiasis contracted in a hospital causes 2,800 to 11,200 deaths yearly in the US.

C. albicans is commonly used as a model organism for fungal pathogens. It is generally referred to as a dimorphic fungus since it grows both as yeast and filamentous cells. However, it has several different morphological phenotypes including opaque, GUT, and pseudohyphal forms. C. albicans was for a long time considered an obligate diploid organism without a haploid stage. This is, however, not the case. Next to a haploid stage C. albicans can also exist in a tetraploid stage. The latter is formed when diploid C. albicans cells mate when they are in the opaque form. The diploid genome size is approximately 29 Mb, and up to 70% of the protein coding genes have not yet been characterized.C. albicans is easily cultured in the lab and can be studied both in vivo and in vitro. Depending on the media different studies can be done as the media influences the morphological state of C. albicans. A special type of medium is CHROMagar Candida, which can be used to identify different Candida species.