The health of your gut plays a significant role in your overall health. It goes beyond digestion. Your gut impacts every system in your body. And, the microbiome is connected to your immune system, mental health, metabolism, and much more. An imbalance in your microbiome with overgrowth of pathogens can contribute to the development of chronic symptoms.
The best method to determine the overall health of your microbiome is to have a comprehensive stool analysis. It helps to identify intestinal health markers, potential autoimmune triggers, dysbiotic flora, normal flora, viral pathogens, parasitic pathogens, and bacterial pathogens.
The importance of the microbiome
Your gut has a diverse community of bacteria. The wide variety of bacteria constitutes your microbiome, which plays a key role in your health. A healthy microbiome has good diversity, balance, and a good supply of beneficial bacteria. It is a foundation for the entire body.
However, if your gut microbiome lacks diversity and has too many harmful bacteria and other pathogens, it has an imbalance of bacteria, which is called dysbiosis. This can increase the risk of inflammation, autoimmune disorders, and other health issues.
How does dysbiosis develop?
Dysbiosis has a number of contributing factors: poor diet lacking in nutrient-dense whole foods and high in processed, artificial food, poor sleep, lack of exercise, poor hydration, excessive stress, and high exposure to toxins. Other factors include poor stomach acid, food sensitivities, poor bile flow, and pathogen overgrowth. If you are experiencing symptoms, testing your gut microbiome will help pinpoint pathogen overgrowth, intestinal health markers, and underlying health issues.
What is the GI MAP?
A comprehensive stool analysis offers a detailed picture of your gut health. Conventional GI physicians pay little attention to diet and lifestyle and typically rely on drugs and surgery to relieve digestive problems. Many natural and holistic health doctors suggest herbs and probiotics to improve your gut microbiome. Still, unless you have an analysis to identify the problems, you won’t know which herbs or probiotics are the right ones. And, you won’t be able to determine if progress has been made. Let’s take a look at what a comprehensive stool analysis shows.
Pathogens
A good stool analysis will identify bacterial, parasitic, and viral pathogens. These commonly cause abdominal pain, diarrhea, bloating, vomiting, and other digestive problems. Some will clear up themselves, but others may last longer causing acute symptoms. For instance, salmonella, clostridium difficile, and a few other pathogens, for example, may lead to reactive arthritis.
A 2008 study published in the Emergency Infectious Diseases showed that bacterial gastrointestinal infections can have both short- and long-term effects. For example, campylobacter infections may increase your risk of ulcerative colitis one year after the original infection occurred. This is why it is important to look for potential pathogens and address them.
Let’s look at what bacterial, viral, and parasitic pathogens a stool analysis can identify.
Bacterial Pathogens
- Campylobacter: It may cause abdominal pain, diarrhea, malaise, and fever
- Clostridium difficile, Toxin A & Toxin B: It may cause inflammation, cramping, fever, diarrhea, and abdominal pain, and may result in reactive arthritis.
- Enterohemorrhagic E. coli (EHEC): It may cause abdominal cramping, fever, fatigue, diarrhea, and nausea
- E. coli: It may cause severe abdominal cramps and diarrhea
- Entroinvasive E. coli (EIEC)/Shigella: It may cause diarrhea, vomiting, fever, chills, abdominal cramping, and fatigue, as well as reactive arthritis
- Enteropathogenic E. coli (EPEC): It may cause bloody and watery diarrhea
- Enterotoxigenic E. coli: It causes diarrhea
- Shiga-like Toxin E. coli (STEC): It may cause abdominal cramps and diarrhea
- Salmonella: It causes vomiting, fever, and severe diarrhea
- Vibrio cholerae: It may cause watery diarrhea, vomiting, thirst, low blood pressure, rapid heart rate, dry mucous membranes, irritability, and restlessness
- Yersinia enteocolicia: It may cause vomiting, fever, diarrhea, and abdominal pain, possibly mimicking Crohn’s disease, and may trigger autoimmune thyroiditis or inflammatory arthritis
Parasitic pathogens
- Cryptosporidium: It can cause diarrhea and reactive arthritis
- Entamoeba histolytica: It may cause diarrhea, dysentery, and fulminant colitis
- Giardia: It can cause diarrhea, cramps, bloating, intestinal malabsorption, malnutrition, weight loss, and steatorrhea
Viral pathogens
- Adenovirus 40/41: It can cause watery diarrhea, fever, and gastroenteritis
- Norovirus GI/GII: It can cause nausea, diarrhea, vomiting, fatigue, abdominal cramps, headaches, and fever.
- Helicobacter pylori (H. pylori) It may cause abdominal pain, vomiting, nausea, peptic ulcers, and other gastrointestinal issues
Normal bacteria
Your microbiome consists of literally trillions of microorganisms. Many are normal that help your body function well. They help protect you from pathogens, extract nutrients, support the gut barrier function, and produce vitamins.
Bacteria have cell walls for strength and protection. The walls have a layer called peptidoglycan, which is a polymer made of sugar mesh and amino acids. Bacteria can be gram-positive or gram-negative depending on the properties of the cell walls.
Gram-positive bacteria have a thick cell wall of about 30 layers of peptidoglycan surrounding the monoderm. Gram-negative bacteria have a thin layer found between diderms. While both gram-positive and gram-negative can be harmful bacteria, gram-negative ones are more resistant to antibodies. A 2017 study published in Frontiers in Immunology found that gram-positive probiotics are more effective against infections and more protective of your immunity.
