Dr Charles Forsyth

General Medical Practitioner


Where appropriate, I use a wide range of gastrointestinal investigations to identify or confirm the underlying causes and mechanisms of the health problems where they might relate to gut function.  I do, of course, use mainstream conventional investigations for identifying or excluding serious gut pathology when it might be suspected, but in many cases they reveal very little, particularly in irritable bowel syndrome.  Food intolerance/allergy, dysbiosis (gut flora imbalance with overgrowth of unfriendly bacteria or yeasts), increased intestinal permeability (leaky gut syndrome), malabsorption (causing multiple nutritional deficiencies), hypochlorhydria (reduced gastric acid production), pancreatic exocrine insufficiency (pancreatic enzyme deficiency), intestinal parasites, secretory IgA deficiency are all very common and one or more of them frequently coexist and are major underlying causes of (or contributing factors to) much of the ill-health we see.   We are very fortunate to have a lot of newer (and some not so new) investigations that have not yet found their way into mainstream medical practice, but are extremely helpful in identifying some of these causes.


Each different microorganism has fairly specific substrate (food) requirements and produces specific fermentation products.  When these fermentation products are not produced by the host, their measurement in the host can be used as a means of identifying the presence, types and levels of organisms present.   The fermentation products we are measuring most often are: hydrogen, methane, a variety of alcohols, D-lactate and hydrogen sulphide.  Unfortunately no one of these is common to all microorganisms, so no single test will detect all organisms.  A negative test only rules out overgrowth of organisms that produce the fermentation product one has tested for.

    1. Gut Fermentation Profile (Biolab) - sadly no longer available.

    2. This is, in my view, one of the best tests for identifying intestinal yeast overgrowth, it can also identify bacterial overgrowth. Twelve blood alcohols are measured one hour after oral glucose, a 3 hour fast and no alcoholic drinks/foods for 24 hours.  Ethanol is produced by a range of yeasts (but not all) including Candida species; other alcohols (eg. methanol, propanols, butanols, glycols) are produced by many bacteria. If limited to one fermentation test, this is my favourite for both fungal and bacterial overgrowth.

    3. Urinary Organic Acids

    4. A number of laboratories offer tests that measure a range of urinary organic acids that can be used as markers for a variety of things including nutritional status, metabolic and detoxification problems, oxidative stress, neurotransmitters and dysbiosis.  Each laboratory differs in exactly what and how many compounds they measure. Some offer profiles just for the dysbiosis markers. These can be very useful tests - they can be done by post, only a urine sample is required and no special preparation needed.  Microbial Organic Acids is my second favourite test for both fungal and bacterial overgrowth.

      1. Microbial Organic Acid Test (MOAT, 20 compounds, by Great Plains Laboratory, USA) via Biolab.

      2. Organic Acid Test (OAT, 73 compounds, by Great Plains Laboratory, USA, www.greatplainslaboratory.com) via Biolab.

      3. There are other laboratories that do organic acids, eg. Metametrix, USA, www.metametrix.com, Genova Diagnostics, USA, www.gdx.uk.net and ELN, Holland, www.europeanlaboratory.nl.

    5. Blood D-lactate (Biolab)

    6. D-lactate is produced by certain specific bacteria, including Enterococcus and Streptococcus species (but also Lactobacillus species), while mammals/humans don’t and metabolise it very poorly, very high levels can produce encephalopathy.  Worth testing in anyone suffering with substantial brain fog.

Hydrogen and Methane Breath Test using Lactulose (Biolab)

A test for identifying gastric and small intestinal bacterial overgrowth.  Following a 12 hour fast and an initial breath sample, a drink containing lactulose is taken. Breath samples are taken every 20 minutes over a three hour period and hydrogen & methane levels are measured. Increased breath hydrogen or methane indicates the presence of bacteria in the stomach or small intestine - a wide range of bacteria, but not all, produce hydrogen and methane.  The use of lactose, fructose or sucrose instead of lactulose enable the investigation of lactose or sucrose intolerance.

Neurotoxic Metabolite Test

A home test kit from: www.proteabiopharma.com.  Work by Professor Kenny De Meirleir & Dr Chris Roelant (soon to be published) indicates that Enterococci, Streptococci & Prevotella species produce hydrogen sulphide - for intestinal bacterial overgrowth.


Intestinal Permeability using PEG400 (Biolab)

This is an excellent test for assessing intestinal permeability since it measures the permeability to not just one size of molecule, but eleven, and can thus identify increased permeability (leaky gut syndrome) or decreased permeability (impaired absoption, or ‘malabsorption’).  It may also give an indication of whether the cause might be food intolerance/allergy or dysbiosis. 

Test procedure: A drink containing PEG 400, a mixture of eleven sizes of molecules, is taken. The different sizes of molecules pass through the gut wall and into the circulation with differing levels of ease. All the urine passed over the next six hours is collected. The quantity of each molecular size of PEG in the urine collection are measured and we can then reconstruct an absorption profile. See information sheet: Leaky Gut Syndrome.

Short-Chain Polypeptides (SCPP’s; Acumen)

Many hormones, cytokines, chemotactic agents and CNS-active metabolites are SCPPs. These substances are also produced during incomplete digestion of proteins. They are relatively small molecules and are easily absorbed into circulation where they can mimic hormones and moderators of immune function. They can also affect CNS metabolism and further disturb endocrine function through inappropriate feedback signals to the pituitary.  There are too many of these substances to measure them individually, so the results are reported as the total concentration of SCPPs for each group according to the number of amino acids. 

