Gut microbiota in the context of "Colonisation (biology)"

Escherichia coli (/ˌɛʃəˈrɪkiə ˈkoʊlaɪ/ ESH-ə-RIK-ee-ə KOH-lye) is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are part of the normal microbiota of the gut, where they constitute about 0.1%, along with other facultative anaerobes. These bacteria are mostly harmless or even beneficial to humans. For example, some strains of E. coli benefit their hosts by producing vitamin K₂ or by preventing the colonization of the intestine by harmful pathogenic bacteria. These mutually beneficial relationships between E. coli and humans are a type of mutualistic biological relationship—where both the humans and the E. coli are benefitting each other. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for three days, but its numbers decline slowly afterwards.

Some serotypes, such as EPEC and ETEC, are pathogenic, causing serious food poisoning in their hosts. Fecal–oral transmission is the major route through which pathogenic strains of the bacterium cause disease. This transmission method is occasionally responsible for food contamination incidents that prompt product recalls. Cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for many days and grow outside a host.

Dietary fiber, fibre, or roughage is the portion of plant-derived food that cannot be completely broken down by human digestive enzymes. Dietary fibers are diverse in chemical composition and can be grouped generally by their solubility, viscosity and fermentability which affect how fibers are processed in the body. Dietary fiber has two main subtypes: soluble fiber and insoluble fiber which are components of plant-based foods such as legumes, whole grains, cereals, vegetables, fruits, and nuts or seeds. A diet high in regular fiber consumption is generally associated with supporting health and lowering the risk of several diseases. Dietary fiber consists of non-starch polysaccharides and other plant components such as cellulose, resistant starch, resistant dextrins, inulins, lignins, chitins, pectins, beta-glucans, and oligosaccharides.

Food sources of dietary fiber have traditionally been divided according to whether they provide soluble or insoluble fiber. Plant foods contain both types of fiber in varying amounts according to the fiber characteristics of viscosity and fermentability. Advantages of consuming fiber depend upon which type is consumed. Bulking fibers – such as cellulose and hemicellulose (including psyllium) – absorb and hold water, promoting bowel movement regularity. Viscous fibers – such as beta-glucan and psyllium – thicken the fecal mass. Fermentable fibers – such as resistant starch, xanthan gum, and inulin – feed the bacteria and microbiota of the large intestine and are metabolized to yield short-chain fatty acids, which have diverse roles in gastrointestinal health.

Prebiotics are compounds in food that foster growth or activity of beneficial microorganisms such as bacteria and fungi. The most common environment concerning their effects on human health is the gastrointestinal tract, where prebiotics can alter the composition of organisms in the gut microbiome.

Dietary prebiotics are typically nondigestible fiber compounds that pass undigested through the upper part of the gastrointestinal tract and help growth or activity of advantageous bacteria in the colon by acting as substrates for them. They were first identified and named by Marcel Roberfroid in 1995. Depending on the jurisdiction, they may have regulatory scrutiny as food additives for the health claims made for marketing purposes. Common prebiotics used in food manufacturing include beta-glucan from oats, resistant starch from grains and beans, and inulin from chicory root.

Cecotropes (also caecotropes, cecotrophs, caecotrophs, cecal pellets, soft feces, or night feces) are a nutrient-filled package created in the gastrointestinal (GI) tract that is expelled and eaten by many animals (such as rabbits, guinea pigs, mice, hamsters, and chinchillas) to obtain more nutrients out of their food. When food passes through the GI tract the first time, the stomach and the small intestine digest the food material, which then moves into the colon, where the food particles are sorted by size. The smaller particles of fiber are moved into the cecum where they are fermented by microbes. This creates useable nutrients which are stored and expelled in cecotropes. The nutrients from the cecotropes are absorbed in the small intestine. The nutrients gained from cecotrophy include short-chain fatty acids, vitamin B, sodium, potassium, amino acids, and protein.

Lagomorphs (a grouping including rabbits, hares, and pikas) are perhaps the most well-known for producing and eating cecotropes, but other monogastric fermenters, such as rodents, also produce cecotropes. Rodents including beavers, guinea pigs, mice, hamsters, and chinchillas are known cecotrophs. Other animals also eat cecotropes, such as the common ringtail possum and the coppery ringtail possum.

The gut–brain axis is the two-way biochemical signaling that takes place between the gastrointestinal tract (GI tract) and the central nervous system (CNS). The term "microbiota–gut–brain axis" highlights the putative role of gut microbiota interacting with brain functions, according to preliminary research. Broadly defined, the gut–brain axis includes the central nervous system, neuroendocrine system, neuroimmune systems, the hypothalamic–pituitary–adrenal axis (HPA axis), sympathetic and parasympathetic arms of the autonomic nervous system, the enteric nervous system, vagus nerve, and the gut microbiota.

Chemicals released by the gut microbiome can influence brain development, starting from birth. A review from 2015 states that the gut microbiome influences the CNS by "regulating brain chemistry and influencing neuro-endocrine systems associated with stress response, anxiety and memory function".

An opportunistic infection is an infection that occurs most commonly in individuals with an immunodeficiency disorder and acts more severely on those with a weakened immune system. These types of infections are considered serious and can be caused by a variety of pathogens including viruses, bacteria, fungi, and parasites. Under normal conditions, such as in humans with uncompromised immune systems, an opportunistic infection would be less likely to cause significant harm and would typically result in a mild infection or no effect at all. These opportunistic infections can stem from a variety of sources, such as a weakened immune system (caused by human immunodeficiency virus and acquired immunodeficiency syndrome), when being treated with immunosuppressive drugs (as in cancer treatment), when a microbiome is altered (such as a disruption in gut microbiota), or when integumentary barriers are breached (as in penetrating trauma). Opportunistic infections can contribute to antimicrobial resistance in an individual making these infections more severe. Some pathogens that cause these infections possess intrinsic resistance (natural resistance) to many antibiotics while others acquire resistance over time through mutations or horizontal gene transfer. Many of these pathogens, such as the bacterium Clostridioides difficile (C. diff), can be present in hosts with uncompromised immune systems without generating any symptoms, and can, in some cases, act as commensals until the balance of the immune system is disrupted. With C. diff and many other pathogens, the overuse or misuse of antibiotics can cause the disruption of normal microbiota and lead to an opportunistic infection caused by antibiotic resistant pathogens. In some cases, opportunistic infections can be labeled as a hospital-acquired infection due to individuals contracting them within a healthcare/hospital setting. In terms of history, there is not one individual that can be attributed for discovering opportunistic infections. Over time and through medical advancement, there have been many scientists that have contributed to the study and treatment options for patients affected by these infections.

The human milk microbiota, also known as human milk probiotics (HMP), encompasses the microbiota–the community of microorganisms–present within the human mammary glands and breast milk. Contrary to the traditional belief that human breast milk is sterile, advancements in both microbial culture and culture-independent methods have confirmed that human milk harbors diverse communities of bacteria. These communities are distinct in composition from other microbial populations found within the human body which constitute the human microbiome.

The microbiota in human milk serves as a potential source of commensal, mutualistic, and potentially probiotic bacteria for the infant gut microbiota. The World Health Organization (WHO) defines probiotics as "living organisms which, when administered in adequate amounts, confer a health benefit on the host."