Why Is There So Much Soluble Fibre In Human Breast Milk?

[HDD]

@HDD
That's really interesting. Thanks for posting that recent update on Dr. Peat's changing perspective on the positive role played by your microbiome in general and fermentable fiber's specific role in promoting beneficial strains of colonic microbiota.
Art Ayers talks a lot about antibiotic properties of various foods too. And you might remember I linked to that article 'Garlic may be your gut's best friend'. Garlic's powerful action against undesirable yeast/fungal overgrowths and pathogenic bacteria while leaving commensal species alone predates modern medicine by millenia.
It's not really surprising is it after all the trouble taken to establish a thriving microbiome in babies. And the anatomical reality of having a huge space ONLY for the proliferation of a healthy mix of bacteria in which the commensals should be in control of the pathogens - the colon ?
But it is indeed heartening to see him keeping up with the latest research !

As stated in the other thread, you knew that I was not pointing out "Peat's changing perspective" but showing that he does use current research.

Here, again, is his current status on gut bacteria:
From 01/2015 interview
"Digestion and Emotion"

Caller: On the last show, you had mentioned that tetracycline destroys harmful intestinal bacteria while preserving the good bacteria. Do we know that for sure? How does it selectively spare the "beneficial" bacteria? I've always heard there is a symbiotic relationship with certain intestinal bacteria that help to absorb certain nutrients. So, I'm assuming that would be considered a beneficial bacteria, if that is true...

RP: I think that the interactions of the intestinal bacteria are too complicated to divide them neatly into beneficial and harmful. In the germ-free animals, they've done experiments with introducing a single species of lactobacillus, and even the supposedly beneficial bacteria will make the germ-free animal susceptible to injury that it wasn't susceptible to before. So, it's the context and interaction of the different bacteria, and generally the healthier a person is, the more sterile their small intestine is.

Caller: So, what do you think of the idea that certain nutrients are absorbed through the actions of so-called beneficial bacteria? Is that kind of a fallacy?

RP: Ya, I think it's...there's a little effect there, but I don't think it makes a big nutritional difference. The totally germ-free animals had extremely efficient digestive systems.

 

[Stuart]

@ HDD
It's not even possible to be even remotely germ free without living your whole life in a germ free bubble. That's exactly why you have a microbiome and why its health is integral to whole body health. Dr. Peat would be only too aware of this. We are talking about the real world, where bacteria and our commensal relationship with them is integral to who we are. 'Commensal' - it means mutualistic. This has been so for all of human history, every single minute of it.
It's actually integral to all life on earth, not just humans. But that's to be celebrated, surely. And certainly not denied.
Did you see the question I posed to you in the other thread? Don't be shy. Have a crack at it

 

[tara]

@Stuart
Are you seriously certain that the only reason we have colons is so we can grow lots of bacteria etc? Really? I would have thought it was just as likely that the large number of bacteria are a side-effect of it's more primary functions.

 

[schultz]

@ HDD
It's not even possible to be even remotely germ free without living your whole life in a germ free bubble.

You've mentioned this several times over the course of the thread. You said that humans will always have the same number of bacteria in the large intestine no matter what we do (paraphrased). What is the purpose of the fibre then? We don't need to feed these bacteria special food if they are always going to be there anyway?

Maybe Peat understands this idea, that it's impossible to be sterile in the "real world", and therefore is just against the idea of having more bacteria than we need. An over-abundance. If it's impossible to get rid of the bacteria, maybe it's very easy to have too many?

I think it comes down to balance. It's sort of a push/pull idea. Human milk has anti-bacterial properties, but also has the fermentable fibre. The milk itself prevents the growth of bacteria but also encourages it via the fibre. Also, the human milk contains a high amount of lauric acid, which I think is bactericidal. All this to me seems to be set up in such a way as to discourage bacteria in the small intestine yet encourage bacteria in the large intestine. Obviously the bacteria are needed in the large intestine, because once properly established and balanced, it seems to keep any one strain of bacteria from flourishing. In this sense, the bacteria in our colon, if properly established, are actually acting like anti-biotics to eachother.

Maybe I'm talking nonsense. It's late (for me) and I may wake up thinking what I wrote is stupid. I blame it on my second brain (or my 2 year old daughter...)

 

[Stuart]

@ HDD
It's not even possible to be even remotely germ free without living your whole life in a germ free bubble.

You've mentioned this several times over the course of the thread. You said that humans will always have the same number of bacteria in the large intestine no matter what we do (paraphrased). What is the purpose of the fibre then? We don't need to feed these bacteria special food if they are always going to be there anyway?

Maybe Peat understands this idea, that it's impossible to be sterile in the "real world", and therefore is just against the idea of having more bacteria than we need. An over-abundance. If it's impossible to get rid of the bacteria, maybe it's very easy to have too many?

I think it comes down to balance. It's sort of a push/pull idea. Human milk has anti-bacterial properties, but also has the fermentable fibre. The milk itself prevents the growth of bacteria but also encourages it via the fibre. Also, the human milk contains a high amount of lauric acid, which I think is bactericidal. All this to me seems to be set up in such a way as to discourage bacteria in the small intestine yet encourage bacteria in the large intestine. Obviously the bacteria are needed in the large intestine, because once properly established and balanced, it seems to keep any one strain of bacteria from flourishing. In this sense, the bacteria in our colon, if properly established, are actually acting like anti-biotics to eachother.

Maybe I'm talking nonsense. It's late (for me) and I may wake up thinking what I wrote is stupid. I blame it on my second brain (or my 2 year old daughter...)

