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©2008 Metametrix, inc. All rights reserved · GI Effects Stool Profiles U.S. patent pending · 70040 rev 0708 v2


Introduction Predominant Bacteria


Proper gastrointestinal (GI) function is critical to adequate

nutritional status and can impact all aspects of body function.

The GI EffectsSM Stool Profiles address key components

of proper GI health including measurement of beneficial

microbial flora, opportunistic bacteria, yeast, parasitic

infection, markers of inflammation, immune function,

and digestion and absorption. The microbial population is

measured using PCR amplification of the genetic material of

each organism, allowing for sensitive detection, and the ability

to detect and identify organisms that cannot be cultured or

are extremely difficult to grow under laboratory conditions.

Reference Range Interpretation

Standard microbiological results are reported as Colony

Forming Units per gram of feces (CFU/gram). One CFU

is equivalent to one microorganism. Metametrix detects

microorganisms by DNA analysis. Each genome detected

represents one cell, or one CFU. Because there are very large

numbers of microorganisms in stool, results are expressed

in standard scientific notation. For example, Bacteroides sp.

may be reported as 2.57 E7, or 2.5 x 107, or 25,000,000 CFU/

gram, which is read as 25 million CFU per gram of feces.

The exponent is kept constant within a section of the report

to facilitate direct comparisons between organisms. The

cutoff for clinical significance for predominant bacteria has

been set at 1E7 (1 x 107), for opportunistic bacteria 1E5 (1 x

105), and for pathogens at 1E3 (1 x 103). Rather than semiquantitative

results (+1 to +4), the new methodology provides

full quantitative analysis.

Abnormal Bacteria, Fungi and/or Parasites


1. Inadequate physical and immune barrier functions

Food sensitivities/leaky gut s yndrome (elevated IgG)

Low intestinal secretory IgA

Gluten intolerance/Celiac disease

Inflammatory bowel disease

Decreased colonic short-chain fatty acids

2. Medication history



Antacids, proton pump inhibitors, and acid-blockers

3. Inadequate digestive and absorptive function


Pancreatic insufficiency

Intestinal inflammation

Rapid transit time

Nutrient insufficiencies

Diet high in red meat, saturated fat, or refined


4. Pathogenic invasion and gut flora imbalances (dysbiosis)

Exposure to pathogens (water/food contamination/

foreign travel/depressed immune system)

Inadequate predominant flora

Treatment Using Four “R” program for

intestinal health

Remove offending foods, medications, gluten (if sensitive) and

reduce poor quality fats, refined carbohydrates, sugars, and

fermented foods (if yeast is present). Consider antimicrobial,

antifungal, and/or antiparasitic therapies in the case of

opportunistic/pathogenic bacterial, yeast, and/or parasite

overgrowth (see below for specific recommendations).

Replace what is needed for normal digestion and absorption

such as betaine HCl, pancreatic enzymes, herbs that

aid in digestion such as deglycyrrhizinated licorice and

marshmallow root, dietary fiber, and water.

Reinoculate with favorable microbes (probiotics such as

Lactobacillus sp., Bifidobacter sp., and Saccharomyces boulardii).

To enhance the growth of the favorable bacteria, supplement

with prebiotics such as inulin, xylooligosaccharides, larch

arabinogalactans, beta glucan, and fiber.

Repair mucosal lining by giving support to healthy intestinal

mucosal cells, goblet cells, and to the immune system.

Consider L-glutamine, essential fatty acids, zinc, pantothenic

acid and vitamin C.

Predominant Bacteria

Microorganisms in the GI tract perform a host of useful

functions, such as fermenting unused energy substances,

communicating with the immune system, preventing growth

of harmful species, regulating the development of the gut,

producing vitamins for the host (such as biotin and vitamin

K), and producing hormones to direct the host to store fats.[1]

Intestinal microflora are also thought to have many beneficial

local and systemic roles such as improving lactose tolerance,

supplying short chain fatty acids (SCFA) as an energy

substrate for the host, anti-tumor properties, neutralizing

certain toxins, stimulating the intestinal immune system,

reducing blood lipid levels and preventing obesity and type

II diabetes.[2] Under normal homeostatic conditions, the

intestinal microflora are of central importance in preventing

colonization by pathogens, termed “colonization resistance.”[3]

Predominant organisms are considered to be beneficial when

they are in balance.

