Chris Kresser, Jeff Leach and the Microbiome

EndlessResearch · Mar 29, 2014

http://chriskresser.com/you-are-what-yo ... jeff-leach

I love Peat...I also love Chris Kresser. You can tell he has a tenacity about digesting information and being skeptical of everything he reads. Plus, he has patients to practice what he preaches on. Anyways, I like to listen to podcasts on nutrition as I walk my dog each day. I listened to the one above, and was hoping smarter people than myself,on the teachings of Ray, could chime in on what they think of what these guys are saying. I searched and someone else here kind of mentioned it, and nobody commented on it. I am really curious and hoping for some counter arguments.

nograde · Mar 29, 2014

I stopped reading here:

... once you start starving your bacteria, you don’t deliver enough substrates, resistant starch and non-starch polysaccharides, when you don’t deliver enough of that stuff from plants, the bacteria have to eat something, so they start eating you.

Chris Kresser: Right.

Jeff Leach: They eat your mucous lining in your colon, and it’s thought that maybe once you start to degrade that protective barrier ...

Sorry, but that sounds ridiculous. Now that the Candida craze is over we need another fear mongering storyline. What about bacteria getting angry when having no fiber and eating your flesh! Come on ...

Kresser should explain why sterile mice live so much longer than their bacteria-laden cousins, and why something simple as feeding activated charcoal increases lifespan in rodents. Did he ever fathom that transit time is what counts, that it's of utmost importance that you get those bacteria out as fast as possible before they release LPS or any other irritating compounds? Kresser chooses irritating fiber as transit time lowering strategy. I choose a healthy metabolism that takes care of the problem by healthy peristalis.

EndlessResearch · Mar 29, 2014

Interesting!

kiran · Mar 29, 2014

First of all the human microbiome is poorly characterized, and Leach admits this.
In addition a lot of information is taken out of context. For instance, the very same bacteria is found in immunocompromised, autistic and healthy people. So we must conclude that the state of the body around it can affect the (mis)behaviour of the bacteria. Additionally, there's not much research on the kind of irritants released by the bacteria. For instance D-Lactic acid can't be used by the body and is a metabolic load. It is released exclusively by bacteria, but the D to L ratio varies, and therefore the effect possibly varies person to person, even if they have the same bacteria.

As for the Hadza, we must keep in mind that they probably share a lot of the same bacteria in very similar circumstances, and a Hadza child has many healthy neighbors with similar diets to inherit his microbiome from. If you transplanted the bacteria on the other hand, it may or may not have the beneficial effect you want, bereft of the context of a shared diet with healthy neighbors.

In summary the microbiome is an individual thing, and in my estimation you're probably better off "keeping it in check", especially since bacteria produce many irritants.

Oh, and endotoxins from the microbiome are incompatiable with a higher metabolic rate!

kiran · Mar 29, 2014

nograde said:
Sorry, but that sounds ridiculous. Now that the Candida craze is over we need another fear mongering storyline. What about bacteria getting angry when having no fiber and eating your flesh! Come on ...

To be fair, Ray doesn't recommend starving them either, just killing/getting rid of the bacteria. Sugar can keep your microbiome calm and happy...

EndlessResearch · Mar 29, 2014

This is great stuff. Thank you!

narouz · Mar 29, 2014

nograde said:
I stopped reading here:

... once you start starving your bacteria, you don’t deliver enough substrates, resistant starch and non-starch polysaccharides, when you don’t deliver enough of that stuff from plants, the bacteria have to eat something, so they start eating you.

Chris Kresser: Right.

Jeff Leach: They eat your mucous lining in your colon, and it’s thought that maybe once you start to degrade that protective barrier ...

Click to expand...

Sorry, but that sounds ridiculous. Now that the Candida craze is over we need another fear mongering storyline. What about bacteria getting angry when having no fiber and eating your flesh! Come on ...

Kresser should explain why sterile mice live so much longer than their bacteria-laden cousins, and why something simple as feeding activated charcoal increases lifespan in rodents. Did he ever fathom that transit time is what counts, that it's of utmost importance that you get those bacteria out as fast as possible before they release LPS or any other irritating compounds? Kresser chooses irritating fiber as transit time lowering strategy. I choose a healthy metabolism that takes care of the problem by healthy peristalis.

Well...this is a bit of a tangled area in Peatdom.

I would say that there is something (Peatish) to the idea that
if the gut bacteria are starved of carbs/sugars
then they will start to "eat you."

