A Wish For More Energy

[GreekDemiGod]

I did a microbiome stool test as indicated by my gastro, will get results back in 20 days.

My microbiome results came back, it's a 17 page PDF and it looks bad. It was compiled/ analyzed by a lab in Germany.
Any thoughts would be welcomed.
I know this forum isn't big on microbiome diversity and puts less emphasis on it, but I could use some perspective.

@Hans @youngsinatra

Sharing part of the results:

Summary of molecular stool diagnostics, indication of:​

Detection of reduced biodiversity
disrupted mucosal protection
microbiome-associated susceptibility to inflammation
microbiome-associated tendency towards Leaky Gut
possible low-grade chronic inflammation ("silent inflammation") caused by
metabolic endotoxaemia
possible bacterial miscolonisation of the small intestine (SIBOS)
microbiome-associated health risks

The analysis of your sample reveals reduced resistance of your microbiome
against infections by enterohaemorrhagic Escherichia coli (EHEC) and
Salmonella.
The analysis of your sample reveals reduced resistance of your microbiome
against infections by Clostridium difficile .
The analysis of your sample reveals a reduced resistance of your microbiome
against infections with noro viruses and rota viruses.

 

[youngsinatra]

My microbiome results came back, it's a 17 page PDF and it looks bad. It was compiled/ analyzed by a lab in Germany.
Any thoughts would be welcomed.
I know this forum isn't big on microbiome diversity and puts less emphasis on it, but I could use some perspective.

@Hans @youngsinatra

Sharing part of the results:

Summary of molecular stool diagnostics, indication of:​

Detection of reduced biodiversity
disrupted mucosal protection
microbiome-associated susceptibility to inflammation
microbiome-associated tendency towards Leaky Gut
possible low-grade chronic inflammation ("silent inflammation") caused by
metabolic endotoxaemia
possible bacterial miscolonisation of the small intestine (SIBOS)
microbiome-associated health risks
The analysis of your sample reveals reduced resistance of your microbiome
against infections by enterohaemorrhagic Escherichia coli (EHEC) and
Salmonella.
The analysis of your sample reveals reduced resistance of your microbiome
against infections by Clostridium difficile .
The analysis of your sample reveals a reduced resistance of your microbiome
against infections with noro viruses and rota viruses.


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I unfortunately have absolutely no knowledge how to interpret these tests and give practical advice. I am generally not that well-versed with gastrointestinal health.

How many rounds of antibiotics have you taken in your life time approximately?

For me all I know is that good motility, stomach acidity and good bile flow are really important to digest food properly first and foremost. I know that some GI doctors and researchers repeatedly said that a very restricted diet (low FODMAP, carnivore, low fiber) if used chronically can worsen GI issues by starving beneficial bacteria and shifting the overall balance towards opportunistic bad bacteria.

Unfortunately, GI issues are really hard to solve. Ray, Danny, many other members in this community and even I tend to circumvent the problem by sticking to very restrictive diets.

You sparked new interest to look into this subject more in the next weeks!

 

[Sefton10]

@Tarmander has got some good knowledge and experience of these types of tests and analyses. I remember listening to a podcast he did on his own results and strategies.

 

[GreekDemiGod]

How many rounds of antibiotics have you taken in your life time approximately?

6-8 times.

It does confirm what I suspected as being my main problems: endotoxin/ LPS overload and bacterial overgrowth.

 

[Hans]

My microbiome results came back, it's a 17 page PDF and it looks bad. It was compiled/ analyzed by a lab in Germany.
Any thoughts would be welcomed.
I know this forum isn't big on microbiome diversity and puts less emphasis on it, but I could use some perspective.

@Hans @youngsinatra

Sharing part of the results:

Summary of molecular stool diagnostics, indication of:​

Detection of reduced biodiversity
disrupted mucosal protection
microbiome-associated susceptibility to inflammation
microbiome-associated tendency towards Leaky Gut
possible low-grade chronic inflammation ("silent inflammation") caused by
metabolic endotoxaemia
possible bacterial miscolonisation of the small intestine (SIBOS)
microbiome-associated health risks

The analysis of your sample reveals reduced resistance of your microbiome
against infections by enterohaemorrhagic Escherichia coli (EHEC) and
Salmonella.
The analysis of your sample reveals reduced resistance of your microbiome
against infections by Clostridium difficile .
The analysis of your sample reveals a reduced resistance of your microbiome
against infections with noro viruses and rota viruses.