For me the whole microbiome thing started to make sense once I learnt about the difference between 'commmensals' ( which do good things in our microbiome, most importantly control the 'pathogens' or bad bacteria) and the pathogenic species, which make us unwell. If all bacteria were bad then there would have been no selective pressure to evolve a colon at all. It would be insane to actually encourage that number of bacteria by providing not only such a big bacteria house, but also ensure that it was well stocked by both the good bacteria (commensals) and food for them to thrive (fermentable fiber) in breast milk. That's why evolution has always seemed such an uncompromising and revealing design tool. Because the constant little improvements over the eons evolutionary change takes place were a bit more likely to be passed down to future generations.
Nature has just worked out that the absolute best way to control the pathogens that are all around us(even within our microbiome itself) is to have a healthy population of good bacteria.
My favourite Peat quote actually recognizes this when he notes : 'We are surrounded by bacteria, so we might as well learn to get on with them. And we have, by having a microbiome in which the good bacteria are our best bet to control the ones which seek to make us ill. Nature has spent many millions of years (millenia before life even emerged onto dry land) perfecting microbiomes. It does seem a bit daft to me to try to second guess that exquisite power of a healthy microbiome to keep us well.
And in that quote, Dr. Peat clearly demonstrates to me that he's not even that far away from realizing that a healthy microbiome is so integral to both who we are, but also to our state of health.
Good night, but don't forget commensals/pathogens - commensals are our friends and pathogens are our mortal enemies. The really neat thing is that the reason they are our immune system allies is that they are also the mortal enemies of the pathogens.
Also, it is important to remember that our colonic microbiota are not just integral to our immune system. they also manufacture vitamins (especially K2 and the B's) foster mineral absorption, and manufacture /mediate hormones. It does so much. Why on earth wouldn't we take dietary steps to ensure all that proceeds smoothly? And until very recently the available food sources ensured that we did automatically.
We have a lot more food choices in the modern world, and we keep making bad ones.

I don't think anything you wrote is stupid Shultz. Even Dr. Peat doesn't seem that aware that there is a world of difference between commensal and pathogenic bacteria. And that difference really is the crux of this entire thread, and also why there is so much fermentable fiber in breast milk - even at the low end of the range you posted.
'Commensals'. It's a beautiful word don't you think? For me it evokes a cooperative bond - that we neglect to our detriment.

 

[Amazoniac]

Not that it will make a difference in anyone's life but..

Symbiosis is an association between two (or more) species meaning 'living together'. The term symbiosis includes a spectrum of relationship, they are mutualism, commensalism and parasitism.
Mutualism is a type of symbiosis that benefits both the organisms. -cut- eg. E. Coli synthesizing K and B vits in the LI.
In commensalism, one of the organisms is benefited and the other is unaffected. -cut- eg. Organisms living on skin that nourish from it. It could become a parasitic relationship if the microbe gains access to some undesired area.
At the other end of the spectrum is the parasitism in which one organism, the parasite benefits from the relationship, whereas the other organism is harmed by it.

edit:
Source - http://www.jaypeedigital.com/Book/BookD ... 9350904749

 

[Stuart]

Yes, I've had globe artichokes two suppers in a row, two each night.
Oops, make that three nights in a row!
I forgot the first night I made HDD's/Such's recipe.

Also, taking the FOS and inulin powder.
I misread the labels when I said I was taking about 30grams/day a few days ago.
I was taking about 15g.
Now I am up to about 30g per day with the powders,
and then there's the artichokes.

I don't think I'm bloating any.
But I am farting quite a bit!
Not violently or painfully or anything.
Just a little bit all day.
The smell is not strange or unusual or particularly strong.
Actually, pretty mild.

Ah, how I love writing about my farts.
I hereby decree that that is firmly pro-Peat!
Nothing very dramatic to report about gut activities, sensations, etc.
Nor about things like mood or energy.
Will update![/font]

You deserve a medal Narouz. Honestly that's a huge increase in fermentable fiber in a very short time. All I can say is that those globe artichokes are are quite remarkable. When I first got my stash of Orafti HP I was immmediately struck by how little gassiness I experienced. Long chain inulin is the bomb I think. It would have been very interesting to see the effect from just the inulin in the globe artichokes without the supplement powders.
But you must have had (a) no SIBO (b) very healthy guts. It could have gone so badly for you (and me ) I'm stoked that you lived to tell the tale. Also, it really is a credit to Peating that your innards are in such fine shape.
On the subject of innards you reported some drama exposing the fleshy interior of the uncooked artichoke, maybe you could soften them in the microwave just to make them easier to prepare for the oil boiling. You know you can (well to be honest, we can buy here, but I expect it's the same in the U.S) cans of marinated artichoke hearts very cheaply at supermarkets. Without the stem though so not as spectacular.
Ages ago you asked whether I'd had any success with topical antifungals. And I wasn't very enthusiastic about any of them. Although I don't have fungal skin stuff going on any more, the skin on my face has always been a bit dry and prone to itchiness - particularly after shaving. On a whim a few days ago, I started using neat ACV as a 'moisturizer' on my face and it seems to have had a truly remarkable positive effect on it , particularly not being itchy whatsoever since. So it well could have been some minor fungal condition . It stings very mildly for about 30 seconds. It's so much more pleasant/honest a feeling than using moisturizers too.

 

[Stuart]

Not that it will make a difference in anyone's life but..

Symbiosis is an association between two (or more) species meaning 'living together'. The term symbiosis includes a spectrum of relationship, they are mutualism, commensalism and parasitism.
Mutualism is a type of symbiosis that benefits both the organisms. -cut- eg. E. Coli synthesizing K and B vits in the LI.
In commensalism, one of the organisms is benefited and the other is unaffected. -cut- eg. Organisms living on skin that nourish from it. It could become a parasitic relationship if the microbe gains access to some undesired area.
At the other end of the spectrum is the parasitism in which one organism, the parasite benefits from the relationship, whereas the other organism is harmed by it.

edit:
Source - http://www.jaypeedigital.com/Book/BookD ... 9350904749

That's really interesting Amazoniac. I wonder why we don't talk about our 'Mutualists'.

