Gastrointestinal tract

intestinegastrointestinaldigestive tract
Helicobacter pylori is a gram-negative spiral bacterium. Over half the world's population is infected with it, mainly during childhood; it is not certain how the disease is transmitted. It colonizes the gastrointestinal system, predominantly the stomach. The bacterium has specific survival conditions that our gastric microenvironment: it is both capnophilic and microaerophilic. Helicobacter also exhibits a tropism for gastric epithelial lining and the gastric mucosal layer about it. Gastric colonization of this bacterium triggers a robust immune response leading to moderate to severe inflammation.

Inflammatory bowel disease

inflammatory bowel diseasesIBDindeterminate colitis
The enteral bacteria can be altered by environmental factors, such as concentrated milk fats (a common ingredient of processed foods and confectionery) or oral medications such as antibiotics and oral iron preparations. Loss of integrity of the intestinal epithelium plays a key pathogenic role in IBD. Dysfunction of the innate immune system as a result of abnormal signaling through immune receptors called toll-like receptors (TLRs)—which activates an immune response to molecules that are broadly shared by multiple pathogens—contributes to acute and chronic inflammatory processes in IBD colitis and associated cancer.

Human gastrointestinal microbiota

gut floragut microbiotaintestinal flora
The human immune system creates cytokines that can drive the immune system to produce inflammation in order to protect itself, and that can tamp down the immune response to maintain homeostasis and allow healing after insult or injury. Different bacterial species that appear in gut flora have been shown to be able to drive the immune system to create cytokines selectively; for example Bacteroides fragilis and some Clostridia species appear to drive an anti-inflammatory response, while some segmented filamentous bacteria drive the production of inflammatory cytokines. Gut flora can also regulate the production of antibodies by the immune system.


diarrhoeadiarrheal diseaseschronic diarrhea
Fecal calprotectin to exclude inflammatory bowel disease. Stool tests for ova and parasites as well as for Clostridioides difficile. A colonoscopy or fecal immunochemical testing for cancer, including biopsies to detect microscopic colitis. Testing for bile acid diarrhea with SeHCAT, 7α-hydroxy-4-cholesten-3-one or fecal bile acids depending on availability. Hydrogen breath test looking for lactose intolerance. Further tests if immunodeficiency, pelvic radiation disease or small intestinal bacterial overgrowth suspected.


antibioticsantibacterialtopical antibiotic
Vaccination either excites or reinforces the immune competence of a host to ward off infection, leading to the activation of macrophages, the production of antibodies, inflammation, and other classic immune reactions. Antibacterial vaccines have been responsible for a drastic reduction in global bacterial diseases. Vaccines made from attenuated whole cells or lysates have been replaced largely by less reactogenic, cell-free vaccines consisting of purified components, including capsular polysaccharides and their conjugates, to protein carriers, as well as inactivated toxins (toxoids) and proteins. Phage therapy is another method for treating antibiotic-resistant strains of bacteria.


proteinsproteinaceousstructural proteins
Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for use in the metabolism. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification.


The vast majority of bacteria, which can range between 0.15 to 700 μM in length, are harmless or beneficial to humans. However, a relatively small list of pathogenic bacteria can cause infectious diseases. Pathogenic bacteria have several ways that they can cause disease. They can either directly affect the cells of their host, produce endotoxins that damage the cells of their host, or cause a strong enough immune response that the host cells are damaged. One of the bacterial diseases with the highest disease burden is tuberculosis, caused by the bacterium Mycobacterium tuberculosis, which killed 1.5 million people in 2013, mostly in sub-Saharan Africa.

Crohn's disease

Crohn’s diseaseCrohn diseaseCrohn
While the cause of Crohn's disease is unknown, it is believed to be due to a combination of environmental, immune, and bacterial factors in genetically susceptible individuals. It results in a chronic inflammatory disorder, in which the body's immune system attacks the gastrointestinal tract, possibly targeting microbial antigens. While Crohn's is an immune-related disease, it does not appear to be an autoimmune disease (in that the immune system is not being triggered by the body itself). The exact underlying immune problem is not clear; however, it may be an immunodeficiency state.


stomach flucholera morbusinfectious diarrhea
It is less common in adults, partly due to the development of immunity. Gastroenteritis usually involves both diarrhea and vomiting. Sometimes, only one or the other is present. This may be accompanied by abdominal cramps. Signs and symptoms usually begin 12–72 hours after contracting the infectious agent. If due to a virus, the condition usually resolves within one week. Some viral infections also involve fever, fatigue, headache and muscle pain. If the stool is bloody, the cause is less likely to be viral and more likely to be bacterial. Some bacterial infections cause severe abdominal pain and may persist for several weeks.