Predominant, Opportunistic, and Pathogenic Bacteria


Low Predominant Bacteria


Dysbiosis: Predominant bacteria should be present at

normal levels in the healthy gut. Bacteroides sp. and

Bifidobacter sp. should be present in the greatest amounts.[4]

Low levels of beneficial fecal bacteria such as Bifidobacter

sp., Lactobacillus sp. and E. coli have been associated with

irritable bowel syndrome, characterized by alternating

diarrhea, cramps, and food intolerance.[5]

Low levels of predominant bacteria increase the

likelihood of acquiring opportunistic and pathogenic


Treatment Options:


Prebiotics such as psyllium, oat bran, oligofructose,

xylooligosaccharide, inulin, beta-glucan, and/or


Increase intake of fresh vegetables and fibers

Address other GI Effects abnormalities

High Predominant Bacteria


Dysbiosis: Predominant bacteria should be present

at normal levels in the healthy gut. Bacteroides sp.

and Bifidobacter sp. should be present in the greatest


Blood infections of Mycoplasma have been linked to

chronic fatigue syndrome and fibromyalgia.[7]

Fusobacterium increases putrification in the colon.

Overgrowth of Lactobacillus sp. could produce D-lactic

aciduria in those with short bowel syndrome. Limit

intake of simple carbohydrates.[8]

Overgrowth of certain Clostridia sp. clusters may play a

role in certain cases of autism.[9, 10]

If Prevotella sp. is in the 5th quintile suspect possible oral/

throat infection.[11]

Treatment Options:

Reduce poor quality fats, refined carbohydrates and

sugars, and encourage intake of fresh vegetables. High

fiber foods might exacerbate patient symptoms.

For Lactobacillus sp. or Clostridia sp. overgrowth,

supplement with Bifidobacter sp. or Saccharomyces boulardii

probiotics, respectively.

May need to use anti-microbial agents

Address other GI Effects abnormalities

Balance flora using appropriate probiotics

Opportunistic Bacteria

Opportunistic Bacteria present


Generally self-limiting and not normally considered


Often exacerbated by low predominant bacteria,

pathogen or parasite infection, poor diet, antibiotic use,

and lowered gut immunity.

Treatment Options:


Prebiotics: Do not use fructooligosaccharide (FOS) if

Klebsiella sp. or Citrobacter sp. are present.

May need to use anti-microbial agents followed by preand


Herbal agents include goldenseal, citrus seed extract,

garlic, uva ursi, oregano oil, and olive leaf extract

Visit www.emedicine.com to search for the pathology

of the individual opportunistic bacteria and treatment


Address other GI Effects abnormalities

Pathogenic Bacteria

Pathogenic Bacteria present

Helicobacter pylori

Helicobacter pylori (H. pylori) bacterium causes peptic ulcer

disease and has been associated with increased gastric cancer

risk. H. pylori is a Type I carcinogen. It is estimated that 50%

of the world’s population is infected with H. pylori.


Acute gastritis with abdominal pain, nausea and

vomiting, usually within two weeks of infection.

Recurrent abdominal symptoms (non-ulcer dyspepsia)

without ulcer disease are common.

Treatment Options (Adult Dosages):

Standard treatment for H. pylori consists of a combination

of 3 or 4 drugs, antibiotics, and proton pump inhibitors,

for 7-14 days. Current recommendations can be found

at www.acg.gi.org. Eradication does not generally exceed


Supplementation with lactoferrin (200 mg/d), prebiotics,

and vitamin C (up to 5 grams), may improve treatment

efficacy, while reducing adverse reactions.[12][13]

Botanical combination treatments have also been shown

to be effective in eradicating H. pylori from the GI tract.

Botanicals* (see page 7)

Pathogenic Bacteria Yeast/Fungi


Clostridium difficile

Suspect recent antibiotic use, especially the cephalosporins,

ampicillin/amoxicillin, and clindamycin.


Cramping, lower abdominal p ain, fever and diarrhea

usually decreases once antibiotics are stopped, though

can continue for up to 4 weeks

Treatment Options (Adult Dosages):

Do not treat if patient is asymptomatic. Stop use of

causative antibiotics.

In severe cases: Vancomycin 125 mg PO qid for 10-14d;

Metronidazole 500 mg PO tid or 250 mg PO qid for


Herbal antibiotics such as berberine or oregano oil

Replete beneficial bacteria, esp. S. boulardii

Campylobacter sp.

