Do Favorable Bacteria PERMANENTLY Colonize The Intestines?

[narouz]

With the other interesting threads now running about the gut microbiome,
I wanted to focus in on one maybe overlooked assumption.
Does the microbiome permanently recolonize?

That is to ask:
if we just leave the gut alone,
eat a good Peat diet, etc...
will the gut, left to its own devices, simply repopulate correctly willy-nilly?

I guess I've been under the impression
that our "healthy" intestinal bacteria reproduces continually--
indeed, from a Peatian point of view,
that they OVER proliferate and are dangerous only in that regard,
not that they eventually dwindle and expire if not re-populated through diet.

Peat does not seem to recommend probiotics (either pills or naturally fermented "probiotics")
under any circumstances.
Even in the event one does a Peatish round of correct antibiotics.

Okay...let me say up front about all that: I don't know.
But in doing some research lately on Candida,
I came across this pretty compelling poster "Jorge."
He argues that there are studies showing that healthy microbiota does not permanently recolonize.
In other words,
we must actively help it recolonize if we seek to maintain it.

Well...this has important implications for the Peat diet.
Peat does seem to agree that we need to maintain a healthy microbiome balance.
It's just that with him, he always sees the challenge from the other side:
how to continually tamp down a natural tendency for gut bacteria--even the "healthy" ones--
to overpopulate.

So anyhow...I just wanted to open a discussion on the assumption we all mostly seem to be making
that the gut microbiome needn't be actively repopulated.

So below please check out this Jorge's argument.
It comes from a forum where the central topic is Candida (I have a thread running on this now).
English is a language he learned late in life,
so it is not the best.
But he has posted on that "Curezone" site for many years,
and I've read a lot of them,
and he seems to me to be a persistent and intelligent seeker/researcher.
His handle over there is "dvjorge" if you want to google for more of his stuff.
In the following post he displays some frustration because, apparently,
people misconstrue what he has said about the microbiome and repopulation:

Yes, THEY DO COLONIZE !!!
I have repeated this a million of times but they DON'T last more than 3 months. I have been in contact with the Gordon Lab that is working in the Genome Proyect. I have discussed it with people who has been investigating it for years. If I go to the Curezone archives where I have posted more than 2000 times, I can find long discussions about it with people who have dedicated years to battle candida. There is reliable scientific information in the web from medical sources that recognize that permanent colonization hasn't been proved. I have dedicated a huge amount of hours to find medical papers demonstrating possible pharmaceutical probiotic colonization that be permanent, but it isn't demonstrated. They colonize but they don't last. After 18 days of stopping supplementation they can be detectable, even after 60 days, but not after 90 days. I don't post garbage. Go to the Probiotic Organization and read about it.

It looks like my bad English isn't well understood. They DO colonize but only temporary. There aren't proves they do colonize permanently. It is a matter of time ( months at best ) that they aren't detectable in feces or biopsies. People need to know that. People need to know that the benefits are as long as you supplement them. You gonna find articles about L. Reuteri, V-299, and other species that have been detectable after 60 days of stopping them, but no longer than 3 months. They decline very fast until there isn't more detection.

An article claiming they can detect them after 18 days don't say me anything since I have read other papers detecting colonization after 60 days. What is important is they do form colonies and growth in the intestines. This is something that has to be seen in the future with pharmaceutical grade probiotic, if it is ever possible.

Jorge.

This is fragment of a Patent Production from one of the larger Pharmaceutical grade Probiotic in the world. It is 2012 patent. I am posting it, but I won't continue arguing about it or any other topic. That time already passed for me. It is your turn to find the true and the best way to recover your health. It has been hard for me and I am doing an effort to help. That is it.

[0004] The gastrointestinal microflora has been shown to play a number of vital roles in maintaining gastrointestinal tract function and overall physiological health. For example, the growth and metabolism of the many individual bacterial species inhabiting the gastrointestinal tract depend primarily upon the substrates available to them, most of which are derived from the diet. See e.g., Gibson G. R. et al., 1995. Gastroenterology 106: 975-982; Christi, S. U. et al., 1992. Gut 33: 1234-1238. These finding have led to attempts to modify the structure and metabolic activities of the community through diet, primarily with probiotics which are live microbial food supplements. The best known probiotics are the lactic acid-producing bacteria (i.e., Lactobacilli) and Bifidobacteria, which are widely utilized in yogurts and other dairy products. These probiotic organisms are non-pathogenic and non-toxigenic, retain viability during storage, and survive passage through the stomach and small intestine. Since probiotics do not permanently colonize the host, they need to be ingested regularly for any health promoting properties to persist. Commercial probiotic preparations are generally comprised of mixtures of Lactobacilli and Bifidobacteria, although yeast such as Saccharomyces have also been utilized.

 

[Suikerbuik]

Do "Favorable" Bacteria PERMANENTLY Colonize the Intestines? No, don't think so.

I put favorable within brackets because even seemingly healthy bacteria can be pathogenic. Healthy bacteria can change their phenotype and become pathogenic. For example extracellular ATP can be trigger or epinephrine which acts as a quorum sensing molecule. Another reason bacteria can permanently change is because they are capable of sharing genetic material via horizontal gene transfer.

Are bacteria found in probiotics favorable bacteria? Depends on which species and what you want to achieve. They -even when death bacteria- alter immune response anyway. Do they colonize? No. May they help establish a better environment? In theory yes, but practice they have little effect if you ask me. I also read (only unreferenced statement) a while ago that an E.coli can be called an E.coli Even though it only shares 60% genetic material.

