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Purpose of running this test:

A key factor in multi-factorial conditions is the infectious disease burden you have in your body. In addition to blood testing for antibody titers for a range of bacterial and viral conditions, there are stool tests that can detect what organisms, normal and pathogenic, are present in your gastrointestinal (GI) tract.

Stool analysis tests can give you an indication of the bacterial and yeast load in your GI tract. My preference is to run more than one GI stool test simultaneously because various tests give related but non-identical information. The Comprehensive Stool Analysis does not limit the organisms it allows to grow. It reports any organisms that grow in a given amount of time. This is a useful tool for detecting a range of non-optimal organisms that may be growing in your gut.

But a Comprehensive Stool Analysis may not pick up very slow growing or oxygen sensitive organisms. Tests that use a DNA probe or include saliva based antibody screens often detect very small numbers of slow growing organisms. This is excellent for determining if slow growing organisms are an issue even if they did not grow on the Comprehensive Stool Analysis. However, DNA probe tests or saliva antibody markers only look for a limited number of organisms. It can identify only those organisms for which their specific DNA probe or the particular antibody assayed is included in the test. For this reason, the combination of a Comprehensive Stool Analysis along with a second GI panel that includes saliva antibody markers and/or DNA probe testing for microorganisms yields more comprehensive data.

The GI Health Panel determines bacterial, parasitic as well as food related issues using a combination of saliva based antigen testing along with the growth of organisms to look for very specific organisms as well as specific toxins or antibodies to individual microbes. This test is useful for slow growing organisms like anaerobes or Clostridia and also looks at Helicobacter pylori antibodies in saliva.

While the H.pylori test that is included in the GI Health Panel is not a DNA based test it does measure antibodies in saliva that the body has produced in response to the presence of H.pylori. When there are concerns about H.pylori (such as chronic acid reflux), I prefer to run this saliva test for H.pylori antibody along with the H.pylori antigen test in stool from DDI. These two tests work well together as one looks at the antibody in saliva produced in response to H.pylori and the stool test from DDI measures evidence of antigens from H.pylori in stool.

The expanded GI Health Panel would make sense if an individual was particularly concerned about parasites or wanted another mechanism to check sensitivity to milk and wheat/gluten rather than the Celiac test.

In addition to looking at specific organisms that are present the idea is to look at BOTH the gut environment as well as specific microbes. In terms of the gut environment, the goal is to have a balanced pH; sufficient elastase; balanced levels of fatty acids reflecting appropriate fatty acid digestion; low levels of inflammatory markers; lack of blood, mucous, or muscle in the stool; and normal ranges of lactoferrin, cholesterol, and triglycerides. A healthy gut environment is more conducive to the growth of appropriate flora rather than non-optimal microbes.

Imbalances in gut microbes can affect your thyroid hormones. Instead of using thyroid peroxidase to make thyroid hormone, your body uses this enzyme to combat abnormal GI organisms. Fluctuating levels of thyroid hormone can result. High levels of T4, the thyroid hormone thyroxine, inhibit glutamate dehydrogenase, which can increase your glutamate levels, reduce alpha keto-glutarate, and give you the symptoms of excitotoxicity.

Marker This table contains the rationale behind my suggestions. These suggestions are for your consideration. Defer your choices to your own health care practitioner, as always.

