Gut dysbiosis is an unknown factor in systemic body odor and halitosis, although secondary TMAU (TMAU2) seems to mainly be accepted as meaning abnormal TMA-production from bacteria. However, most seem to feel they have a gut problem, and it seems there could be a connection, especially in gut-smells body odor.
One of the leading labs in testing for 'gut dysbiosis' and similar underlying problems, is Metametrix based in Duluth Georgia. They have recently pioneered DNA testing of microbes in stool samples, which means they can identify far more strains of bacteria than normal stool-culture testing. Their website is always worth a visit: Metametrix website
Cass Nelson-Dooley, M.S, Clinical Consultant at Metametrix Clinical Laboratory, has kindly given us an interview, with contributions by Mr. Tony Hoffman, on the work at Metametrix, and how it may apply to metabolic body odor and halitosis. Thank you Cass and Metametrix.
This is part 1 of 2
Part 2 is here
Metametrix questions
Intro and general questions
Would you like to summarise the history of Metametrix and what they do ?
The mission of Metametrix is to improve health worldwide by providing clinical laboratory tests that identify nutritional imbalances and toxicities underlying chronic diseases. Metametrix Clinical Laboratory has been around for 25 years, providing innovative laboratory tests to integrative clinicians. For example, we offer vitamin blood tests, fatty acid blood tests, and food allergy tests. Almost two years ago, we released a ground-breaking test, called the GI Effects, which measures stool bacteria, fungus, and parasites with DNA analysis. We are the first ones in the world to offer such a test.
The mission of Metametrix is to improve health worldwide by providing clinical laboratory tests that identify nutritional imbalances and toxicities underlying chronic diseases. Metametrix Clinical Laboratory has been around for 25 years, providing innovative laboratory tests to integrative clinicians. For example, we offer vitamin blood tests, fatty acid blood tests, and food allergy tests. Almost two years ago, we released a ground-breaking test, called the GI Effects, which measures stool bacteria, fungus, and parasites with DNA analysis. We are the first ones in the world to offer such a test.
How much do you think is known about the gut ecology and states of dysbiosis currently ? Is there more to discover?
I think that we have some good ideas about gut ecology and dysbiosis currently but there is always more to discover. The human GI tract is very long and our tools for measuring what happens in the GI tract are limited. For example, until now, it was very difficult to know what was happening with bacteria in the anaerobic (no oxygen) regions of the GI tract. Stool tests were done by culture, so environmental oxygen would make it very hard to grow and measure these “oxygen-hating” bacteria. I think new technologies such as RT-PCR will help us find out much more about the microbiota of the human GI tract.
I think that we have some good ideas about gut ecology and dysbiosis currently but there is always more to discover. The human GI tract is very long and our tools for measuring what happens in the GI tract are limited. For example, until now, it was very difficult to know what was happening with bacteria in the anaerobic (no oxygen) regions of the GI tract. Stool tests were done by culture, so environmental oxygen would make it very hard to grow and measure these “oxygen-hating” bacteria. I think new technologies such as RT-PCR will help us find out much more about the microbiota of the human GI tract.
Is the general rule for a symbiotic gut something like: a bit of lactobacillus in the lower small intestine, a lot of bifidobacteria in the right side of the colon, and non-carb type bacteria in the lower left?
I think Lactobacillus and Bifidobacteria have enjoyed all of the attention when it comes to healthy GI bacteria, mostly because these bugs can grow aerobically and can be packaged for sale. While the GI tract contains hundreds of different species, 30-40 species from only 5-6 genera make up 99% of the total biomass. Therefore, measuring the predominant genera offers a good snapshot of the colon environment. The anaerobic bacterial genera measured in the GI Effects test are those known to be present in humans: Bacteroides species (sp.), Prevotella sp., Fusobacteria sp., Mycoplasma sp., Clostridium sp., Lactobacillus sp., Bifidobacter sp., and E. coli. I think the more diversity of organisms, the better. Some studies show that as we age, the biodiversity of our GI bacteria decreases, making us more vulnerable to pathogens.
