Thursday, November 6, 2014

UPDATES: Current LiveFeed with AmGut Scientists! Also The Gut Guardian Podcast: Episode 05 – WEED THY GUT

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NOW!: Post any questions for American Gut researchers!

Jamie Binn at Redefining Human has set up an AMA (ask-me-anything) for us and other curious gut explorers! Thank you so much Jamie!

Go to twitter.com and please post with #redefininghuman hashtag. I've posted a few already this morning.

SEARCH: https://twitter.com/search?q=%23redefininghuman

Daniel is #3 at AmGut, super geeky nerdy comp sci. Enbriette is a hard core biologist.



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Don't forget to look at their Kickstarter and being a citizen researcher on the gut. I just signed up for some kombucha and the $250 level (will get my name on their episode).

KICKSTARTER for REDEFINING HUMAN: THE MICROBIOME DOCUMENTARY


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The Gut Guardian Podcast: Episode 05 – WEED THY GUT

Test results are in. You’ve got overgrowths of the wrong microbes. Dr. Grace and Matt examine the process of weeding out these misplaced microbes and recreating a symbiotic gut flora. Testing is the first step, and after listening to this episode you will have the tools needed to begin your weeding process.

Enjoy the episode!


Show Notes

00:00
00:00

42 comments:

Anonymous said...

No twittar for me...question:

Why does it take soooo flipping long to get American gut tests back now? At first 6mo, now over 1 year?
W. T. F. ?

Brett England said...

Grace ~ Once again, enjoyed the podcast. Lots of good info!

Had a question about the stress component - specifically, the possible role of trigger points in digestive health...As we age, via sitting, sucking in stomach, stress, etc - we invariably accumulate trigger points {poor blood flow, etc} throughout the pelvic floor {abs, gluts, abductors, hip flexors etc.} which can form an electrical network for inflammatory activity. (neuroinflammation...Compounding this process would be conditions such as IBS/IBD, etc. where there is excessive clinching of that area over time leading to extremely low blood flow..My understanding is that these hypersensitive points typically cannot be unwound with yoga or acupuncture or other classic ways of stress reduction - but rather require deep myofascial release, coupled with meditative/breathwork...I've run across practitioners who state that once you "heal your gut" these points fade, however, I wonder if they might be mistaking a trigger point becoming inactive, versus actually disappear. Meaning, via an "anti-inflammatory" type of diet these issues tend to calm but are easily reactivated...In FMT studies, C Diff has a great success rate (90+%), however, that rate seems to drop to around the 50+% mark (and a high rate of reoccurance) in IBS/IBD which both have the neuroinflammatory component...Another example might be antibiotic treatment of SIBO in which the patient might have success in clearing the bacteria, but is required to take Zelnorm on a continued basis following...Anyhow, just wanted to get any input you might have on trigger points role in gut health.. Thanks! Brett.

Anonymous said...

Tests results this summer: overgrowth of Citrobacter fruendii and Morganella Morganii.
Bugs were tested sensitive against Bactrim DS and berberine. Things that seem to help some: Arginine/Citrulline;Goldenseal;Sage;Apple Cider Vinegar. Things that help a lot: Bactrim DS, Thyme. I took a course of 4 weeks of Bactrim DS and it helped immensely. I took potato starch, homemade kefir, homemade kombucha, and the Prescript Assist during and after the course of Bactrim to try to repopulate the gut. I've had some success but it seems like slowly the symptoms are returning. Inulin and Fodmap foods give me instant heartburn. Any ideas on how to weed out these guys? The are seeming to be resilient.

lisao said...

Anon,

What do you have IBS? You have to be patient it can take many months, really a few years. I had a major turn around and complete remission of Ibs/colitis symptoms a couple of years ago using berberine. The berberine actually sat in my cupboard for 2 years or so because I tried to take a capsule a day and by day three was sick as a dog. I just thought it wasn't for me. I eventually realized it was just super effective and gave me really bad die off. I had to reduce to 1/3 of a cap and stay on that for several days and then add another third and gradually increase then I could tolerate. Within about a week I could eat things I hadn't been able to for a long time, primarily carbs: starches and disaccharides. I got diarrhea from those things before. I took berberine off and on for a few months and started learning stuff like what is on dr Lius blog from Richard nikoley, dr ayers etc. it was a slow but steady cycle of improvement. I've never tested because of the expense and I'm skeptical personally about just how accurate they really are but may do some testing in future. I've had great improvements in number of things: sleep, hormonal balance, no more pms or horrible cramps, I'm almost off thyroid meds, have to drop to only a tiny amount of thyroid. One hold out problem for me is weight. I have added some strength training and that seems to be making some changes so maybe that was the thing missing. Also just read a post on Richard nikoleys site from a guy who says his weight dropped when he added a great variety of fibers: glucomannan, chitosan, beta glucan, psyllium...
There must have been like a dozen in the list of what he is consuming. I'm taking a few things but not near than many. Will try to get as much from food as possible as grace recommends. I think mushrooms have a lot of beta glucan, konjac noodles have glucomannan. It's taken me two years to get where I am and I'm not done. Don't know how long you've been at this but have patience cause it's not a quick fix.

lisao said...