Gut Environment

Elastase Long chain fatty acids For imbalances in the levels of elastase and long chain fatty acids, consider 1 or 2 Special Digestive Enzymes (SDE) with each meal, along with 1 or more FOK capsules daily for pancreatic support, and support for pancreatin and digestive enzymes. If this is not sufficient to get elastase levels into the normal range, then also consider an ACAT/BHMT capsules with each meal. Run a HMT and UTM to rule out high thorium, since thorium can bind and inhibit digestive enzymes.
Short chain fatty acids (SCFA)Fat StainTriglyceridesCarbohydrates Imbalances in the levels of these compounds suggest problems with fat digestion and carbohydrate absorption. If these are out of balance, consider 1 or 2 Special Digestive Enzymes (SDE) with each meal. In addition, Biotin and low dose Adenosyl B12 help with fat digestion and are key nutrients for imbalances in SCFA. Order a MAP test to rule out ketosis, as well as a UAA to look at overall nutrient absorption. If high levels of carbohydrate are seen and/or there are low amino acids on a UAA, then consider Bowel Support nucleotide blend /or Leaky Gut nucleotide blend, as well as VitaOrgan, AminoAssist and Ora-Placenta. SCFA also play a regulatory role with respect to T cells and inflammation, so consider T cell and B cell support capsules for immune support if SCFA are out of balance.
Propionate High levels of propionate, or propionic acid, may be produced by intestinal bacteria, such as Propionibacterium, after the use of antibiotics, in particular clindamycin. Carnitine and Carnosine may offset the impact of high levels of propionic acid.
Butyrate Increased butyric acid, or butyrate, may be due to Fusobacterium or Roseburia. Consider Goldenseal, a component of Naturomycin, to address butyrate.
Acetate When acetate is high, check the CSA / GI for signs of yeast infection, as the acetaldehyde produced by Candida can be converted to acetate, or acetic acid. This conversion uses Molybdenum, so be sure molybdenum is supported, or that Black Bear Spray is in place. The processing of acetaldehyde also may use the cofactor PQQ, so consider Ultimate B as a natural source of PQQ.
Vegetable fibers and Muscle fibers High vegetable and muscle fibers suggest poor digestion. Consider 1 or 2 Special Digestive Enzymes(SDE) with each meal. Not all digestive enzymes are equal, and many do not have sufficient pancreatin. The reason I recommend SDE is that they are higher in pancreatin, along with a more complete range of additional digestive enzymes. Consider low dose Muscle Support nucleotide blend and low dose Ion Transport nucleotide blend. The Muscle Support nucleotide blend may help keep muscle breakdown in a more normal range. The Ion Transport nucleotide blend may aid in balancing excess mucous in the gut that can contribute to digestive issues.
Cholesterol If your cholesterol levels are high, you can consider low dose Red Rice Yeast. When using any supplement or medication that helps to keep cholesterol in a normal range, also use CoQ10.
LysozymeLactoferrinWhite blood cellsMucus Red blood cells Occult blood These compounds are all markers of inflammation, and may also indicate infection. When they are high, consider AHCY/SHMT compound, SHMT Spray, and/or extra Lactoferrin to take the pressure off of your body to produce lactoferrin, and to prevent its depletion in your system. To help with inflammation, and to have these markers stay in the normal range, consider Inflammatory Pathway Support capsules and/or Inflammove, as well as Bowel Support nucleotide blend, Cytokine Balance nucleotide blend, as well as General Support nucleotide blend. For the presence of red blood cells, consider Vitamin K and Mastica Gum. Rule out Helicobacter pylori and hemolytic E.Coli as causes of blood in your stool. For excess white cells, consider Myrrh. Also, check lithium levels on a UEE and HMT, because lithium can be stimulating for white cells. If lithium is low, consider Be Calm Spray, All in One, and, if needed, Lithium Orotate. For excess mucus, consider Ion Transport nucleotide blend, Muscle Fatigue Support compound and Serraflazyme.
Gut pH Ideally, your gut pH should be around 7. Levels that are too low may grow the non-optimal microbes that are able to thrive at a low pH, such as H.pylori, E.coli and Streptococci. In addition, a low gut pH makes it difficult for healthy, normal flora such as Lactobacillus and Bifidobacter to colonize the area. Low pH may mask the growth of other non-ideal organisms, so a full picture of your microbial imbalances may not be seen until your gut pH is closer to 7. For this reason, even if no dysbiotic flora are noted, if your GI pH is at 5, there may still be a range of imbalanced flora that are simply not being identified. In these cases, it is suggested that another set of stool tests, CSA and GI Effects, be run once the low pH has been addressed. Wide swings in pH, for instance a pH of 5 on a CSA, and a pH of 7 or 8 on a GI Effects test, when both samples have been taken during the same time period, may indicate H. pylori. While H. pylori is attracted to a low pH, it then produces urease, which increases the gut pH so that it can thrive. Separate tests for H. pylori can be run to rule out this possibility. In addition, a breath test