Acinetobacter junii is rarely a cause of disease in humans. A. junii has mainly been associated with bacteremia in preterm infants and pediatric oncologic patients. Acinetobacter junii is one of more than 50 different species belonging to the genu

Actinobacteria is one of the largest bacterial phyla, comprised of Gram-positive bacteria.

Actinomycetales are considered low abundance colonizers of the gastrointestinal tract with primary residence on the skin.

Adenoviruses are non-enveloped DNA viruses. Adenovirus is a cause of acute gastroenteritis in infants, young children, the elderly and immuno-compromised patients. The Adenovirus serotypes most frequently associated with gastroenteritis are Adenov

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.

- Alistipes does not contribute significantly to short chain fatty acid production. - A diet rich in animal protein and fat increases the abundance of Alistipes. - High abundance of Alistipes was identified as a possible predictor of successful

Alistipes does not contribute significantly to short chain fatty acid production. A diet rich in animal protein and fat increases the abundance of Alistipes. High abundance of Alistipes was identified as a possible predictor of successful weight loss

Ascaris is a worm that infects the small intestine, but its life cycle includes migration through the circulation to the heart and lungs, and into the oropharynx. Infection is acquired through the ingestion of embryonated eggs in contaminated soil or

The phylum Firmicutes constitutes the most diverse and abundant group of gastrointestinal microbiota which are grouped into four classes, Bacilli, Clostridia, Erysipelotrichi, and Negativicutes. They make up approximately 39% of the gut microbiota, o

Imbalanced bacteria are usually neither pathogenic nor beneficial to the host GI tract. Imbalances can occur when there are insufficient levels of beneficial bacteria and increased levels of commensal bacteria. Certain commensal bacteria are reported

Species in the genus Bacteroides carry out broad metabolic functions, including degradation of complex plant polysaccharides, proteolytic activities, de-conjugation of bile acids, mucosal barrier integrity, short chain fatty acid production, fatty ac

Bacteroides pectinophilus contributes to breakdown of dietary pectins which are prebiotics. Pectins are complex, plantderived carbohydrates that are indigestible by human enzymes, but can be easily degraded by certain commensal bacteria in the gut.

Species in the genus Bacteroides carry out broad metabolic functions, including degradation of complex plant polysaccharides, proteolytic activities, de-conjugation of bile acids, mucosal barrier integrity, short chain fatty acid production, fatty ac

The predominant genera in the human colonic microbiota are Bacteroides and Prevotella, which belong to the major phyla Bacteroidetes.

Species in the genus Bacteroides carry out broad metabolic functions, including degradation of complex plant polysaccharides, proteolytic activities, de-conjugation of bile acids, mucosal barrier integrity, short chain fatty acid production, fatty ac

Bacteroides zoogleoformans is part of the Bacteroides genus. Species in the genus Bacteroides carry out broad metabolic functions, including: - degradation of complex plant polysaccharides, - proteolytic activities (=the breakdown of prote

Considered amongst the most beneficial commensal bacteria in the human gut, Bifidobacterium spp. are able to degrade monosaccharides, galacto-, manno-, and fructo-oligosaccharides, as well as some complex carbohydrates. Many of the non-digestible oli

Most Campylobacter infections in industrialized countries are caused by C. jejuni, C. coli, and C. lari with an estimated 1.5 million cases of foodborne illness due to Campylobacter per year in the US. Campylobacter spp. are responsible for approxima

Simple sugars are absorbed in the small intestine and should not be appreciably present in the colon because they are a primary energy source for pathogenic or dysbiotic bacteria and yeast.

Consumption of a Western diet has been shown to increase Catenibacterium mitsuokai in the human gut microbiota. Catenibacterium mitsuokai ferments glucose, mannose, galactose, fructose, sucrose, maltose, cellobiose, lactose and salicin in the prod

Charcot-Leyden crystals are formed from the breakdown of immune cells, especially eosinophils, and may be seen in the stool of patients with parasitic diseases. The crystals are indicative of immune response and can sometimes be seen in association w

Citrobacter spp., a gram-negative bacterium and member of the Enterobacteriaceae family, is considered dysbiotic at 3+ or greater. Citrobacter freundii complex (including C. freundii, C. braakii, C. gullenii, C. murliniae, rodentium, C. wermanii, C.

