Wednesday, December 18, 2013

Crowd-Sourced Science n=4

Allan Folz's Gut Microbiome Study, n=4


I *heart* science and I love places like indiegogo which encourage all kinds of experimentation and projects whether it's techno or food-related.  It's truly a brilliant evolution.

Allan Folz and his family of 4 are doing a gut microbiota study: Resistant Starch & Gut Biome Family Science Project for six weeks, testing pre- and post-microbiome.  Allan cultures his own viili heirloom yogurt, a type of Swedish or Finnish yogurt. As we know yogurt that has live probiotics has many health benefits for us. One study in rodents showed that yogurt with live cultures improved 'rodent swagger', leaner body mass, and testicular size in males and improved fertility (brood size) and nesting instincts (successful weaning) in female rodents. "Mice That Eat Yogurt Have Larger Testicles", Scientific American, 2012.


Besides contributing to the first RS n=4 study with pre- and post-microbiome 16S rRNA pyrrosequencing outcomes,  first-tier funding ($250) for this crowd-sourced experimentation includes a personal tour of Oregon Wine Country in Yamhill County and a hand written thank you.


Allan's goal:
(1) The goal of this project is to measure and compare the effects of resistant starch dose-responses on gut biome in as reasonably controlled a manner as possible by selecting an otherwise typical and healthy family that lives and eats together.
(2) A secondary goal of this project is to provide a proof-of-concept and, perhaps, a template for future crowd-sourced, small-scale diet and health experiments.




Study Design:

Purchased two "Microbes for Four" swab kits from the American Biome Project.

Provided a stool swab -- 2 children, 2 adults

Over the course of a 6 week study period food journal will be maintained for each participant and provide a daily diet supplement of resistant starch in the form of Bob's Red Mill Unmodified Potato Starch. Each participant will follow a unique supplementation regimen:

a) adult 1 - 2 TBSP PS mixed in water, consumed on an empty stomach

b) adult 2 - 4 TBSP PS mixed in water, consumed on an empty stomach

c) child 1 - 1 TBSP PS  plus 1 TSP whole psyllium husk mixed into yogurt

d) child 2 - 1 TBSP PS mixed into yogurt

At the conclusion of the study period the four test subjects will provide a second stool swab for comparison purposes. The lab results from both swabs will be shared publicly on the internet.

Allan: Our current diet is almost entirely home-cooked meals somewhere between primal/paleo-ish and WAPF. None of us has supplemented with potato starch previously. We do eat, a few times a week up to almost daily, an heirloom strain of viili yogurt that I culture myself. More details, including a fairly typical week of meals for us are recorded at the project blog.



Microbiome 16S rRNA pyrrosequencing Testing: PRE v. POST

Additional testing depends on several factors: funding, information garnered and availability.  AmGut is wonderful and provides the bacterial and Archae enteroprofiling. On the other hand, functional medicine laboratory testing provides valuable information about the other gut ecosystem including profiling for fungi, parasites, worms and pathogenic overgrowths, as well digestive enzyme capacities and pH.

Disclaimer: I am working for Allan!



Sample food diary  (follow up HERE)

Food Journal: Thurs, Dec 12
Breakfast:
Child 1 - 2 eggs scrambled, melted cheese on top; yogurt w/ granola
Child 2 - ditto
Adult 1 - coffee & half-n-half
Adult 2 - coffee & half-n-half

Lunch:
Child 1 - don't know
Child 2 - don't know
Adult 1 - yogurt w/ granola; 2 egg omelet w/ deli ham; 1 corn tortilla
Adult 2 - ditto

Dinner:
All - roasted pork loin; brown rice, cabbage, onion, etc; sliced up fresh pineapple on the side

Evening snack:
1 c Milk & 6 squares (~0.7oz) 85% dk chocolate

26 comments:

Tim Steele said...

I gave $25! Hope more give--this will be the ultimate bio-hack. C'mon people, you won't get a chance like this ever again--all you need is a PayPal account and 5 minutes.