for urease produced by H.pylori can be run by your doctor and may be the most sensitive test for this organism. pH strips can be used at various points throughout the day to check your progress in balancing gut pH prior to rerunning GI tests. Check pH in the morning, mid or late day, and again before bed. Alternately, supplements can be added for 6 to 8 weeks. Once your pH is close to 7, you can rerun GI tests to both reassess your gut environment, as well as get a more complete picture of your gut microbes. Supplements to help address low gut pH include VitaOrgan, Stomach pH Balancing nucleotide blend, Buffer pH, and/or low dose Potassium Bicarbonate or sodium bicarbonate, depending on your need for sodium or potassium on a HMT and UEE. Lack of B12 may also be a factor in causing a low gut pH. Consider a HMT and UEE to assess cobalt levels as an indicator of B12 levels, and support B12 as needed. Because lithium plays a role in B12 transport, be sure both lithium and potassium are in balance prior to adding extra B12. Support for lithium can include Be Calm Spray, All in One and Lithium Orotate. Tin may also cause an acidic pH, so rule out high tin on a HMT and UTM. Also, acidic conditions may increase iron levels, and iron increases bacterial virulence. A HMT and UEE can be run to check iron. Consider SHMT support and/or Lactoferrin to help with high iron. Acidosis can occur secondary to mitochondrial dysfunction, so consider a MAP test to rule out mitochondrial concerns. Acidosis can lead to pancreatic issues, in which case you can consider SDE, FOK capsules, and VitaOrgan. If the pH is very high, above pH 7, rule out non-optimal anaerobes as an issue. They can be the cause of increased pH. Consider Anaerobic X nucleotide blend, IgY Immune capsules and the appropriate antibiotic herbs and other support listed later in this chapter. High pH conditions in your GI tract may limit copper uptake, which can impact the processing of serotonin, dopamine and histamine, so consider a neurotransmitter test, as well as a MAP test, to check on neurotransmitter levels and their breakdown.
sIgA Secretory IgA is a marker for immune response in your gut. It is produced by the mucosal lining of your gut. High Ig A may be due to inflammation or indicate infection. Inflammation can be supplemented into a healthy normal range with Bowel Support nucleotide blend, Cytokine Balance nucleotide blend, Inflammatory Pathway Support capsules, or Inflammove. Your immune system can be supported with T cell and B cell support capsules. Your gut lining can be supported with Colostrum, specifically colostrum that is high in sIgA, to take the pressure off of your GI tract to either produce or deplete its own IgA stores. In addition, if your sulfur levels are not high on a HMT or UEE, consider using Glucosamine/Chondroitin Plus to support your gut lining. VitaOrgan may also be helpful for the GI mucosa.
Overall basic approach to imbalanced and dysbiotic flora  Natural herbs can be used to help limit growth of undesired organisms, along with probiotics and supplements that address biofilms. Consider the use of BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut. In addition to the two Naturomycins and grapefruit seed extract (GSE capsules or GSE liquid), consider BactiSolve to aid with biofilm if you have no shellfish allergies. If you have shellfish allergies, then consider low dose sources of EDTA including MetalAway, EDTA capsules, EDTA soap and/or EDTA soak. In addition to these more general suggestions for imbalanced flora, consider the use of specific RNA Microbial nucleotide blends and specific immunfactors (IMF). Since iron increases bacterial virulence, consider Lactoferrin, AHCY/SHMT compound, and/or SHMT Spray to help with iron.
Rotate probiotics Rotating specific probiotics lays the groundwork for normal flora in your gut. A healthy gut environment helps normal flora proliferate. In turn, healthy normal flora makes it more difficult for imbalanced or dysbiotic flora to grow. The probiotics that can be rotated include Suprema dophilus, NutriClean, and Lactobacillus. These products have a range of Lactobacillus species, including L.acidophilus, L.reuteri. L.rhamnosus, L.johnsonii, as well as Bifidobacter. Also, include normal yeast flora, such as Saccharomyces boulardii. Eliminate Streptomyces, Streptococcus, Enterococcus and Prevotella in probiotic supports. Lactobacillius species ferment sugars to lactic acid, which provides an environment in the large bowel that protects against infection. Bifidobacter species assist digestion, and protect against the development of allergies and cancer. Other bacteria will flourish if numbers of Lactobacilli and Bifidobacter decline for any reason. Diet has a huge influence on the gut flora, as well as gut pH. For instance, a diet high in sugar can contribute to high levels of yeast. Certain diets may cause a greater tendency toward ketosis, such as the Specific Carbohydrate Diet or the Paleolithic Diet. Diets that are too high in protein can cause excess ammonia. Diets that are high in glutamate, glutamine or high levels of fermented food, can increase excitotoxins. Diets high in sulfur may increase your need for molybdenum and B12. Work with your health care provider on a healthy, balanced diet.

