Wednesday, July 23, 2014

Read: "Gory Details -- Here’s the poop on getting your gut microbiome analyzed"

Interesting read:

"Here’s the poop on getting your gut microbiome analyzed"

I asked two different companies to analyze my gut microbiome. American Gut (left) gave nearly opposite results to those from uBiome (right) with respect to the major phyla of bacteria in a duplicate sample.

For more gut stool analysis consider the following functional medicine labs:

Stool -- Genova Diagnostics, Biohealth, Great Plains, Doctor's Data, etc
Urine -- Genova Diagnostics (ONE, Nutri Eval, Organix, etc)

The stool testing gives a partial view of what's inside that the Am Gut and uBiome lack -- protozoa, helminths, parasites, pathogenic yeasts, fungi, and the pathogenic bacterial overgrowths compared with symbiotic, beneficial commensal populations (E coli, Bifido, Enterococcus, Lacto, SBOs, etc)

Urine testing gives a partial view of what's going out of the gut

Caveat: all the current testing is imperfect including functional medicine testing, but what they can reveal are the (more stable) pathobionts and yeasts, which usually survive and thrive once colonization resistance and gut barriers are no longer functioning well or at all.  Recently 16S pyrosequencing was done as part of the Ribosomal Database Project (RDP) on a sample of healthy Korean gut microbiota. Geographical differences were seen compared to other Asian and American countries however between Korean guts, there was homology and core phylogenetic similarities.

In 8 Koreans (below), their guts were tracked monthly for 3 time points. Temporally, great shifts are notable on nearly every gut. I think it indicates clearly that our gut is like a playground. Kids, toddlers, nannies and teenagers all vie for spots and it's constantly shifting over time. Studies show even between meals, the microbiota show significant shifts. A diet protocol can shift populations in only day.

Temporal Month-to-Month Microbiota Shifts
Korean RDP, 2011


aerobic1 said...

Yes, Grace, that is indeed a good read. The author could certainly not be the one to blame for this disparity. This appears to be a case where the race to be first to the marketplace with microbiome testing got ahead of the technology, or lack thereof. The next phase of technology advancements and collection procedures will likely address these types of discrepancies.

Dr. B G said...

Exactly. GDX is not perfect in technology either and I suspect the other companies as well.

Bifido analysis is completely done imperfectly with the Masaii and other gut studies. New primers and technology and standardization/QC (alcohol v non alcohol collections, etc) hopefully will correct the 'misinterpretations'.

It is still a far cry improvement from culture based tech which missed 10-100-fold strains!

They still all currently miss the mycobiome for yeasts/fungi - as well as as you are aware viruses, phages, and spirochetes.

Anonymous said...

thanks for posting this, although I must confess I am now even more confused. I can't tell whether it is worth the trouble to get my gut biome analyzed. It FEELS (not saying it IS, saying it FEELS) like consulting an astrologer at this point -- if two labs give completely contradictory results then I'm not even sure of the point of submitting samples. Woudl be grateful for any thoughts you could share. Are some labs better than others? Does this mean that, for the layperson, it makes sense to hold off until testing protocols improve?

Unknown said...


About a 1.5 years ago I was diagnosed with Reactive Arthritis. Didn't take medication and AIP Paleo instead, couldn't walk for 5 months.

Rollercoaster with health since then.

Problems: bloating, unable to eat inulin or starch (joint, skin, anxiety problems result), often tired, get extremely tired after meals early in day, and foggy-headed.

I have done FMT twice, with some good results. But I still clearly have issues.

Where should I start?? See a naturopath? Get a comprehensive stool analysis? Get an OAT test? I have no idea what I should be doing to feel normal again!!!

Dean said...

Dr. BG,

In this article,, you mentioned lymphoma. While the article referenced in the post,, speaks a lot to biome effects on immunity, it doesn't mention any information leading to later development of lymphoma as a response to auto-immunity.

Do you have more you could share on any theories you have concerning the biome's effects leading to lymphoma?


aerobic1 said...