Before AND After, kids AND adults, it doesn't get better than this!
Tim

Mark L said...

I did $25. I figure it is a small way for me to pay back for the benefit that I think I'm getting from potato starch.

Dr. B G said...

Mark L,

RU getting a lot of perceivable and tangible benefits? And PS is just a bag of lega WHITE POWDER..... *evil laugh, all the way to the bank LAUGHING LAUHGIN LAUGHING*

Ok seriously. Probiotics are awesome (in clinical trials and anecdotally) and guess what my favorite brands use as the 'fiber/prebiotic'??

THese 3 below cured my (1) YEAST and (2) SEVERE GLUTEN AND DAIRY INTOLERANCES:

--SBO Clostridium butyricum
http://www.iherb.com/Advanced-Orthomolecular-Research-AOR-Advanced-Series-Probiotic-3-Natural-Probiotic-Formula-90-Veggie-Caps/43463

--SBO Bacillus licheniformis (found in raw dairy, ground dwelling birds like free range chickens, ducks, eggs)
http://www.bodybiotics.com/

--Floramend (some strains might be in the homemade heirloom viili yogurt that Allan and his family are using)
http://www.iherb.com/Thorne-Research-FloraMend-Prime-Probiotic-30-Veggie-Caps/41208

Don't forget to look on the label, 'other ingredients' listed.

THANK YOU MARK, LUV LUV LUV UUUUUUUUUU!!! Ur a rockstar!

Jean said...

A famous physician in Europe explain that prebiotic and probiotic is a nonsense to treat SIBO because this stuff increase the power of bad bacteria.

For him probiotic increase fermentation by the production of H2

For theatment he give essentiel oil (carvacrol..), mushrooms, biliary salt and physial exercise...

I've stopped my HSO probiotic because he explain that increase my SIB!!!

thank for your help

Dr. B G said...

Hi Jean,

Thanks for your comment again!

I kinda agree with your famous Euro doc. Some people with severe, refractory SIBO/SIFO should not get a synbiotic (prebiotic + probiotic) immediately until they've stopped for 1-2wks the foods the gut has immunoreactivity to (gluten, dairy, soy, corn, egg whites, nuts, etc -- basically the TOP 7-10 foods they are currently eating).

However after the severe immunoreactivity is improved, the role of fiber (RS + NSP) combined with appropriate probiotics (fermented foods, Lacto, Bifido, S. boulardii and the Soil-Based Organisms) have immense benefits to heal SIBO/SIFO very quickly, safely and effectively.

Also I agree with him on the treatment, the WEEDING effects using ' essentiel oil (carvacrol..), mushrooms, biliary salt and physial exercise.' I do the same!

Mushrooms have both FERMENTABLE FIBERS (b-glucan, etc) and antifungal and antimicrobial compounds.

However to cure the intestinal permeability you need to SEED and FEED the microbiota. Seeding will crowd the remaining pathogens and pathobiont growth as well as prevent further new growths. FEEDING is obvious.

After implantation, zoo animals need to be nourished and nurtured.

Let me know what he has against the science, which to me, says it all despite its infancy and the new discovery that SIFO/SIBO is associated with nearly every chronic condition in medical history...


Good review and discusses the soil and role of resistant starch:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552567/pdf/2001-1326-1-6.pdf


"Supply of Pre- and Probiotics Reduces Bacterial Infection Rates After Liver Transplantation—A Randomized, Double-Blind Trial"
http://onlinelibrary.wiley.com/doi/10.1111/j.1600-6143.2004.00649.x/pdf

Dr. B G said...

Jean,

HSOs trump other probiotics because our guts co-evolved with them. The strains are found in all of our ancestral fermented foods and naturally of course on roots and shoots of our vegetables, potatoes, and tubers.

Here are some listed benefits besides reducing the pathogenicity of nasty microbial strains that lodge during SIFO/SIBO.