Specific Microbes listed alphabetically

Specific herb suggestions are derived in part from Buhner, Stephen Harrod. Herbal Antibiotics: Natural Alternatives for Treating Drug-resistant Bacteria. North Adams, MA: Storey Pub., 2012. Print.
Anaerotruncus colihominis This organism is an anaerobe related to Clostridia. Consider Naturomycin and IgY Immune capsules.
Akkermansia muciniphila This organism may be a beneficial probiotic that can help with obesity and aid in breaking down excess mucus in your gut. Indirectly, this may be a help for H. pylori and those who are CFTR+.
Bacteroides Rhubarb and IgY Immune capsules may be a help for anaerobes, particularly for Bacteroides. Consider the use of BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Barnesiella Barnesiella may have a protective effect against certain drug resistant organisms.
Butyrivibrio crossotus This organism is an anaerobe related to Clostridia. Consider Naturomycin and IgY Immune capsules. Consider the use of BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Campylobacter Consider Garlic, an ingredient in Naturomycin, along with IgY Immune capsules for bacteria that grow anaerobically. Certain Campylobacter species induce antibodies that react with neuromuscular junctions. This can create ‘molecular mimicry’ such that your immune system can produce antibodies that cross react with neuromuscular junctions. It is important to eradicate this organism. Campylobacter is related to H.pylori, so the use of HELX nucleotide blend and Peptimycin may be considered.Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Clostridia This organism is an anaerobe. Clostridia has been implicated in a range of behavioral and language issues. It is critical to address this organism. Use Microbial CLX nucleotide blend, Peptimycin, IgY Immune capsules and Bay leaf. Consider BOTH Naturomycin Spray and Naturomycin capsulesbecause they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Collinsella aerofaciens This organism is an anaerobe. Use Naturomycin and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Coprococcus eutactus This organism is an anaerobe related to Clostridia. Consider Naturomycin and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Desulfovibrio piger This organism can produce hydrogen sulfide which can inhibit mitochondrial function directly. A positive Hydrogen Sulfide Urine Test may indicate severe gut dysbiosis, which can be due to overgrowth of Desulfovibrio or Prevotella. Hydrogen sulfide is known to inhibit mitochondria and block the oxygen carrying capacity of hemoglobin. It also greatly increases the toxicity of heavy metals by enhancing their absorption. Hydrogen sulfide can also affect neurotransmitter levels, so consider a NT test and a MAP test if consistently high levels of Desulfovibrio or Prevotella are noted on a CSA test and GI Effects test.  This organism is an anaerobe. Consider Naturomycin and IgY Immune capsules, be sure levels of Molybdenum and B12 are adequate, or consider the use of Black Bear Spray or Black Bear Drink. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Enterobacter This organism is an anaerobe. Consider Sage, Naturomycin, and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Enterococcus Enterococcus is the cause of a number of hospital acquired infections or issues in individuals with compromised immune systems. The concern with Enterococcus is that it is resistant to many standard antibiotics. Natural herbs that have been reported to act on Enterococcus include Sage and Oregano.