Something I think is useful to share is info I've learned about berberine. It used to be thought that berberine worked because of being antimicrobial. It is now understood that it doesn't itself change the microbes in the gut. It works by modulating the immune system in the gut so that the gut then defends itself and eradicates infections. It increases immunoglobulins and immune cells like phagocytes and modulates their function. It normalizes mucus secretion and closes tight junctions. We probably don't know all that it does. When Chinese scientist Zhao Liping studied it he found that pathogenic microbe numbers went down and beneficial ones increased in the gut.

It's mode of actions suggests it is not resistance promoting. Personally, I don't believe that the natural anti microbials are resistance promoting, particularly herbs because of their complexity. They attack microbes in so many different ways it is impossible for them to deal with. Herbs contain hundreds if not thousands of different chemical constituents working together synergistically and often attack microbes in dozens of different ways shutting down numerous metabolic pathways. Pharma antibiotics however are very simple and only attack typically in one way. I have not experienced natural antimicrobials becoming ineffective like I have say nystatin or antibiotic drugs, even using them for years.

Dr. B G said...

lisao --

Awww you are talking about WILBUR! I luv the brilliant dude!!

Absolutely, diversity yields the best guts -- resilience, immunoprotection, longevity and optimal health because it nourishes the most diverse gut flora!

The 7 Steps ultimately fills in all of the fiber needs -- bionic fiber just got edited -- both versions

Congratulations on your 'slow but steady cycle of improvement'! My ultimate goal is a speedy, pain free and full gut recovery for anyone seeking it. We will hopefully get there together, that's my dream. I appreciate all of your kind insights and sharing!

Thank you for your thoughts on berberine. It is wonderful and awesome stuff, no? The natural botanicals that our DNA and physiology are accustomed to for millenia make me reach rapidly for these 'tools'.

If you are considering restoring the full gut of symbionts, you may want to consider holding and discontinuing on the high dose potato starch because it appears to 'skew' the gut. There will be a series later but after reviewing several gut profiles, what stands out is the low amount of bifido longum and other gut symbionts when people take high dose potato starch/RS2 (even with other fiber). 7 Steps overcomes because RS3 and NSP fiber are high (~20-60g/day) and Version B has high dose inulin. But most people don't follow this fully or cannot until some gut recovery happens.

Email me if you want this study -- it demonstrates the potentially damaging effects of how high dose RS2 skews the gut flora profile toward high Bacteroides and other RS2-eaters, which are already overcompensated in gut dysbiosis (B-Prevotella, Klebsiella, Bacteroides fragilis and others): http://www.ncbi.nlm.nih.gov/pubmed/22909308

RS2 at high dose lowers
--Roseburia
--Other cluster XIVa (needed for gluten, dairy, peanut, food, allergen tolerances)
--F. prausnitzii (highest% of all healthy stool flora)
--BIFIDOBACTERIA LONGUM (because it eats inulin, and not RS2/starches)

As discussed in the last 2 podcasts, B longum has a vital and ancestral role as an ancient gut guardian. We do not want to compromise its abundance and starve it by feeding RS2-eating bifido strains (I call these hamster bifido LOL). It is wonderful you point out berberine -- there is evidence it restores or even increases bifidobacteria from pathological dysbiosis. Thx! In your health journey, have you addressed B longum? In every disease of Western civilization, B longum is missing. In elderly, B longum, Roseburia and Akkermansia are DEPLETED. Centenarians on the other hand have rich amounts B longum and likely of all the above! Roseburia is our key butyrate producer along with F prausnitzii.