Peat has said that something like that can happen on low-carb type diets.
He has said that when the bacteria have enough sugar to eat,
they don't usually create problems.
But when they don't have enough sugar,
they sort of bore into the stomach lining
(and even through it?) in search of food.
I say "bore."
That's not exactly right, I don't think.
But it seems like Peat described
some kind of nasty way those bacteria penetrate the stomach lining.
Perhaps with sucking tubes or something?
And with some nasty results, which I confess I don't clearly recall.
Perhaps the bacteria or the endotoxin they create
is able to escape into the bloodstream that way?
Or maybe it is that that is how one gets what is called a "leaky gut,"
which allows bad stuff to get into the bloodstream.
Maybe those starved bacteria do make lots of tiny holes.

At least for myself, I've never felt perfectly clear
on some aspects of Peat's view of stomach bacteria and how it should be handled.
He has said that animals with sterile guts are healthier.
But he also then qualified that by saying that
that elevated health ended when those animals ran into bacteria from the environment.
He said something like:
since we live amidst bacteria, we might as well learn to live with them.

I know he takes antibiotics from time to time to suppress intestinal bacteria.
What I've never been real clear on is:
would he endorse the post-antibiotic use of yogurt or kefir or even probiotics?
His comments above seem to me to amount to a tacit acceptance of their limited use.
I could be wrong about that,
but a completely sterile gut, like one after a solid dosing of antibiotics,
would seem to be a problem waiting to happen:
better to reintroduce some strains of "helpful" bacteria to defend against
the possible invasion of bad bacteria.
Yes, Peat has said that even the "helpful" bacteria create stuff unhelpful to us humans.
Still...better to accept some of that than to leave a vacuum enticing to really bad bacteria...?

Peat has said in interviews that this area involves a matter of balance.
In so saying, it seems to me
he doesn't see the goal as the complete annihilation of all intestinal bacteria.

nograde · Mar 29, 2014

@narouz: Peat said that about candida which definitely has invasive capabilities. It does that maybe, as Peat said, to suck off nutrients from blood and/or plasma when no other food is available. I've never heard of gut bacteria "eating" mucosa if they are starved. Mucosal destruction as I understand is always mediated by your own immune system via inflammation. This in turn could create crypts where bacteria settle to cause even more inflammation.

nograde · Mar 29, 2014

Well, I might have missed this recent finding:

http://www.sciencedaily.com/releases/20 ... 131036.htm
On the trail of mucus-eaters in the gut

However, I think there is still a long way to go from bacteria eating mucus to bacteria eating your mucosal (epithelial) tissue.

narouz · Mar 29, 2014

nograde said:
@narouz: Peat said that about candida which definitely has invasive capabilities. It does that maybe, as Peat said, to suck off nutrients from blood and/or plasma when no other food is available. I've never heard of gut bacteria "eating" mucosa if they are starved. Mucosal destruction as I understand is always mediated by your own immune system via inflammation. This in turn could create crypts where bacteria settle to cause even more inflammation.

He didn't say they ate mucosa.
He said, as I recall, that when deprived of sugar/carbs,
they sought food by boring or otherwise devilishly penetrating into
and maybe even through
the intestinal wall.

Filip1993 · Mar 30, 2014

I feel best with little to no fiber in my diet.

Mittir · Mar 30, 2014

One guy is an acupuncturist and another guy is an anthropologist.
I do not know how much biology and physiology these two person know
to teach others what happens with gut flora.
Dr Ayers from coolinginflammation.blogspot.com has a PhD in
cell biology and teaches at university. He has been writing
about gut flora and it's effect on health. His recommendation
differs with RP in some issues but he is a scientist.
People might find his post more informative.

@narouz
Candida
RP mentioned that candida type yeast
grows filament and get into places for food if they are not fed sugar.
But he also mentioned that carrot salad will quickly kill these kind of yeast.
Any other type of anti-yeast substance should do the same.
He did not say anything about other type of bacteria growing filament.
Low thyroid people often have SIBO ( Small intestine Bacterial Overgrowth)
type problem. A good thyroid function will get rid of this problem.
RP mentioned Lactase and other carbohydrate digesting enzymes
are low in hypothyroid people. IIRC Hypothyroid people are also low in
hydrochloric acid production. Hypo people do have low peristalsis
I think health gurus often diagnose SIBO as candida problem.
Their approach is to kill bacteria by starving them with a low-carb diet
without understanding the root cause. Low-carb worsens thyroid function