 

[EnoreeG]

So I am still left in the dark as to whether Ray Peat is, or is not informed on current microbiome studies. The interview leaves me thinking he is an unchanged man regarding the last several years of study, whether he's read any studies or not. It is up to each of us to decide whether this is a positive or a negative. To me, it just leaves a large question mark as to what Ray knows of recent studies.

There is a thread called "20 questions with Ray Peat" from 09/2014 that Dr. Peat has kindly replied to 10 of the questions. If you look at his replies, you will find studies from 2014 along with older studies. There is no doubt in my mind that Dr. Peat is up to date on current research.

From the thread:

2. marcar72 - "Ask him for more insight on what could be the cause of "high anxiety/panic attacks" quite a few of us members have been experiencing lately. Is it RT3 clearing, low serotonin, or maybe a B vitamin deficiency? A thorough answer from him covering all the possible causes in a checklist type answer would be awesome!

Ray Peat - When things are working properly, tissues are activated according to their use in adapting to the environment, and produce CO2 in proportion to their response; CO2 adjusts the blood supply while promoting mitochondrial energy production and regulating energy use. It stimulates normal breathing, while stabilizing (restraining activity of) nerves and other tissues. In the absence of oxygen (or presence of injury that prevents its use), lactate is produced instead of CO2, and displaces CO2 from the system, activating emergency alarm systems, potentially creating vicious circles of hormone changes and inflammation. Intestinal irritation (e.g., undigested food and bacterial toxin) releases large amounts of serotonin. Serotonin (named for its ability to constrict blood vessels) impairs oxygen use and increases lactate production. Hypothyroidism reduces tissues' ability to use oxygen and produce CO2, and slows digestion, increasing a tendency to produce serotonin, which activates stress hormones, etc.
Bag breathing can increase the carbon dioxide in the tissues, helping to reduce lactate production, but stabilizing the metabolic system is the real solution. With high glycogen stores, minor stresses don't tip the system into glycolytic metabolism easily.

===Physiol Behav. 2004 Sep 15;82(2-3):357-68.
Anxiety and aggression associated with the fermentation of carbohydrates in the
hindgut of rats.
Hanstock TL, Clayton EH, Li KM, Mallet PE.
School of Psychology, University of New England, Armidale, NSW 2351, Australia.
Lactic acid accumulation in the caecum and colon resulting from the fermentation
of carbohydrates can lead to deleterious effects in ruminant and monogastric
animals, including humans. In the present study, we examined the behavioural
effects of two types of commonly consumed foods: soluble and fermentable
carbohydrates (FCs). Thirty-six male Wistar rats were fed either a commercial rat
and mouse chow, a soluble carbohydrate (SC)-based diet or an FC-based diet.
Social interaction, anxiety, aggression and locomotor activity were examined by
employing a social interaction test and a light/dark emergence test, while
physical parameters of hindgut fermentation were examined after sacrifice, either
3 or 21 h after feeding. Results showed that anxiety (spending less time in the
light compartment during the light/dark emergence test) and aggression (increased
fighting during the social interaction test) were increased following raised
concentrations of fermentation end products, such as lactic acid and volatile
fatty acids (VFAs) in the caecum of rats. These associations occurred regardless
of dopamine and 5-HT concentrations in the prefrontal cortex (PFC) and provide
evidence supporting a general effect of FCs on behaviour. Possible mechanisms of
action along with similarities between a rat and human model of acidosis are
discussed.

Proc Soc Exp Biol Med. 1986 Dec;183(3):299-310.
Relationship between dietary fiber and cancer: metabolic, physiologic, and
cellular mechanisms.
Jacobs LR.
The relationships between fiber consumption and human cancer rates have been
examined, together with an analysis of the effects of individual dietary fibers
on the experimental induction of large bowel cancer. The human epidemiology
indicates an inverse correlation between high fiber consumption and lower colon
cancer rates. Cereal fiber sources show the most consistent negative correlation.
However, human case-control studies in general fail to confirm any protective
effect due to dietary fiber. Case-control studies indicate that if any source of
dietary fiber is possibly antineoplastic then it is probably vegetables. These
results may mean that purified fibers alone do not inhibit tumor development,
whereas it is likely that some other factors present in vegetables are
antineoplastic. Experiments in laboratory animals, using chemical induction of
large bowel cancer, have in general shown a protective effect with supplements of
*poorly fermentable fibers such as wheat bran or cellulose. *In contrast, a number
of*fermentable fiber supplements including pectin, corn bran, oat bran,**
**undegraded carageenan, agar, psyllium, guar gum, and alfalfa have been shown to**
**enhance tumor development. *Possible mechanisms by which fibers may inhibit colon
tumorigenesis include dilution and adsorption of any carcinogens and/or promoters
contained within the intestinal lumen, the modulation of colonic microbial
metabolic activity, and biological modification of intestinal epithelial cells.
Dietary fibers not only bind carcinogens, bile acids, and other potential toxins
but also essential nutrients, such as minerals, which can inhibit the
carcinogenic process. Fermentation of fibers within the large bowel results in
the production of short chain fatty acids, which in vivo stimulate cell
proliferation, while butyrate appears to be antineoplastic in vitro. Evidence
suggests that if dietary fibers stimulate cell proliferation during the stage of
initiation, then this may lead to tumor enhancement. Fermentation also lowers
luminal pH, which in turn modifies colonic microbial metabolic acidity, and is
associated with increased epithelial cell proliferation and colon carcinogenesis.
Because dietary fibers differ in their physiochemical properties it has been
difficult to identify a single mechanism by which fibers modify colon
carcinogenesis. Clearly, more metabolic and physiological studies are needed to
fully define the mechanisms by which certain fibers inhibit while others enhance
experimental colon carcinogenesis.