Contaminated animal food sources are the primary cause,

especially poultry and red meat. Dogs may also become

infected from rodents and birds and infect humans. Suspect

hydrochloric acid insufficiency and/or secretory IgA



Symptom onset is generally abrupt. Influenza-like

symptoms are common, including headache and malaise.

GI symptoms include abdominal pain, nausea, and

vomiting. The degree of diarrhea varies. Campylobacter sp.

has been associated with reactive arthritis.

Treatment Options (Adult Dosages):

Generally self-limiting infection not requiring treatment

Support rehydration if diarrhea is present

If infection persists treat with Erythromycin: 500 mg

erythromycin stearate, base, or estolate salts (or 400 mg

ethylsuccinate) every 6h PO.

Entero-hemorrhagic Escherichia coli


Also referred to as Shiga toxin-producing E. Coli (STEC).

Suspect ingestion of contaminated food, especially

undercooked ground beef, raw milk, unpasteurized apple juice,

water, and lettuce.


Typical symptoms include severe abdominal cramping,

watery or bloody diarrhea, and vomiting. In some cases

(up to 10%) it can cause hemorrhagic colitis or hemolytic

uremic syndrome.

Treatment Options:

The infection is generally self-limiting

Rehydrate if diarrhea is present

Antibiotic therapy hasn’t proven useful in EHEC infection

and can predispose to development of hemolytic uremia

Streptomycin, sulfonamides, and tetracycline have

demonstrated resistance to many EHEC strains

Probiotic/prebiotic therapy


Yeast/Fungi present

Commonly identified species: Candida, Rhodotorula,

Geotrichum, Sacchoromyces, Trichosporon, Candida are detailed

below. If other commonly identified species are reported,

consider patient symptoms and degree of infection to decide

if anti-fungal therapy is warranted. Saccharomyces sp. may be

reported if patient is supplementing with S. boulardii. Restore

proper predominant microflora populations and address all

other imbalances found on the GI Effects test report.

Candida sp.

Candida sp. is a normal inhabitant of the gastrointestinal

flora and is present in 40-65% of the human population

with no harmful effects. However, in conditions allowing for

overgrowth, Candida sp. is the most common causal agent of

opportunistic fungal infections. The esophagus is the most

commonly infected site, followed by the stomach then the

small and large bowel. Approximately 15% of people develop

systemic candidiasis.


Gastric pain, nausea and vomiting, gas, bloating,

intestinal permeability, imbalance in gut microflora,

opportunistic bacterial infection

Treatment Options:

Reduce intake of refined carbohydrates and sugars

Prescriptive agents: fluconazole, intraconazole,

ketoconazole, nystatin

Herbal agents (use in combination for greater efficacy):

oregano oil, berberine, goldenseal, undecylenic acid,

caprylic acid, grapefruit seed extract, uva ursi, garlic (allicin)

S. boulardii aids in the growth of beneficial bacteria,

crowds out yeast, and helps with immune support

Avoid fructooligosaccharide (FOS) as it may feed the yeast

Yeast/Fungi Present: taxonomy unavailable

Uncommon yeast/fungi is present, and one that likely colonizes

other animals, or has not been identified as pathogenic to

humans. Infection with Candida, Rhodotorula, Geotrichum,

Saccharomyces, and Trichosporon species have been ruled out. If

present at +2 or below, it is likely that this yeast is transient due

to ingestion of molds or other yeasts, and is not problematic to

humans. Consider patient symptoms before treating.

Yeast/Fungi Parasites


Treatment Options:

Reduce intake of refined c arbohydrates and sugars

If presentation is consistent with a fungal infection, use

antifungals followed by prebiotics and probiotics

Avoid FOS powder as it may feed the yeast

Address other abnormal results on the GI Effects test

first, with the expectation that rare yeast/fungi will be

crowded out when healthy conditions are restored


Parasite present

Pharmaceutical recommendations for each parasite are

from the 2007 publication in The Medical Letter, “Drugs for

Parasitic Infections.”[14]

Blastocystis sp.

Blastocystis sp. is transmitted via fecal-oral route or from

contaminated food or water. Seven subspecies have

been identified and Blastocystis sp. 4 infection has been

correlated with disease. Blastocystis sp. 2 is considered to be



May include diarrhea, cramps, nausea, fever, vomiting,

abdominal pain or fatigue. Blastocystis sp. has been

associated with irritable bowel syndrome, infective

arthritis and intestinal obstruction. In certain cases,

chronic fatigue may be the only complaint.

