Environment (diet), Not Genetics, Mainly Shapes Gut Bacteria Composition

haidut

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As many forum users know, studying the microbiome is the current hot topic in biochemistry and imbalances in the microbiome are used to explain everything from depression, to CVD, to cancer. A major argument advanced in the microbiome analysis field is that genes are the main driver of the microbiome composition. That composition can be altered by antibiotics and possibly by pro/pre biotics intake but the argument is that such changes are temporary and the microbiome sooner or later reverts back to its genetically predetermined state.
This study below found that the situation is the exact opposite, and it was the genes that played a minor role and environment the biggest. If that is the case, and the microbiome has such an important role in virtually all chronic diseases, then our diet suddenly seems a lot more important than just counting calories. We are what we eat, truly.

https://www.nature.com/articles/nature25973
https://www.the-scientist.com/?arti...ics--Primarily-Shapes-Microbiome-Composition/
"...“For years we’ve been constantly told . . . that the environment in the microbiome may play some role, but it’s kind of minor,” says Jack Gilbert, a microbiologist at the University of Chicago who was not involved in the study. “We now see that yes, genomics plays a minor role in shaping the microbiome. The fact that environment has a much bigger role in driving the microbiome than genetics pinpoints the fact that the environment is playing a much more fundamental role in influencing disease onset and disease progression than genetics is.”"
 

Vinero

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Do you think fiber-rich foods have a negative impact on the gut microbiome? I am currently experimenting with eating a lot of buckwheat and dark chocolate for their high magnesium content. But they also have a lot of fiber.
 

haidut

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Do you think fiber-rich foods have a negative impact on the gut microbiome? I am currently experimenting with eating a lot of buckwheat and dark chocolate for their high magnesium content. But they also have a lot of fiber.

Insoluble fiber is fine, as is charcoal, at least in my opinion. Large amounts of soluble fiber like pectin is probably not a good thing.
 

Amazoniac

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Shaping the intestinal microbiota by diet: A realistic target? - Gerhard Rogler

[9-10] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957428/
[11-12] Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome
[17] https://www.sciencedirect.com/science/article/pii/S0016508516352660
[18] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697132/
"During EEN [exclusive enteral nutrition] treatment, representation of KEGG modules relevant to the biosynthesis of biotin and thiamine, two B-complex vitamins, decreased. This may be indicative of the reduction in bacteria that bear genes encoding for these vitamins during EEN, such as bifidobacteria and E. coli spp., or changes in the synthesis of short or medium-chain fatty acids that requires these vitamins. Alternatively, supply of these vitamins through EEN may induce bacterial redundancy or indolence to produce them."​
[20] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049827/
[21] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583329/
 

haidut

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Shaping the intestinal microbiota by diet: A realistic target? - Gerhard Rogler

[9-10] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957428/
[11-12] Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome
[17] https://www.sciencedirect.com/science/article/pii/S0016508516352660
[18] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697132/
"During EEN [exclusive enteral nutrition] treatment, representation of KEGG modules relevant to the biosynthesis of biotin and thiamine, two B-complex vitamins, decreased. This may be indicative of the reduction in bacteria that bear genes encoding for these vitamins during EEN, such as bifidobacteria and E. coli spp., or changes in the synthesis of short or medium-chain fatty acids that requires these vitamins. Alternatively, supply of these vitamins through EEN may induce bacterial redundancy or indolence to produce them."​
[20] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049827/
[21] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583329/

Wow, what an extensive list. Thanks.
 

Amazoniac

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"Pectin is a natural part of the human diet, but does not contribute significantly to nutrition. The daily intake of pectin from fruits and vegetables can be estimated to be around 5 g (assuming consumption of approximately 500 g fruits and vegetables per day)."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5332253/

"The texture is a fundamental characteristic of yogurt. It can be improved by the use of gelling, thickening, or stabilizing agents Lucey and Singh (1998). Among these additives, water‐soluble macromolecules or hydrocolloid, the pectin is mainly extracted from apple pomace and citrus peel. Pectin is widely used as a functional ingredient in the food industry due to its ability to form aqueous gels and has been used in jams and jellies, fruit preparations, fruit drink concentrates, fruit juice, desserts, and fermented dairy products (Everett and McLeod 2005).

