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.


The vast majority of bacteria, which typically range between 1 and 5 micrometers in length, are harmless or beneficial to humans. However, a relatively small list of pathogenic bacteria can cause infectious diseases. One of the bacterial diseases with the highest disease burden is tuberculosis, caused by the bacterium Mycobacterium tuberculosis, which kills about 2 million people a year, mostly in sub-Saharan Africa. Pathogenic bacteria contribute to other globally significant diseases, such as pneumonia, which can be caused by bacteria such as Streptococcus and Pseudomonas, and foodborne illnesses, which can be caused by bacteria such as Shigella, Campylobacter, and Salmonella.


diarrhoeadiarrheal diseaseschronic diarrhea
This occurs with inflammatory bowel diseases, such as Crohn's disease or ulcerative colitis, and other severe infections such as E. coli or other forms of food poisoning. Inflammatory diarrhea occurs when there is damage to the mucosal lining or brush border, which leads to a passive loss of protein-rich fluids and a decreased ability to absorb these lost fluids. Features of all three of the other types of diarrhea can be found in this type of diarrhea. It can be caused by bacterial infections, viral infections, parasitic infections, or autoimmune problems such as inflammatory bowel diseases. It can also be caused by tuberculosis, colon cancer, and enteritis.


stomach flucholera morbusinfectious diarrhea
Gastroenteritis is defined as vomiting or diarrhea due to inflammation of the small or large bowel, often due to infection. The changes in the small bowel are typically noninflammatory, while the ones in the large bowel are inflammatory. The number of pathogens required to cause an infection varies from as few as one (for Cryptosporidium) to as many as 10 8 (for Vibrio cholerae). Gastroenteritis is typically diagnosed clinically, based on a person's signs and symptoms. Determining the exact cause is usually not needed as it does not alter management of the condition.


Some microorganisms that are seen to be beneficial to health are termed probiotics and are available as dietary supplements, or food additives. Microorganisms are the causative agents (pathogens) in many infectious diseases. The organisms involved include pathogenic bacteria, causing diseases such as plague, tuberculosis and anthrax; protozoan parasites, causing diseases such as malaria, sleeping sickness, dysentery and toxoplasmosis; and also fungi causing diseases such as ringworm, candidiasis or histoplasmosis.


Phage therapy infects pathogenic bacteria with their own viruses. Bacteriophages and their host ranges are extremely specific for certain bacteria, thus they do not disturb the host organism and intestinal microflora unlike antibiotics. Bacteriophages, also known simply as phages, infect and can kill bacteria and affect bacterial growth primarily during lytic cycles. Phages insert their DNA into the bacterium, where it is transcribed and used to make new phages, after which the cell will lyse, releasing new phage able to infect and destroy further bacteria of the same strain. The high specificity of phage protects "good" bacteria from destruction.

Gut flora

gut microbiotaintestinal floragut bacteria
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.

Crohn's disease

Crohn’s diseasechronCrohn
The later hypothesis describes impaired cytokine secretion by macrophages, which contributes to impaired innate immunity and leads to a sustained microbial-induced inflammatory response in the colon, where the bacterial load is high. Another theory is that the inflammation of Crohn's was caused by an overactive T h 1 and T h 17 cytokine response. In 2007, the ATG16L1 gene has been implicated in Crohn's disease, which may induce autophagy and hinder the body's ability to attack invasive bacteria.


lactobacilliDöderlein vaginal bacillusLactic acid bacteria
In addition, Lactobacillus species can be administered as probiotics during cases of infection by the ulcer-causing bacterium Helicobacter pylori. Helicobacter pylori is linked to cancer, and antibiotic resistance impedes the success of current antibiotic-based eradication treatments. When Lactobacillus probiotics are administered along with the treatment as an adjuvant, its efficacy is substantially increased and side effects may be lessened. Also, Lactobacillus is used to help control urogenital and vaginal infections, such as bacterial vaginosis (BV).

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.


septicemiasepticaemiablood poisoning
Sepsis is caused by an inflammatory immune response triggered by an infection. Most commonly, the infection is bacterial, but it may also be fungal, viral, or protozoan. Common locations for the primary infection include the lungs, brain, urinary tract, skin, and abdominal organs. Risk factors include very young age, older age, a weakened immune system from conditions such as cancer or diabetes, major trauma, or burns. An older method of diagnosis was based on meeting at least two systemic inflammatory response syndrome (SIRS) criteria due to a presumed infection.