Diverse plant polysaccharides and fiber yield a robust and healthy gut -- when you do gut testing, I would be curious if the fingerprint is similar to the ones discussed here for IBS or pre-CRC or autoimmunity?
Part 3: Don't Take Resistant Starch If You Have Moderate to Severe Irritable Bowel Syndrome (IBS) Temporarily
Part 4: Don't Eat Raw Resistant Starch (RS2) If Pre-Cancerous or Cancerous for Colorectal Cancer, Temporarily
Part 5: Don't Take Raw Potato Starch (RPS) Temporarily If You Have an Autoimmune Disorder

Dr. B G said...

lisao -- have you seen this? Nearly every Western disease shows depletion of Roseburia and when treatment works, Roseburia is shown to increase or be restored. Eat disease state has a gut 'fingerprint' and I believe in the future, medicine shall treat according each patient's individual and unique gut 'fingerprint.'

Roseburia and B longum consume similar food-fuel: INULIN and oligosaccharides.


http://www.ncbi.nlm.nih.gov/pubmed/24021287
A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis.
Machiels K, Joossens et al


OBJECTIVE:
Bacteria play an important role in the onset and perpetuation of intestinal inflammation in inflammatory bowel disease (IBD). Unlike in Crohn's disease (CD), in which dysbiosis has been better characterised, in ulcerative colitis (UC), only small cohorts have been studied and showed conflicting data. Therefore, we evaluated in a large cohort if the microbial signature described in CD is also present in UC, and if we could characterise predominant dysbiosis in UC. To assess the functional impact of dysbiosis, we quantified the bacterial metabolites.

DESIGN:
The predominant microbiota from 127 UC patients and 87 age and sex-matched controls was analysed using denaturing gradient gel electrophoresis (DGGE) analysis. Differences were quantitatively validated using real-time PCR. Metabolites were quantified using gas chromatography-mass spectrometry.

RESULTS:
Based on DGGE analysis, the microbial signature previously described in CD was not present in UC. Real-time PCR analysis revealed a lower abundance of Roseburia hominis (p<0.0001) and Faecalibacterium prausnitzii (p<0.0001) in UC patients compared to controls. Both species showed an inverse correlation with disease activity. Short-chain fatty acids (SCFA) were reduced in UC patients (p=0.014), but no direct correlation between SCFA and the identified bacteria was found.

CONCLUSIONS:
The composition of the fecal microbiota of UC patients differs from that of healthy individuals: we found a reduction in R hominis and F prausnitzii, both well-known butyrate-producing bacteria of the Firmicutes phylum. These results underscore the importance of dysbiosis in IBD but suggest that different bacterial species contribute to the pathogenesis of UC and CD.

KEYWORDS:
INTESTINAL BACTERIA; ULCERATIVE COLITIS

Dr. B G said...

Anon

Thx-- I asked AmGut but no ETA for changes. Sorry. Use Genova stool 2200 ;) $99. You may contact me.


Brett,
I do believe in the value of trigger points. When I get deep tissue whether from a TCM practitioner or day spa masseuse, it changes my physiology. I suspect the microbial junk from our leaking guts block and fill up our lymph vessels... thoughts!?? So acupuncture, exercise, trampolines, and deep tissue may be several modalities to 'release'. I'd love to hear more.

IBS/IBD are autoimmune imho. We can have auto-antibodies to the MMC or neuromuscular junctions. How they get foiled up, I dunno. Certainly immunoboosting to stop antibody production helps -- antioxidants, polyphenols, gut rehab, Roseburia and B longum and the soil probiotics, balancing TH1 TH2 and TH17 and all likely to be key. Thank you for your insights and wonderful clinical thoughts!

Dr. B G said...

Anon

I appreciate you taking the time to post your results here. Look forward to hearing more about your health and gut journey!

I had 3 things -- parasitic, yeast and the same as you M. morganii overgrowths. This is what worked for me and I was taking Floramend which contains Bifidobacteria longum (shelf stable -- able to buy in China). I took soil probiotics as well and ate high fiber paleo-Asian with brown and black rices and heirloom potatoes, mountain yams. Every gut is different so you need to consider what gut flora needs boosting, what needs shifting out with probiotics and prebiotics.

There is yeast likely confounding (like my case) -- none of the current testing now will quantify fungi well. Just presume imho because under pathological dysbiosis, the yeasts turn pathobiont and somehow fail to culture on the standard media. GDX just chnaged to culture which is too bad (cheaper of course).

http://drbganimalpharm.blogspot.com/2013/09/my-n1-pre-and-post-microbiome-digestion.htm

Anonymous said...

The sound quality was much, much better on this podcast.

Esha said...