Treatment Options:

Blastocystis sp. can be prevented by personal hygiene and

sanitary conditions

Clinical significance of infection by these organisms is


Metronidazole 750 mg PO tid x 10d or iodoquinol 650

mg PO tid x 20d or trimethoprim/sulfamethoxazole 1 DS

tab PO bid x 7d have been reported to be effective

Infection is difficult to get rid of, botanicals may not

be strong enough. Use of broad spectrum antiparasitic

botanicals is most effective.*

Botanicals* (see page 7)

Clonorchis sinensis (Chinese Liver Fluke)

Clonorchis sinensis is found in pickled, smoked, salted,

imported, or undercooked freshwater fish.

Symptoms :

Frequently asymptomatic. Inflammation and intermittent

obstruction of the biliary ducts. Acute abdominal

pain, nausea, diarrhea and eosinophilia can occur. In

long-standing infections, cholangitis, cholelithiasis,

pancreatitis and cholangiocarcinoma can develop.

Treatment Options:

Praziquantel, 75 mg/kg/d PO in 3 doses x 2d

Albendazole 10 mg/kg/d PO x 7d

Botanicals* (see page 7)


Water, including swimming pools, is a common source of

contamination as it is resistant to chlorine. Outbreaks are

associated with raw milk and meat, and Cryptosporidium is a

likely cause of traveler’s diarrhea.


Watery diarrhea is the most frequent symptom, and can

be accompanied by dehydration, weight loss, abdominal

pain, fever, nausea and vomiting. May be very severe in

immunocompromised patients.

Treatment Options:

Usually self-limiting in an immunocompetent person,

with symptoms lasting 1-2 weeks

If symptoms persist look for possible water


Nitazoxanide, 500 mg PO bid x 3d for persistent


Botanicals* (see page 7)

Dientamoeba fragilis

Fecal-oral transmission and water contamination are common

sources. Often accompanies pinworm.


Diarrhea, fatigue and abdominal bloating, although

often asymptomatic. In chronic infections, abdominal

tenderness, nausea and weight loss may be present.

Treatment Options:

Iodoquinol, 650 mg PO tid x 20d; Paromomycin, 25-35

mg/kg/d PO in 3 doses x 7d; Tetracycline, 500 mg PO qid

x 10d or Metronidazole, 500-750 mg PO tid x 10d

Botanicals* (see page 7)

Endolimax nana or Entamoeba hartmanni

Endolimax nana and Entamoeba hartmanni are considered to

be non-pathogenic amoeba. Detection is significant in that it

means the patient has ingested something contaminated with

fecal material. Increased personal hygiene is recommended.



Entamoeba histolytica

Entamoeba histolytica is the only amoeba considered

pathogenic. Contaminated food or water, pets, sexual contact,

and fecal-oral route are possible sources of transmission. Cysts

are sensitive to chlorinated water.


Range from asymptomatic t o fulminating colitis

(resembling ulcerative colitis), dysentery, and

extraintestinal lesions on the liver, lung, brain, skin and

other tissues

Treatment Options:

Asymptomatic carriers should be treated in order to

avoid spread

For asymptomatic patients: Iodoquinol, 650 mg PO tid x

20d; Paromomycin, 25-35 mg/kg/d PO in 3 doses x 7d or

Diloxanide furoate, 500 mg PO tid x 10d

For mild to moderate intestinal disease: Metronidazole,

500-750 mg PO tid x 7-10d or Tinidazole, 2 g once PO

daily x 3d followed by either Iodoquinol, 650 mg PO tid

x 20d or Paromomycin, 25-35 mg/kg/d PO in 3 doses x


For severe intestinal and extraintestinal disease:

Metronidazole, 750 mg PO tid x 7-10d or Tinidazole, 2

g once PO daily x 5d followed by either Iodoquinol, 650

mg PO tid x 20d or Paromomycin, 25-35 mg/kg/d PO in

3 doses x 7d

Botanicals* (see page 7)

Enterobius vermicularis (pinworm)

Enterobius vermicularis is transmitted from fecal-oral route.

Females emerge from the anus and lay eggs on the perianal

surface. Eggs can survive on bed linens and fabrics for 2-3



Nocturnal perianal pruritus which can lead to skin

bacterial infection, abdominal pain and anorexia. It may

enter the vagina and has been associated with some cases

of cystitis.