Psychiatry Res. 1989 May;28(2):181-91.
Prolactin and sodium lactate-induced panic.
Hollander E1, Liebowitz MR, Cohen B, Gorman JM, Fyer AJ, Papp LA, Klein DF.
Sodium lactate infusions reliably induce panic attacks in panic disorder patients but not in normal controls, but the mechanism underlying this response is unknown. We studied the plasma prolactin response to infusion of 0.5 molar sodium lactate in 38 patients with panic disorder or agoraphobia with panic attacks, and 16 normal controls. As expected, baseline plasma prolactin was significantly higher in female subjects than in male subjects. However, the males who experienced lactate-induced panic had significantly elevated baseline prolactin levels compared to male nonpanickers and controls. Prolactin levels increased in all groups during lactate infusion, which may reflect osmotic effects, but were blunted in the late panickers compared to nonpanickers and controls. The elevated baseline prolactin for male panickers supports a relationship between prolactin and anticipatory anxiety. The blunted prolactin response for late panickers suggests a net diminution, rather than a sensitization, of prolactin response in panic anxiety.

Endocrinol Jpn. 1960 Dec;7:261-70.
The role of serotonin in carbohydrate metabolism. III. The effect of serotonin on
blood lactate level of rats.
UI M, WARASHINA Y, KOBAYASHI B.

Endocrinol Jpn. 1960 Dec;7:271-8.
The role of serotonin in carbohydrate metabolism. IV. Mechanism of serotonin
hyperlactacidemia.
UI M, WARASHINA Y, KOBAYASHI B.

1. Effect of serotonin on blood lactate level of rats were examined.
2. Serotonin, administered intravenously, subcutaneously or intraperitoneally, caused a rise of blood lactate.
3. Effectiveness of serotonin in causing hyperlactacidemia was far more than that of epinephrine if considered on the basis of physiological concentration in circulation.
4. Serotonin had no effect on blood glycolysis both in vivo and in vitro.
5. The possibility that serotonin may act primarily on carbohydrate metabolism in peripheral and/or hepatic tissues are discussed.


J Am Soc Nephrol. 2014 Apr;25(4):657-70.
The gut microbiome, kidney disease, and targeted interventions.
Ramezani A(1), Raj DS.
(1)Division of Renal Diseases and Hypertension, The George Washington University,
Washington DC.
The human gut harbors >100 trillion microbial cells, which influence the
nutrition, metabolism, physiology, and immune function of the host. Here, we
review the quantitative and qualitative changes in gut microbiota of patients
with CKD that lead to disturbance of this symbiotic relationship, how this may
contribute to the progression of CKD, and targeted interventions to re-establish
symbiosis. Endotoxin derived from gut bacteria incites a powerful inflammatory
response in the host organism. Furthermore, protein fermentation by gut
microbiota generates myriad toxic metabolites, including p-cresol and indoxyl
sulfate. Disruption of gut barrier function in CKD allows translocation of
endotoxin and bacterial metabolites to the systemic circulation, which
contributes to uremic toxicity, inflammation, progression of CKD, and associated
cardiovascular disease. Several targeted interventions that aim to re-establish
intestinal symbiosis, neutralize bacterial endotoxins, or adsorb gut-derived
uremic toxins have been developed. Indeed, animal and human studies suggest that
prebiotics and probiotics may have therapeutic roles in maintaining a
metabolically-balanced gut microbiota and reducing progression of CKD and
uremia-associated complications. We propose that further research should focus on
using this highly efficient metabolic machinery to alleviate uremic symptoms.

J Agric Food Chem. 2008 May 28;56(10):3554-60.
Purple carrot (Daucus carota L.) polyacetylenes decrease
lipopolysaccharide-induced expression of inflammatory proteins in macrophage and
endothelial cells.
Metzger BT(1), Barnes DM, Reed JD.
(1)Department of Animal Science, University of WisconsinMadison, 1675 Observatory
Drive, Madison, Wisconsin 53706, USA. [email protected]
Carrots ( Daucus carota L.) contain phytochemicals including carotenoids,
phenolics, polyacetylenes, isocoumarins, and sesquiterpenes. Purple carrots also
contain anthocyanins. The anti-inflammatory activity of extracts and
phytochemicals from purple carrots was investigated by determining attenuation of
the response to lipopolysaccharide (LPS). A bioactive chromatographic fraction
(Sephadex LH-20) reduced LPS inflammatory response. There was a dose-dependent
reduction in nitric oxide production and mRNA of pro-inflammatory cytokines
(IL-6, IL-1beta, TNF-alpha) and iNOS in macrophage cells. Protein secretions of
IL-6 and TNF-alpha were reduced 77 and 66% in porcine aortic endothelial cells
treated with 6.6 and 13.3 microg/mL of the LH-20 fraction, respectively.
Preparative liquid chromatography resulted in a bioactive subfraction enriched in
the polyacetylene compounds falcarindiol, falcarindiol 3-acetate, and falcarinol.
The polyacetylenes were isolated and reduced nitric oxide production in
macrophage cells by as much as 65% without cytotoxicity. These results suggest
that polyacetylenes, not anthocyanins, in purple carrots are responsible for
anti-inflammatory bioactivity.