Hello, Dr Grace! Thanks for the great podcast:)

I’ve got a question about yeasts developing resistance to antifungals. I use Bacillus subtilis and Bacillus amyloliquefaciens as antifungals (gluten intolerance disappears, no liver problems and they don’t irritate the gut... well, at least in my case), but is it possible that yeast will become resistant to SBO? On some forums i read about how soil-based bacteria actually eat candida (do they?..) and others say Bacillus subtilis is like other antifungals and the initial success will wear off as candida adapts to it... I hope the question is not too silly)))

Dr. B G said...

Anon!~
Yes! Thank you for your comment, Matt is spectacular at the tech aspects.

Esha,
Cool! Congrats on your reversal of food intolerances! YAY!
Where do you purchase the B amyloliquefaciens? I've not heard of that one.
I concur -- Bacilli line our small intestines and colon and are vital for digestion. They have enzymes like lactase, gluten/gliadin-ases, proteases, etc. In addition to bifido, soil and bacilli probiotics, I regained the ability to break down dairy and gluten like yourself!

Our gut ecosystems act in harmony when there is no dysbiosis, however under aggressive situations I believe they microcritters exert there territorialism. Candida perhaps is one of the most ancient and thus has wily ways of maintaining their spots. We are no longer connected to Bacilli, bifido, and other soil SBO probiotics, sadly. Each has many mechanisms I believe to collaborate harmoniously with Candida, another natural companion in a healthy, eubiosis (normal) gut.

Saccharomyces (like brewers yeast and fungi on the skin of fruit growing in humid geographies) secretes a coconut oil like fatty acid
Capric acid secreted by S. boulardii inhibits C. albicans filamentous growth, adhesion and biofilm formation.

Lactobacilli competes in the same geographic niches as fungi (moist, acidic areas -- guts, vaginas, bladders). They make an entire PHARMACY OF ANTIFUNGALS. lol YAY vaginas!

Bacilli also secrete biofilm busters against microbes and fungi.

There are likely ways for resistance naturally with evolution but because these are low dose, non-systemic microbial by-products and thus, highly selective -- they are not likely to produce the pattern of resistance.

Our indigenous gut core flora have many ways to 'limit' Candida -- plants do too. Garlic (allicin) are biofilm busters too.

http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed&from_uid=20706577

Esha said...

Grace, thanks for the answer!

Where do you purchase the B amyloliquefaciens? I've not heard of that one.

I buy this product: http://vetom.ru/content/view/201/116/ It’s available in our local drugstore and quite effective – at least for candida and gluten-induced sinusitis.

Lactobacilli competes in the same geographic niches as fungi (moist, acidic areas -- guts, vaginas, bladders). They make an entire PHARMACY OF ANTIFUNGALS. lol YAY vaginas!

Uph... i failed to find probiotic lactobacilli that fight yeast... There are lots of studies that they do and i used to read and reread those papers over and over again, but... somehow... my candida is FOND of lactos!! :/ Symbionts?.. My list of bacteria that are really truly helpful in suppressing yeasts includes only B bifidum, Propionibacterium, B subtilis and B amyloliquefaciens plus unknown bugs in sauerkraut (my liver hated it, but it’s super great for candida, after sauerkraut my liver reacted to Propionibacterium as well). Oh, yes, and nameless critters in fermented sausages too.

I’m a newbie in this microbiota thing and only planning to try B coagulans, Clostridium butyricum and different bifido strains in strep-free probiotics:)

I concur -- Bacilli line our small intestines and colon and are vital for digestion. They have enzymes like lactase, gluten/gliadin-ases, proteases, etc. In addition to bifido, soil and bacilli probiotics, I regained the ability to break down dairy and gluten like yourself!

I can’t come to terms with dairy yet) But gluten – yesss)) With bacilli it’s quite a source of energy, btw, a 180 degree turn in reaction. Amazing))

Dr. B G said...

Esha,

Russians are so advanced in microbial rx's. Have you tried the L bulgaricus yet? Supposedly this is very antifungal as well.

http://www.medicalinsider.com/bacterial.html

Have you seen the potential antifungal herbals yet? Some of these helped me as well besides removing the offensive mercury which candida loves to affiliate with.

Why do you avoid the strep ones? Does it trigger strep? If so, then if it were me, I would consider immuno boosters. Candida can suppress the immunity like mad. Yes ENERGY IS NICE TO HAVE. Congratulations to make substantial progress with the bacilli probiotics on candida!

Great immuno boosters I have found are the liver support and biocurcumin. The gallbladder, liver and pancreatic biliary trees get all CONGESTED AND F*KCED completely during microbial translocations of dysbiotic gut flora and deficiencies of Bifidobacteria longum.
http://www.iherb.com/FutureBiotics-Detox-Daily-Liver-Support-60-Veggie-Caps/7318

Are your liver tests < 12 (normal for hawwwt grrrls; <15 hot boys)?