In my opinion, reactive arthritis is exactly what it states, it’s a reaction (a symptom) and should not be confused with a root cause of disease. It is generally associated with an infection. Mayo Clinic states it can be caused by one or more of the following:
• Chlamydia
• Salmonella
• Shigella
• Yersinia
• Campylobacter

Symptoms can be one or more of the following:
• Pain and swelling of certain joints, often the knees and/or ankles
• Swelling and pain at the heels
• Extensive swelling of the toes or fingers
• Persistent low back pain, which tends to be worse at night or in the morning

There are probably many more bacterial infections that will inflict RA too. In my case my RA was cause by Lyme disease which is a result of a bacterial infection from Borrelia burgdorferi. Once I treated it properly my RA was totally gone and was pain-free.

From my perspective, I would suggest you look for a an expert in Infectious Disease who can run a full evaluation including a number of immune function and blood culture tests looking for specific antibodies which can help draw a roadmap to what the root cause of your issues. Once that root cause is identified and properly treated it will likely result in improvements in your RA. My preference is to look for an Integrative MD or specialist who is well practiced in this type of problem. If it is serious infection, it may take a variety of prescription, herbal and possibly homeopathic agents to get you on the right road. I would also focus on correcting and maintaining gut function and integrity. Just my opinions. Good luck.

Dr. B G said...

Thanks Aerobic1 for generous thoughts!


Your gut is pretty f*kcered it sounds like, despite the benefits of FMT because the root causes are not elucidated yet and the gut fully rehab'd.

For reactive arthritis, immunity, adrenals, thyroid and gut all require attention I think. Don't give up. The answers won't be easy but worth pursuing.


Ck out the functional medicine labs either on your own or with your functional/integrative medicine practitioner.

Dr. B G said...


for ya... gluten can trigger because it induces permeability particularly for celiacs. For non-celiacs, permeability is still the notable event that leads to gut dysbiosis and aberrant DNA damage and growths. VLC actually can potentially induce cancers and lymphoma due to the lack of butyrate from bacterial fermentation of plant fiber and starches. Guess where ketone bodies, beta-hydroxy-butyrate, derives from? The substrate is butyrate from the gut. Butyrate also plays important roles for DNA correct editing as an HDAC inhibitor. In order for fermentation that extends the entire length of the 1.5 m colon, the entire spectrum of fiber is needed: insoluble, soluble/viscous, and cooked resistant starches. RPS is great for butyrate but sadly alone it performs suboptimally by failing to both ferment to the end of the colon (only caecum) and failing to lower stool pHs in clinical animal and human trials.

Dig Dis. 2011;29(2):166-71. doi: 10.1159/000323879. Epub 2011 Jul 5.
Bacteria as trigger for chronic gastrointestinal disorders.
Marteau P1, Chaput U.
Author information
Apart from acute infections, microorganisms may also induce or perpetuate chronic inflammatory diseases and reversible or irreversible proliferation of various cells in the gastrointestinal tract (the extreme being adenocarcinoma and lymphoma). Helicobacter pylori is not only involved in the pathogenesis of lymphoma and gastric adenocarcinoma. The steps and mechanisms of the carcinogenic process involve host predisposition, environmental factors, and strain virulence. The steps of lymphoma genesis include chronic inflammation, acquisition of mucosa-associated lymphoid tissue in the stomach, proliferation of the B lymphocytes in an inflammatory context, acquisition of genetic anomalies and dysregulation of the NF-κB pathway. The role of Campylobacter jejuni in immunoproliferative small bowel disease has also been shown and eradication of this bacterium can cure the lymphoma at its early stage. The evidence for the role of some bacteria in colon cancer development is discussed. Opportunistic pathogens are detected in the stools or mucosa of a proportion of subjects with Crohn's disease. They include Mycobacterium avium paratuberculosis, adherent invasive Escherichia coli, and Clostridium difficile. A dysbiosis has been repeatedly observed in patients with inflammatory bowel disease. Instability of the dominant microbiota and decreased biodiversity (especially in the firmicutes phylum) are major characteristics. The decrease of Faecalibacterium prausnitzii seems to have a prognostic value to predict relapse of Crohn's disease after surgery. Finally, important perspectives are opened by new tools such as metagenomics and metabolomics of the gastrointestinal ecosystems. Major tracks concern irritable bowel syndrome, colon cancer and obesity.

Dr. B G said...

(cont) Dean...