Bioactives in minimally processed carrots
March 24, 2011
Source: Teagasc
Summary:
Researchers are developing an understanding of how bioactive compounds in vegetables are affected by passage through the food chain. They assessed the impact of Modified Atmosphere Packaging, which is used to preserve ready-to-eat vegetable products such as carrot disks at the point of sale during chill storage.
Researchers at the Teagasc Food Research Centre, Ashtown, as part of the Irish Phytochemical Food Network, are developing an understanding of how bioactive compounds in vegetables are affected by passage through the food chain. They assessed the impact of Modified Atmosphere Packaging, which is used to preserve ready-to-eat vegetable products such as carrot disks at the point of sale during chill storage.
Polyacetylenes are natural products found in certain plants that have been related to a reduction in the risks of developing diseases such as certain types of cancers and other important diseases. Carrots contain relatively high contents of polyacetylenes. Recent studies have focussed on the polyacetylenes from carrots because their bioactive properties could have beneficial health effects.
They can be classified into four groups depending on the impact they have on human health -- anti inflammatory and anti-platelet; anti fungal and anti-viral; anti-bacterial and anti-mycobacterial; and, cytotoxicity and anti-cancer. Falcarinol has emerged as the most active polyacetylene in carrots in terms of cytotoxicity against cancer cell lines.
Researchers at the Teagasc Food Research Centre, Ashtown, as part of the Irish Phytochemical Food Network, are developing an understanding of how bioactive compounds in vegetables are affected by passage through the food chain. They assessed the impact of Modified Atmosphere Packaging, which is used to preserve ready-to-eat vegetable products such as carrot disks at the point of sale during chill storage.
In an article for TResearch, the Teagasc research and innovation magazine, Dr Juan Valverde and colleagues outline the results of their analysis. The results show that Modified Atmosphere Packaging is a useful way to retain polyacetylenes levels in carrots. None of the three major polyacetylenes in carrots showed significant difference from the control.

Thank you HDD. Finally, this (and also your later post with quotes from "Digestion and Emotion" is MUCH more what I was looking for to explain Ray's current perspective on some current issues regarding gut microbes (and also fiber).

Briefly, I think it is telling that Ray is being asked these questions. It shows the gut microbiome is on the minds of his followers, and answers are needed.

Also, briefly, I think with just these last 2 posts from you, that fairly reliably, Ray has not changed his stance on the value of either fiber or microbes to either a human, or specifically to the human gut. At least from what I can tell, he never in all the comments and studies cited seems to concede that he must "move more toward" some other point of view. For my purposes and satisfaction, I believe Ray has not changed his stance. Some of the studies he cites are saying the question is still open (for instance, as to causes of cancer related to specific fiber, but not others), but I believe if you look at the bulk of citations Ray uses, he wishes his audience to conclude that both fiber and microbes are unnecessary to health, and in many cases may be deleterious.

With that said, I think anyone who wishes to "follow Peat" to the letter should follow him. Those who have a question about this should still inquire. It's quite simple. If the question is still arising for Peat to answer, it shows at least that there are two sides to the issue. And since the question seems to arise more often now than in the past, it shows that Ray may not be answering the question to someone's satisfaction. It will all work out in the end. No worries. I really wish all here the best of luck in finding health. I don't care which way each turns to find truth, or how persistent you may be to do so. We each have different priorities.

The way I decide for myself is to try to stay open to the whole field of available theories and studies regarding health. I especially appreciate hearing about studies and theories that are contrary to either my bias, or the current consensus. That is why I like this forum. It represents something outside the current consensus.

When I question what Ray Peat says, it is to try to likewise point minds toward ideas that might enhance others' frame of reference. With respect to the citations you just provided, I would like to point out that, for instance, in the "Purple carrot" study we find

Carrots ( Daucus carota L.) contain phytochemicals including carotenoids,
phenolics, polyacetylenes, isocoumarins, and sesquiterpenes. Purple carrots also
contain anthocyanins. The anti-inflammatory activity of extracts and
phytochemicals from purple carrots was investigated by determining attenuation of
the response to lipopolysaccharide (LPS).

Now all of these phytochemicals are abundant in many other fruits and vegetables. Even the one which I think Ray singles out as especially protective against cancer, polyacetylene, is found in other vegetables. So it's nice to read some other studies besides the ones that Ray cites, to learn more on this. By doing so, I at least realize I have great choice in the vegetables I eat, and don't have to restrict myself to carrots. For instance, in

Effects of C17-Polyacetylenes on cell proliferation

Epidemiological studies have provided evidence that a diet high in fruit and vegetables is associated with a reduced risk for the development of certain types of cancer, cardiovascular diseases, diabetes, and other diseases (1−7). Compounds associated with the health promoting effects of vegetables are glucosinolates and other organosulfur compounds and their degradation products, carotenoids, phytosterols, polyphenols, vitamins, and dietary fibers (1,7). The mechanisms for the protection of these classes of natural products are mostly unknown and may only in part explain the health effects of vegetables. Consequently, in recent years focus has been on other types of potential health promoting compounds. One of these groups of compounds is aliphatic C17-polyacetylenes of the falcarinol-type (Figure ​(Figure1)1) (7−13), which are common in carrots and related vegetables such as parsley, celery, parsnip, and fennel (10,11,14) as well as in medicinal plants such as ginseng (15,16). Polyacetylenes of the falcarinol-type have shown many interesting bioactivities including anti-inflammatory (11,13,16), antiplatelet-aggregatory11,16−18, cytotoxic (10,11,16,19,20), and antitumor activity (9,22) as well as activity against bacteria and mycoplasma (21). [emphasis added]

I think Peat has selected the carrot, out of all the vegetables available to humans, as the best compromise (in his mind) between having to have some unavoidable fiber, and getting some anti-microbial and cytotoxic properties. Whether the carrot is the best "compromise" food for this goal, I don't know. Whether that severe a compromise is necessary, I also don't know. But I think it's nice to find out why it is that Ray suggests carrots in the first place. And then go on from there. In my mind, it's ALWAYS important to go on from there.

I just will never be happy with one man's take on interpreting the universe. But I totally support others' preference to do the opposite. We should be happy within ourselves.

 

[EnoreeG]

The more the bacterial bulk, the more the resultant endotoxins,

Also a ‘healthy’ microbiome can consist of prominent species having LPS it’s not really pathogen related. See for example bacteroidetes or prevotella. However, endotoxemia is something that involves more than having those bacteria down there.
http://www.nature.com/news/2011/110420/full/news.2011.249.html

Hello Suik.

Will you provide a study that shows an instance of a fecal sample showing a prominent species (or even one of the three genera supposedly found to always be dominant per your cited paper) which contain components consisting of lipopolysaccharide (LPS)? I would really like to see this on paper. It would be significant for all of us trying to establish or maintain health via whatever changes we might make in our gut microbiota!