Esha said...

Grace,

Have you tried the L bulgaricus yet?

I have. L bulgaricus and L acidophilus give me real bad sinusitis, no luck with lactos for me :(

Why do you avoid the strep ones? Does it trigger strep?

Yep – joint & muscle pain, stuffy nose, high temperature. My body treats probiotic strep as an infection, go figure))

Are your liver tests < 12 (normal for hawwwt grrrls; <15 hot boys)?

I’m yet to do the tests, since next week, i think. Sonography showed only S-shaped gallbladder, the rest is ok. I hope i’m a hawt girl:)))

Have you seen the potential antifungal herbals yet?

In my first attempts to gain health i took tons of antifungals, GSE, coconut oil etc. and at first they did help against candida, but hurt the gut lining, i guess – after a while i got super sensitive, extremely weak, constipated, often dizzy. Raw potato helped to heal the gut (it’s RS2 + some unique very healing substances), i feel much better now but still afraid to try strong antifungals... I only do propolis, a little coconut oil, spices and herbal teas, take liver herbs and bacteria.

http://www.iherb.com/FutureBiotics-Detox-Daily-Liver-Support-60-Veggie-Caps/7318

I’ll order, thank you:)

Esha said...

Is bio-curcumin the same as turmeric? I use turmeric quite a lot, even in drinks))

Dr. B G said...

Esha, HAWT GUT GODDESS!

S shaped gallbladder? Do you think you have impaired digestion, low acid, low bile or low pancreatic enzymes? This often happens during dysbiosis of the gut and candida infections. I urge stool/urine testing because it is not uncommon to find other pathogens and pests in addition to candida. The response to antimicrobials (trypsin inhibitors) in potato is not surprising and may indicate the vipers in the upper gut. The trypsin inhibitor content is not low in tubers, and is why we do not eat raw tubers commonly or ancestrally without fermentation, cooking and other treatments! Trypsin, chymotrypsin and pepsin are vital for breaking down carnivorous substrates in the upper gut.

We are different from HERIBIVOROUS HAMSTERS ;)

Have you read the comments for weeding on the other threads?

Yes sounds like the candida and other dysbiotic factors may create high histamine for you. Have you tried the bifido probiotics which work hand in hand with bacilli in the upper gut?

There can be adverse effects with raw potatoes in the pancreas and significant protein malnourishment. Most people with SIBO/SIFO already have compromised protein digestion (lack of enzymes), no bile and low gastric acid.


J Nutr. 1989 Nov;119(11):1598-609.
Pancreatic response in rats and mice to trypsin inhibitors from soy and potato after short- and long-term dietary exposure.
Gumbmann MR1, Dugan GM, Spangler WL, Baker EC, Rackis JJ.

The effects on the pancreas of chronic (95 wk) dietary exposure to protease inhibitors from soy and potato were compared in rats and mice. Soy and potato trypsin inhibitor (TI) concentrates were prepared from defatted raw soy flour and potato juice, respectively, by selective precipitation and ultrafiltration. Animals were fed a diet in which casein supplied approximately 20% protein. Each concentrate (less than 1% of the diet) was added to provide 100 and 200 mg of trypsin inhibitor activity per 100 g of diet. In short-term (28 d) experiments in rats, both sources of TI decreased the apparent nutritional quality of casein and produced pancreatic hypertrophy consistent with a hormonally mediated feedback mechanism for pancreatic adaptation to diet that is interactive with the nutritional status of the animal. After long-term feeding (95 wk), soy and potato TI produced dose-related pancreatic pathology in rats consisting of nodular hyperplasia and acinar adenoma, which was typical of that associated with raw soy flour. Although mice responded similarly to rats to soy TI in short-term (28-d) feeding experiments, they were resistant to the formation of these lesions following long-term feeding. This considerable species variation in propensity to develop preneoplastic and neoplastic lesions of the pancreas is not predicted by the short-term hypertrophic and hyperplastic response of the pancreas to TI.

Dr. B G said...

Esha~ biocurcumin is much more bioavailable, potent and strong. For me it lowers my blood sugars too much; I can't take it without having to eat more which is annoying. Turmueric is great but often too weak.

Stylooke said...

Hi Grace,

Thanks for the awesome podcasts!

Can B. animalis/lactis be beneficial? Or is it a non-human animal species only?

Cheers, Nils

Dr. B G said...

