Did you know that you can have your bowel flora assessed in detail? And that you can do it on your own?
Ubiome is the first direct-to-consumer bowel flora assessment service that uses the same cutting-edge technology as the Human Microbiome Project at the National Institutes of Health.
I’ve used their service and find it invaluable in charting serial changes as you proceed through your program of cultivating the “garden” called bowel flora. An assessment is easy to perform and costs $89, no doctor’s order required. They are also at the forefront of a movement that I find VERY exciting: the crowd-sourcing of answers in health. If you permit, your data will be added to their research database, an enormous undertaking that will, like the Human Microbiome Project, be yielding some fascinating observations.
Here’s an excerpt from a Ubiome email they recently sent:
The Lowdown On Brown
“We love your poop. It’s so wonderfully rich in information about the microbiome, unlocked when we analyze it using DNA sequencing technology to reveal the make up of the three to six pounds of bacteria you carry in and on your body.
“But what exactly is poop? Since so much (excuse the expression) ‘passes’ through our lab, you might not be too surprised that we know a thing or two about its ingredients.
“First and foremost, feces contains a boatload of water. About 75% to be exact.
“Put that aside, however, and things get more interesting.
“About 50 to 80% of the remainder is bacteria, both living and dead. This is the stuff we’re focused on.
“On top of that there’s protein, undigested food residue (more on this in a minute), waste material from food, cell membranes, fats, salts and material released from your intestines and liver (e.g. mucus).
“If you’re anything like the average person you’ll produce around half your own body weight in feces every year.
“That’s a lot.
“Fortunately we require the tiniest proportion of this when you send in a gut microbiome test sample to us. It’s also far less yucky than you might imagine: simply swab your used toilet paper to collect just enough to turn the tip of the cotton swab brown.
“Poop is generally brown, by the way, largely because of a pigment called bilirubin produced when your red blood cells break down.
“And speaking of toilet paper, although it might seem as if you’re forever buying the stuff, this relatively minor inconvenience has to be better than living in Ancient Rome.
“In those days you’d have wiped yourself with a communal sponge rinsed in a bucket of water or vinegar after use. Nice.
“Oh yes, one last thing about that undigested food residue in your poop. (It’s okay, just about everyone has it, as some food is simply indigestible.)
“The outside of corn kernels is a perfect example. While you’ll probably have no trouble processing the insides, the hulls are made of cellulose so they generally pass through your body intact.
“Examine your poop after eating yellow corn, therefore, and you’ll likely spot what looks like intact kernels – actually just the “skins”.
“In fact they can provide a neat way to time how long your body takes to digest food.
“Like we said, your poop can tell you an enormous amount. All you have to do is listen.
“Or at least send a little of it our way.”
Disclaimer: I have no relationship with Ubiome beyond being a customer.
Does anyone have any info abut d mannose? I have had 2 uti infections in 2 months. I found out about d mannose . It seems to be helping. I will soon go on a maintenance dose of it. I’m hoping for no more antibiotics. I do take a good probiotic daily. I would love o start loosing the weight on the wheat belly plan. I think the utis were stalling me.
«… info about d mannose?»
I’m sure you’ve seen the same web info that I was able to find. Formal testing so far hasn’t been adequately controlled to be conclusive, but this supplement appears to work as well as the nitrofurantoin antibiotic that is a commonly prescribed – and of course wouldn’t have the adverse biome impact of an AB.
Using a quality d_mannose supplement might be preferable to consuming, say, cranberries or other fruits high in it, because the supplement form typically contains no sugars other than a gram or two of d_mannose (no glucose, no fructose).
Cutting blood sugar is also key in controlling UTIs, which are thought to feed on sugars. Consistent with that, UTIs are more common in diabetics.
«I do take a good probiotic daily.»
Which one? And have you added ~20 grams of prebiotic fiber to your daily diet?
«I would love to start loosing the weight on the wheat belly plan.»
From a UTI perspective, the very-low-carb aspect of Wheat Belly Total Health is as important as the wheat-be-gone.
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Thanks. I take NOW brand 50 billion probiotic one time a day on an empty stomach. I am on a keto gluten and grain free diet. I only eat 20 grams or less of carbs. I will continue d mannose to avert another uti. I have a lot of other issues,since I was on antidepressant meds and benzodiazepines for many years. I have become an expert in detoxing from these. I may not be loosing much on the scale, but I do feel much better.
«I take NOW brand 50 billion probiotic…»
That product may have only Lactobacillus strains, and no Bidifobacteria. See:
https://drdavisinfinitehealth.com/2014/04/gastrointestinal-recovery-after-the-wheat-battle-is-won/
If this is just for the UTI, a probiotic alone may suffice, but for general gut health, you also want to provide substrate in the form of prebiotic fibers or resistant starches, at about 20 grams per day (this feeds those bacteria). Prebiotic fiber can be chosen to have no impact on net carbs.