View attachment 52772View attachment 52773View attachment 52774View attachment 52775View attachment 52776View attachment 52777View attachment 52778View attachment 52779

Dropping the pH alone might make a good change. Lactospore (Bacillus coagulans) produce lactate which drops the pH. This will have a very beneficial effect on modulating the microbiome. These bacteria foster in various environments, so just changing the environment can help a lot.
Black cumin is also good. And lastly, I'd add Bai zhu. It's great for the microbiome.

 

[GreekDemiGod]

@Tarmander has got some good knowledge and experience of these types of tests and analyses. I remember listening to a podcast he did on his own results and strategies.

I found these 3 episodes on his channel. I'll give them a watch.


View: https://youtu.be/Bxfh3730Jc4


View: https://youtu.be/DqXunUjlap4


View: https://youtu.be/hEPJs1vmuqg

 

[GreekDemiGod]

Torn between pushing it with the Peat/ bio-energetic approach to gut health VS following more mainstream advise: increase biodiversity, fiber intake, butyrate/ SCFA being the main energy source of colonocytes, and preventing/ healing a leaky gut. What if Peat is wrong on this. Yet Haidut and co. keep pushing the "all gut bacteria is dangerous, fiber causes cancer" hypothesis.
The simple fact that there exists healthy, vibrant starch-eating people should at least make everyone on this forum question Peat's approach to gut health.
I started eating oatmeal again last few days, and it made me feel satiated for hours, while on no-starch diet, I would barely be able to not eat for 3-4 hours, cause I would become weak and hungry.
Next week I will have my consultation with the gastro, so let's see what his recommendations/ treatment will be. He will likely suggest pre-biotics, perhaps some antibiotics for my bacterial overgrowth.

All the bio-energetic tips that I've tried have not made a permanent difference, and only give band-aid/ mild effects:
Thiamine high-dose
coffee everyday
Magnesium
Cascara
Activated Charcoal
L-Glutamine
Inosine
high salt intake
high SFA intake
high animal protein
Taurine
TUDCA
Milk thistle
Oregano oil
B-complex
...

All these just don't really work in fixing a bacterial overgrowth.

 

[Korven]

Torn between pushing it with the Peat/ bio-energetic approach to gut health VS following more mainstream advise: increase biodiversity, fiber intake, butyrate/ SCFA being the main energy source of colonocytes, and preventing/ healing a leaky gut. What if Peat is wrong on this. Yet Haidut and co. keep pushing the "all gut bacteria is dangerous, fiber causes cancer" hypothesis.
The simple fact that there exists healthy, vibrant starch-eating people should at least make everyone on this forum question Peat's approach to gut health.
I started eating oatmeal again last few days, and it made me feel satiated for hours, while on no-starch diet, I would barely be able to not eat for 3-4 hours, cause I would become weak and hungry.
Next week I will have my consultation with the gastro, so let's see what his recommendations/ treatment will be. He will likely suggest pre-biotics, perhaps some antibiotics for my bacterial overgrowth.

All the bio-energetic tips that I've tried have not made a permanent difference, and only give band-aid/ mild effects:
Thiamine high-dose
coffee everyday
Magnesium
Cascara
Activated Charcoal
L-Glutamine
Inosine
high salt intake
high SFA intake
high animal protein
Taurine
TUDCA
Milk thistle
Oregano oil
B-complex
...

All these just don't really work in fixing a bacterial overgrowth.

I don't agree either with the notion that all gut bacteria are dangerous or bad, or that starch is bad for everyone. It's an ecosystem where you actually want certain bacterial strains to thrive, e.g. bifidobacterium and akkermansia, since these crowd out LPS-producing bacteria.

However there is no cookie-cutter recipe on how to improve the microbiome, since everyone has a unique ecosystem of gut critters, which makes it very confusing. For instance. it is recommended to lower fat/protein and eat more carbs for hydrogen sulfide SIBO, or when there is too much proteobacteria. If you feel like you have tried all the standard Peat recommendations then there is no harm in experimenting with prebiotics and probiotics. Joel Greene recommends human milk oligosaccharides, red apple peels and red phenols to get back bifido and akkermansia populations. Bifidobacterium longum is a good, safe probiotic to try.