Nils,

Glad you are enjoying! They are super fun. I think Matt and I talk too much about poop

All bifido are wonderful. Please don't misunderstand. But B longum like all the ancestral strains that make us human, not hamsters, are special.

Consider our microbiota as an organ. Each ancestral strain has a role that is interrelated and interdependent on its neighbors and friends. You disturb one, you will disturb them all. I think it is possible to use other bifido as 'crutches' but why? it is so easy to replenish and feed well (inulin, oligos from beans/grains/beets).

Potato starch will lower B longum. It is a fact of competition in the gut and selective feeding of non-longum strains.

When B longum is 'amputed', so is immunity and health ultimately. They are just our 'microbial fingerprint' and consequences exist when theyre absent, sadly, from what I observe.

The anatomical position of B longum (fig 1b). Sick guts don't have it. Genova stool and urine testing can now elucidate the quantity and presence of B longum. Sadly ubiome and amgut do not have the depth to go the species level.
http://aem.asm.org/content/75/6/1534.full.pdf+html

Stylooke said...
This comment has been removed by the author.
Stylooke said...

Hi Grace,

Thanks for your response. Reason why is because I bought a B. Longum supplement only to find out there were less than 500k live bacterias in the capsule. So that's probably not gonna work. I found some fermented dairy with B. lactis, which is why it peaked my interest!

I've had multiple rounds of antibiotics during my life (penicillin, amoxicilline, minocycline) and I've taken isotretinoin. Leaving my gut in a state of dismay! I have permanently dry lips! Oh and I probably made it even worse with high dosing RS2 because of all the hype..

Lately I've been taking prescript assist and paleo with lots of legumes and onion/garlic/shallot. But it hasn't helped that much so far.. Bifido might be the missing link, I'll make sure to find a B. longum supplement with some actual numbers in it ;)

Thanks for everything youre doing!

Bo said...

Hi Grace! Thanks for a fantastic blog. As someone who was quite recently diagnosed with Crohn's it's been very helpful and fascinating to follow yours and your colleagues work on gut flora and gut health. Am hopeful about the prospect of getting to the root of this weird disease.

I read that you had updated your bionic fiver formulas, what did you change? I've recently ordered the Gdx FX stool test. Should I wait until I get the results before implementing the bionic fibers or start right away? Which one is best to start with?

Thanks!
Bo

Esha said...

Grace,

There can be adverse effects with raw potatoes...

Yes, I am apprehensive of raw potatoes... and that’s the reason i tried to switch to potato starch several times, but in my case it has nearly none of raw potato benefits. You see, i can’t do antimicrobials without healing the gut lining at the same time. First comes tinnitus, then weakness, then sensitivities – the downward spiral... I plan to add psyllium (no psyllium here, have to order), nettle, vitamin K (it does help), cabbage juice and check for ulcers (should have done it in the first place, i know:))). I no longer eat raw potatoes on a regular basis:)

Have you tried the bifido probiotics which work hand in hand with bacilli in the upper gut?

Yes – B bifidum (helpful but constipating) and B lactis (makes me extremely skinny). I’ll buy B longum, of course. Only I’ll have to order it (time...), all probiotics with B longum I can get here come with streps. They put streps everywhere, so annoying!

Thank you for your suggestions and urging for tests! Initially i was veeery reluctant to check the gut))

robert said...

Actually Grace, Ubiome does go to species level for some bacteria. You need to look in the raw taxonomy.

Here's mine revealing bifidobacterium logum and bifidobacterium catenulatum. Anyone feel free to look and comment. Help is always needed.

https://drive.google.com/file/d/0Bwcb-Gc6FPfhNmYwT09VMWRKMmM/view?usp=sharing

Dr. B G said...

robert

NEAT O

but what does it mean it's all a big jumble????! wtf

Yours says (thanks for sharing)

for both B frag and B longum == 'count 6' etc. What is ubiome's normal for B longum? Which page did you acquire the raw taxa?

It seems the higher the 'count' the more abundant?

robert said...

I don't even understand. Chronic fatigue brain combined with some dyscalculia makes this a terribe jumble. Sorry to send you to another page but...
But this page explains it, I think.

https://autodidactauthor.wordpress.com/2014/10/29/ubiome-raw-data-taxonomy/

robert said...

Oh, it was on the dashboard in beta.ubiome.com. I forgot that some people have the old style and I don't know if it's there.

Dr. B G said...

May you be so kind to send the link? Thx! I use beta

Dr. B G said...

robert,

IT looks like B longum is less than B fragilis or the same 0.0016%.

I'm sorry to hear about the brain fog. Thank you for taking the time to share your information.