Citrobacter spp., a gram-negative bacterium and member of the Enterobacteriaceae family, is considered dysbiotic at 3+ or greater. Citrobacter freundii complex (including C. freundii, C. braakii, C. gullenii, C. murliniae, rodentium, C. wermanii,

This trematode infects the bile ducts. Infection occurs through consumption of encysted metacercariae in raw, dried, or pickled fish imported from endemic areas, which include Japan, Korea, China, Taiwan, and Vietnam. Light infection is usually as

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.

C. difficile may cause diarrhea following the production of two toxins, enterotoxin A and cytotoxin B. C. difficile is the most common cause of nosocomial infectious diarrhea in developed countries and is the major cause of antibiotic-associated

Appropriate digestion and metabolism of complex dietary carbohydrates from plants drives healthy diversity in the gut microbiota. Clostridium methylpentosum ferments the naturally occurring sugar L-rhamnose that is released by microbial breakdown of

Stool is normally brown because of pigments formed by bacteria acting on bile introduced into the digestive system from the liver. While certain conditions can cause changes in stool color, many changes are harmless and are caused by pigments in food

Stool normally contains about 75% water and ideally should be formed and soft. Stool consistency can vary based upon transit time and water absorption.

Coprobacillus cateniformis ferment glucose and other common sugars primarily to acetic and lactic acid, and to a lesser extent butyrate and valerate.

The Cryptosporidium parasite causes disease in humans through ingestion of infectious oocysts in contaminated water or food, and by direct contact with fecal material from individuals or animals actively shedding oocysts. Two species of Cryptosporidi

Dialister invisus is generally considered an endodontic pathogen (Endo is the Greek word for inside and odont is Greek for tooth). Dialister invisus is often associated with periodontitis, caries, halitosis, and endodontic in

Dialister invisus is generally considered an endodontic pathogen (Endo is the Greek word for inside and odont is Greek for tooth). Dialister invisus is often associated with periodontitis, caries, halitosis, and endodontic in

D. fragilis infects the large intestine. This parasite does not have a cyst stage, and cannot survive long outside the body alone. It may be spread in pinworm (Enterobius vermicularis) eggs. Infection is common worldwide, including in the United Stat

Dorea is a genus within the Lachnospiraceae family that is in the Firmicutes phylum. Dorea species are known to produce hydrogen and carbon dioxide as end-products of glucose fermentation and may be associated with bloating.

Elastase is a pancreatic enzyme that digests and degrades a number of proteins. A finding of low elastase in a formed stool specimen is an indicator of pancreatic exocrine insufficiency. Moderate pancreatic insufficiency is defined at 100-200 μg/m

Entamoeba histolytica is a protozoan parasite that infects an estimated 34 to 50 million people per year worldwide, and kills 100,000 individuals annually. The disease caused by E. histolytica, amebiasis, is common in tropical areas with poor sanitar

Enterobacter cloacae complex is part of the Enterobacteriaceae family. E cloacae complex is a group of six closely related species with similar resistance patterns: E. cloacae, E. asburiae, E. hormaechei, E. kobei, E. ludwigii, and E. nimipressura

Enterobacteriaceae is a large family of bacteria within the Proteobacteria phyla. Enterobacteriaceae is inclusive of normal commensal species, harmless opportunists, and many of the more familiar pathogens, such as Salmonella, Escherichia coli, Klebs

This nematode inhabits the large intestine and migrates to the anus at night, where it deposits eggs on the perianal surface. Pinworm is the most common worm infection in the United States. School-age children, followed by preschoolers, have the high

ETEC is a major cause of traveler’s diarrhea in adults in industrialized countries and a leading cause of infant diarrhea in developing countries. ETEC is estimated to cause 200 million episodes of diarrhea and approximately 380,000 deaths in c

E. coli O157 is a member of the pathogenic enterohemorrhagic E. coli strains (also known as verocytotoxin producing or Shiga-toxin producing E. coli (STEC)), and is an uncommon but serious cause of gastroenteritis. Infection with E. coli O157 often c

Eubacterium hallii and Eubacterium rectale are both part of the Lachnospiraceae family that is in the Firmicutes phylum.

Faecalibacterium prausnitzii is one of the most abundant butyrate producing bacteria in a healthy gastrointestinal tract.