It can lead to septic shock, if the immune response is severely pronounced. Moreover, endotoxemia of intestinal origin, especially, at the host-pathogen interface, is considered to be an important factor in the development of alcoholic hepatitis, which is likely to develop on the basis of the small bowel bacterial overgrowth syndrome and an increased intestinal permeability. Lipid A may cause uncontrolled activation of mammalian immune systems with production of inflammatory mediators that may lead to septic shock. This inflammatory reaction is mediated by Toll-like receptor 4 which is responsible for immune system cell activation.


Microbes can make nutrients and minerals in the soil available to plants, produce hormones that spur growth, stimulate the plant immune system and trigger or dampen stress responses. In general a more diverse set of soil microbes results in fewer plant diseases and higher yield. Microorganisms can form an endosymbiotic relationship with other, larger organisms. For example, microbial symbiosis plays a crucial role in the immune system. The microorganisms that make up the gut flora in the gastrointestinal tract contribute to gut immunity, synthesize vitamins such as folic acid and biotin, and ferment complex indigestible carbohydrates.

Coeliac disease

celiac diseaseceliac spruecoeliac
Membrane leaking permits peptides of gliadin that stimulate two levels of immune response, the innate response and the adaptive (T-helper cell mediated) response. One protease-resistant peptide from α-gliadin contains a region that stimulates lymphocytes and results in the release of interleukin-15. This innate response to gliadin results in immune-system signalling that attracts inflammatory cells and increases the release of inflammatory chemicals. The strongest and most common adaptive response to gliadin is directed toward an α2-gliadin fragment of 33 amino acids in length. The response to the 33mer occurs in most coeliacs who have a DQ2 isoform.


lactobacilliDöderlein vaginal bacilluslactic acid bacteria
In children, Lactobacillus strains such as L. rhamnosus are associated with a reduction of atopic eczema, also known as dermatitis, due to anti-inflammatory cytokines secreted by this probiotic bacteria. .In addition, lactobacillus with other probiotic organisms in ripen milk and yogurt progress the immunity in the mucous intestine in humans through rising the number of LgA Some Lactobacillus species have been associated with cases of dental caries (cavities). Lactic acid can corrode teeth, and the Lactobacillus count in saliva has been used as a "caries test" for many years. Lactobacilli characteristically cause existing carious lesions to progress, especially those in coronal caries.


septicaemiablood poisoningseptic
The early phase of sepsis characterized by excessive inflammation (sometimes resulting in a cytokine storm) may be followed by a prolonged period of decreased functioning of the immune system. Either of these phases may prove fatal. On the other hand, systemic inflammatory response syndrome (SIRS) occurs in people without the presence of infection, for example, in those with burns, polytrauma, or the initial state in pancreatitis and chemical pneumonitis. However, sepsis also causes similar response to SIRS. Bacterial virulence factors, such as glycocalyx and various adhesins, allow colonization, immune evasion, and establishment of disease in the host.

Tumor necrosis factor alpha

To study whether acute exercise induces a true anti-inflammatory response, a model of ‘low grade inflammation’ was established in which a low dose of E. coli endotoxin was administered to healthy volunteers, who had been randomised to either rest or exercise prior to endotoxin administration. In resting subjects, endotoxin induced a 2- to 3-fold increase in circulating levels of TNF. In contrast, when the subjects performed 3 hours of ergometer cycling and received the endotoxin bolus at 2.5 h, the TNF response was totally blunted. This study provides some evidence that acute exercise may inhibit TNF production.


A common example of an irreversible inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2 enzymes that produce the inflammation messenger prostaglandin. Other enzyme inhibitors are poisons. For example, the poison cyanide is an irreversible enzyme inhibitor that combines with the copper and iron in the active site of the enzyme cytochrome c oxidase and blocks cellular respiration. As enzymes are made up of proteins, their actions are sensitive to change in many physio chemical factors such as pH, temperature, substrate concentration, etc. The following table shows pH optima for various enzymes. Enzymes serve a wide variety of functions inside living organisms.


In a multicellular organism's immune system, phagocytosis is a major mechanism used to remove pathogens and cell debris. The ingested material is then digested in the phagosome. Bacteria, dead tissue cells, and small mineral particles are all examples of objects that may be phagocytized. Some protozoa use phagocytosis as means to obtain nutrients. Phagocytosis was first noted by Canadian physician William Osler (1876), and later studied and named by Élie Metchnikoff (1880, 1883). Phagocytosis is one of the main mechanisms of the innate immune defense. It is one of the first processes responding to infection, and is also one of the initiating branches of an adaptive immune response.