What I see is something celiac or spectrum. A lot of vipers, very few angels. Bifido is more than 1000-fold below normal.

Bifido (avg= ~1%) 0.0032%
B. longum (should be 40-50% and it is!! lol) 0.0016%

The vipers might be Proteobacteria, fusobacteria (starch eaters), staph and pseudomonas. What do you see?

Decent amounts of roseburia, F praus and R bromii. But these may be overgrowths. What is your diet and what has worked so far?

Yeasts, protozoa, and helminths aren't evaluated in ubiome as you are aware.

robert said...

my diet is rice, potato, nixtamalized corn tortillas, lots of meat, salad, carrot, tomato, onion as main ingredients. My diet reduced down to these things as there was little left to eat.
Had great success just feeling even throughout the day by making sure to get protein with every meal and discovering the corn flour as a carb source though don't know it's effects on gut flora. Had trouble with every type of flour I tried as a replacement.

Having to type like this or do intellectual work causes burning back and intense pressure on top of head and in frontal lobes and muscle spasms around neck and upper back. Feels like a raging sea storm.

I've tried/ am trying, pure bifido products to try and raise them but haven't felt any difference so far.

Have tried mutaflor and aor probio 3 as I didnt see any enterococcus and I hear it plays well with e coli nissle.

I may have felt a slight shift but difficult to tell. The cold weather has arrived and I seem to have trouble with my sense of temperature - I feel very hot but my actual temperature is low. I found in the past that around 4 celcius I begin to feel a normal temp and slightly more relaxed.

I feel like I'm locked up within myself and my emotional responses are limited. Quite curious. Thoughts are moving within a very limited range, same ones repeating constantly. I recognise that large parts of me are offline but don't know what.

I've typed myself out. I'll finish later.

Dr. B G said...

Esha

You said 'First comes tinnitus, then weakness, then sensitivities' -- I'm sorry to hear -- is it die-off? When massive amounts of yeast/candida and microbes leave their prior 'real estate' they leave gaps on the epithelium as well as release cell wall LPS or metabolites that are neurotoxic. For me going slow and taking bentonite clay/charcoal were huge beneficial buffers.

That is too bad about the strep, why? Is it in the culture supernatant? I have similiar body fat burning responses with mixtures of prebiotics for bifido (version A (new) and B of BIONIC FIBER)!



Nils
Looking forward to how you do and the gut journey! 'high dosing RS2 because of all the hype..' Probably -- it is clear RS2 'dosage' may cripple healing guts by suppressing all the barrier protectors: roseburia, human bifido (not animal), F praus and Akkermansia.



Bo,
IBD/CD has a distinct microbial pattern -- loss of bifidos and high vipers. Look at the Part 4 CRC post. This is IBD too which riases risk of colorectal cancer 4 to 20-fold. Same broken barrier, vipers and loss of ancestral gut allies.

http://drbganimalpharm.blogspot.com/2014/10/dont-eat-raw-resistant-starch-rs2-if.html

Dr. B G said...

robert,

"I feel like I'm locked up within myself and my emotional responses are limited. Quite curious. "

I felt that same when I had mercury/titanium reactions, yeast/parasite overgrowths and CFS. Good luck. You need to find all the root problems then systematically work on them. They are all inter-related but tie to the toxins and gut. My gut was a sewage because of mercury and antibiotics. Circus of morons! lol Do you think the head/sinus/neck symptoms are a result of yeast and dental amalgams?

robert said...

I think they could well be a result of mercury - mouthful! Luckily the day I stopped using toothpaste and switched to bar soap was the day I never developed another cavity. I've looked up the nearest dentist who could remove it and his rates seemed reasonable. I'm on benefits that don't cover my living expenses but I've okay'd the early use of my inheritance to deal with this once and for all, hopefully.

Meantime, I'm using Bimuno. Going to get proper help as there's no way to sort this on my own. I wasn't able to read or even speak properly, let alone write, for some years so regaining some use is helping me to start attempting some changes. If I could acquire your professional services that would be great! or if you can recommend someone or what to look for.

Two things that helped ( whilst I remember) were ashwagandha and boswellia. They helped me to feel less extreme head pressure and I regained my fine motor control.

I looked for an easy way to post my results for others to see. I looked at this http://metagenomics.anl.gov/ but got too confused and now I'm not sure if it even allows public displays. Nice graphs though!

Thank god for spell check!

Robert

Kor said...