Additionally, the paper you cited seemed to have been published quite prematurely. Like one of those things that can use a Subject Title to rivet the audience to attention, and then the text under-delivers on the facts.

Also to question in that paper, was that the populations studied were all from developed countries. The paper should have included samples from peoples of third world countries, based on what has already been found to be important differences between "developed" and "primitive" microbiomes, don't you agree?

 

[Suikerbuik]

FYI (I am not sure what you mean with prematurely): http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html,

Additional ones:
http://www.nature.com/ncomms/2015/150325/ncomms7505/pdf/ncomms7505.pdf
http://www.nature.com/ncomms/2014/140415/ncomms4654/pdf/ncomms4654.pdf

 

[goodandevil]

Hey- I just wanted to give my interpretation of gut biomes. I think both good bacteria, and an abiotic state are both healthy. Perhaps a biotic is moreso. Then, either "healthy gut bacteria" or an abiotic state would be desirable. Then the question becokes, to me: do bacteria belong in the small intestine, or anywhere outside of the colon? I feel they do not. However, I would venture to posit that bacteria is good in.the colon, else we would have no.apparendix. it reeuces the argument to spatial terms, vs an all-or-nothing viewpoint

 

[EnoreeG]

FYI (I am not sure what you mean with prematurely): http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html,

Additional ones:
http://www.nature.com/ncomms/2015/150325/ncomms7505/pdf/ncomms7505.pdf
http://www.nature.com/ncomms/2014/140415/ncomms4654/pdf/ncomms4654.pdf

I meant by "prematurely" exactly what your 2nd reference refers to:

...the full extent of human gut microbial diversity remains underexplored. Extant people living traditional
lifestyles are especially under-studied, limited to one population of hunter-gatherers from Tanzania 1, and three rural agriculturalist communities in Burkina Faso 2, Malawi and Venezuela 3...

To test whether subsistence traditions harbour distinct microbial communities, we compared relative abundance of taxa between each of our populations. The three populations show differences in taxonomic distribution at the phylum level (Fig. 2a), with 8 out of 20 phyla having a significant difference in abundance in at least 1 population (False Discovery Rate (FDR)-corrected Kruskal–Wallis test: P o 0.0006)

and

Finally, we compared genus-level taxa abundance profiles
between our populations, and those from two previous studies of
remote agrarian and hunter-gatherer human gut microbiomes
1,3.
PCoA of a Bray–Curtis distance matrix generated from genus-
level taxa tables shows a clear separation between traditional and
urban-industrial microbiomes (Fig. 3a), consistent across the
three different studies.

While that study didn't single out the particular Genera mentioned in your article that I say is "premature", it certainly shows there is massive differences in microbiomes at Phyla, Class, Order and Family levels dependent on many different variables like food, agriculture, medicines.

In fact, most studies trying to do a survey and comparisons of microbiomes don't even go to the species level because they lose certainty by trying to do so because of the shotgun methods used. This is another reason to say that any study claiming to have determined, at the Genus level, what 3 Genera are going to comprise the total set of "most dominant" in every microbiome, such that no human microbiome will ever be found to contain any other but one of those 3 Genera in the most dominant position is, well, premature, it seems to me.

At this point in time, unless a study is dealing with a single species to test it's antimicrobial characteristics, or it's pathogenicity, gut microbiome studies tends to forget about particular species and even Genera and look at weighting across the higher level classifications.

Is this different than the way you see the issue of already determining the 3 dominant Genera of gut microbes?

 

[XPlus]

I didn't forget about you Eno.

1. We don't keep the bacteria in the colon, etc. by design, but there's little we can do to eliminate them.

If that was the case, then we would have evolved to keep the GI completely sterile. That point I made was actually more supportive to your case.

2. They are going to persist as long as we are alive, (the commensals, at any rate) but otherwise they aren't regulated by the liveliness of our organism, and as stressors overwhelm the body and weaken it physiologically, the commensals will continue to fight for us and protect us. They don't turn-coat and become pathogens when the going gets tough. All they want is a good diet of their favorite foods, and that is not our gut lining.

There are documented cases of “commensals” turning pathogenic. Flesh eating bacteria and some bacteria that cause persistent sinus infections are an example of this.
https://en.wikipedia.org/wiki/Staphylococcus_aureus
https://en.wikipedia.org/wiki/Methicill ... cus_aureus

This one is a very interesting read
http://www.ncbi.nlm.nih.gov/books/NBK8526/

Opportunistic pathogens are those isolated from patients whose host defense mechanisms have been compromised. They may be the agents of disease (e.g., in patients who have been predisposed to urinary tract infections with Escherichia coli by catheterization). Finally, some bacteria, such as Lactobacillus acidophilus, are considered to be nonpathogens, because they rarely or never cause human disease. Their categorization as nonpathogens may change, however, because of the adaptability of bacteria and the detrimental effect of modern radiation therapy, chemotherapy, and immunotherapy on resistance mechanisms. In fact, some bacteria previously considered to be nonpathogens are now known to cause disease. Serratia marcescens, for example, is a common soil bacterium that causes pneumonia, urinary tract infections, and bacteremia in compromised hosts.

There are some funny contradictions in here
http://www.kitchenstewardship.com/2012/ ... n-the-gut/

There doesn’t seem to be consensus on the idea of “friendly” bacteria. There’s lot of hoopla assuming the friendliness of the tiny parasitic predators.

3 We are never much capable of "regulating the bacterial presence". Other than using anti-biotics, or changing our diet, and those are only approximations of what I would consider "regulation".