Irritable bowel syndrome

IBSbowelirritable bowel
Evidence has demonstrated that the release of high levels of proinflammatory cytokines during acute enteric infection causes increased gut permeability leading to translocation of the commensal bacteria across the epithelial barrier; this in turn can result in significant damage to local tissues, which can develop into chronic gut abnormalities in sensitive individuals. However, increased gut permeability is strongly associated with IBS regardless of whether IBS was initiated by an infection or not. A link between small intestinal bacterial overgrowth and tropical sprue has been proposed to be involved in the cause of post-infectious IBS.

Urinary tract infection

urinary tract infectionscystitisbladder infection
It is believed that the bacteria are usually transmitted to the urethra from the bowel, with females at greater risk due to their anatomy. After gaining entry to the bladder, E. Coli are able to attach to the bladder wall and form a biofilm that resists the body's immune response. Escherichia coli is the single most common microorganism, followed by Klebsiella and Proteus spp., to cause urinary tract infection. Klebsiella and Proteus spp., are frequently associated with stone disease. The presence of Gram positive bacteria such as Enterococcus and Staphylococcus increased.


proteinsprotein synthesisproteinaceous
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.


carbohydratessaccharidecomplex carbohydrates
Saccharides and their derivatives include many other important biomolecules that play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development. Starch and sugars are the most important carbohydrates in human diet. They are found in a wide variety of natural and processed foods. Starch is a polysaccharide. It is abundant in cereals (wheat, maize, rice), potatoes, and processed food based on cereal flour, such as bread, pizza or pasta.


Many such drugs are reversible competitive inhibitors that resemble the enzyme's native substrate, similar to methotrexate above; other well-known examples include statins used to treat high cholesterol, and protease inhibitors used to treat retroviral infections such as HIV. 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.


Other enzymes like hyaluronidase, lipase, collagenase, elastase, ribonuclease, deoxyribonuclease also play an important role in preventing the spread of infection and degradation of essential microbial biomolecules leading to cell death. It is possible for cells other than dedicated phagocytes (such as dendritic cells) to engage in phagocytosis. Some white blood cells in human immune system perform phagocytosis by gulping in some pathogenic and disease causing cells. Leukocytes generate hydrogen cyanide during phagocytosis, and can kill bacteria, fungi, and other pathogens by generating several other toxic chemicals.


allergiesallergicallergic reaction
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.

Lactobacillus rhamnosus

L. rhamnosusL. rhamnosus GGLactobacillus rhamnosus GG
The Lactobacillus rhamnosus and L. reuteri species are most commonly found in the healthy female genito-urinary tract and are most helpful to supplement in order to regain control over dysbiotic bacterial overgrowth during an active infection. L. rhamnosus sometimes is used in yogurt and dairy products such as fermented and unpasteurized milk and semi-hard cheese. While frequently considered a beneficial organism, L. rhamnosus may not be as beneficial to certain subsets of the population; in rare circumstances, especially those primarily involving weakened immune system or infants, it may cause endocarditis.


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.


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.


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.


The Fc receptors are isotype-specific, which gives greater flexibility to the immune system, invoking only the appropriate immune mechanisms for distinct pathogens. Humans and higher primates also produce "natural antibodies" that are present in serum before viral infection. Natural antibodies have been defined as antibodies that are produced without any previous infection, vaccination, other foreign antigen exposure or passive immunization. These antibodies can activate the classical complement pathway leading to lysis of enveloped virus particles long before the adaptive immune response is activated.


Chronic inflammation has been hypothesized to directly cause mutation. Inflammation can contribute to proliferation, survival, angiogenesis and migration of cancer cells by influencing the tumor microenvironment. Oncogenes build up an inflammatory pro-tumorigenic microenvironment. Some hormones play a role in the development of cancer by promoting cell proliferation. Insulin-like growth factors and their binding proteins play a key role in cancer cell proliferation, differentiation and apoptosis, suggesting possible involvement in carcinogenesis.

Pasteur Institute

Institut PasteurHellenic Pasteur InstitutePasteur Institute of Paris
Yersin looked for the germ responsible for the infection specifically in these plague-spots, tumors caused by the inflammation of the lymphatic glands which become black because of the necrosis of the tissue. After many microscopic exams he was able to state that in most of the cases the bubonic plague bacterium was located in these buboes; but in the meanwhile the Japanese scientist Kitasato also declared that he had isolated the bacterium, even though the description he provided was dissimilar to the one given by Yersin.