Individuals who have pancreatic insufficiency secondary to pancreatic or biliary tract disease may be unable to efficiently digest and absorb fat normally. The microscopic fecal fat test is a reliable marker for fat malabsorption, and evaluation enzy

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 mic

G. duodenalis, a single celled protozoa, is the most frequent cause of non-bacterial diarrhea in the United States. The Centers for Disease Control and Prevention (CDC) estimates as many as 2.5 million cases of Giardia infection occur annually in the

The adult nematodes attach to the wall of the small intestine and suck blood. The hookworm life cycle also includes migration through the circulation to the heart and lungs, and into the oropharynx. Infection occurs when larvae from fecally-contamina

Iodamoeba buetschlii is considered nonpathogenic or commensal. Infection occurs via fecal-oral route, and indicates increased risk of exposure to potential pathogens.

Klebsiella spp. are gram-negative bacilli belonging to the Enterobacteriaceae family and closely related to the genera Enterobacter and Serratia. Klebsiella spp. are considered dysbiotic in the amount of 3 - 4 +. Klebsiella spp. are widely distribute

Klebsiella spp. are gram-negative bacilli belonging to the Enterobacteriaceae family and closely related to the genera Enterobacter and Serratia. Klebsiella spp. are widely distributed in nature and in the gastrointestinal tract of humans. In humans,

The Lachnospiraceae family is a diverse group of butyric acid producers, which have been associated with beneficial microbial and epithelial cell growth. Consumption of a Mediterranean diet decreased levels of species belonging to Lachnospiraceae.

Decreased and normal levels of Lactobacillus spp. have been reported in patients with irritable bowel syndrome. Lactobacillus spp. abundance was shown to be lower in the active phase of ulcerative colitis. Lactobacillus levels were shown to be increa

Lactobacillus species is a type of bacteria. There are lots of different species of lactobacillus. Lactobacillus bacteria are commonly found in the human gut, mouth and vagina. They are considered generally as “good bacteria”

The presence of mucus in the stool may be due to prolonged irritation to the intestinal mucosa and may be secondary to a proliferation of gastrointestinal enteropathogens such as bacteria, yeast, or parasites. It can also be associated with an inflam

Muscle fibers in the stool are an indicator of incomplete digestion. Bloating, flatulence, feelings of “fullness” may be associated with increase in muscle fibers. The presence of muscle fibers in the stool is an indicator of incomplet

Mycoplasma hominis is from the Tenericutes phylum. Tenericutes are cell wall-less bacteria that do not synthesize precursors of peptidoglycan. Tenericutes consist of four main clades designated as the Acholeplasma, Spiroplasma, Pneumoniae and Homi

Norovirus affects people of all ages causing 19 to 21 million illnesses in the US per year. It is the leading contributor to acute gastroenteritis (AGE) across all age groups. While infections can occur year-round, Norovirus outbreaks tend to peak in

In many cases, a positive occult blood results from gastrointestinal bleeding from the upper small intestine or higher. Gastric ulceration could, for example, result in a finding of occult blood rather than blood in the feces. However, a positive fin

The abundance of Parabacteroides spp., major anaerobic producers of acetate and succinate is increased with a high fat diet and is positively correlated with body weight. Parabacteroides spp., along with certain Bacteroides spp., have been shown to d

The abundance of Parabacteroides spp., major anaerobic producers of acetate and succinate is increased with a high fat diet and is positively correlated with body weight. Parabacteroides spp., along with certain Bacteroides spp., have been shown to d

P. hominis is considered nonpathogenic or commensal. It lives in the large intestine. Exposure occurs via fecal-oral route, and indicates increased risk of exposure to potential pathogens.

Phascolarctobacterium faecium can produce short-chain fatty acids, including acetate and propionate, and may be associated with metabolic effects and mental state of the host.

Proteobacteria (phylum) Proteobacteria include a wide variety of pathogens, including species within the Escherichia, Shigella Salmonella, Vibrio, and Helicobacter genera. The phylum includes a number of species that are permanent residents of the

Red Blood Cells (RBC) in the stool may be associated with a parasitic or bacterial infection, or an inflammatory bowel condition such as ulcerative colitis. Colorectal cancer, anal fistulas, and hemorrhoids should also be ruled out.