Since you’re into this bacterial business, I assume you aware that even small changes in the environment, such as temperature affect their reproduction. This is why – for example – body temperature raises during fever. It’s to control the replication of the pathogens.
Accordingly, someone who’s hypothyroid with relatively lower body temperatures will offer a more pleasant environment for the bacteria to thrive. (1)
Also, enzyme, bile and acid production depends on physiological health. Starting from the thyroid to the salivary glands, liver, pancreas and the stomach . (2)
Stomach acid s is especially an interesting factor. With PH as low as 1 it’s very potent against bacteria. That’s why we usually only get sick when we’re tired. Because all bodily systems including adrenals and digestion are weak and the bacteria can easily change the acidity around them to survive. In the normal functioning of processes it’ll be very difficult for them to survive. (2.1)
Digestive enzymes work better at higher temps. So when someone temps are good there’s not much food left for the bacteria. (2.2)
Co2 protects oxygen within the system, so the largely anaerobic population of the gut will not like it much when you live in the higher altitudes or simply supplement more Co2. (3)
Light exposure is another factor that adds to resistance against bacteria. Dead matter decays at a faster rate in the dark. (4)
All the parameters I mentioned in 1-4, when their function is optimal, not only work against bacterial presence but also provide clear examples that the variables involved in our physiological function can be manipulated to control bacterial growth. In other words, they can be pushed synergistically either up or down and their movement can alter bacterial populations.
If you want a real life demonstration of this, I urge you to plant some tomatoes. When the tomatoes are ripe enough, remove one from the same plant and leave it in the kitchen sink for few days. Compare this to the fruit still unpicked on the plant. There should be clear difference which one is still intact.

4. So I don't see a time of human physiological weakness when what we've in health been calling "commensal" bacteria suddenly become non-symbiotic or non-mutualistic.

Refer to number 2

5. So ultimately, I don't see the threat that you do. But ultimately, I see that a set of commensal friends remains true to the end, because by their very nature, they realize through all of evolution that their very life depends on us staying alive and providing them a source of their preferred food, which is plant fiber, and not host protoplasm. In some way, the commensals must realize that host death means their death. Likewise, in some way, the pathogens must realize that host death means their final victory and they can multiply for a while, then need to make spoors as they've consumed the host, until they can transfer to another host.

https://en.wikipedia.org/wiki/Decomposi ... rjournal-8
“The small amount of oxygen remaining in the body is quickly depleted by cellular metabolism and aerobic microbes naturally present in respiratory and gastrointestinal tracts, creating an ideal environment for the proliferation of anaerobic organisms. These multiply, consuming the body's carbohydrates, lipids, and proteins, to produce a variety of substances including propionic acid, lactic acid, methane, hydrogen sulfide and ammonia. The process of microbial proliferation within a body is referred to as putrefaction and leads to the second stage of decomposition, known as bloat”
This not only supports my previous argument for oxygen, it shows that our parasitic friends can’t wait for us to die so they can feast on our dead bodies. This supports another point I mentioned earlier that bacteria simply exist to feed and replicate. There isn’t a magic mechanism that regulates their behavior and keeps them from not harming us; because they love us or perhaps because they’re aware we’re the source of their food. Tell them to stay away from your kitchen sink the next time you prepare food.

The machine doesn’t understand that the loop should stop, unless you programme it to do so.

Further Reading
http://australianmuseum.net.au/decompos ... a#bacteria

That's just me. I am totally not afraid of bacteria.

Regardless.

Good for you :P

@HDD
That's really interesting. Thanks for posting that recent update on Dr. Peat's changing perspective on the positive role played by your microbiome in general and fermentable fiber's specific role in promoting beneficial strains of colonic microbiota.
Art Ayers talks a lot about antibiotic properties of various foods too. And you might remember I linked to that article 'Garlic may be your gut's best friend'. Garlic's powerful action against undesirable yeast/fungal overgrowths and pathogenic bacteria while leaving commensal species alone predates modern medicine by millenia.
It's not really surprising is it after all the trouble taken to establish a thriving microbiome in babies. And the anatomical reality of having a huge space ONLY for the proliferation of a healthy mix of bacteria in which the commensals should be in control of the pathogens - the colon ?
But it is indeed heartening to see him keeping up with the latest research !

As stated in the other thread, you knew that I was not pointing out "Peat's changing perspective" but showing that he does use current research.

Here, again, is his current status on gut bacteria:
From 01/2015 interview
"Digestion and Emotion"

Caller: On the last show, you had mentioned that tetracycline destroys harmful intestinal bacteria while preserving the good bacteria. Do we know that for sure? How does it selectively spare the "beneficial" bacteria? I've always heard there is a symbiotic relationship with certain intestinal bacteria that help to absorb certain nutrients. So, I'm assuming that would be considered a beneficial bacteria, if that is true...

RP: I think that the interactions of the intestinal bacteria are too complicated to divide them neatly into beneficial and harmful. In the germ-free animals, they've done experiments with introducing a single species of lactobacillus, and even the supposedly beneficial bacteria will make the germ-free animal susceptible to injury that it wasn't susceptible to before. So, it's the context and interaction of the different bacteria, and generally the healthier a person is, the more sterile their small intestine is.

Caller: So, what do you think of the idea that certain nutrients are absorbed through the actions of so-called beneficial bacteria? Is that kind of a fallacy?

RP: Ya, I think it's...there's a little effect there, but I don't think it makes a big nutritional difference. The totally germ-free animals had extremely efficient digestive systems.

You deserve a clap for digging this

 

[Suikerbuik]

I am no microbiologist, nor pretend to be one. Species, genera, family, .. I think, for this particular issue, it is just fine based on higher level classifications e.g. phyla.

I thought referring to a study showing that gram-negative are a normal and sometimes prominent species of a healthy microbiome would elucidate. They have divided, or named enterotypes, based on certain metabolic functions (and not only constituent) and found 3 types, as can be read in the study. Perhaps forget about it as it doesn’t matter for this subject.

Endotoxins came from pathogenic microbes that, in a healthy person will be a very small subset of the microbiota, and thus will be producing a very small amount of endotoxins, as in lipopolysaccharides, and thus there is no worries in that situation about serotonin, etc. on down the cascade.