Dig Dis. 2011;29(6):554-61. doi: 10.1159/000332967. Epub 2011 Dec 12.
Contribution of gut microbiota to colonic and extracolonic cancer development.
Compare D1, Nardone G.
Author information
It is estimated that 20% of malignancies worldwide can be attributed to infections, i.e. about 1.2 million cases per year. A typical example of the association between bacterial infection and gastrointestinal malignancies is Helicobacter pylori infection with both gastric cancer and mucosa-associated lymphoid tissue lymphoma. Bacteria are an important component of the human body. The human intestine contains >500 different types of microorganisms, the 'gut microbiota', that play important functions such as energetic metabolism, proliferation and survival of epithelial cells, and protection against pathogens. Chronic alteration of intestinal microbiota homeostasis, 'dysbiosis', could promote many diseases, including cancer. The mechanisms by which bacteria may induce carcinogenesis include chronic inflammation, immune evasion, and immune suppression. There are three effector pathways of T helper (Th) cell differentiation: Th1 responses promoted by procarcinogenic signal transducer and activator of transcription (Stat)1 and Stat4 signaling, Th2 responses promoted by Stat6 signaling, and Th17 responses promoted by Stat3 signaling. Interestingly, Th1 responses, driven by IL-12 and characterized by IFN-γ production, are typically anticarcinogenic, whereas Th17 responses are activated in various cancers. Furthermore, a T regulatory response, driven by IL-10 and TGF-β, counterbalances the proinflammatory effect of Th17 responses. Elevated numbers of T regulatory cells suppress the innate and adaptive immune responses, thereby contributing to tumor progression. The emerging relationship between gut microbiota and cancer has prompted new ways of thinking about cancer prevention and has led to the development of noninvasive diagnostic tests and innovative treatments, such as with probiotics. However, although in vitro and animal model studies suggest a protective anticancer effect of probiotics, the results of human epidemiological studies are controversial.

Anonymous said...

Brock said...

Genova recommends stopping probiotics 2 weeks prior to testing, do you follow this rule?

Dr. B G said...

No. I consider probiotics a drop in the proverbial gut flora ocean

Anonymous said...

I've been dealing with chronic bloating (severe, both gas, water, and stored up feces I think) and constipation after visiting China 8 months ago. I was on antibiotics at the time (doxycycline and amoxicillin, only briefly for each) and then got sick in China (diarrhea for a week). Ever since then, my digestive problems started as well as severe acne.

I guess my gut flora is completely out of whack, but I'm thinking i may still have parasites and other pathogens.
Would the GI Effects 2200, or one of the mroe specific tests, along with something better for parasites like the ParaWellness test be the best thing to do right now? I've had improvements only from fiber supplements and eating tons of food (much more than I should be) helps push things through and allow me to go.

I'm probably somewhat hypothyroid as well from some simple blood tests I had done, but I don't think that's really related to this considering it had a clear trigger for me (getting sick in China)

Thanks, Sean

Dr. B G said...

Dr Sean
I think u are right on!!

This is a decent company as well for parasite eval

Pre china, like you I had no parasites

But post china, somewhere (or in Cali during our freq visits) picked up one. Dave Asprey on our Bulletproof podcast and I talk about his parasite as well. Fun. But very common and misdiagnosed all the time. Yeasts can mimic parasitic damage as well but GI fx by GDX or other functional medicine stool/urine testing will reveal.

With the gut being the size of moon compared to the real estate in the USA, when it is perforated and broken, cortisol and thyroid hormones are vastly drained. Seek some adrenal support whilst the gut is healing and it will speed recovery

Anonymous said...

Thanks so much Dr. B G.

So for the GI Effects, I'd need to find a practitioner who can order the test for me? Do you think the 2200 is worth it in my case? Is there one that's just as accurate as the Gi effect but cheaper?

Also, which probiotics would help after Amoxicillin, Flagyl, Cipro, and doxycycline courses?

Thanks, Sean

Dr. B G said...

All the tests are imperfect but I like the GDX, biohealth, doctors data and great smokies ones. After those antibiotics there are mass extinctions ;) If you've on the SAD then gluten, n6 and refined carbs/sugar have done untold devastation to the flora as well