Bacillus Subtilis HU58 -
Bacillus Subtilis has been extensively studied on a genetic and functional level. There are several probiotic products in the pharmaceutical and agricultural markets that utilize this powerful probiotic. One very interesting function of Bacillus Subtilis is its ability to produce nearly 12 strong antibiotics that are potent fighters of opportunistic and harmful bacteria. Bacillus Subtilis HU58 offers MegaSporeBiotic the ability to prevent harmful bacteria growth in a variety of conditions. In addition, HU58 produces a very healthy compound called Nattokinase. Nattokinase is secreted from vegetative cells of Bacillus subtilis and has been shown to reduce blood pressure, reduce cholesterol and reduce excessive clotting by fibrinolysis. Along with Nattokinase, Bacillus subtilis also produces a number of other nutrients that have systemic health benefits such as B vitamins and Vitamin K2. Bacillus subtilis HU58 offers MegaSporeBiotic the important function of fighting off pathogenic bacteria and producing key nutrients in the gut itself. In addition, HU58 is an extremely potent immune stimulator. It has the function of germinating in the small intestines to some degree and this offers the effect of broad-spectrum immune stimulation.

Bacillus Licheniformis –
A probiotic often found with Bacillus subtilis and other bacillus species, licheniformis has been shown to have a potent effect of preventing the growth of harmful bacteria via the production of a common antibiotic called bacitracin. It is also a potent immune stimulator. Another very important feature of bacillus licheniformis is its ability to produce highly effective and stable protease enzymes in the gut that assist in the digestion and absorption of proteins. Lastly, licheniformis also produces the whole spectrum of B vitamins in the gut including folic acid and biotin and acts as an important nutrient factory in the digestive system.

Bacillus Coagulans –
A very well studied probiotic in the spore family that has a profound effect on inflammatory conditions such as IBS and Crohn’s. Bacillus coagulans offers MegaSporebiotic an expanded effect of controlling these common inflammatory bowel conditions in addition to its potent immune boosting activity. Coagulans has the unique attribute of producing lactic acid and specifically the L+ optical isomer of lactic acid, which has been shown to have a more profound effect on immune stimulation and gut defense than the other forms of lactic acid produced by conventional probiotics. Coagulans is also a tremendous colonizer and thus assures proper colonization of MEGAsporebiotic, which in turn will produce the beneficial effects required. Coagulans also plays a key role in digestion of food and absorption of nutrients. In fact, Coagulans can digest incoming fat to reduce the uptake of cholesterol. Coagulans adds another dimension to MEGAsporebiotic, giving it a potent ability to fight inflammatory conditions, aid in digestion and prevent the growth of harmful bacteria.
http://www.gomegaspore.com/faqs/

Jean said...

Thank you for this GREAT answer.

I feel great with RS+psyllium and HSO probiotic

Anonymous said...

Hi Dr. BG!
I'm reading all I can here and on freetheanimal.

I have a few questions
What's your thoughts on Threelac? Is it good/useful?
And where do you place candida overgrowth in this gut health equation...? Any thoughts on candida specifically?


Is HSO = SBO or what? I think all this reading in various places makes me a bit confused!

Thank you for your time!
/EM

The Natural said...

Hi Dr. BG, the Body Biotics has this warning on its label. What do you think of this? I have never heard of Psyllium Husk stripping away microbes:

"The use of psyllium seed husk with Body Biotics™ is discouraged because of its indiscriminate stripping away of both friendly and unfriendly bacteria. Use of psyllium seed husk could minimize the positive health benefits of Body Biotics™"

T-Nat

The Natural said...

Dr. BG, wanted to let you know that your blog has been blocked at my work place by our new web filter under "Marijuana" category :-)

Can't understand how FTA passes but yours fails :-)

LOLs but it does really suck for me :-(

T-Nat

Keith Bell said...

