Supplementing E. coli

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In this thread I will outline my ongoing attempt to remodel my gut microbiom using E. coli bacteria and other probiotics and prebiotics.

Two months ago I send my stool sample to Ubiome, and at the same time to a German lab (ordered online). The Ubiome results took more than 6 weeks to get back (probably due to a hold up on the border).

Good news is, both lab tests came back with equal results. Giving that they both use quite different ways of testing the sample (to Ubiome you send back a small cotton stick, to the other lab I had to send back a whole small bottle full of poop), that gave me confidence that they are both actually doing a pretty good job at testing.

The major findings:
Interestingly Ubiome said that I am deficient in GABA and Serotonin producing bacteria:

ecoli3.jpg
ecoli4.jpg
Indeed from 2011 to Jan 2018 I took a SSRI for anxiety and panic disorder. Since one year I don't take it anymore but feel that I should, as stepping out of the general comfort zone comes again with panic attacks, which during that time have been rare.

The bacterii mentioned here are Lactobacillus and Bifidobacterium, as well as Streptococcus and Enterococcus.

On a different page Ubiome basically shows 0% Lactobacillus and Bifidobacterium. Personally I don't know if it is truly 0% but it seems to be low.

ecoli5.jpg

The German lab has the same findings:

ecoli1.jpg
ecoli2.jpg

They didn't test for Streptococcus, but for a different bacteria which Ubiome doesn't seem to test for, or at least it doesn't include it in their major findings. And that bacteria is E. coli.

While most of us associate E. coli with the consumption of some bad food and some days being ill, it is actually quite a necessary citizen of the gut. It provides the anaerobe living conditions which other bacterii like Lactobacillus and Bifidobacterium need for survival. Now you can see why these are missing, too. They don't have any good habitat to live in.

Any supplementing with probiotics would be absolutely futile without addressing the E. coli problem first.

Streptococcus and Enterococcus on the other hand get their daily food via so called cross feeding by byproducts from Lactobacillus and Bifidobacterium. Again, it is no surprise that these are missing, too.

In conclusion, the low level of both GABA and Serotonin producing bacteria start with the absolute lack of E. coli bacteria in my gut. I don't know what caused this in the first place (no use of Antibiotics as far as I can remember), but that problem would have to be addressed first.

The solution:

Thankfully there is the possibility for supplementing with E. coli without getting sick doing so. Already 1917 there was the Nissle strain of E. coli discovered in Germany. While being very beneficial for the body it has no side effects. Many things could be written about that strain, but you can find all the information on the English Mutaflor website:

https://www.mutaflor.com/mutaflor-w...=false&cHash=b4e7d1c7a0d545f53d051a2226ff3b9b

In Germany you can get it in three different forms:
a) Mutaflor
b) Mutaflor Mite: which is around 1/5 of the dose per capsule of the Mutaflor. It is used in the first two weeks for easing into the program.
c) Mutaflor Suspension: which is so low concentrated that it is used to treat new born babies. It seems that some of these poor creatures already have to go through antibiotic treatment. These are then used to rebuild the gut from the get go. By the way, this is the best sign that you are really not dealing with any harmful species here.

The goal is to take 2 capsules in the morning of the normal Mutaflor for 3 months. One package with 100 capsules comes around 100 bucks, so it is not the cheapest of probiotic treatments. The capsules have to be stored in the fridge and have to be ordered in a way that they are delivered cool.

Personally I startet two weeks ago with the Mutaflor Mite, and are now taken 2 capsules per day of the normal Mutaflor with no ill effects.

At the same time I am using another probiotic to build up the Lactobacillus and Bifidobacterium. Personally I used Dr. Wolz Darmflora Plus Select Intens, which is not only the strongest probiotic I could find when it comes to bacteria per capsule. But it also has the widest variety of them. Also many strains are included which I have come along regarding treatment of depression etc. The content is as follows:

100 x 10^9 cultures:
Lactobacillus acidophilus
Lactococcus lactis
Bifidobacterium lactis
Lactobacillus salivarius
Lactobacillus reuteri
Lactobacillus delbrueckii subsp. bulgaricus
Bifidobacterium breve
Lactobacillus gasseri
Lactobacillus fermentum
Lactobacillus rhamnosus
Bifidobacterium longum
Bifidobacterium infantis
Lactobacillus brevis
Streptococcus thermophilus
Lactobacillus paracasei
Lactobacillus casei
Lactobacillus plantarum
Bifidobacterium bifidum

An English product website would be:
https://www.wolz.de/en/products/for-a-healthy-intestinal-tract/darmflora-plus-select-intens-dr-wolz/

You can see that this product also includes one strain of Streptococcus, which hopefully later helps with the Serotonin production. At the moment there is no way of supplementing Enterococcus.

At the moment I take 2 of the capsules in the morning and 2 in the evening, as intended by the manufacture. With no ill effects.

I will give it some time and then will additionally supplement with Inulin as a prebiotic to feed these bacteria. I am still waiting a litte bit, because obviously I don't want any of the guys already living in my gut feasting on the delicious Inulin and further growing. The new kids on the block need a little HQ first and then hopefully will have a better chance fighting their grounds.

