GI-MAP by Diagnostic Solutions

Adenovirus serotypes 40 and 41 cause acute gastroenteritis (inflammation of the stomach and intestines) primarily in children.

Akkermansia muciniphila may represent 3–5% of the microbial composition in the healthy human intestinal tract, and have a crucial role in the regulation of the gut barrier and other homeostatic and metabolic functions.

The distribution of hookworm (Necator americanus and Ancylostoma duodenale) is worldwide, with particular prevalence in rural areas of the moist tropics where there is inadequate sanitation and people walk barefoot. The two species produce indistinguishable thin-walled eggs that hatch in soil. Infection is usually acquired by walking barefoot in soil contaminated with human faeces. The larvae undergo several moults before infective larvae are produced.

Antigliadin antibodies (AGAs) are antibodies of the IgA and IgG classes found in the serum of celiac disease patients. These antibodies mainly target gliadin-derived peptides, which are the main proteins of gluten. AGAs are not specific for celiac disease as they are also found in patients with other gastrointestinal diseases such as gastritis, gastroenteritis, and IBD.

Ascaris lumbricoides, an intestinal roundworm, is one of the most common helminthic human infections worldwide.

Ascaris lumbricoides is the largest intestinal nematode of man. The female worms are larger than the males and can measure 40 cm in length and 6 mm in diameter. They are white or pink and are tapered at both ends. 

Beta-glucuronidase is an enzyme that breaks the tight bond between glucuronic acid and toxins in the intestines. The liver and intestine bind toxins, steroid hormones and some dietary components to glucuronic acid. That is a protective process that limits absorption and enterohepatic reabsorption of toxins, and enhances excretion. A high level of activity of Beta-glucuronidase in the gut is not desirable. A low level of Beta-glucuronidase activity is not known to be of any direct clinical consequence.

Bacillus spp. are spore forming bacteria, ubiquitous in the environment. B. cereus in particular is a frequently recognized cause of toxin-induced acute gastroenteritis.

Other infections caused by this genus include:

- sepsis

- pneumonia

- endocarditis

- central nervous system (CNS) and ocular infections

Gram-negative species of the Bacteroidetes phylum. Immune-modulating normal gut species. Believed to be involved in microbial balance, barrier integrity, and neuroimmune health (Hsiao 2013). High levels may result from reduced digestive capacity or constipation. Low levels may contribute to reduced anti-inflammatory activity in the intestine.

Bacteroidetes are the most prominent gut microbes in much of the world. They are thought to help protect against obesity because they do not digest fat well.

Gram-positive genus in the Actinobacteria phylum. Present in breast milk. Colonizes the human GI tract at birth. Common in probiotics. Thrives on a wide variety of prebiotic fibers.

Blastocystis hominis is found throughout the world in both people with and without symptoms. It is a non-pathogenic parasite. Non-pathogenic parasites are present in the gastrointestinal tract and generally are self-limiting and do not cause illness. However, some research shows an association between non-pathogenic parasites and gastrointestinal symptoms.

C. difficile is an opportunistic anaerobic bacterium which causes symptoms ranging from mild diarrhea to pseudomembranous colitis when the normal flora has been altered (as in antibiotic use).

C. difficile produces two toxins:

- Toxin A is a tissuedamaging enterotoxin,

- while toxin B is referred to as a cytotoxin.

Calprotectin is a calcium-binding protein with antimicrobial properties. It accounts for 60% of neutrophil cytosolic content and is also found in monocytes and macrophages. Calprotectin is released from the intestinal mucosa into the stool in intestinal inflammation. 

When people worry about eating undercooked chicken, they usually focus on getting sick from salmonella bacteria. But another common type of bacteria called campylobacter can also make you ill if you eat poultry that isn’t fully cooked.

Commensal fungi that can be pathogenic to immunocompromised patients. Causes vaginal yeast infections and can be fatal in systemic infections. May cause diarrhea. Has been suggested to cause a cluster of symptoms including GI complaints, fatigue, and muscle or joint pain but evidence is weak.

Commensal fungi that can be pathogenic to immunocompromised patients. Causes vaginal yeast infections and can be fatal in systemic infections. May cause diarrhea. Has been suggested to cause a cluster of symptoms including GI complaints, fatigue, and muscle or joint pain but evidence is weak.