Treatment Options:

Mebendazole, 100 mg PO once, repeat in 2 weeks;

Pyrantel pamoate, 11 mg/kg base PO once (max. 1 g),

repeat in 2wks

Albendazole, 400 mg PO once; repeat in 2wks

Botanicals* (see page 7)

Giardia lamblia

Giardia lamblia is a flagellate considered to be a pathogen

and the most common cause of diarrheal disease worldwide.

Transmitted via contaminated water, food or the fecal-oral



Often asymptomatic. Incubation period is 1-3 weeks and

symptoms range from acute diarrhea, to chronic diarrhea

with bloating, intestinal malabsorption, steatorrhea

(possibly due to bile salt deconjugation) and weight

loss. Generally self-limiting, however 30-60% develop

chronic giardiasis. Unusual presentations include allergic

manifestations such as urticaria, reactive arthritis, and

biliary tract disease. May induce lactose intolerance, B12

deficiency and reduced sIgA.

Treatment Options:

Metronidazole 250 mg PO tid x 5-7d

Avoid fatty foods as giardia feeds on bile salts

Paromomycin, 25-35 mg/kg/d PO in 3 doses x 5-10d; or

Furazolidone, 100 mg PO qid x 7-10d; or Quinacrine,

100 mg PO tid x 5d

Botanicals* (see page 7)

Necator americanus and

Ancylostoma duodenale (hookworm)

Necator americanus and Ancylostoma duodenale are transmitted

via skin contact with contaminated soil, or oral ingestion

of the larvae. Worms can travel to the lungs or attach to the

mucosa of the GI and suck blood.


Itching and a rash at the site of penetration. While a light

infection may cause no symptoms, heavy infection can

cause anemia, abdominal pain, diarrhea, loss of appetite

and weight loss. Has been associated with reactive


Treatment Options:

Albendazole, 400 mg PO once; Mebendazole, 100 mg PO

bid x 3d or 500 mg once, or Pyrantel pamoate, 11 mg/kg

(max. 1g) PO x 3d

Botanicals* (see page 7)

Schistosoma mansoni

Schistosoma mansoni is transmitted through skin contact with

contaminated water or oral ingestion. Larvae can migrate to

the lungs and liver and can live for 25-30 years. Eggs secrete

an enzymatic substance that destroys surrounding tissues.


Infection is generally asymptomatic unless there is

repeated exposure leading to heavy worm burden. Severe

infection can lead to myalgias, abdominal pain, diarrhea,

cough, tender liver, ulceration of the intestinal mucosal

layer. It has been linked with reactive arthritis and


Parasites Botanical Treatments


Treatment Options:

Praziquantel 4 0 mg/kg/d in 2 doses x 1d, or

Oxamniquine 15 mg/kg once

Botanicals* (see below)

Strongyloides sp.

Strongyloides sp. is transmitted via skin contact with contaminated

soil, or oral ingestion of the larvae. Larvae are

carried to the lungs or are swallowed and mature in the small



Itching and a rash at the site of penetration. While a

light infection may cause no symptoms, heavy infection

can cause epigastric pain, nausea and vomiting, gas,

and alternating constipation and diarrhea. Has been

associated with reactive arthritis.

Treatment Options:

Thiabendazole 50 mg/kg/d in two doses x 2d; Ivermectin

200 mcg/kg/d x 1-2d, or Albendazole 400 mg/d x 3d

Eradication is difficult, recheck stool in 3 months

Botanicals* (see below)

Taenia sp. (tapeworm)

Taenia sp. is transmitted by undercooked, infected beef.

Maturation from cyst to worm takes 2 months. Taenia sp. can

grow 4-8 meters long and can live 25 years.


Often asymptomatic. Symptoms include GI complaints

such as abdominal pain, anorexia, weight loss or malaise.

Vitamin B12 deficiency may result.

Treatment Options:

Praziquantel, 5-10 mg/kg PO once, Niclosamide, 2 g PO once

Botanicals* (see below)

Trichuris trichiura (whipworm)

Trichuris trichiura is transmitted from ingested feces

contaminated soil, or underwashed vegetables. It is the

most common helminth infection. T. trichiura can become

embedded in the intestinal villi, feeds on tissue secretions and

can cause eosinophilin. Larvae hatch in the small intestine

and take up residence in the large intestine. Adult female lay

eggs for up to five years.