Dietary supplement

dietary supplementsnutritional supplementnutritional supplements
In humans, the large intestine is host to more than 1,000 species of microorganisms, mostly bacteria, numbering in the tens of trillions. "Probiotic" in the context of dietary supplements is the theory that by orally consuming specific live bacteria (or yeast) species, it is possible to influence the large intestine microbiota, with consequent health benefits.


allergiesallergic reactionallergic
Allergic diseases are caused by inappropriate immunological responses to harmless antigens driven by a TH2-mediated immune response. Many bacteria and viruses elicit a TH1-mediated immune response, which down-regulates TH2 responses. The first proposed mechanism of action of the hygiene hypothesis was that insufficient stimulation of the TH1 arm of the immune system leads to an overactive TH2 arm, which in turn leads to allergic disease. In other words, individuals living in too sterile an environment are not exposed to enough pathogens to keep the immune system busy.


lymphocyteslymphocyticlymphoid cells
A lymphocyte is one of the subtypes of a white blood cell in a vertebrate's immune system. Lymphocytes include natural killer cells (which function in cell-mediated, cytotoxic innate immunity), T cells (for cell-mediated, cytotoxic adaptive immunity), and B cells (for humoral, antibody-driven adaptive immunity). They are the main type of cell found in lymph, which prompted the name "lymphocyte". The three major types of lymphocyte are T cells, B cells and natural killer (NK) cells. Lymphocytes can be identified by their large nucleus. T cells (thymus cells) and B cells (bone marrow- or bursa-derived cells) are the major cellular components of the adaptive immune response.

Urinary tract infection

cystitisurinary tract infectionsbladder infection
Chronic prostatitis in the forms of chronic prostatitis/chronic pelvic pain syndrome and chronic bacterial prostatitis (not acute bacterial prostatitis or asymptomatic inflammatory prostatitis) may cause recurrent urinary tract infections in males. Risk of infections increases as males age. While bacteria is commonly present in the urine of older males this does not appear to affect the risk of urinary tract infections. Urinary catheterization increases the risk for urinary tract infections. The risk of bacteriuria (bacteria in the urine) is between three and six percent per day and prophylactic antibiotics are not effective in decreasing symptomatic infections.

Lactobacillus rhamnosus

L. rhamnosusL. rhamnosus GGLactobacillus rhamnosus GG
Lactobacillus rhamnosus is a bacterium that originally was considered to be a subspecies of L. casei, but genetic research found it to be a species of its own. It is a short Gram-positive heterofermentative facultative anaerobic non-spore-forming rod that often appears in chains. Some strains of ''L. rhamnosus'' bacteria are being used as probiotics, and are particularly useful in treating female-related infections, most particularly very difficult to treat cases of bacterial vaginosis (or "BV").


The immune response to the bacteria can cause sepsis and septic shock, which has a high mortality rate. Bacteria can also spread via the blood to other parts of the body (which is called hematogenous spread), causing infections away from the original site of infection, such as endocarditis or osteomyelitis. Treatment for bacteremia is with antibiotics, and prevention with antibiotic prophylaxis can be given in high risk situations. Bacteremia is typically transient and is quickly removed from the blood by the immune system. Bacteremia frequently evokes a response from the immune system called Sepsis, which consists of symptoms such as fever, chills, and hypotension.


Toxins produced by microorganisms are important virulence determinants responsible for microbial pathogenicity and/or evasion of the host immune response. Biotoxins vary greatly in purpose and mechanism, and can be highly complex (the venom of the cone snail contains dozens of small proteins, each targeting a specific nerve channel or receptor), or relatively small protein. Biotoxins in nature have two primary functions: Some of the more well known types of biotoxins include: The term "environmental toxin" can sometimes explicitly include synthetic contaminants such as industrial pollutants and other artificially made toxic substances.


malabsorption syndromeintestinal malabsorptionmalabsorption of nutrients
Enteroscopy for enteropathy and jejunal aspirate and culture for bacterial overgrowth. Capsule Endoscopy is able to visualise the whole small intestine and is occasionally useful. Colonoscopy is necessary in colonic and ileal disease. ERCP will show pancreatic and biliary structural abnormalities. 75 SeHCAT test to diagnose bile acid malabsorption in ileal disease or primary bile acid diarrhea. Glucose hydrogen breath test for bacterial overgrowth. Lactose hydrogen breath test for lactose intolerance. Sugar probes or 51 Cr-EDTA to determine intestinal permeability. D-xylose absorption test for mucosal disease or bacterial overgrowth. Normal in pancreatic insufficiency.