Grace,
What does it mean that a single tablet of CandiBactin BR had me vomiting desperately for 4 hours last night. Continuous even after everything was out. Worst night of my life! had a similar horrible experience with goldenseal root and also with chlorella.

had mercury amalgams replaced a year ago but still trying to figure out the root of my candida issues. main things im trying to resolve are acne around my mouth, brainfog, general cfs and poor poop. rs3 seems to worsen acne.

What do u think about EDTA for mercury?

Esha said...

“That is too bad about the strep, why? Is it in the culture supernatant?”

Grace, I’m a liar, I have found today B longum without any other bacteria))) But it really often goes either with Streptococcus or L acidophillus, don’t know why. I’ll try it tomorrow or the day after tomorrow! So curious)) Does it feel different than other bifidos?

Anonymous said...

Rob, sounds like you may have something in your gut that is producing ammonia. Hard to know without testing as Grace always says but if it is ammonia, L-citrulline which is found in watermelons and cucumber can help get rid of it. It will take a week or so to notice a difference but it might be worth a try.

Anonymous said...

Hi Grace,

If one were to have limited funds, what would you recommend...an OAT test or stool test? I'm kinda thinking the OAT test but would love your advice. My two kids need some testing and we can't do all four at once.

Dr. B G said...

Esha

Keith sent this today -- 'most bifidobacteria strains were tested in combination with other probiotics (lactobacilli and propionibacteria) and/or food-starter bacteria (Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus and Lactococcus lactis) (Table 2); thus, the reported beneficial effects cannot be exclusively assigned to a specific bifidobacterial strain.'

http://www.wjgnet.com/1007-9327/pdf/v20/i41/15163.pdf

For me I just feel better -- before I took shelf stable products in China like FloraMend with B longum.
http://www.iherb.com/Thorne-Research-FloraMend-Prime-Probiotic-30-Veggie-Caps/41208

This worked very well for me but ALAS we ran out and I didn't renew for the last few months. (MISTAKE) Under any stressful conditions we need more probiotics and relaxation ;) I have the same effects when I push bifido with prebiotics Version B -- body fat loss too and have to eat more. Have you tried green banana flour? It has botanicals that heal microulcerations, peptic ulcer and colitis fast.

Esha said...

Grace,

Yea, I hate these freaky reactions of mine, when everyone (studies included) extols the benefits of live yogurts or acidophilus probiotics and i get real sick from them. Pure bifidos are better in my case (tried it both ways), I wouldn’t mind LGG or L plantarum though and i’m fine with propionibacteria.

“Have you tried green banana flour?”

Most of the products mentioned in your blog are not available here (exotic) or much cheaper when bought on Amazon or iherb. I mean to try them only it takes time till they arrive. I’m fine with green bananas though, thanks for reminder. Also I started drinking nettle tea for gut healing and for now it seems pretty effective, never knew it’s antifungal btw. Going to try sea-buckthorn oil too.

robert said...

Dr. B G said...

The vipers might be Proteobacteria, fusobacteria (starch eaters), staph and pseudomonas. What do you see?

Just at the end of a serious cold and feeling able to look into the question 'what do you see?'. Must be the high dose Bifido and Bimuno from last week kicking in!

I see domination of Families Ruminococcaceae and Lachnospiraceae both accounting for just over 71% about equally.

Bacteriodaceae is 3.9% (Bacteriodetes in toto 7.26%).

Alphaproteobacteria are the only proteo's in which I am high (2.17%), these made almost entirely of Thalassospira.
Gamma (pseudomonas very low) and delta are low end of average distribution, Beta is normal.

Fusobacteria are very low (0.00130%).

Staphylococcaceae are very low, 0.00240%.

Genus level - what stands out are the high Coprococcus (6.16%). High Dorea (2.23) and high Dialister(1.65). All outside of top of average range. Obviously high Ruminococcus at 13%.

Tannerella also off top of average distribution (0.425%).

Akkermansia very low (0.162%)

Pretty much everything low to very low. Sulfurihydrogenibium (?)is off the scale at the bottom end.

I'm amazed by the very low levels of pretty much everything. I can't know what the 13.72% of unclassified bacteria are. I wonder what hides in this section?

I've finally got to (partial) grips with the raw taxonomy. It's great just how much species level info there is. Excuse me for being a dumbo but does the normalisation used just helps us to compare against others samples, as a percentage of our sample?

Cheers Robert

Ben said...

Hey Grace! I have emailed you a few times about doing a consult. I am looking to do another stool test (can you really get the Genova 2200 for $100) and if I can really get one at that cost I would love to do one asap. Also, possibly get a urine organix acids test. Do I need to email you at a different address or just practice more patience? :-)

Thanks for all you do!