But others of us thought that:

The more the bacterial bulk, the more the resultant endotoxins, thus the more serotonin and so on down the cascade resulting in more threat, more stress on the immune system, etc.

Does anyone else remember that phase? Did we settle that? Or only to each of us a different conclusion?

So, firmicutes generally containing gram-positive species and bacteriodetes generally containing gram-negative species. Like firmicutes, bactereoidetes are found as a prominent constituent in the metagenome of healthy people and help producing butyrate, so I’d not consider them pathogenic. Increasing the bulk of bacteria containing a fair amount of bacteroidetes does simply result in more LPS – not equal to endotoxemia!

My thoughts on species:
I think all the 16s rRNA sequencing even up to species level is really limiting (useless maybe??). Okay, great for scientists writing papers and interested in evolutionary biology maybe, but for people interested in reality and health? Fairly useless imo.

At least when talking for myself here, I’m not interesting what name they have, or if they have corresponding 16s rRNA. We should all give them the name OTU if you ask me (operational taxanomic unit).

We should start measuring what they do. Normally you can do so by giving a thing a name, for example a banana like his brother or sister has an almost 100% identical DNA sequence and they operate in ‘predictable’ ways compared to each other (given identical circumstances). It doesn’t matter where you pick it from.
But a species? They say that two ‘identical’ species, lets say E.Coli can still be named an E.Coli while only having 60% similarity in DNA. It’s like comparing humans to dinosaurs??? (kidding of course). I may look up some references. Perhaps I have some (saying with doubt), but heard it a few times during conferences so I don’t think it’s nonsense.

 

[Amazoniac]

Hat tip, XPlus. The majority of people that experience microbial intestinal problems are due to a weakened organism and not a strengthened microbe..

Suiker, those quotes that HDD posted by Ray reinforce what you're trying to say: it won't matter to identify them because as soon as you change the context, the response can be completely different..

 

[narouz]

In this sense, the bacteria in our colon, if properly established, are actually acting like anti-biotics to eachother.

Maybe I'm talking nonsense. It's late (for me) and I may wake up thinking what I wrote is stupid. I blame it on my second brain (or my 2 year old daughter...)

No, I think it makes good sense, schultz. :)

 

[narouz]

Hat tip, XPlus. The majority of people that experience microbial intestinal problems are due to a weakened organism and not a strengthened microbe...

Amazon-
Your re-affirming the terrain argument.
Is the root of health the microbiome?
Or is it the more general health/energy of the organism?

Why prioritize one over the other?
Mightn't it be both?

It seems to me you used to be the kind of guy
whose default diagnosis was "it's all rooted in the gut/microbiome."
Maybe I'm wrong about that.
But if true, what caused your shift?

There are many on the forum who suffer some stubborn form of gut problems.
Despite dedicated Peating.
Would you still think that, in their cases,
they are still neglecting some aspect of their health/nutrition/energy
besides the gut/microbiome?

By the way,
did you note The Return of The Tri-Ball Prince!?
I think it was your capper, pboythewildseducer, that lured him back down from the astral plane....

 

[Stuart]

Suiker, those quotes that HDD posted by Ray reinforce what you're trying to say: it won't matter to identify them because as soon as you change the context, the response can be completely different..

I think this is so important. The role of microbiota in a healthy digestive tract - from mouth to the prodigious numbers in the colon is so complex. Eventually we'll probably have deciphered all of the breathtakingly complex mechanisms and feedback loops, but it could take hundreds of years. We are only in the very infancy of properly understanding the integral role bacteria play in our health.
Perhaps that's why observing and respecting the enormous effort taken to establish and feed an infant's microbiome serves as an ongoing reminder of what is a priority.
There are so many studies out there which laymen and professionals alike use to justify this or that dietary practice. And the work has to be done of course. We are a curious species after all. But it uses up so much bandwidth! And is so heavily influenced by tribal loyalties to particular dietary philosophies.
But in the interim, isn't it also a good idea to not lose sight of what nature provides for babies as the clearest indication of what we should eat?
If our physiology changed in significant ways (like the colon atrophying for instance ) with age then obviously dietary optimums would be completely different. But even after decades of eating a diet that is inspired by the attitude that the microbiome is at best irrelevant to health, the colon will still be a huge bag full of a mix of good and bad bacteria, whose interractive and participatory role with every aspect of our health and well being, including neurological, has continued without a moment's respite. Some humans lose the ability to metabolize lactose after weaning of course, particularly asians, but most Europeans have developed lactase persistence.

I wonder why Dr. Peat thinks there is so much fermentable fiber in breast milk? One of you lot in the U.S. should ask him. Perhaps he thinks the microbiome is important to babies' health but isn't after weaning? He's clearly an almost poetic master of the quotable quote. I'd love to know what his take would be.

 

[Stuart]

Hat tip, XPlus. The majority of people that experience microbial intestinal problems are due to a weakened organism and not a strengthened microbe...

Amazon-
Your re-affirming the terrain argument.
Is the root of health the microbiome?
Or is it the more general health/energy of the organism?

Why prioritize one over the other?
Mightn't it be both?

It seems to me you used to be the kind of guy
whose default diagnosis was "it's all rooted in the gut/microbiome."
Maybe I'm wrong about that.
But if true, what caused your shift?

There are many on the forum who suffer some stubborn form of gut problems.
Despite dedicated Peating.
Would you still think that, in their cases,
they are still neglecting some aspect of their health/nutrition/energy
besides the gut/microbiome?

By the way,
did you note The Return of The Tri-Ball Prince!?
I think it was your capper, pboythewildseducer, that lured him back down from the astral plane....

I think it's both too. Even the appendix was once thought to be an unnecessary 'appendage'. Sob!!
I'd also love to hear what led Amazoniac to taking a more hierarchical perspective.
Did he used to be the Stuart of Peatdom?
Maybe in time I'll be corrupted too.