Often asymptomatic and self-limiting. Symptoms

depend on the amount of worms present and the degree

of mucosal involvement. Severe infection can result

in bloody diarrhea, abdominal pain, nausea and irondeficiency


Treatment Options:

Mebendazole, 100 mg PO bid x 3d or 500 mg once;

Albendazole, 400 mg PO x 3d, or Ivermectin, 200 mcg/

kg PO daily x 3d

Botanicals* (see below)

Parasite Present: taxonomy unavailable

The DNA probe identified kingdom protozoan, but genus and

species probes for known human pathogens were negative.

Suspect that the protozoan identified is likely NOT a human

pathogen, and probably a transient, non-colonizer of the

human GI. Evaluate patient symptoms and inflammatory

markers on the GI Effects test. If symptoms are consistent

with a parasite infection, consider treatment.

Treatment Options:

Address other abnormal results in the GI Effects test first,

with the expectation that a rare parasite will be crowded out

when healthy conditions are restored.

Consider exposures such as pets, sushi, camping, or

foreign travel

If presentation is consistent with parasite infestation, use

a broad spectrum antiparasitic treatment followed by preand


Botanicals* (see below)

*Botanical Treatment

Individualized pharmaceutical interventions are listed below each parasite. Common botanical anti-parasitic herbs for each parasite listed

include black walnut, quassia, garlic, berberine, grapefruit seed extract, oil of oregano, barberry, and artemesia. When treating parasites

with botanicals, it is recommended to use a blend of several, to lengthen treatment duration, and to rotate antiparasitic agents

Adiposity Index • Drug Resistance Genes • Short Chain Fatty Acids (SCFA)


Adiposity Index

Adiposity Index imbalanced: high firmicutes

and low bacteroidetes

Research has indicated that obesity has a microbial component

that alters caloric yield from ingested food.[18] Altering the

gut microbiota may also improve insulin sensitivity and oral

glucose tolerance.[19] Treatments for obesity that result in

lowering the percentage of Firmicutes may assist in weight



Bacteria classes known to increase c aloric extraction

from food are present


The Firmicutes class consist of Clostridia sp., Streptomyces

sp., Lactobacillus sp., Mycoplasma sp., Bacillus sp. (see

results under “Predominant Bacteria”)

The Bacteroidetes class consist of Bacteroides sp. and

Prevotella sp. (see results under “Predominant Bacteria”)

Treatment Options:

Balance predominant bacteria using 4R protocol

Remove opportunistic bacteria, especially Bacillus sp.

Supplement with Bifidobacter sp. and S. boulardii

Reduce refined carbohydrates

Address all GI Effects imbalances

Drug Resistance Genes


Bacterial resistance to antibiotic class

Treatment Options:

Avoid using class of antibiotics for which patient has

drug resistance gene

Drug resistance names and antibiotics



Gentamicin, Kanamycin, Tobramycin (aminoglycosides)

Target Organism:

Gram-positive bacteria (cocci), namely Enterococci



Methicillin (Beta-Lactam)

Target Organism:

Aerobic, Gram-negative

vanA, vanB, vanC


Vancomycin and Teicoplanin (glycopeptides)

Target Organism:

Gram-positive bacteria, particularly beta-lactamase-producing

organisms such as Staphylococcus

gyrB, ParE


Ciprofloxacin and later generation quinolones

Target Organism

Gram-positive and Gram-negative bacteria



Penicillin (Beta-Lactam)

Target Organism:

Broad spectrum

Short Chain Fatty Acids (SCFA)

Depressed total SCFA or N-Butyrate

Beneficial SCFA come from dietary carbohydrates that have

escaped digestion or absorption in the small bowel, or from

prebiotics that have undergone fermentation in the colon.

They are also produced by fermentation of fiber by anaerobic

bacteria in the large bowel. Production of SCFA in the

intestinal lumen plays an important role in the maintenance of

the intestinal barrier. Short chain fatty acids and specifically

n-butyrate serve as the fuel for the colonocytes.[20] Butyrate has

been shown to be protective against colon cancer.


Low anaerobic bacteria (see “Predominant Bacteria”)

Antibiotic treatment

Insufficient fiber intake/poor diet

Slow transit time (more time for SCFA absorption)

Treatment Options:

Consider pre- and probiotic supplementation if the

predominant bacteria are low

Psyllium, oat bran, oligofructose, inulin

xylooligosaccharide, beta-glucan, or arabinogalactan

Increase dietary intake of fruits and vegetables

In ulcerative colitis, Crohn’s or those at risk for colon

cancer, consider butyrate enemas or enteric-coated

butyrate supplements

Enemas are contraindicated for those with GI bleeds

SCFA • Inflammation Immunology


Elevated total SCFA or N-Butyrate

Presence of short chain fatty acids and n-butyrate are essential

for the health of the colon. In general, high-normal levels of

these in the stool could mean that there is optimal fiber intake

and a balanced bacterial population. However, extremely

elevated SCFAs and n-butyrate in the stool could indicate

underlying GI abnormalities and need to be evaluated in

conjuction with the other GI Effects markers. Values of 184

mM/g or greater are above the 95% confidence interval.