Here is a RP quote explaining all these

Ray Peat said:
Polysaccharides and oligosaccharides include many kinds of molecules that no human enzyme can break down, so they necessarily aren’t broken down for absorption until they encounter bacterial or fungal enzymes. In a well maintained digestive system, those organisms will live almost exclusively in the large intestine, leaving the length of the small intestine for the absorption of monosaccharides without fermentation. When digestive secretions are inadequate, and peristalsis is sluggish, bacteria and fungi can invade the small intestine, interfering with digestion and causing inflammation and toxic effects. Lactose malabsorption has been corrected just by correcting a deficiency of thyroid or progesterone…Sometimes having a daily carrot salad (grated, with salt, olive oil, and a few drops of vinegar) will stimulate (and disinfect) the small intestine enough to prevent fermentation.http://www.functionalps.com/blog/2012/0 ... aw-carrot/

Sterile gut

RP used that rat study to make a point that presence of bacteria is a burden to the body.
But he also added, since we live in a bacteria filled world one is expected to have
variety of bacteria inside them and to build resistance against bacteria. He is not recommending a rat like
sterile gut. But his idea is to minimize bad bacteria and to keep all the bacteria in large intestine
area, where they belong. He mentioned that lactose eating bacteria are much safer than other types.
But he also mentioned in another place that some lactose bacteria causing problems.
Milk drinking keeps those bacteria alive and multiplying, it also help with elimination.
He mentioned that people with bad bacteria have problem with pectin, not with good
balance of bacteria. Dr Ayers also think starch feed bad bacteria.

narouz · Mar 30, 2014

Mittir said:
Candida
RP mentioned that candida type yeast
grows filament and get into places for food if they are not fed sugar.
But he also mentioned that carrot salad will quickly kill these kind of yeast.
Any other type of anti-yeast substance should do the same.
He did not say anything about other type of bacteria growing filament.

I expect you're right about what Peat said on this, Mittir.
But, just based upon my imperfect memory listening to his interviews,
I don't recall him singling out Candida as the only intestinal bacteria
capable of this intestinal-wall-penetrating action.
Well, actually, Candida is a fungus, right?
Maybe Peat was using the term "bacteria" loosely, meaning to encompass fungus also.
But I don't recall Peat narrowing this whole problem area of "leaky gut"
(or gut penetrated/compromised) to fungus.
On Candida, I just recall him, in some interview,
briefly casting doubt on it
being the widespread problem
mainstream alternative (if I can use that term) health thinking sees it as.
I recently listened to the KMUD "Endotoxin" interview,
and don't recall Candida being mentioned,
not that that contradicts what you say about Peat's view of it.

"Filaments."
Yes, that was the "nasty" mechanism of the bacteria I couldn't recall.
In my memory, Peat didn't single out and specify Candida as the only filamenting evildoer,
but this may well be the case.

I do remember Peat saying that carrots and bamboo shoots, regularly consumed,
should get rid of troublesome/overgrown bacteria most of the time.
But he did say that there are some types of intestinal bacteria
which can survive carrots/bamboo.
He did say those cases were "rare," though.

Mittir said:
But he also mentioned in another place that some lactose bacteria causing problems.
Milk drinking keeps those bacteria alive and multiplying, it also help with elimination.

This is interesting. Would those bacteria include some of the most common strains
used in commercial yogurts and kefirs, I wonder?
Presumably, then, milk drinking could be a problem for some.
I hadn't heard this.
I did hear Peat say that even many
of what are commonly thought of as the "helpful" bacteria
produce unhelpful stuff in the gut.
To me, then, it seems their most helpful quality
is that they simply occupy space
and thereby squeeze out the niche for potentially bad bacteria.
This is where I, personally, feel somewhat in the dark about Peat's exact view.

The last little bit, "it also help with elimination"...that's a little confusing.....

Mittir · Mar 30, 2014

@narouz
I had to listen to Josh Rubin interview on Glycemia again.
( His interviews are worth listening 100 times)
At 1 hour 11 minute, Josh asked RP about over growth of Candida
RP mentioned a bacteriologist named Rene Dubos showed ( probably with picture)
a candida type yeast grew some kind of filament when deprived of glucose.
RP mentioned that lactose feeding bacteria helps with forming stool.
I think It probably has the same mechanism of Lactulose type non-digestble
sugar used in constipation.

narouz · Mar 30, 2014

Thanks, Mittir.
I don't think I've ever listened to that Rubin interview,
so I'll download it.

"RP mentioned that lactose feeding bacteria helps with forming stool."

Okay, I was reading your previous post wrong;
thought it was saying that lactose-feeding bacteria caused trouble.
In your reference, Peat looks like he's saying they may help,
at least in part.
Re-reading your earlier post now,
I guess you're saying Peat thinks it goes both ways with lactose-feeders:
they do some good, and they also do negative things.