Chilomastix mesnili is a nonpathogenic flagellate that is often described as a commensal organism in the human gastrointestinal tract.

Gram-negative bacteria in the Proteobacteria phylum.

Gram-negative bacteria in the Proteobacteria phylum. High levels may indicate increased intestinal inflammatory activity.

Autoimmune Association: Rheumatoid arthritis

Markers in this class are important producers of short-chain fatty acids, and have many well-documented roles in promoting a healthy intestinal barrier, immune balance, and protection against pathogens.

Cryptosporidium is notorious for being spread by swimming pools. A number of Cryptosporidium outbreaks have occurred after contamination of public swimming facilities. Cryptosporidium can cause gas, bloating, diarrhea, and abdominal pain. In a healthy, immune-competent person, this is a selflimiting infection and can be cleared within 2-3 weeks.

This parasite causes an intestinal infection called cyclosporiasis.

Epidemiology:

- Herpes virus that has infected 60% of the US population

- One in three children have contracted CMV by five years old

- Passed around in child daycare centers

Desulfovibrio is a genus of gram-negative sulphate-reducing bacteria. This genus has been positively correlated to IBD, colorectal cancer (in animal model), ulcerative colitis, liver disease and autism.

Desulfovibrio spp. is predominant member of Sulfate-reducing bacteria in human gut microbiota. Sulfate-reducing bacteria (SRB) are anaerobic microorganisms that conduct dissimilatory sulfate reduction to obtain energy, resulting in the release of a great quantity of sulfide. They are commonly isolated from environmental sources, but are also present in the digestive tract of animals and humans. 

Different species of Desulfovibrio: Desulfovibrio desulfuricans, Desulfovibrio piger, Desulfovibrio fairfieldensis Desulfovibrio legallii

The bacteria produce hydrogen sulfide (H2S), a metabolite which can influence cell signaling and reduce oxidative stress at low concentrations and pose toxicity at higher concentrations.

Dientamoeba fragilis is a parasite that lives in the large intestine of people. This protozoan parasite produces trophozoites; cysts have not been identified. The intestinal infection may be either asymptomatic or symptomatic.

Pancreatic elastase is an enzyme that digests protein. It’s only produced by the pancreas and when it is seen in the stool, it’s an excellent biomarker of how well the pancreas is performing.

Epidemiology:

- Fecal contamination of food or water

Clinical Implications:

- Considered non-pathogenic; individuals may be asymptomatic

- May be indicative of dysbiosis, conservative treatment may be indicated if clinical presentation is consistent with enteroparasitosis.

Entamoeba coli are intestinal amebae that are found in the large intestine. They generally are not considered pathogenic. However, when these amebae are found in stool samples it can indicate the presence of other potentially pathogenic organisms.

Entamoeba histolytica is a disease-causing parasite that can affect anyone, although it is more common in those who lived or travelled in tropical areas with poor sanitary conditions. Diagnosis can be difficult since, under a microscope, it looks similar to other parasites such as Entamoeba dispar and Entamoeba hartmanii. The latter two parasites generally do not cause illness.

Gram-negative genus in the Proteobacteria phylum. Closely related to E. coli (in the same taxonomic family). High levels may indicate increased intestinal inflammatory activity. Low levels may indicate reduced mucosal health.

Gram-positive species in the Firmicutes phylum. High levels may result from reduced stomach acid, PPI use, compromised digestive function, SIBO or constipation. High natural resistance to some antibiotics, which may result in overgrowth.

Gram-positive species in the Firmicutes phylum. High levels may result from reduced stomach acid, PPI use, compromised digestive function, SIBO or constipation. High natural resistance to some antibiotics, which may result in overgrowth.

Gram-positive genus of lactate-producing bacteria in the Firmicutes phylum. High levels may be due to reduced digestive capacity, constipation or small intestinal bacterial overgrowth. Low levels may indicate insufficiency of beneficial bacteria.

What is enterohemorrhagic E. coli?

Escherichia coli (or simply E. coli) is one of the many groups of bacteria that normally live in the intestines of healthy humans and most warm-blooded animals. E. coli bacteria help maintain the balance of normal intestinal bacteria against harmful bacteria.

However, there are hundreds of types or strains of E. coli bacteria. Different strains of E. coli have different characteristics.