Has anyone considered resistant starch as antibiofilm? I've been wondering how fungi would react to RS in SIFO. Apparently, fungi would produce amylase as would some bacteria. Amylase busts biofilm. But would RS feed fungi? Or would amylase production be enough to keep populations in check?
http://link.springer.com/article/10.1007%2Fs12010-011-9526-2
http://benthamscience.com/open/openaccess.php?tomicroj/articles/V005/21TOMICROJ.htm
http://www.hindawi.com/journals/bmri/2013/150653/
http://synapse.koreamed.org/Synapse/Data/PDFData/0184MB/mb-34-128.pdf
http://pelagiaresearchlibrary.com/european-journal-of-experimental-biology/vol3-iss4/EJEB-2013-3-4-26-34.pdf

Fungi also produce lactic acid and ethanol from potato starch:
http://digital.library.adelaide.edu.au/dspace/handle/2440/47204
http://aem.asm.org/content/52/5/1055.full.pdf
http://link.springer.com/article/10.1007/s00449-005-0398-0#page-1

So, the basic hypothesis is that RS may be forcing microbes to produce enzymes, acids and alcohols which serve to clean up shop in the small intestine, right where they live in their slimy biofilm matrix communities. Of course, you can also take amylase supplement (also thought to degrade histamine), but the results may not be as well-targeted as with RS.

Tim, apologies for all the links.

Keith Bell said...

General article on the health benefits of amylase includes possibly lowering autoimmune response:
http://www.globalhealingcenter.com/natural-health/the-health-benefits-of-amylase/

Keith Bell said...

The first link may help explain synergy espoused by Dr. B G in combining SBOs with RS:
http://link.springer.com/article/10.1007%2Fs12010-011-9526-2

Here's more about amylase production by bacillus subtilis:
http://www.pacificjournals.com/ajbor/pdf/06-2010/short_communication/23-28.pdf
http://link.springer.com/article/10.1007%2Fs00449-004-0391-z#page-1

nice vintage review here:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1243542/

Bacillus subtilis also produce lactic acid, but how interesting it's also used to manufacture hyaluronic acid which is very healing in little known gut application:
http://www.biopharma.novozymes.com/en/hyaluronic-acid/Frequently-asked-questions/Pages/default.aspx

Keith Bell said...

Fulvic acid is another product of SBOs who produce it from mucopolysaccharides of plants, basically the same as starch.
http://www.grjournals.com/portals/grjournals/JASA/Vol2%20Issue8/JASA-2012-28-188-711-721.pdf

http://www.supremefulvic.com/documents/html/fulvic_acid.php#Humic_Deposits

I believe hyaluronic acid (HA) is a type of mucopolysaccharide. Here's an informative/funny piece about the sticky potato diet of a long-lived, healthy Japanese community attributed to HA in their soil:
http://www.youtube.com/watch?v=PefdHNnDuv4

Merriest, happiest, healthiest, all.

Gillian said...

Dear Dr. Grace, Keith, and others... Its me again, with a slightly deviant topic. Tater lightly suggested I find a new doctor.... my doctor just suddenly died. Overnight. Since that post, less than a week ago. I did feel like he cared and was helping, and now I'm at a loss again. Still reeling. He was a friend as well. Anyway, so I have no one to ask this question to right now. One of my many problems is (isn't it amazing when the gut is messed up, so much else is too? And the viscious cycle gets more enmeshed...) that I have extremely low T3 levels (lowest my doctor had ever seen by a lot, 26 when it should be 100 I guess) but normal T4 levels. I avoid soy--even natto and the fermented stuff because of it. But for Christmas I was given some wonderful sounding tea... but with soy lecithin in it (darn commercialism that must pollute everything). With euthyroidism, low T3 levels, how important is it to avoid soy lecithin? I know Dr. Grace has blogged on the thyroid before. Dr. Chris Kresser posted on soy lecithin saying it wasn't that big of a concern except for those with soy allergies, but he didn't address the thyroid too much.

Again, I do not mean to be demanding or annoying. But seeking health, and wisdom, and am deeply grateful for any advice (intelligible, lay people advice, Keith. LOL)

Merry Christmas. Gillian

Gabriella Kadar said...

Gillian, I have the same prob, low T3. My endo started me on Cytomel (synthetic T3). Blood test coming up early January.