Escherichia coli Consider the use of ECX nucleotide blend, Cranberry*, Goldenseal*, Garlic*, Juniper Berry*, Sage, Mastica Gum, grapefruit seed extract (GSE capsules or GSE liquid), Mycoceutics and IMF 5 and IgY Immune capsules. *The starred items are ingredients in Naturomycin. Certain E. coli species have a capsule that is identical to human neuronal tissue. This can create ‘molecular mimicry’ such that the immune system can also induce antibodies that cross react with neuronal tissue. It is important to work with your doctor to address high levels of this organism. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Faecalibacterium prausnitzii This may be a helpful organism, but if its levels are high, it may be associated with symptoms and health problems. This organism is an anaerobe. Consider Naturomycin and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Fusobacterium These organisms have been associated with numerous problematic health conditions. Fusobacterium ultimately increases TNF-alpha, so it may play a role in mucosal inflammation. Fusobacterium may also be the cause of high butyric acid (butyrate) on CSA and GI tests. Because TNF-alpha can increase the activity of CBS, consider a UAA to check that taurine levels are not too high. See the section on taurine in Chapter 5. Consider Goldenseal, Naturomycin, IgY Immune capsules, and low dose TNF nucleotide blend. Consider BOTH Naturomycin Spray and Naturomycin capsulesbecause they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Haemophilus This organism is an anaerobe. A number of species of Haemophilus cause significant infections and so the presence of this organism should be taken seriously. Consider NaturomycinGarlic*, Goldenseal*, Sage, grapefruit seed extract (GSE capsules or GSE liquid), thyme, Oregano*, Mycoceutics, and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Helicobacter pylori This organism is an anaerobe. H.pylori plays a role in acid reflux, as well as gastric ulcers. It has also been linked to duodenal ulcers and gastric cancer. The presence of H.pylori should be taken seriously and addressed. See the DVD by Dr. Yasko, and Gastrointestinal Balance and Neurotransmitter Formation by Drs. Yasko and Mullan. Consider HELX nucleotide blend, Peptimycin, Carnitine, Potassium Bicarbonate or sodium bicarbonate, TNF nucleotide blend, Oregano, Cranberry, Magnesium, and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsulesbecause they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Klebsiella Species of Klebsiella can cause serious infection and thus should be addressed. Consider KLX nucleotide blend, Juniper Berry, Uva Ursi, Goldenseal, Sage, Wormwood, thyme, Oregano, Echinacea, and Mycoceutics. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Methanobrevibacter Smithii This organism is an anaerobe. High levels of this bacterium are often found in people with multiple health conditions. It is often high in those with anorexia, however,it may actually help process polysaccharides. Consider Naturomycin and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Morganella morganii This organism may reflect the use or overuse of antibiotics. It can play a role in urinary tract and other infections. It can break down tryptophan, so it may be involved with serotonin imbalances. Check tryptophan levels on a UAA and serotonin on a NT test. Consider Sage and BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Mycoplasma This organism is an anaerobe. Mycoplasma can cause pneumonia and has been associated with neurological and psychiatric problems. Consider Anaerobic X nucleotide blend, IMF 9 and IgY Immune capsules.
Odoribacterspp. Consider oral Naturomycin Spray.
Oxalobacter formigenes High levels of Oxalobacter may be due to high oxalate in your system. Consider a MAP test and work on oxalate if it is high. See the Oxaloacetic acid section of Chapter 4 for more information on this. High oxalate may be due to yeast and fungal infestation. These factors can be investigated with a CSA test and GI Effects test, among others.