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Thanks, Bob!
You got me running to the refrigerator…..my DH’s beloved sliced cheese has natamycin.. He says he can eat MY cheese now…SCORE!!
re: You got me running to the refrigerator…..my DH’s beloved sliced cheese has natamycin.
The full spectrum of any hazards posed by anti-fungals are not yet scoped. I see this as a cost-of-convenience issue. For hard cheeses, giving up the convenience of pre-shredded, pre-sliced or pre-crumbled cheeses dramatically reduces the amount of AF required.
Cottage cheese and yogurt are another matter. Reading labels matters there. And, sigh, unless you want to make your own, it was already a challenge to find a full-fat yogurt not loaded with sugars or adverse artificial sweeteners.
So is kombucha good for the gut? I’ve bought a couple glasses, tastes kind of like soda. It’s carbonated. Does have some cane sugar in it but it saids organic.
I guess they have it as just the tea with no carbonation?
What are your thoughts on Spirulina (the super algae)?
«So is kombucha good for the gut?»
Dr. Davis doesn’t seem to have commented on it apart from one favorable remark on the Cureality forum. The issues with it, apart from inflated vendor claims, are net carbs, quality control, and if you make your own – strain drift and contamination over time with the starter.
For a commercial product, rely on the Nutrition Facts panel (if available, otherwise research the product on line). A typical commercial kombucha may have added sugar, a few grams of residual sugar, or other net carbs, per serving. Just factor it into the net carb budget. The original fermented sugar is usually no longer sugar, and presumably ceases to be any form of rapidly digestible carb.
«It’s carbonated.»
That’s an acid load you don’t need, but which is likely not a major concern.
«Does have some cane sugar in it but it said organic.»
Organic cane sugar mainly flags the producer as a charlatan, as there is likely no measurable pesticide residue after refining. The vendor is just pandering to what they probably think is a nutrition fad. Either they are fools, or they think they customers are.
«I guess they have it as just the tea with no carbonation?»
Or see if you can find it with safe added alternative sweeteners (they have to use real sugars prior to fermentation).
«What are your thoughts on Spirulina (the super algae)?»
There are cheaper ways to obtain the known beneficial micronutrients.
Contaminants are a concern. Microcystin toxicity is a concern.
Consumerlab.com has tested some products containing spirulina, and a significant fraction of them are “NOT APPROVED” by CL due to things like arsenic, lead, aerobic bacteria and label violations. Two vendors responded to CL with non-denial denials.
By the way, assume “super” is a warning label on a food or food-like substance. It has even less legal meaning than “natural”. Caveat emptor.
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You have to be careful when you interpret this data. To me, the variability in it makes it fairly meaningless. See:
http://blogs.scientificamerican.com/oscillator/which-bacteria-are-in-my-poop-it-depends-where-you-look/
I’m also not sure there’s enough data about what these bacteria do or how to increase one over the other. There’s really very little data showing that if you do change your microbiome, you’d get a benefit from this. It’s one thing to say that a certain bacteria is associated with some condition; it’s another to say that reducing or increasing that bacteria would have a beneficial effect.
For me, there’s not enough randomized controlled trials on people in this area to be concerned about this.
«You have to be careful when you interpret this data.»
Yep, and the base article here isn’t advocating interpretation, saying “… and find it invaluable in charting serial changes …”.
«To me, the variability in it makes it fairly meaningless.»
Certainly a ‘second opinion’ would be indicated before undertaking any extreme steps, like FMT or perhaps even probiotic enema. And thanks for the link. It rather looks as if the American Gut results aren’t terribly useful at all.
«I’m also not sure there’s enough data about what these bacteria do or how to increase one over the other.»
Compare any Hazda result to any typical American result, and it’s clear that there’s a huge amount to learn. uBiome is a useful tool in this early stage of understanding this.
«There’s really very little data showing that if you do change your microbiome, you’d get a benefit from this.»
Here’s what people have on the table:
You can test your biome a couple of times and get result A, with some generous error bars.
You then add 20-50 grams of varied prebiotic fiber to your daily diet, do a course of a quality probiotic, and experience some combination of: lowered blood pressure, lowered blood glucose, improved sleep, vivid dreams, improved bowel movements, improved mood, elevated mental alertness, etc. Hmmm, so you run another couple of tests and get result(s) B, which turn out to be very unlike A.
Oops. An unavoidable situation results in a course of antibiotic. You feel like your old self (terrible), and decide to get another couple of samples run. Result C is more like A than B. Perhaps it’s deficient in some strains found in the probiotic. This might provide some guidance on what to do next. In any event, you’ve added quite a bit to the database.