Two negatives: price (expensive) dosing schedule (twice per day 6 hours apart.)

If you normally have not had problems (i.e. not on Synthroid), maybe if you are too low carbs, it can push T3 down.

Tim Steele said...

Merry Christmas everybody!

Keith - here's a present for you:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC92288/

Concerning biofilms, RS from raw starch granules may not only bust biofilms as you suggest, but create their own to protect themselves. And there's a picture of it in the study I linked!

Gillian - sorry to be the predictor of doom...hope everything works out for you.

Grace - Thanks for letting me have so much leeway around here, I feel I have learned more than I shared.


Dr. B G said...

Merry Christmas Tim! Thx for the link.

One of the saccharolytic Clostridium listed that colonize and degrade RS granules is C butyricum (from the article). As Keith posted this and other SBOs secrete their own amylases which are biofilm busters as well. It's nice to have confirmation.

How was your experience taking the AOR Probiotic-3 which contains C butryicum? Ur consumption of dirt and soil is not negligble like is urban plebs! ...So I wonder if you saw quantifiable differences as the ones that are reported by me or others on this blog.

My kids and I have problems with heavy metals so I try to limit any unnecessary exposures.

What do you think the content of heavy metals from Bobs red mill potato starch might be? Have you considered asking them or any organic producers?

I will have to start asking. Here in China aluminum is reported from the processed starch and flours. Aluminum toxicity is reported pretty high here even 1/3 of people tested. Potato starch like all starches have to be pounded, dried and air blown on metal, then pried off the metal and the starch is the run over magnets to remove metal shards and filings.

Tim Steele said...

Hi, Grace - Did you see that Allan's family RS project is almost fully funded! Can't wait to see their results.

yes, I've been popping a few of the Probiotic-3 supps aweek since October, I figured that since Alaska is a frozen wasteland for 6 months out of the year, it would be a good way to keep my gut bugs topped off. Jackie has been taking them regularly along with potato starch and is commenting daily about how regular she is for the first time in her life.

Jeremy, our 30yo son, and health nut has been reading RS blog posts the last 2 days and bought a bag of Bob's Red Mill yesterday.

Now that I have 2 close family members hooked on the white stuff, I had to convince them it was safe. We found several papers that indicate Solanine is not an issue, Sulfur is sometimes used in the production of PS, but is always listed on the tech data sheets as being 2ppm or less in US and 50ppm or less from production abroad--FDA has a safety limit on sulfur of something like 50 micrograms per KG of bodyweight, and calls Potato Starch 'Generally Recognized as Safe', deferring to the USP requirements, which are more lax than food grade requirements.

As to Aluminum, I see from http://www.ncbi.nlm.nih.gov/pubmed/12042058 that aluminum is used as an anti-caking agent in MODIFIED potato starch, but not unmodified food grade starches.

I would love to see a complete breakdown of any trace chemicals or metals found in commercially available starches, but I think that since potato starch is a food item, it comes with a basic promise that it is safe from contaminates in the US, anyway. Somebody at FTA wrote to Bob's asking about GMO status and they indicated that all their potatoes used are GMO free and they were getting them certified so they could start labeling their PS GMO-free.

I was looking at several starch manufacturers websites and they said all the metal used in the starch making process is stainless steel. Still, I guess there is always a concern about impurities in all our foods and supplements.

I need to start making my own potato starch. I tried it last summer and found I could easily get 3-4TBS from a couple big potatoes.

If anyone is concerned about the safety of potato starch or any of the other starches people are using (mung bean, plantain, tapioca, Hi-Maize), I think the only other alternatives for RS2, raw starch granules are raw potato or dried plantains. I keep a bag of dried plantains around and find them easy to make and good to eat.

Cheers to everyone who donated to Allan's project!

Keith Bell said...

Tim, thanks for the lovely gift, first of the day other than waking up this morning.