I think Lactobacillus and Bifidobacteria have enjoyed all of the attention when it comes to healthy GI bacteria, mostly because these bugs can grow aerobically and can be packaged for sale. While the GI tract contains hundreds of different species, 30-40 species from only 5-6 genera make up 99% of the total biomass. Therefore, measuring the predominant genera offers a good snapshot of the colon environment. The anaerobic bacterial genera measured in the GI Effects test are those known to be present in humans: Bacteroides species (sp.), Prevotella sp., Fusobacteria sp., Mycoplasma sp., Clostridium sp., Lactobacillus sp., Bifidobacter sp., and E. coli. I think the more diversity of organisms, the better. Some studies show that as we age, the biodiversity of our GI bacteria decreases, making us more vulnerable to pathogens.
Is stool DNA testing likely to be as good as stool microbial testing will get?
I think DNA analysis in stool testing is an enormous leap forward in technology. In the Manual of Clinical Microbiology they state, “PCR is the best developed and most widely used nucleic acid amplification strategy…These techniques have sensitivity unparalleled in laboratory medicine, have created new opportunities for the clinical laboratory to have an effect on patient care and have become the new ‘gold standards’ for laboratory diagnosis of several infectious diseases.” With DNA analysis, we are seeing the microbial population with more sensitivity and specificity than ever before. Doctors and scientists trained on the older culture techniques have to view DNA results with a fresh perspective. I think that stool microbial testing will continue to evolve and improve in ways that we can scarcely imagine today.
I think DNA analysis in stool testing is an enormous leap forward in technology. In the Manual of Clinical Microbiology they state, “PCR is the best developed and most widely used nucleic acid amplification strategy…These techniques have sensitivity unparalleled in laboratory medicine, have created new opportunities for the clinical laboratory to have an effect on patient care and have become the new ‘gold standards’ for laboratory diagnosis of several infectious diseases.” With DNA analysis, we are seeing the microbial population with more sensitivity and specificity than ever before. Doctors and scientists trained on the older culture techniques have to view DNA results with a fresh perspective. I think that stool microbial testing will continue to evolve and improve in ways that we can scarcely imagine today.
You mentioned that in your GIfx results, there appears a trend of 3 clusters of dysbiosis? Could you elaborate on this?
Among the nine genera that we are measuring, some tend to grow together while excluding others. So, we are advancing our ability to discriminate one type of bacterial overgrowth from another. At this point, we do not know which cluster might be more associated with formation of malodorous products.
Among the nine genera that we are measuring, some tend to grow together while excluding others. So, we are advancing our ability to discriminate one type of bacterial overgrowth from another. At this point, we do not know which cluster might be more associated with formation of malodorous products.
Are you finding parasites to be a common problem? Mainly protozoan?
We see parasites in about 18% of people. Some parasites are more common than others. Based on our in-house research the population data shows about 6% of people have Blastocystis hominis, 5.5% Necator americanus (or hookworm), and 5.3% Cryptosporidium.
We see parasites in about 18% of people. Some parasites are more common than others. Based on our in-house research the population data shows about 6% of people have Blastocystis hominis, 5.5% Necator americanus (or hookworm), and 5.3% Cryptosporidium.
How big a problem is candida in your results and would you like to make any comments about candida?
In the population that submits stool tests to us, we see about 12% Candida. This is less than observed by stool culture. According to our data that discrepancy is due to false overgrowth in transport media. We will publish more on this soon. We also assess the upper GI tract for Candida overgrowth using an excellent marker of Candida called D-Arabinitol. It can be measured in urine and there is a lot of research on this compound in blood as a measure of invasive candidiasis.
In the population that submits stool tests to us, we see about 12% Candida. This is less than observed by stool culture. According to our data that discrepancy is due to false overgrowth in transport media. We will publish more on this soon. We also assess the upper GI tract for Candida overgrowth using an excellent marker of Candida called D-Arabinitol. It can be measured in urine and there is a lot of research on this compound in blood as a measure of invasive candidiasis.