Prevotella Although some probiotic mixes include Prevotella, or consider it normal flora, this program does not. Prevotella species ferment to produce hydrogen sulfide. Hydrogen sulfide inhibits mitochondrial function directly. So, a positive Hydrogen Sulfide Urine Test may indicate severe gut dysbiosis, which can be due to overgrowth of Prevotella. Hydrogen sulfide is known to inhibit mitochondria and block the oxygen carrying capacity of hemoglobin. It also greatly increases the toxicity of heavy metals by enhancing their absorption. There does not appear to be an antibiotic to which Prevotella is sensitive, but it is purported to be reduced by taking bile salts such as ursodeoxycholic acid as in Cholacol or ACAT/BHMT capsules. Neem can also be used and is extremely safe. Neem works by making microbes less sticky so they cannot adhere to the lining of the gut. Hydrogen sulfide can also affect neurotransmitter levels, so consider a NT test and a MAP test if consistently high levels of Prevoltella are noted on CSA and GI tests. In extreme cases, Prevotella species have been found in brain and lung abscesses.Consider Anaerobic X nucleotide blend, Neem, Cholacol or ACAT/BHMT capsules, Molybdenum and B12 or Black Bear Spray. Consider IgY Immune capsules for anaerobes. Consider BOTH Naturomycin Spray and Naturomycin capsulesbecause they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Proteus Consider Garlic, Sage, and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs adds another level of broad spectrum support and may help balance the microbes in your gut.
Pseudoflavonifractor spp. Rhubarb and IgY Immune capsules may be a help. Consider the use of BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Pseudomonas Pseudomonas species can cause serious infection, so this organism should be addressed, working with your doctor as always. Pseudomonas may be inhibited by hypothiocyanite and thiocyanate, so you can consider using Ion Transport compound, which contains sources of these compounds. Consider Microbial PSX nucleotide blend, Juniper Berry, Garlic, grapefruit seed extract (GSE capsules or GSE liquid), thyme, Oregano, Uva Ursi, Goldenseal, Cranberry, Mycoceutics, aloe, Ion Transport nucleotide blend, and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Roseburia spp. Along with Fusobacterium, Roseburia may be a source of butyric acid or butyrate. This organism is an anaerobe. Consider Naturomycin, IgY Immune capsules and Goldenseal. Consider BOTH Naturomycin Spray and Naturomycin capsulesbecause they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Ruminococcus spp This organism is related to Clostridia. It is an anaerobe. Consider Naturomycin and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Salmonella Salmonella is associated with significant infection in the gut and should be taken seriously. Consider Microbial SALX nucleotide blend, Ashwagandha, Juniper Berry, AHCY/SHMT compound, SHMT Spray or Lactoferrin to help with iron, and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Shigella Shigella can cause significant infections and should be taken seriously. Consider Goldenseal, Garlic, grapefruit seed extract (GSE capsules or GSE liquid), Sage, Mycoceutics, AHCY/SHMT compound and SHMT Spray or Lactoferrin to help with iron. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Staphylococcus Certain species of Staph, for example Staph aureus, have an outer protein that inhibits the ability of immunoglobulins to function optimally. Staph may be inhibited by hypothiocyanite and thiocyanate, so you can consider Ion Transport compound, which contains sources of these compounds. To support the immune system, consider T cell and B cell support capsules. Consider STAX nucleotide blend, Garlic, Goldenseal, Wormwood, Juniper Berry, grapefruit seed extract (GSE capsules or GSE liquid), thyme, Oregano, Mycoceutics, aloe, Ion Transport nucleotide blend, IMF 5 and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Streptococcus Aside from species of Strep that are known to cause infection, some species of Strep are often included in probiotic mixes. This program eliminates the use of these probiotics because Streptococcus fermentation produces large amounts of lactic acid. This may incline you to acidosis. Lactic acid is metabolized in your liver by lactate dehydrogenase. High levels of lactic acid may indicate bowel overgrowth with Streptococcus. Fermentation produces two isomers of lactic acid, L-lactate and D-lactate. D-lactate is the problem. The body cannot metabolize D-lactate. It accumulates in mitochondria and may cause inhibition of mitochondrial energy production. For this reason, consider using MitoForce when your levels of Strep