Bacterial overgrowth[21]

Rapid transit time (less time for SCFA absorption)[22]


Pancreatic insuffiency resulting in carbohydrate

maldigestion and increased bacterial fermentation

Bacterial fermentation of blood[24]

Treatment Options:

Address all GI imbalances including bacterial

overgrowth, parasite infection, gluten intolerance, food

allergy, vitamin, mineral, or essential fatty acid (EFA)

deficiency, or chronic NSAID usage.

Normalize transit time

Pancreatic enzymes, betaine HCl, or digestive herbs.


Elevated Lactoferrin, WBCs, or Mucus present

Lactoferrin is an iron-binding glycoprotein released from

neutrophils during inflammation. It is a marker of leukocyte

activity and is a primary component of the host’s first line

immune defense against infection.


Mucosal inflammation

Bacterial or yeast overgrowth

Parasite infection

Inflammatory bowel disease, e.g. Crohn’s, ulcerative


Treatment Options:

Due to infection:

Remove pathogens

Probiotics and prebiotics to replenish beneficial bacteria

and establish proper balance

Enhance the endogenous immune (sIgA) defense by

supplementing with L-glutamine, S. boulardii and/or


Due to non-infectious inflammation, e.g. Inflammatory

Bowel Disease:

Balance the intestinal flora, if indicated

Anti-inflammatory herbs and nutrients, e.g. turmeric,

ginger, EPA/DHA, quercetin, antioxidants

Mucosa support, e.g. vitamin A, zinc, folic acid, aloe

vera, licorice, L-glutamine, butyrate (for UC), N-acetyl

glucosamine, slippery elm

Rule out food sensitivities

Test Interferences:

Colostrum has a high concentration of lactoferrin, so

those breast feeding or supplementing with colostrum

could show false positives

False negatives can be seen in those with severe immune



Depressed Fecal sIgA


Chronic stress



Immuno-suppressing medication

Treatment Options:

Support gut mucosa, e.g. glutamine, probiotics (S.

boulardii, Bifidobacteria), colostrum, immunoglobulins,

essential fatty acids, zinc, and stress reduction

Support immune function

Elevated Fecal sIgA


Immune response to eliminate pathogenic organisms in

GI tract

Sensitivities to foods

Treatment Options:

Support immune function

Remove pathogens, parasites, opportunistic bacteria,


Rule out food sensitivities

Elimination diet

Elevated Anti-Gliadin Antibody


Gluten enteropathy or sensitivity in colon

Treatment Options:

Remove gluten on trial basis

Consider Celiac Profile

Consider nutrients and herbs for mucosal healing

Additional Tests

Additional Tests • Digestion


Additional Tests

Depressed pH


Bacterial overgrowth

Carbohydrate maldigestion (increases bacterial

proliferation and the production of SCFAs)

Lipid malabsorption

Rapid transit time (less time for SCFA absorption)

Treatment Options:

Support digestion and absorption

Supplementary plant or pancreatic enzymes, betaine

HCl, disaccharidases (if needed)

Normalize transit time

Address all GI Effects imbalances

Elevated pH


Decreased bacterial production of SCFAs

Insufficient flora, dietary fiber, or water

Inadequate acid-producing organisms such as

Lactobacillus sp.


A high meat diet can stimulate ammonia production in

the bowel

Slow transit time (more time for SCFA absorption)

Elevated pH increases risk for colon cancer

Treatment Options:

Supplement with probiotics

Increase dietary fiber (esp. soluble) and water to increase

SCFA production and normalize transit time

Support digestion

Supplementation with betaine HCl or herbs to stimulate

gastric acid production, including ginger, peppermint, etc.