One E. coli strain that causes a severe intestinal infection in humans is known as enterohemorrhagic E. coli (EHEC). It’s the most common strain to cause illness in people. It’s different from other E. coli because it produces a potent toxin called Shiga toxin. This toxin damages the lining of the intestinal wall, causing bloody diarrhea.

Eosinophil Activation Protein (EDN/EPX) is a protein released by activated eosinophils which has strong cytotoxic characteristics. 

Cytotoxic means that a substance or process can damage cells or cause them to die. "Cyto" means cell and "toxic" means poison.

The protein plays a significant role in a variety of inflammatory and mast-cell mediated pathologies in addition to fighting pathogens, particularly viral infections.

- One of the most common viruses worldwide; infects 90–95% of the population

- Commonly contracted in childhood and causes mild symptoms

- Gram-negative genus in the Proteobacteria phylum.

- Normal gut flora.

- Escherichia coli (E. coli) is the primary species in this genus.

- Most E. coli are nonpathogenic (pathogenic E. coli strains are measured separately).

Faecalibacterium prausnitzii is one of the most important bacteria in the human gut flora and makes up to 5-10% of the total number of bacteria detected in stool samples from healthy humans. Faecalibacterium prausnitzii has a crucial role in maintaining gut physiology and host wellbeing.

Gram-negative Bacteroidetes and grampositive Firmicutes are bacterial phyla that dominate the entire human digestive tract, including the mouth, nose, throat, and colon.2 An abnormal result in one or both of these phylum suggest imbalanced normal microbes in the GI tract. Further, high Firmicutes and low Bacteroidetes (resulting in a high F/B ratio) suggest microbial imbalance which may be related to increased caloric extraction from food, fat deposition and lipogenesis, impaired insulin sensitivity, and increased inflammation.

An abnormal result in one or both of these phylum suggest imbalanced normal microbes in the GI tract.

Gram-negative Bacteroidetes and grampositive Firmicutes are bacterial phyla that dominate the entire human digestive tract, including the mouth, nose, throat, and colon. 

Autoimmune Association: Systemic sclerosis or inflammatory bowel disease.

May cause disease in immunosuppressed patients. Low levels may be a dietary artefact; certain strains are used to make soft cheeses.

Giardia infection (giardiasis) is one of the most common causes of waterborne disease in the United States.

Helicobacter pylori (H. pylori) infection occurs when H. pylori bacteria infect your stomach. Helicobacter pylori has been evolving with human beings for well over 50,000 years, since they migrated out of Africa. H. pylori colonization has been implicated in a variety of gastroduodenal diseases.

Gram-negative bacteria in the Proteobacteria phylum. Common residents of the oral cavity and respiratory tract. May cause diarrhea, gas, abdominal pain, and bloating; Common after long-term antibiotic use; May release histamine in the gut; High levels may indicate increased intestinal inflammatory activity.

Klebsiella species are gram-negative bacteria normally found in the intestinal tract that are associated with a wide range of small intestinal disorders including:

- alterations of motility,

- diarrhea,

- gas,

- abdominal pain,

- and bloating.

Gram-positive genus of lactate-producing bacteria in the Firmicutes phylum. Many strains used as probiotics.

Bacterial species in the Actinobacteria phylum. Higher levels have been associated with Crohn’s disease and rheumatoid arthritis.

Family of bacteria-like microbes that produce methane. Facilitates carbohydrate fermentation and short-chain fatty acid production by beneficial bacteria. High levels linked to chronic constipation, as well as some types of SIBO and IBS. Low levels may indicate reduced production of short-chain fatty acids and may be associated with inflammation.

Gram-negative group in the Proteobacteria phylum. May produce histamine. High levels may indicate increased intestinal inflammatory activity. High levels may cause diarrhea, and may also be associated with SIBO.

Hookworms are soil-transmitted nematode parasites that can reside for many years in the small intestine of their human hosts; Necator americanus is the predominant infecting species.

Norovirus GI & GII, or Norwalk virus, is the most common cause of non-bacterial gastroenteritis in the world. It is widely known for causing the stomach flu on cruise ships. Three genotypes of this diverse virus, GI, GII, and GIV, can infect humans.