Pectin, a family of complex heteropolysaccharides consisting predominantly of partially methoxylated galacturonic acid residues, is extensively distributed in almost all of the fruits and vegetables as the structural unit of fresh cells and the junction between the cells. Its structure is based on 1, 4‐linked ‐d‐galacturonic acid, interrupted by l‐rhamnose residues with side chains of neutral sugars (mainly d‐galactose and l‐arabinose) (Guo et al. 2012).

To overcome pollution problems and to get more return in the citrus industry, these residues can be utilized in the production of pectin, which has a wide application in the food and pharmaceutical industries. The aim of this study was to extract pectin from orange peel (Citrus sinensis) which is a by‐product of the juice industry. The pectin was then incorporated at different levels in order to improve the texture and sensorial characteristics of yogurt during the fermentation as well as storage period."​

But the reason I opened was to find how much they usually add to products. They suggested at the end of the study the addition of pectin "in rate of 0.6%". A cup of yogurt would have 1.5g of added pectin.

People here consume tend to consume more than 500g of fruits and vegetables a day. This seems to be a quality issue.
 

Birdie

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"cherries, grapes, and strawberries contain small amounts of pectin"
Nice, I love those fruits.
It's hard to find jams without pectin added. I sometimes find them at Ross or Home Goods, otherwise way too expensive.
I know Ray has pointed to grapes as being beneficial, and maybe cherries? Strawberries are limited because of the zillions of tiny seeds.

You'd think tiny amounts of pectin are harmless, unless somebody is allergic... I avoid pectin where there are larger amounts. For example, uncooked apples..
So we cook them.
 

Birdie

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@haidut thanks for this study and for all of them that you post.
Very convenient to forward this kind of thing to people who might be curious.
 

biffbelvin

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I find it hard to fathom that 'it's genetics' thinking rooted itself into discourse around intestinal flora.

We're talking about colonies of foreign objects here, not the organisms cells. How could they not be dominated by environmental factors...
 

Vinero

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Update: my experiment ended badly. Eating a lot of Buckwheat and Dark chocolate for their magnesium content backfired.
The fiber irritated my intestines badly. I got stomach cramps and anxiety from it. I'm back to eating a low-fiber diet again,
White rice, Meat, Milk, Coffee and Coke.
 

Amazoniac

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Update: my experiment ended badly. Eating a lot of Buckwheat and Dark chocolate for their magnesium content backfired.
The fiber irritated my intestines badly. I got stomach cramps and anxiety from it. I'm back to eating a low-fiber diet again,
White rice, Meat, Milk, Coffee and Coke.
But you ate them just because of their magnesium content or you actually carveI mean, craved them?
 

robknob

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Soluble fibers can feed good bugs but they also form a gel and slow transit time, whereas insoluble fiber increases transit time. I suspect a pectin "allergy" is just a herx reaction as the good bugs out compete the bad causing a die off and endotoxin release, combined with slow transit.
 

Amazoniac

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I ate them for their high magnesium content, but unfortunately they contain too much fiber which irritates my gut.
So no intuition? All but especially the more fermentable foods deserve this attention.
herx reaction
What about Jarisch? I'm sure he would be pretty disappointed. Are you "allergic" to Austrians?
 

Owen B

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I picked up (generated?) some candida recently and had to back track my diet and find out the culprit(s).

I had bought some non-fat Stonyfield Farms yogurt. Very watery consistency with sugar and pectin. (Most yogurts have one or more different kinds of gums and pectin).

So I was horrified to find out in researching pectin that it only takes if the sugar content of the surrounding fluid is 50-60%. A lot of pectin, plus sugar = candida. (Plus whatever else the pectin may cause).
 

haidut

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I picked up (generated?) some candida recently and had to back track my diet and find out the culprit(s).

I had bought some non-fat Stonyfield Farms yogurt. Very watery consistency with sugar and pectin. (Most yogurts have one or more different kinds of gums and pectin).

So I was horrified to find out in researching pectin that it only takes if the sugar content of the surrounding fluid is 50-60%. A lot of pectin, plus sugar = candida. (Plus whatever else the pectin may cause).

There are maybe 2-3 brands of yogurt in WholeFoods that do not use any gums/pectin. I will find out the exact names and share. But yes, most brands (organic or not) use pectin/starch and/or at least one of the gums.
 
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