Rotaviruses are classified into seven serogroups (A-G); however, only groups A, B, and C are human pathogens. The Group A Rotaviruses are responsible for the majority of infections. Globally, Rotavirus is estimated to cause more than 125 mill

Imbalanced bacteria are usually neither pathogenic nor beneficial to the host GI tract. Imbalances can occur when there are insufficient levels of beneficial bacteria and increased levels of commensal bacteria. Certain commensal bacteria are reported

Members of Ruminococcus sensu produce acetate, but not butyrate. Ruminococcus gnavus, like Akkermansia muciniphila is a mucin degrading specialist. HIGHER LEVELS: - Higher levels of Ruminococcus spp. were associated with non-alcoholic fatty liv

Members of Ruminococcus sensu produce acetate, but not butyrate. Ruminococcus gnavus, like Akkermanisia muciniphila is a mucin degrading specialist. 

Salmonella are facultative anaerobic bacteria in the family of Enterobacteriaceae. There are two species of Salmonella, Salmonella enterica and Salmonella bongori that include over 2,600 different serotypes. The majority of the pathogenic serotypes o

Fecal Secretory IgA is a marker of gut secretory immunity and barrier function. Immunoglobulin A (IgA) is an antibody playing a critical role in mucosal immunity and is produced in greater quantities than all other types of antibody combined. I

E. coli are a diverse group of bacteria that normally live in the intestines of humans and animals. Although most strains of these bacteria are harmless, some produce toxins that can make you sick and cause diarrhea (loose stool/poop) such as Sh

Shigella spp. are non-sporulating bacteria that belong to the family Enterobacteriaceae. Shigella infections account for 5% to 20% of all diarrheal episodes throughout the world, and although these infections are commonly seen in children younger tha

Streptococcus agalactiae, also known as Lancefield’s group B streptococcus (GBS), is a gram-positive facultative anaerobe. Found in around 30% of healthy adult gastrointestinal tracts and vaginas, it can cause severe infections. The bacterium i

Imbalanced bacteria are usually neither pathogenic nor beneficial to the host GI tract. Imbalances can occur when there are insufficient levels of beneficial bacteria and increased levels of commensal bacteria. Certain commensal bacteria are reported

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, n

Higher abundance of S. salivarius and S. thermophilus (Firmicutes phylum) have been associated with a moderate to severe disease course in newly diagnosed ulcerative colitis (UC) patients. These findings are in accordance with a study that showed

Higher abundance of S. salivarius and S. thermophilus (Firmicutes phylum) have been associated with a moderate to severe disease course in newly diagnosed ulcerative colitis (UC) patients.

Higher abundance of S. salivarius and S. thermophilus (Firmicutes phylum) have been associated with a moderate to severe disease course in newly diagnosed ulcerative colitis (UC) patients. These findings are in accordance with a study that showed tha

Higher abundance of S. salivarius and S. thermophilus (Firmicutes phylum) have been associated with a moderate to severe disease course in newly diagnosed ulcerative colitis (UC) patients. These findings are in accordance with a study that showed tha

Higher abundance of S. salivarius and S. thermophilus (Firmicutes phylum) have been associated with a moderate to severe disease course in newly diagnosed ulcerative colitis (UC) patients. These findings are in accordance with a study that showed tha

Strongyloides infects the duodenum and jejunum, but its life cycle also includes migration through the lungs. Infection occurs when larvae penetrate the skin of humans or are passed via the fecal-oral route. Strongyloidiasis is endemic throughout th

These cestodes usually infect the intestinal tract, but Taenia solium may also invade the CNS. Transmission is by ingesting cysts in raw or undercooked meat. Taenia solium transmission may also occur via the fecal-oral route, which increases chance o

T. trichiura is a nematode that infects the large intestine. Infection is spread via the fecal-oral route. The parasite is found principally in the tropics and subtropics. Mild asymptomatic infections are common in rural parts of the southeastern USA

Vegetable fibers in the stool may be indicative of inadequate chewing, or eating “on the run”.

Veillonella are anaerobic, gram-negative cocci, part of the normal flora of the mouth, gastrointestinal tract, and vaginal tract.

Vibrio cholerae is one of the most common causes of diarrhea worldwide. While diarrhea associated with V. cholerae is predominately seen in the Indian subcontinent, South East Asia, Africa, and South America, sporadic cases of V. cholerae-induced dia

White Blood Cells (WBC) and Mucus in the stool can occur with bacterial and parasitic infections, with mucosal irritation, and inflammatory bowel diseases such as Crohn’s disease or ulcerative colitis. Elevated levels of WBCs in the stool ar

Yeast may normally be present in small quantities on the skin, in the mouth and intestine. While small quantities of yeast may be normal, yeast observed in higher quantities is considered abnormal.