 

[Korven]

My microbiome results came back, it's a 17 page PDF and it looks bad. It was compiled/ analyzed by a lab in Germany.
Any thoughts would be welcomed.
I know this forum isn't big on microbiome diversity and puts less emphasis on it, but I could use some perspective.

@Hans @youngsinatra

Sharing part of the results:

Summary of molecular stool diagnostics, indication of:​

Detection of reduced biodiversity
disrupted mucosal protection
microbiome-associated susceptibility to inflammation
microbiome-associated tendency towards Leaky Gut
possible low-grade chronic inflammation ("silent inflammation") caused by
metabolic endotoxaemia
possible bacterial miscolonisation of the small intestine (SIBOS)
microbiome-associated health risks

The analysis of your sample reveals reduced resistance of your microbiome
against infections by enterohaemorrhagic Escherichia coli (EHEC) and
Salmonella.
The analysis of your sample reveals reduced resistance of your microbiome
against infections by Clostridium difficile .
The analysis of your sample reveals a reduced resistance of your microbiome
against infections with noro viruses and rota viruses.


View attachment 52772View attachment 52773View attachment 52774View attachment 52775View attachment 52776View attachment 52777View attachment 52778View attachment 52779

I guess the problem is that any fibers or prebiotics that feed good gut bacteria also feed bad bacteria. It looks like you have a klebsiella overgrowth (among other things) which feeds on undigested starch.

How do you restore a healthy gut microbiome?

I don't know it seems to be pretty difficult in some cases. First you have to get rid off the pathogenic bacteria or SIBO and then try to reach some sort of homeostasis where healthy bacteria re-populate to keep things in check. I have had some success using both antibiotics à la Peat (augmentin, doxycycline) and probiotics and prebiotics, mainly lactoferrin.

 

[moa]

@GreekDemiGod It seems the colon has so much endotoxin that only a fraction would be lethal if injected into bloodstream.

Having that much endotoxin and having twice that much is irrelevant, the more important is how much is absorbed.

Sibo is one possible cause for greater absorption, since small intestine is supposed to be sterile.

slow peristaltism and gut permeability could be the other.

i think insoluble fiber like carrots is better for water retention, increase bulk than oats. and pectin, inulin (and some rs) is better for feeding butyrate and other good bacteria than mucilage like oats. carrots contain lot of pectin.

buckwheat, artichokes, apples, carrots. occasional Riboflavin with regular b coagulans help restore good bacteria and butyrate production.

zinc is a critical cofactor (besides magnesium and butyrate) in the gut protection mechanism against endotoxins.

For sibo, i found thiamine to help long term. and bitter, including coffee also helps long term. thiamine levels are always low without supplementation, when you are peating, especially if you eat low pufa high sugar and coffee long term.

Bifidobacterium longum is a good, safe probiotic to try.

b infantis is good and b. longum too, safe to take. but i found b coagulans safer and much more beneficial long term.

I've tried to make my own yogurt with b. infantis/longum and it's safe indeed with limited and very short term benefits compared to b coagulans (that is both very safe long term and effective).

i think bifodo and lactobacillus probiotics are good to prevent or cure against occasional food poisoning, in that case i would take a huge pill with 50 billion or more once.

 

[Apple]

Torn between pushing it with the Peat/ bio-energetic approach to gut health VS following more mainstream advise: increase biodiversity, fiber intake, butyrate/ SCFA being the main energy source of colonocytes, and preventing/ healing a leaky gut. What if Peat is wrong on this. Yet Haidut and co. keep pushing the "all gut bacteria is dangerous, fiber causes cancer" hypothesis.

I think Haidut said he just eats normal foods like anyone else. I guess that implies lots of starches , oats or whatever. Haidut doesn't even drink milk because there is smth off in it

 

[Osukhan]

I don't agree either with the notion that all gut bacteria are dangerous or bad, or that starch is bad for everyone. It's an ecosystem where you actually want certain bacterial strains to thrive, e.g. bifidobacterium and akkermansia, since these crowd out LPS-producing bacteria.