are high. Some Strep species, such as Strep pyogenes, contain components that are similar to those of human cardiac, skeletal, and smooth muscle, heart valve fibroblasts, and neuronal tissues. This can create ‘molecular mimicry’ so that your immune system may produce antibodies that cross react with heart, joints and brain leading to movement disorders. It is important to eliminate this organism. Strep infection also increases your levels of TNF alpha. High TNF alpha has been implicated in Tourettes syndrome, OCD behavior, “stims”, PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections), perseverative speech, rheumatoid arthritis and leaky gut. Consider STRX nucleotide blend, Garlic, Echinacea, rosemary, Sage, barberry, Goldenseal, Oregon Grape, grapefruit seed extract (GSE capsules or GSE liquid), Mycoceutics, Juniper Berry, IMF 5 and IgY Immune capsules. Also, consider AHCY/SHMT compound for DPPIV and as a source of lactoferrin. Consider TNF nucleotide blend. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Streptomyces This is an anaerobic bacterium. Consider Anaerobic X nucleotide blend and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Veillonella spp. This organism is an anaerobe and is resistant to a number of antibiotics, so use an herbal combination. Consider Naturomycin and IgY Immune capsules. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Candida Consider Garlic, Candisol, Mycology Support nucleotide blend, Goldenseal, Juniper Berry, IMF 7 and grapefruit seed extract (GSE capsules or GSE liquid). Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Parasites Consider Naturomycin Spray, Naturomycin capsules, and Paradex. Consider De Witt’s syrup if needed. Consider BOTH Naturomycin Spray and Naturomycin capsules because they contain different herbs that work together for optimal results. Naturomycin Spray is a source of the following herbs: Echinacea, Cranberry, Elderberry, lomantium, Dandelion Root, Skullcap, and Goldenseal. Naturomycin capsules are a source of the following herbs: berberis, Myrrh, Bay leaf, Cranberry, Neem, Oregon Grape, Elderberry, olive leaf, Oregano, black walnut, Juniper Berry, Garlic, Uva Ursi, Wormwood and pumpkin. The use of grapefruit seed extract (GSE capsules or GSE liquid) along with these herbs creates additional broad spectrum support and may help balance the microbes in your gut.
Additional Considerations
BH4 levels
Aluminum
Studies indicate that bacteria can hold on to toxic metals, including aluminum. Running a UTM and HMT to check aluminum, especially as you begin to work on non-ideal microbes, gives you a sense of the level of retention of aluminum in your body, as well as the rate of its excretion. Aluminum is known to compromise tetrahydrobiopterin (BH4) formation. BH4 is needed to produce serotonin and dopamine. Consider a Neopterin / Biopterin Profile Urine Test, as well as a MAP test and a UAA. These tests can indicate issues with BH4 levels. Supplements should include a source of EDTA which may help with aluminum, such as MetalAway, EDTA soap or soak, or EDTA capsules. Also, support for natural healthy levels of BH4 can include MTHFR A1298C Liver Support capsules and BH4.

 

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Related Tests to Run

MAP tests are useful to look at a number of GI related issues, including the balance of kynurenic and quinolinic acid that may be increased with bacterial infection. This ratio is important because quinolinic acid can serve as an excitotoxin. MAP tests also reveal information on your need for BH4, the production of which may be compromised due to bacterial infection. They contain data on the breakdown of serotonin, which may also be a consequence of bacterial infection.

UTM/UEE testing is also useful, because bacterial infection may lead to increased stores of toxic metals, particularly aluminum and other toxins. Thorium and tin may impact digestion and gut pH. UAA tests are useful in conjunction with a CSA / GI as gut imbalances can directly play a role in nutrient absorption.

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