The fecal occult blood test (=FOBT) looks for blood in your feces. “Occult” (=hidden) means that the blood amount is so small that it cannot be seen with the naked eye. The bleeding does not change the color of the stool or result in visible bright red blood. Therefore, the blood is found only by testing the stool for blood in the laboratory.

Epidemiology:

Fecal contamination of food or water

Clinical Implications:

- Considered harmless, a non-pathogen

- Infected individuals are usually asymptomatic

- May contribute to dysbiosis

- Also colonizes dogs, cats, and other animals

Prevotella spp. is known for its ability to degrade complex plant polysaccharides (carbohydrates) and fiber.

Opportunistic Bacteria associated with Autoimmunity. 

Gram-negative bacteria in the Proteobacteria phylum. High levels may indicate increased intestinal inflammatory activity; May contribute to loose stools or diarrhea; Pets or wild animals can be a source

Gram-negative bacteria in the Proteobacteria phylum. High levels may indicate increased intestinal inflammatory activity; May contribute to loose stools or diarrhea; Pets or wild animals can be a source.

- Gram-negative bacteria in the Proteobacteria phylum.

- Pseudomonas aeruginosa are normal flora in the human gastrointestinal (GI) tract, which on occasion cause GI tract infection.

Gram-negative bacteria in the Proteobacteria phylum. High levels may indicate increased intestinal inflammatory activity and may cause abdominal cramping and loose stools. Some strains of P. aeroginosa may produce toxins that can damage cells.

- Common in soil, plants, bathrooms, and in beverages like milk, juice, and water. 
- May be a commensal (=living in a relationship in which one organism derives food or other benefits from another organism without hurting or helping it). 
- Can cause disease in immunosuppressed patients.

A genus of Gram-positive anaerobic bacteria in the Clostridia class that inhabit the human colon. The Roseburia genus has five well-characterized species, all of which produce short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate. Roseburia can also produce butyrate from acetate promoting balance in energy homeostasis. The genus is widely recognized to influence colonic motility, support immunity, and suppress inflammation.

As the most abundant class of antibody found in the human intestinal lumen, secretory IgA (sIgA) is recognized as a first line of defense in protecting the intestinal epithelium from enteric pathogens and toxins. It is used to assess gastrointestinal barrier function.

Epidemiology

- Fecal contamination of ingested foods (undercooked meat, unpasteurized milk, juice, and water)

Clinical Implications

- Symptoms may include severe abdominal cramps and diarrhea

- Toxins may elicit strong inflammatory response

Gram-positive bacteria in the Firmicutes phylum. High levels may result from reduced digestive capacity, and intestinal inflammatory activity. Some strains may produce toxins and contribute to loose stools or diarrhea.

Gram-positive bacteria in the Firmicutes phylum. High levels may result from reduced digestive capacity, and intestinal inflammatory activity. Some strains may produce toxins and contribute to loose stools or diarrhea.

The steatocrit is a measure of the amount of fat in stool.

Streptococcus is a member of Gram-positive lactic acid-producing bacteria (LAB) that belonged to Firmicutes phylum. Many strains of Streptococcus are non-pathogenic and occur as commensal flora on the skin, the oral cavity, nasopharynx, upper respiratory tract, urogenital, and gastrointestinal tracts.

Taeniasis in humans is a parasitic infection caused by the tapeworm species Taenia saginata (beef tapeworm), Taenia solium (pork tapeworm), and Taenia asiatica (Asian tapeworm).

Humans can become infected with these tapeworms by eating raw or undercooked beef (T. saginata) or pork (T. solium and T. asiatica). People with taeniasis may not know they have a tapeworm infection because symptoms are usually mild or nonexistent.

Taenia solium tapeworm infections can lead to cysticercosis, which is a disease that can cause seizures, so it is important to seek treatment.

Epidemiology:

- Fecal contamination of produce or person-to-person contact

- Prevalent in Asia, Africa, South America, and rural southeastern United States

H. pylori virulence factor OipA (Outer Inflammatory Protein A) - associated with gastric cancer and peptic ulcer.

Zonulin is a protein that opens intercellular tight junctions in the gut lining (the connections between epithelial cells that make up the gastrointestinal lining). Zonulin increases intestinal permeability in the jejunum and ileum and is considered a biomarker for barrier permeability.