In 1-2 months I will also get another test done by the German lab (Ubiome would take too long), to see if there is already some changing taking place. But I expect the whole treatment to take at least 3 months.
 

roller

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While most of us associate E. coli with the consumption of some bad food and some days being ill, it is actually quite a necessary citizen of the gut. It provides the anaerobe living conditions which other bacterii like Lactobacillus and Bifidobacterium need for survival. Now you can see why these are missing, too. They don't have any good habitat to live in.
oh my, e.coli ??? may explain some things...
i was wondering, which were involved, but i never saw that anaerob e.coli is needed for other aerobes (lacto/bifido...)
 
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lafarfelue

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Great idea to keep track of it like this. Wishing you the best of luck :thumbsup:

I was found to be low in e coli too. That's one of the key strains that CFS Discovery/Dr Lewis tests for, as it is apparently commonly low in pwME.

Mutaflor helped kick things more into order, though it was a tough first 2 weeks. I haven't taken it since the initial time as I didn't feel it have much effect after that. However I do regularly take Lactobacillus rhamnosus (LGG), another one that is apparently also often low in pwME.

Helping my gut (including reducing carbs and sugars) helped me regain maybe 10-15% or more functionality. When I'm bad with my diet and probiotic supplementation, I can feel the difference with increased PEM and brainfog.

Again, best wishes to you, hope it helps!
Descr
 
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Nope, that is an autolysate. That is basically the content of the bacteria without cell wall and proteins. People use it in the hopes of activating their immune system. Probably similar to homeopathic medicine. But obviously it is not useful at all as a probiotic to recolonize the gut.

Enterococcus is not regarded as save on most countries (US for example), in the other countries it is used as a probiotic - for animals.

See for more:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085487/

Mutaflor helped kick things more into order, though it was a tough first 2 weeks. I haven't taken it since the initial time as I didn't feel it have much effect after that. However I do regularly take Lactobacillus rhamnosus (LGG), another one that is apparently also often low in pwME.
What have been the side effects in the first 2 weeks? And how long did you take it after that?
 

lafarfelue

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What have been the side effects in the first 2 weeks? And how long did you take it after that?

The effects lasted longer (maybe 2 months of feeling worse than usual?) but the first 2 weeks were the absolute worst of it.

It was like a heavy crash. My body felt like lead, I had really bad brainfog, sore throat, flu feeling etc. My guts were in overdrive... there was a lot of gas! I don't really remember much else because I was just focussed on getting through it each day. I can understand how difficult it would be for people who are severe.

I didn't pay any attention to how my detox pathways/phases were working. I should have but I wasn't really able to take more information in before starting the probiotics anyway. This is IMO an important aspect worth at least being aware of.

I took the Mutaflor until it ran out and kept taking the LGG until that ran out too.

Now I regularly cycle through oil of oregano for as long as I can manage without crashing (sometimes only a couple of days), followed by LGG + Dr Ohhira's probiotics + kombucha.
 
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Sadly this link just points to three weak studies in vitro.

However I wrote an email to the company that produces Symbioflor 1. First information: it does indeed include both an Autolysat BUT also living bacteria, so that is good.

But they also provided me with a study (produced in-house as far as I can see) that shows that the Enterococcus of Symbioflor 1 are unable to colonize the gut in a sustainable way.

I attached the study to this post.

They gave a man 10ml of Symbioflor 1 (that is 10 times the recommended daily dose of 1ml) and could not detect Enterococccus (other than the ingested ones) inside his poo.

In a second attempt they gave him 50ml (that is 50 times the recommended dose - and by the way - a full bottle of Symbioflor 1, which comes in 50ml bottles). The Enterococcus could be found inside his gut for the next 6 days, declining everyday, but then no more.

The study states:
"In conclusion, both probiotic Symbioflor products tested here are able to survive passage through the human GIT but, in contrast to E. coli, Ent. faecalis is only able to colonise the gut transiently."

So one would have to take a whole bottle every week for probiotic attempts. That is probably the reason why Symbioflor is not marketed as a probiotic at all by the company, but as a treatment for Sinusitis etc. I will definitely try a few drops in the future though.


The effects lasted longer (maybe 2 months of feeling worse than usual?) but the first 2 weeks were the absolute worst of it.
Did you by any chance did testing prior and after?

The good news, which I did not mention in the first post is that I don't have any dysbiosis at all. I wonder if that could have led to your problems, bad bacteria dying off? Mhm.
 

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The one I linked to was Symbioflor2, not Symbioflor1.

I'm interested in what you are doing, having worked on rebuilding my microbiome after chemotherapy 4 1/2 years ago, oral antibiotics 2 years ago, then IV antibiotics a year ago. I've had some success, but it is a difficult thing to do.

After the chemo, I used Xymogen ProBioMax 100 and an organic Paleo diet with lots of non-starchy vegetables, and 18 months later, I had, in the words of my doctor, "one of the best stool tests I've ever seen."