Beneficial bacteria
- Akkermansia muciniphila: This bacteria is a mucus degrader that helps to support mucus production and mucosal health.
- Bacteroides fragilis: This gram-negative bacteria is important for microbial balance and neuroimmune health.
- Bifidobacterium spp.: This is a gram-positive bacteria found in breast milk that helps to colonize the gut at and after birth.
- Clastridia: This is an important bacteria in the large intestine that helps to protect the gut from pathogens, support immune balance, and promote a healthy mucosal barrier.
- Enterococcus spp.: This is a gram-positive lactate-producing bacteria.
- Faecalibacterium prausnitzii: This bacteria supports anti-inflammatory processes and mucosal health and homeostasis.
- Lactobacillus spp: This a lactate-producing bacteria often found in probiotics
- Enterobacter spp: This is a gram-negative bacteria closely related to E. coli.
Opportunistic bacteria
A comprehensive stool analysis should also identify opportunistic pathogens that may cause
inflammation, chronic symptoms, illness, and disease. Symptoms like abdominal pain, loose stools, diarrhea, and constipation are common when these opportunistic bacteria are present in high amounts. Overgrowth of opportunistic bacteria can be a greater problem if you consume a poor diet, use antibiotics, have a compromised immune system, or have a fungal or parasitic infection.
Additional overgrowth or dysbiosis:
- Bacillus spp.: High levels may be connected to constipation, SIBO, and other digestive issues
- Enterococcus faecalis, Enterococcus faecium: High levels may occur due to SIBO, constipation, or other digestive issues, as well as antibiotic use
- Methanobacteriaceae: High levels occur with SIBO, IBS, and chronic constipation, and low levels may be linked to inflammation or low short-chain fatty acid production
- Morganelia spp. High levels may mean inflammation and may lead to diarrhea or SIBO
- Pseudomonas spp., Pseudomonas aeruginosa: High levels may occur due to inflammation and lead to loose stools and cramping
- Staphylococcus spp, Staphylococcus aureus: High levels may cause inflammation. Certain strains may cause diarrhea due to toxins
- Streptococcus spp.: High levels may occur because of low stomach acid, SIBO, constipation, or inflammation
Potential autoimmune triggers
- Citrobacter spp, Citrobacter freundii:. High levels may mean high inflammation in the gut and may be linked to rheumatoid arthritis
- Fusobacterium spp: High levels are associated with inflammation and autoimmunity (1). Klebsiella spp., Klebsiella pneumoniae: It can lead to abdominal pain, bloating, gas, and diarrhea, or symptoms of inflammatory bowel disease.
- Mycobacterium avium subsp. Paratuberculosis: High levels of this bacteria have been linked to rheumatoid arthritis and Crohn’s disease
- Prevotella capri: They have been linked to rheumatoid arthritis
- Proteus spp.m Proteus mirabilis: High levels may mean inflammation in the gut and may lead to diarrhea or loose stools
Parasites
Typically, parasites enter a body through contaminated food and drink. Some are non-pathogenic, but most are not and live inside your gastrointestinal tract. Parasitic infections can lead to bloating, gas, constipation, diarrhea, digestive issues, chronic pain, fatigue, headaches, depression, and other symptoms. Parasite overgrowth can cause inflammation, cravings, and gut dysbiosis.
Protozoa
Blastocystis hominis: It causes abdominal pain, diarrhea, nausea, vomiting, fatigue, fever, symptoms of IBS, and infective arthritis .
Chilomastix mesnili: It causes diarrhea, cramping, abdominal pain, nausea, vomiting, and weight loss
Dientamoeba fragilis: It causes diarrhea, nausea, vomiting, abdominal pain, fatigue, fever, loss of appetite, and weight loss, but may also be asymptomatic
Endolimax nana: It is often asymptomatic but may cause gut dysbiosis
Entamoeba coli: It may cause gut dysbiosis
Pentatrichomonas hominis: It is usually asymptomatic but may cause gut dysbiosis
Worms
- Ancylostoma duodenale and Necator americanus (hookworm): It may cause rashes or itching, then may lead to abdominal pain, fatigue, diarrhea, weight loss, loss of appetite, iron-deficiency anemia, and coughing
- Ascaris lumbricoides (roundworm): It may cause fever, coughing, and wheezing, and later may lead to abdominal pain, nausea, vomiting, dry cough, pancreatitis, and appendicitis
- Trichuris trichiura (whipworm): It often remains asymptomatic but may cause diarrhea with mucus or blood
- Taenia spp. (tapeworm): It may remain asymptomatic but may also cause abdominal pain, constipation, nausea, headaches, weakness, diarrhea, anemia, loss or increased appetite, hyperexcitability, and pruritus ani
In addition, a comprehensive stool analysis should provide detailed information on intestinal health markers, digestion, GI markets, gut mucosal and immune health, gut inflammation markers, and some genetic markers.
Final thoughts
Your gut health plays a critical role in your overall health. Your gut microbiome health is connected to your immune system, metabolism, mental health, and other areas. Imbalance in your microbiome and various pathogen overgrowth may contribute to the development of autoimmune and other chronic health issues.
A comprehensive gut test helps identify bacterial pathogens, parasitic pathogens, viral pathogens, normal flora, dysbiotic flora, potential autoimmune triggers, and all intestinal health markers. This will enable your functional doctor to develop a specific treatment plan to rebalance your gut and improve your health naturally.