«For me, there’s not enough randomized controlled trials on people in this area to be concerned about this.»
As you wish. Because there’s probably no patent-protected potions that will come out of it, formal science is apt to be decades behind. This grass roots game has considerations, but it’s a game worth playing.
PS – Don’t eat the grass seeds.
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The test sounds intriguing. I’ll have to look into it.
With the mention on digested particles seen in stools, I’ve been pleased with how EZ water lessens, to virtually eliminates that from my experience. With an IBD condition, that is a concern for me. I view EZ water as being is similar to magnesium and other minerals found in water in a natural state. With tap water, I’m guessing EZ is missing.
«I view EZ water as …»
I view it as an unknown factor. I looked it up the last time it was mentioned on this blog, and again today, and can find only highly polarized opinions about it, with a bit too many supporters from the astral plane subculture.
I don’t think Pollack did himself any favor describing Exclusion Zone water as the “4th phase” of water. Physics had already co-opted that phrase for other states, and H3O2 is arguably no more “water” than is H2O2 (hydrogen peroxide).
Seems harmless enough – so if it works for you, is cheap, and you’re confident it’s not placebo effect, have at it.
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ubiome: “About 50 to 80% of the remainder is bacteria, both living and dead. This is the stuff we’re focused on.”
Potential customers need to fully grasp that statement. uBiome presently only sequences bacteria. The gut biome also includes eukaryotic parasites, fungi, protozans, viruses and yeasts, and you won’t get any data on them.
Does that matter? Does anyone else test the whole biome? Will uBiome eventually get around to the other lifeforms? Open questions; but in the meantime what they do offer seems like an astonishingly useful service for the modest price.
«The gut biome also includes eukaryotic parasites, fungi, protozans, viruses and yeasts…»
And on that theme, I was just tonight reading the label on some grated cheese, and saw an ingredient I didn’t recognize, and one which raised an eyebrow: natamycin
This is an anti-fungal agent used in cottage cheese, sour cream, yogurt, shredded cheeses, cheese slices and packaged salad mixes. In countries other than the US, it may be used on meats, such as sausages. Natamycin-cyclodextrin inclusion complexes have been developed for the protection of beverages, and apparently are present at high doses.
Macrolide polyenes of this kind are also sold as drugs, and used to treat fungal infections and overgrowths.
If any intestinal fungi are beneficial, does this additive depress their numbers?
Perhaps more ominously, for pathogens like candida, is natamycin breeding resistant fungi?
http://www.ncbi.nlm.nih.gov/pubmed/25862309
“Development of natamycin resistance has been observed in Candida spp. colonising the intestinal tract of patients following natamycin treatment of fungal infections. Horizontal gene transfer among different Candida spp. and within Aspergillus fumigatus spreads resistance. Therefore, it cannot be denied that use of natamycin for preservation of yoghurt and beverages may foster development of resistance to polyenes in Candida spp.”
Grated cheese products also routinely have anti-caking agents, so in the case of the package I was examining, I wasn’t at all surprised to see the vague “cellulose” listed. Such agents are often wheat-sourced.
For grated cheese, the solution for avoiding both hazards is to buy cheese in big blocks, and grate it yourself. Waxed cheese is probably ideal, as plastic-wrapped may still have some anti-fungal surface treatment (although dramatically less than pre-grated cheese).
Whole Foods put natamycin on their “Unacceptable Ingredients for Food” list in 2003.
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Wow, what a terrific observation, Bob. Perhaps we should explore just how common this additive is?
«Perhaps we should explore just how common this additive is? »
It looks like the biggest problems are cottage cheese and yogurt. It’s easier to avoid in shredded, sliced and crumbled cheeses by not buying them in those forms. We’re accidentally avoiding the cottage cheese and yogurt hazard by making our own, but that’s a fair bit of work.
Slate ran a little natamycin cheer-leading piece last December:
http://www.slate.com/articles/life/food/2014/12/natamycin_safety_whole_foods_has_banned_it_but_what_does_the_science_say.html
“… when natamycin is used for the surface treatment of food products it poses no health risk, in part because it is so poorly absorbed by the body.”
If you have properly functioning intestinal tight junctions, which wheat eaters will not.
“But multiple studies have shown natamycin to be safe for human consumption.”
There was no discussion of gut biome.
Wiki tells us “There is no evidence that natamycin, at either pharmacological levels or levels encountered as a food additive, can harm normal intestinal flora, but definitive research may not be available.”
Translation: no biome effects could have been identified, because no one has looked.
Natamycin, of course is only one anti-fungal agent. All of them, including the legacy sorbic acid, need to come under the dysbiosis microscope.