After the oral antibiotics, I used Xymogen ProBioMax, PrescriptAssist, and Symbioflor2. I had 0 lactobacilli and bifidobacteria. My doctor said "They have nothing to stick to," and we added in Thorne Research FiberMend and Klaire Labs GOS and switched to Xymogen ProBioMax350, which helped them come back. I was approaching normal.

We tried the IV antibiotics to save my microbiome, but it wiped it out anyway. I was down to 17% diversity. Tried the same protocol, ProBioMax350 plus FiberMend plus GOS plus sheep yogurt. Not much change after 4 months. Switched to the Gut Institute BifidoMax 1 trillion with the FiberMend. Now up to 36% diversity, but .02% lacto and bifido. UBiome says to drink milk and eat grains, which I'm allergic to, though I've eaten sheep yogurt or cheese almost daily.

The question I'm having is why, after huge quantities of lacto and bifidobacteria, plus prebiotics, do I have so few actually sticking. Or, does it really matter? No one knows what ideal microbiome composition is.

UBiome says my bacteria are actually metabolizing everything pretty normally and I don't have the undigested food I did 9 months ago, but I don't feel that things are "normal."

I used to have faith in probiotics and being able to manipulate the microbiome. But now I'm not so sure. I'm curious as to how your experiment goes.
 
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Ah I see, because on that link they have a few studies on Symbioflor 1. and since you talked about Enterococcus before I was assuming that you wanted to point out something regarding 1. Yes, Symbioflor 2 seems to be a good supplement for E. coli as well.

In two days I will start taking Inulin. Later I may try a more diverse prebiotic mix (similar to the supplements that you mention). In two weeks I am thinking about taking a first test. The reason is that in three weeks I have a doctors appointment that I am waiting a couple of months for already. A first test result may come in handy, but I would have to stop taking the probiotics for 2 days before taking the test.

Interestingly Ubiome mentions that 0% of Lacto and Bifido is quite common (see picture in first post), on the other hand we get all these studies showing that certain kind of strains are beneficial (for example for depression). So as you I am also not so sure about things to expect.

The last few days my blood sugar is even lower than normal. Could be a side effect of the probiotics, but also an unrelated glitch.
 
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Now up to 36% diversity, but .02% lacto and bifido. UBiome says to drink milk and eat grains, which I'm allergic to, though I've eaten sheep yogurt or cheese almost daily.
Is the Ubiome recommendation to drink milk and eat grains to help increase lacto and bifido or something else. I would really like to add more grains into my diet but am afraid they will worsen my microbiome.

The question I'm having is why, after huge quantities of lacto and bifidobacteria, plus prebiotics, do I have so few actually sticking.
That's a question I have too. Why is it so difficult to change the microbiome for so many of us?
 
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A first test would be useful. I do them every 3-6 months. I have definitely seen changes, and knowing what you did to promote tgem van be helpful.
Is the Ubiome recommendation to drink milk and eat grains to help increase lacto and bifido or something else. I would really like to add more grains into my diet but am afraid they will worsen my microbiome.
As im allergic to corn, quinoa, and gluten, I worry too. If we don't eat them, do we really need bacteria who digest them? Maybe not. UBiome says I have no gluten consuming bacteria, but as I'm celiac, and have bern in a GF diet for 8 years, I'm not sure that's a problem

That's a question I have too. Why is it so difficult to change the microbiome for so many of us?
That is exactly the question. I'm eondering if the FUT2 gene status is a factor, or perhaps that it's some combo of the meds and supplements, which I need for other reasons, are discouraging them. The studies that claim the microbiome bounces back quickly after antibiotics are dead wrong in my book.
 

pamojja

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The major findings:
Interestingly Ubiome said that I am deficient in GABA and Serotonin producing bacteria:



Indeed from 2011 to Jan 2018 I took a SSRI for anxiety and panic disorder. Since one year I don't take it anymore but feel that I should, as stepping out of the general comfort zone comes again with panic attacks, which during that time have been rare.
I never been on SSRI, nor did I ever suffer from anxiety of depression. But my result from 2017 showed even worse result:

Sleep Microbes:
- Serotonin-producing microbes (Streptococcus and Enterococcus): 0.14x than Selected Samples
- GABA-producing microbes (Lactobacillus and Bifidobacterium): <0.05x than Selected Samples
 

pamojja

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How was your sleep at time of sampling?
Just answered their new questionnaire, and found already can't remember such details of the day taking the sample. However, at that time and for the many years of chronic disease I needed at least 10 hours of sleep per day, still unrefreshed. Confounded by the diagnosis: PAD (2009), COPD ('13), T2D ('16) - and improvements again: T2D controlled with diet, 2015 a 60% walking-disability from PAD revoked again, last year checked COPD improved, no further monitoring needed.
Moreover: since about 1 year with a lot of pacing, but then also challenging it - no PEM anymore! And since just about 1 month: sleeping needs after many years seems to come down from the usual 10 hrs/d. Still often interupted (for going to the toiled), but relatively much more refreshing.
 
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