Test procedure: A blood sample is taken 1 to 2 hours after a meal that includes proteins. The foods chosen should reflect the usual main meal of the day and have regard for any dietary restrictions already in place. Failure to do this can lead to false negative findings. 

Increases in SCPPs are associated with increased gut permeability and/or inadequate protein digestion (insufficiency of digestive enzymes and/or stomach acid). However, raised levels are sometimes found in patients without any clinical evidence of gut dysfunction.  Indications for the test include unexplained endocrine disorder and immune dysfunction as well as digestive/permeability problems. Download more information: SHORT-CHAIN POLYPEPTIDES.pdf.  See information sheet: Leaky Gut Syndrome.

Urinary D-Xylose (Biolab)

This is a very useful test for identifying poor small intestinal absorption.  D-Xylose is a naturally occurring simple sugar that is normally readily absorbed by the small intestine, is not metabolised by the body and is readily excreted unchanged in the urine.  Changes in intestinal absorption are therefore accurately reflected in the amount that appears in the urine.

Test procedure: A five hour urine collection is made after drinking 5 grams of D-Xylose in a glass of water.  The total urine volume is measured and a sample sent to the laboratory, where the D-Xylose concentration is measured.  See information sheet: Malabsorption.


For any coeliac tests to be reliable you must be regularly eating gluten grains/wheat - the likelihood of false negatives progressively increases the longer the abstinence.

Blood tests

  1. Tissue Transglutaminase (tTG, IgA) - the most specific test

  2. Endomysial antibodies (IgA)

  3. Reticulin antibodies (IgA)

  4. Gliadin antibodies (IgA & IgG)

IgA deficiency is common in coeliac disease (10 times more than the general population) and this may lead to false negative antibody test results in some patients - IgA should therefore be measured at the same time as these tests. By measuring both IgG & IgA antigliadin antibodies, this test may also identify gluten sensitivity in IgA deficient patients and may also identify those who are gluten sensitive but do not have true coeliac disease (as defined by characteristic histological changes on jejunal biopsy samples).  See information sheet: Wheat, Gluten & Grain Sensitivity.  I now mostly use The Doctors Laboratory (TDL) Coeliac Screen, which includes all four of these.


There are now a huge range of very useful tests available including very comprehensive and accurate microbiology (assessment of normal and abnormal intestinal flora: bacteria, yeasts, parasites, together with assessment of their sensitivities to a range of both natural and synthetic antimicrobial agents), markers of inflammation, digestion, absorption, metabolism and immunology.

Comprehensive Stool Tests

  1. Comprehensive Stool Analysis (Doctor’s Data, USA, www.doctorsdata.com): includes elastase and sIgA, via Biolab £200.

  2. Comprehensive Digestive Stool Analysis 2.0 + Parasitology (CDSA2.0+P, Genova Diagnostics, USA, www.gdx-uk.net): This is their most comprehensive test (about £291).

  3. GI Effects Comprehensive Stool Profile (Genova) www.gdx.uk.net  This test includes most of the CDSA2.0+P above and adds microbial DNA analysis.  About £304.

Stool Microbiology:

    1. Comprehensive Parasitology (Doctor’s Data, via Biolab; Two samples: £115; Three samples: £125: Bacteriology, Mycology, Parasitology + six normal flora (Lactobacillus sp, Bifidobacteria sp, Bacteroides sp, E coli sp, Enterococcus sp, Clostridia sp.) + Sensitivities of pathogens found to 7 natural and 4 synthetic antifungals and 7 natural and 6 synthetic antibacterials.

    2. Stool Microbiology (Doctor’s Data, via Biolab; £76): Bacteriology and Mycology + six normal flora (Lactobacillus sp, Bifidobacteria sp, Bacteroides sp, E coli sp, Enterococcus sp, Clostridia sp.) + Sensitivities of pathogens found to 7 natural and 4 synthetic antifungals and 7 natural and 6 synthetic antibacterials.

    3. Comprehensive Parasitology Genova (about £152) www.gdx.uk.net 

Stool Parasitology - to identify intestinal parasites only.  See separate information sheet.

    1. Genova Diagnostics (about £108)

Pancreatic Elastase 1 (available on NHS + Genova Diagnostics (about £100), Doctor’s Data (about £114), TDL (about £95)): a non-invasive marker in stool for pancreatic enzyme insufficiency; included in the full comprehensive profiles of all three companies.

Calprotectin (available on NHS + TDL & The London Clinic about £46; included in Genova’s CDSA2.0) - this is most reliable test for gastrointestinal mucosal inflammation (eg. when trying to exclude inflammatory bowel diseases, eg Ulcerative colitis and Crohn’s disease). Doctor’s Data’s CSAP includes Lysozyme and Lactoferrin, while Metametrix’s GI Function Profile includes Lactoferrin - which are ok but not as reliable.

Secretory IgA - to identify poor mucosal immune defence - sIgA is the main immune defence in the gut.

    1. Salivary: Genova (about £65).

    2. Stool: Doctor’s Data & Genova - included in their full comprehensive profiles


Salivary Endothelial Growth Factor (EGF - Acumen about £60): a non-invasive marker, elevated levels occur in  hyperchlorhydria, stomach cancer & some upper gastrointestinal infections; low levels may be due to hypochlorhydria (low stomach acid).

Candida Antibodies (IgA/ IgG; Genova (about £70)): can be a useful indicator of intestinal candidiasis, but can yield false negatives in some situations.  Salivary or blood sample.

Gastrointestinal Investigations

   INVESTIGATIONS: Nutritional  Gut  Toxins  Microbial  Mitochondrial  DNA Adducts