If Candida was discussed in that interview,
what did Peat have to say about it, beyond what you've noted?
When I've heard him talk about it,
he has seemed dismissive, sort of like he is about Lyme disease:
not saying it doesn't exist, but that it is way over-diagnosed.

What would you imagine Peat would recommend
following antibiotics for intestinal bacterial overgrowth?
Nothing?
Some yogurt or kefir?

Blossom · Mar 31, 2014

I think paleo's focus on the microbiome is just a misguided attempt to reconcile all the digestive issues that develop when the body lacks enough sugar(broadly speaking) to maintain an adequate gastrointestinal mucosa. I'm just an ordinary Jane but if you don't eat enough carbs(generally speaking) the body will start to prioritize the use of what little is consumed. This is interpreted by our body as a famine condition and digestion always takes a back seat in any emergency scenario. We all have a microbiome and I think keeping it happy is giving our fellow travelers a good home. I believe this may be part of what Peat means by eating enough sugar(generally speaking)to keep them happy. I don't think we can maintain our mucosa without sugar( fruit, honey, lactose..etc.). When a coherent view of the organism is lacking lots of things are mistakenly asserted to the detriment of many people. My microbiome has never been happier and at one time I had 18 anti fungal treatments in one year. Once again, for me personally Ray Peat has been right about everything.

EndlessResearch · Mar 31, 2014

Wow...this is all amazing stuff. I just saw Chris as a Danny Roddy kind of guy. Not trained in one specific area, and willing to look into numerous modalities...obviously not too interested in Peat besides his post on Fructose which is totally against the scientists of the Paleo-shpere like Matt Lalonde and Robb Wolf. I find myself cherry picking from a lot of people that I look up to in holistic health like Peat, Chek, Chris, and more. I am one of those paralysis through analysis people though, and can read all day about these topics, but when it comes to actually USING them in my own life, I just end up arguing with myself on what works for me. People always say the Peat way is such an easy way to eat, but it is much different than what I am used to, or what I even enjoy eating. I did get myself over my lactose intolerance though after reading Peat, but still have problems with eating a lot of it when it comes to using the bathroom if you know what I mean. My lady is super allergic to shellfish (or so she claims), so oysters are something I have to go out for and do by myself or with friends....same with liver for that matter. Everyone's eating mass quantities of haagen dazs suggestions gives me diarrhea and my intestines rumble throughout the night and I experience gas. There are no ripe tropical fruits where I live, and ingredients are important to me so I really like to buy local, organic, and in season produce. I know it is all a feel thing, and honing in a routine is what I just have not gotten down yet. I just like a really wide variety of food, and coffee, eggs, cheese, ripe tropical fruit, OJ, organ meat, milk, gelatin, honey, and sugar get old to me after a while...not to be confused that I don't enjoy consuming these things. I guess it is all give and take when it comes to my inner turmoil. Thanks again for the insight on the original topic!

EndlessResearch · Mar 31, 2014

So I found some counter arguments to Ray's work by a person called "Stabby Raccoon" under a youtube video. Kind of hard for me to decipher so I was hoping for some insight and counter arguments. Here is what he said...