Did you know you can have too much of a good thing in butyric acid, actually damaging the intestinal lining? We're not yet hearing about resistant starch overdose and I hope we don't . . . I haven't used it yet, but plan on experimenting as I believe everyone needs an improved small intestine. And I believe in being proactive as treatment and prevention are one and the same.

paradoxical butyrate causes damage: http://www.nature.com/pr/journal/v61/n1/full/pr20079a.html

butyric acid causes damage including histamine excess: http://www.ncbi.nlm.nih.gov/pubmed/8906631

http://carcin.oxfordjournals.org/content/20/4/539.abstract

Grace, I'm far from expert in heavy metal detox, but have been reading about fulvic acid for this purpose and impressed, even including mercury. I wonder just how good it really is . . .


Dr. B G said...

ALLAN~!!!

CONGRATULATIONS!!!!!


Keith ~
My brain is still on holiday mode. Will get back to biz in a little while...


Tim~
I'm allergic to nickel so that might explain why I haven't felt well on Simplot brand of PS when I take higher doses for a long time. I've felt noticeably better off for some reason.

So potato starch may potenially have shavings and metal contamination from stainless steel which is nickel and Steele. Lol ahah.

Even USP grade supplements have problems with heavy metal toxicities. The specs and QA don't often include the metal screening. It takes the manufacturer or third party lab testing like Consumer Labs to screen and test. In USA and globally around the world, metals in the food and supplements are overlooked.

I appreciate all that you've shared and provided. It is quite genius to use potato starch to temporarily fill in and hack the gut ecology. The supplement manufacturers (Probiotic-3, FloraMend, MEGASPORE) are using PS as a prebiotic ALREADY but to use massive doses like one would you Metamucil is absolutely clever and brilliant.

I have to concede that you are the most persistent pimp and persuasive 'drug' dealer of white powder I've ever run across. Lol

Dr. B G said...

Keith ~

Will look into fulvic acid. Thanks for the link that soil based organisms produce fulvic acid -- that's a source i don't mind! Cheap and readily available hopefully and produced daily. I think obtaining a healthy gut ecosystem with a full suite of commensals and mutualistd is one of the greatest hurdles people face when trying to think about metal chelation. Hormones too -- HPA, gut and thyroid.

PMC3849008

Gillian said...

So where does fulvic acid come from? If you take SBOs, does it naturally come with it? Or does Keith recommend a supplement?

And I guess there were no answers to the soy lecithin.

Tim Steele said...

Keith - interesting studies on excess butyrate damaging colon cells and causing other problems. Looks like it's mostly cause for concern in babies and the ill, and a good reason not to take butyrate supplements, especially in enema form.

I think the problem with most people, though, is quite the opposite--an extreme lack of buytrate.

It will be great when really smart people figure out exactly how much we need and where it should come from.

Keith Bell said...

Thanks for considering, Tim. Did you know autistic children are high in clostridium? Perhaps the types they're high in, however, aren't the butyrate producers, i.e, cluster IV.

But it still makes me wonder if RS would be contraindicated in autism as butyric acid is known elevated.
http://www.esciencecentral.org/journals/clostridium-bacteria-and-its-impact-in-autism-research-thinking-outside-the-box-of-neuroscience-JCDSHA.101.pdf

http://link.springer.com/article/10.1007/s10620-012-2167-7#page-2

But that doesn't negate the value of RS if the main mechanism of success is cleansing the small intestine. I'm informally monitoring a few epileptics who have just begun testing RS and so far, so good, though one report of seizure in the beginning of use, not surprising. Then things improved and she said after over 20 years of trying to heal her gut, RS has been the best thing so far. If RS can cure seizure of gut origin, I'd say that's a pretty massive win.


Keith Bell said...

Gillian, I'm just beginning to learn about fulvic acid. It is a product of SBOs and there are several supplements on the market. I'm not sure if it's made in the gut. It's normally associated with peat/humus soils. It increases nutrient absorption in plants and has a long list of attributes. After a few minutes of researching it yourself, I'm sure you can teach me about it . . . it is known to bust biofilm:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849008/?report=classic