Address all GI Effects imbalances

Positive Occult Blood


Bleeding in upper GI tract due to peptic ulcer,

inflammatory bowel disease, parasite infection, colon

cancer, hemorrhoids [25, 26]

Rule out false positive from red meat

Treatment Options:

Repeat occult blood test on two more occasions

Address all GI Effects imbalances

Rule out iron deficiency anemia

Consider sigmoidoscopy or colonoscopy to identify

source, treat accordingly

Anti-inflammatory medical food

Anti-inflammatory diet

Food allergens

Positive RBCs


Bleeding in lower GI from hemorrhoids, intestinal

polyps, or tears around the anus due to constipation

Those with compromised liver function are more likely to

develop hemorrhoids

Treatment Options:

Treat constipation if present

Consider colonoscopy to identify source, treat


Assess liver function

Soothe and repair gut mucosa

RBCs, occult blood


Depressed Elastase 1

Elastase 1 is a digestive enzyme excreted by the pancreas,

exclusively, and has a direct correlation with pancreatic

function. Elastase 1 results are not affected by pancreatic

enzyme replacement therapy.[27,28] Optimal levels are > 500.


Suppressed pancreatic function

Gallstones or post-cholecystectomy

Chronic pancreatitis



Cystic fibrosis

Treatment Options:

Support digestion with betaine HCl with pepsin, or plant

or pancreatic enzymes or digestive herbs

Bile salts, taurine, or cholagogues (esp. if high

triglycerides and constipation)

Relax while eating and chew thoroughly

Support diabetes regulation

Elevated Vegetable Fibers, Triglycerides




Pancreatic insufficiency

Bile salt insufficiency (if elevated triglycerides)

Inadequate chewing (if elevated vegetable fibers)

Treatment Options:

Support digestion with betaine HCl with pepsin, plant or

pancreatic enzymes or digestive herbs

Bile salts, taurine, or cholagogues (esp. if high

triglycerides and constipation)

Relax while eating and chew thoroughly


Digestion • Absorption

Elevated Putrefactive SCFA


Protein maldigestion


Pancreatic insufficiency

Malabsorption, esp. if elevated long chain fatty acids or


Bacterial overgrowth of the small intestine

Treatment Options:

Support digestion with betaine HCl with pepsin, plant or

pancreatic enzymes or digestive herbs

Treat any underlying pancreatitis

Consider nutrients and herbs for mucosal support:

L-glutamine, Zn, EFAs, Vitamins A, E, and C,

pantothenic acid, N-acetyl glucosamine, glycyrrhiza, aloe

vera, slippery elm, etc.

Eliminate infection, address gluten intolerance, and food



Elevated LCFA, Total Fat, or Cholesterol


Malabsorption due to diarrhea, intestinal dysbiosis,

parasites, colitis, gluten intolerance, food allergy,

essential fatty acid deficiency, pancreatic or bile salt

insufficiency and/or chronic NSAID usage [29]

High dietary fat intake

Medications designed to bind and eliminate fats

If elevated cholesterol, suspect malabsorption, high

dietary intake or increased mucosal cell turnover

resulting from inflammation [30, 31]

Bacterial overgrowth of the small intestine (esp. if

elevated SCFAs)

Bacterial enzymes can also impair micelle formation,

resulting in lipid malabsorption

Treatment Options:

Support digestion with supplementary plant or

pancreatic enzymes, betaine HCl, digestive herbs, bile

salts or cholagogues, taurine or glycine, if indicated

Address food sensitivities or gluten intolerance

Check vitamin (esp. fat-soluble), mineral, and EFA status

Support mucosal health with nutrients such as

L-glutamine, Zn, EFAs, Vitamins A, E, and C,

pantothenic acid, N-acetyl glucosamine, glycyrrhiza, aloe

vera, slippery elm, etc.

Address all GI Effects imbalances

Botanical Sensitivities References



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Botanical Sensitivities

When treating with botanicals, it is recommended to use a broad spectrum product. Treatment with botanicals might also require

a longer duration than treatment with pharmaceuticals. Antimicrobial botanicals may be rotated and/or administered in a pulsatile

fashion to improve efficacy. Listed below are the active ingredients tested for each botanical used in antimicrobial blends.

Botanical Active ingredient

Wormwood (Artemesia) Artemisinin

Olive leaf Oleuropein

Uva Ursi (Bearberry) Arbutin

Garlic Alliin

Undecylenic acid (from castor bean) Undecylenic acid

Oil of thyme Thymol

Oil of oregano Carvacrol

Goldenseal Berberine

Cat’s Claw Quinic acid
Black Walnut 5-hydroxy-1,4-naphthoquinone