"I've read some of his articles and there's some value to them but I see his articles as more of a springboard for hypotheses rather than something to adhere to. Over-reliance on animal studies and purely mechanistic speculation, and under reliance on strong human experimentation is a bad way to go about things. Some disagreements: He thinks that fiber causes an increase in endotoxin in the blood stream because it feeds gram negative bacteria. Actually it reduces it because it feeds bacteria that product short chain fatty acids that improve tight junction permeability. He thinks that eating polyunsaturated fats increases lipid peroxidation. It can, particularly if they're heat-treated, but there's no evidence that whole food versions do and it's pretty much eliminated by having sufficient natural vitamin E and carotenoids around. Although replacing saturated fatty acids with omega-6 fatty acids is generally detrimental, replacing them with omega-6 and omega-3 fatty acids is generally beneficial. His theories would predict that it would actually be worse when you add the omega-3, yet this is not the case. Fish oil is generally not of good quality but consuming extra vitamin E, like people do when they consume most foods high in omega-6, prevents that lipid peroxidation and enhances the function of the omega-3 fatty acids. He thinks that eating fat increases endotoxin levels, but this is probably only in the absence of those molecules that regulate intestinal tight junctions. Consuming a great deal of your calories as fructose isn't anti-stress, it chronically elevates adrenaline levels. Not to say that sugar is necessarily bad, but living off of it might be, especially according to his criteria of badness. What else? Low fat diets have downsides, the only diet that probably doesn't have macronutrient insufficiency downsides if 40 carbs 40 fats 20 protein. The muscle meat thing is mostly unproven it can elevate cortisol levels temporarily but it's very temporary and it's associated with improved mood. Methionine restriction may be the reason why low "muscle meat" diets are good but if you're consuming enough glycine it's the same effect, properly regulated methylation. So there's an area where he gets it very right. Though it's probably detrimental to see everything as good and bad. He literally seems to think that there are good and bad hormones and nutrients and some of themneed to be eliminated as much as possible, yet a lot of the time this isn't necessary, you may just need to correct its regulation. That goes for free fatty acids too, he thinks that they cause insulin resistance. They can but only if your cellular lipid metabolism is poor. Which reminds me, he seems to be against intense exercise because it causes DNA damage and increases endotoxin levels, yet that's actually prevented by some antioxidants like vitamin c, and the oxidative stress from exercise is probably a net benefit. This is where it would be good to look at more reliable evidence rather than speculating about mechanisms, especially when we have so much good evidence on exercise. That reminds me the lack of exercise, omega-3 fats, fiber and muscle meats may exacerbate lipotoxicity, I think he's created a self-fulfilling prophecy where his extreme dietary and lifestyle restriction has created intolerances to fats. However I still do regard some of his articles as useful."

Mittir · Mar 31, 2014

narouz said:
I guess you're saying Peat thinks it goes both ways with lactose-feeders:
they do some good, and they also do negative things.

Yes, but he only cites one study he read showing lactose bacteria
causing problem. So it is much safer with small amount of risk.
IIRC He speculated lactic acid was causing the problem.

narouz said:
If Candida was discussed in that interview,
what did Peat have to say about it, beyond what you've noted?
When I've heard him talk about it,
he has seemed dismissive, sort of like he is about Lyme disease:
not saying it doesn't exist, but that it is way over-diagnosed.

He said similar things about MS. He treated many people with MS diagnosis
with thyroid. He is not saying MS does not exist, probably because he does not
have studies to claim that. In case of Candida he is saying that over growth of
candida yeast does happen but he sees it as a result of low thyroid and weak
digestive system. Lyme falls into that low thyroid category. IIRC He is more dismissive
about Lymes. He is a scientist he does not always express what he believes to be true
unless he has some evidence to support that.

narouz said:
What would you imagine Peat would recommend
following antibiotics for intestinal bacterial overgrowth?

Daily carrot salad is killing bacteria everyday and
keeping intestine clean. Good thyroid function will increase digestive power
and keep things moving. We are also keeping bad bacteria and total bacteria low
by not eating food that bacteria feast on.

Mittir · Apr 1, 2014

EndlessResearch said:
So I found some counter arguments to Ray's work by a person called "Stabby Raccoon" under a youtube video. Kind of hard for me to decipher so I was hoping for some insight and counter arguments. Here is what he said...

That sounds like another self trained scientist doing their critiquing of RP's works.
All most all the bloggers who criticize RP use those same line of attack.
As if they all got the same memo. I think he did not read RP's articles in details
and even if he did he did not understand any of it. Most people who criticize RP
do not read his articles. They attack him based on some quotes and lines they heard
somewhere else.
I think even a 5th grader knows that you can not do book report
without reading the book. But critiquing is different, you have to read the book
and you have to understand what author is saying and then you give your
counter argument. Anyone can be film critique or music critique.
You only have to watch the movie and write whatever you feel like.
It does not work like that in science. You learn high school level science and
the then you go to college, there you learn more advance science.
Then you go to graduate school, there you learn research method and you
choose field of specialization. It is funny how people who do not even know
high school level science throwing around studies to prove their claim.
Most of them do not even read the full text, they think they can read abstract and
know it all. A 5th grader can sit in front of computer and google up 100 studies to
support a claim or disprove a claim. These self trained health gurus are not much
better than a 5th grader. Most of these health gurus have financial motives to
discredit RP. If RP is right then they have to admit all the books they sold,
all the blog post they wrote and all the clients they fooled were based on their
ignorance. It is not easy.
I think it is a better use of time to read RP articles in detail or any other
article by real scientists. Just avoid self proclaimed scientists.
You can always check authors academic background and field of specialization
before you decide to read their articles. Since this field is full of conflicting
studies ,it takes a lot of time for average person to find a good source of
information.

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Chris Kresser, Jeff Leach and the Microbiome

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