However there is no cookie-cutter recipe on how to improve the microbiome, since everyone has a unique ecosystem of gut critters, which makes it very confusing. For instance. it is recommended to lower fat/protein and eat more carbs for hydrogen sulfide SIBO, or when there is too much proteobacteria. If you feel like you have tried all the standard Peat recommendations then there is no harm in experimenting with prebiotics and probiotics. Joel Greene recommends human milk oligosaccharides, red apple peels and red phenols to get back bifido and akkermansia populations. Bifidobacterium longum is a good, safe probiotic to try.

second this!
im a big fan of Joel Greene as well, i think i may have recommended his book in this thread in the past.

 

[youngsinatra]

I am also looking for ways to improve gut health currently. Has anyone of you tried water kefir? I think that is the next thing I‘ll try.

 

[GreekDemiGod]

Joel Greene recommends human milk oligosaccharides, red apple peels and red phenols to get back bifido and akkermansia populations. Bifidobacterium longum is a good, safe probiotic to try.

Apples are high in FODMAP and bother me.

 

[GreekDemiGod]

b infantis is good and b. longum too, safe to take. but i found b coagulans safer and much more beneficial long term.

I will try B. Coagulans, Hans also recommended it earlier.

 

[Highserotonin90]

@GreekDemiGod Could organic coffee, ACV or herbal enemas help you? I'm considering them but as usual connecting the dots is never easy.

 

[youngsinatra]

I will try B. Coagulans, Hans also recommended it earlier.

Yes. I heard very good things about this. It powerfully enhances bile flow.

 

[GreekDemiGod]

This is madness. I notice that even pulp-free grapefruit juice bloats me.

 

[GreekDemiGod]

So I had the follow-up consultation with the gastroenterologist. He interpreted my stool test analysis.

very low diversity
overgrowth of: Bilophila 2.3x, Klebsiella 39x, Suturella 2.5x, C.Diff 19x.

Said he doesn't recommend taking anymore antimicrobials or antibiotics because my diversity is already very low and that will only exacerbate that. But instead recommends to slowly build up the microbiome with beneficial species, and through diet, with the purpose of increasing my diversity.

He gave me a treatment and some dietary recommendations to follow for at least 6 months.

- a prebiotic complex: Megapre from Microbiome Labs containing Fructooligosaccharides, Xylooligosaccharides, Galactooligosaccharides
- a probiotic complex: Megasporebiotic containing Bacillus Licheniformis, Bacillus Subtilis, Bacillus Clausii, Bacillus Coagulans(the one you guys recommended)
- a prokinetic to increase motility/ transit time
Magnesium Oxide for constipation

MegaPre™ contains a proprietary blend of functional fibers that specifically feed these keystone bacteria. This unique blend is made up of clinically-tested-and-published, non-digestible oligosaccharides, derived from non-GMO green and gold kiwi fruit, non-GMO corn cob, and rBST-free cow’s milk.
MegaPre™ is a cutting-edge Precision Prebiotic™ supplement made up of clinically-tested, non-digestible oligosaccharides that can increase microbial diversity and selectively feed beneficial, keystone bacteria like Akkermansia muciniphila, Faecalibacterium prausnitzii, and Bifidobacteria.

The dietary recommendations were to:
- slowly increase diversity of fruits and vegetables(for their prebiotic effect)
- No gluten and no lactose
- minimize sugar consumption as much as possible.
- meat and eggs as desired.

That was about it. I will follow it and see where it goes. The focus on vegetables/ fiber is surely anti-Peat, but at this point, I will stop trying to force the Peat framework, when it clearly hasn't given me results.
And I've also been reading today how sugar can make things worse when dysbiosis is present. So I'm going to try to eliminate all added sugar, with the exception of honey in smaller quantities.
I suspect that Peat might have been very wrong on his low fiber, high sugar approach and "all bacteria is bad" hypothesis. I definitely feel more vulnerable to stress when eating no fiber/ high sugar & fructose, whereas when I increase fiber/ prebiotics, I quickly feel more stress resillent.

 

[Runenight201]

When will you be doing the follow up test? Very curious to see what the results are. I hope they are positive and you start feeling much better