If someone has dysbiosis and a simple-carb addiction, would candida be the main suspect, or is there other usual suspects?
When someone has gut symptoms suggesting dysbiosis and a simple-carb addiction I try to be open-minded to other causes besides Candida. I think some people assume the patient has Candida when they actually have bacterial overgrowth. I’ve seen cases where the patient results show various bacteria species are very high and Candida is not an issue at all! I think the excessive bacteria can suppress the fungal growth. I also wonder about adrenal exhaustion and neurotransmitter status when people crave sugars. I think dysbiosis can often be a side effect of food intolerances. This is why laboratory testing is so important for doctors and patients. You can find out the cause of your symptoms instead of shooting in the dark.
When someone has gut symptoms suggesting dysbiosis and a simple-carb addiction I try to be open-minded to other causes besides Candida. I think some people assume the patient has Candida when they actually have bacterial overgrowth. I’ve seen cases where the patient results show various bacteria species are very high and Candida is not an issue at all! I think the excessive bacteria can suppress the fungal growth. I also wonder about adrenal exhaustion and neurotransmitter status when people crave sugars. I think dysbiosis can often be a side effect of food intolerances. This is why laboratory testing is so important for doctors and patients. You can find out the cause of your symptoms instead of shooting in the dark.
How big a problem is poor digestive function in your results?
On the GI Effects test, we commonly see patients who show problems digesting fat, protein, or that have poor pancreatic function. Sometimes the clinician expects to find that the patient has a parasite due to abdominal pain and actually the pain appears to be caused by problems digesting and absorbing nutrients from the diet.
On the GI Effects test, we commonly see patients who show problems digesting fat, protein, or that have poor pancreatic function. Sometimes the clinician expects to find that the patient has a parasite due to abdominal pain and actually the pain appears to be caused by problems digesting and absorbing nutrients from the diet.
What type of symptoms would someone with over-dominant lactobacillus have and how common is it? Would taking Bifidobacter on its own always be ok?
It is possible to have too much of a good thing- namely Lactobacillus sp. Normally this occurs when people eat too many refined carbohydrates or if they’ve had a surgical procedure in the small intestine. A diet rich in simple carbs and poor absorption can feed the Lactobacillus. Similarly, alterations in the anatomy of the small intestine can create pockets where Lactobacillus can thrive. We measure Lactobacillus in the GI Effects Profile and also we look at the metabolite, D-Lactate in urine. I think treatment with a diet low in refined sugars, a probiotic (Bifidobacteria or Saccharomyces boulardii), and fiber, can help.
It is possible to have too much of a good thing- namely Lactobacillus sp. Normally this occurs when people eat too many refined carbohydrates or if they’ve had a surgical procedure in the small intestine. A diet rich in simple carbs and poor absorption can feed the Lactobacillus. Similarly, alterations in the anatomy of the small intestine can create pockets where Lactobacillus can thrive. We measure Lactobacillus in the GI Effects Profile and also we look at the metabolite, D-Lactate in urine. I think treatment with a diet low in refined sugars, a probiotic (Bifidobacteria or Saccharomyces boulardii), and fiber, can help.
Does the Organix Dysbiosis urine test complement the stool test? Or could it be overlapping the same result?
The results of the Organix Dysbiosis Profile and the GI Effects Profile are used in conjunction to assess the health of the whole GI tract. The Organix Dysbiosis Profile is a urine test that measures bacterial and fungal by-products. These organisms are growing in the small intestine, where the by-products are absorbed and are present in the person’s circulation and eventually in the urine. In contrast, the stool results reflect the health of the colon. I also think a food antibodies test is useful when trying to see into a person’s GI health.
The results of the Organix Dysbiosis Profile and the GI Effects Profile are used in conjunction to assess the health of the whole GI tract. The Organix Dysbiosis Profile is a urine test that measures bacterial and fungal by-products. These organisms are growing in the small intestine, where the by-products are absorbed and are present in the person’s circulation and eventually in the urine. In contrast, the stool results reflect the health of the colon. I also think a food antibodies test is useful when trying to see into a person’s GI health.
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