There's also a swedisch study showing that it's the whole-microbiome (including interactions that matters). They had thin mice and fat mice. Put them together and showed which bacteria passed onto the fat mice than became thin. They noticed about 39 species transfered. However when they composed a probiotic with those 39 bacteria and gave a new set of fat mice that probiotic they didn't became thin..

Difficult subject if you ask me. Immensely complex we know really little about it.

 

[narouz]

Do "Favorable" Bacteria PERMANENTLY Colonize the Intestines? No, don't think so.

I put favorable within brackets because even seemingly healthy bacteria can be pathogenic. Healthy bacteria can change their phenotype and become pathogenic. For example extracellular ATP can be trigger or epinephrine which acts as a quorum sensing molecule. Another reason bacteria can permanently change is because they are capable of sharing genetic material via horizontal gene transfer.

Are bacteria found in probiotics favorable bacteria? Depends on which species and what you want to achieve. They -even when death bacteria- alter immune response anyway. Do they colonize? No. May they help establish a better environment? In theory yes, but practice they have little effect if you ask me. I also read (only unreferenced statement) a while ago that an E.coli can be called an E.coli Even though it only shares 60% genetic material.

There's also a swedisch study showing that it's the whole-microbiome (including interactions that matters). They had thin mice and fat mice. Put them together and showed which bacteria passed onto the fat mice than became thin. They noticed about 39 species transfered. However when they composed a probiotic with those 39 bacteria and gave a new set of fat mice that probiotic they didn't became thin..

Difficult subject if you ask me. Immensely complex we know really little about it.

Hmmm...the fat mice/thin mice experiment would seem to point to general "terrain" point-of-view.
The terrain of the thin mice was different somehow from the terrain of the fat mice.
The macrobiome composition was not the decisive factor in thinness/fatness.
Maybe a result or reflection of healthy terrain, rather than a cause of it...?

Well, okay.
This might be viewed as support of Peat's general attitude about microflora:
it will take care of itself if one works on creating a healthy terrain.
Even, presumably, after one takes a Peatish round of antibiotics.
He does seem to think there is a general tendency toward overpopulation of gut flora,
and even if composed by the good guys they need persistent tamping down
by carrots, etc.
And by not fueling them with starch and wrong fiber.

Peat has said that we've evolved as an organism with intestines which
deal with the threats posed by bad bacteria
by counterbalancing them with (generally) favorable bacteria.

And I guess you'd have to say Peat does advise persistent intervention with the microbiome--
with the carrot salad, avoidance of starch, etc.

So one wonders why another kind of intervention bolstering good microbiome health/balance
would be wrong.
Another kind of intervention in the form of regular consumption of
what are regarded generally as favorable intestinal bacteria.

What you note above, Suiker, might argue that such intervention is unnecessary or useless.
But not harmful...I wouldn't think.

On the other hand there's a lot pointing to healthy microbiomes being a causative actor, even star actor,
in overall health.
If favorable bacteria do not automatically or permanently repopulate,
seems like there's a good argument to supplement them regularly.
The down side would seem to be a little burdensome lactic acid,
depending upon what form used.
The upside might be the proper balancing of the microbiome--a foundation, perhaps, of good health.

Isn't there evidence that some of the healthiest, longest-lived people on the planet
had diets containing substantial amounts of fermented foods?

 

[Such_Saturation]

Narouz , if you want to try probiotics so bad, just do it. Give in and we won't stop you, but report your findings. There's no point in procrastinating. But anyway, if the the environment is favorable, they will stay. Otherwise you would become sterile after a while.

 

[narouz]

Narouz , if you want to try probiotics so bad, just do it. Give in and we won't stop you, but report your findings. There's no point in procrastinating. But anyway, if the the environment is favorable, they will stay. Otherwise you would become sterile after a while.

Oh Such, I'm way past that.
I have and I am.
(I haven't tried Nystatin enemas yet though! )

No, in this thread I'm just opening for exploration the possibility
that Peat's firm anti-probiotic stance
might beneficially be tweaked by some people at some times.

Is the following not a reasonable line of thinking?
1. Peat says certain pharma antibiotics might be helpful sometimes.
2. Yet he says probiotics even in that context are still counter-productive or at least unnecessary.
3. But we seem to be agreeing here that favorable microflora do not permanently recolonize;
that is: if we want them in our guts we need to replenish them.
Somehow.
Probiotics are an obvious method.

Just questioning Peat orthodoxy.
Is that not perfectly Peatian?

As someone who has taken antibiotics because I "needed" them--
appendectomy several years ago, possible dental infection recently--
and who has tried Peatian short-courses experimentally a couple of times over the years...

...it wouldn't seem unreasonable that I disturbed the microbiome balance
and that one consequence of that might be an overgrowth of fungus/yeast/Candida.

I don't think I'm the only one on this forum who has taken antibiotics.
I know Charlie has.
And I know that we both got white tongue effect afterwards.
Flowers of sulfur never resolved it, for me.

Just be nice to hear what others' experiences are in this regard.

 

[Suikerbuik]

I see there are some threads about the same subject going on. I'll just reply here.

Hmmm...the fat mice/thin mice experiment would seem to point to general "terrain" point-of-view.
The terrain of the thin mice was different somehow from the terrain of the fat mice.

I don't think it's the terrain in this regard. All fat mice are grown in the same way. It is the complexity we cannot understand yet. Incomplete measurements is one reason.

What do you mean with macrobiome composition?

What is your definition of favorable bacteria? And what is the goal you have in mind with them?

What you note above, Suiker, might argue that such intervention is unnecessary or useless.
But not harmful...I wouldn't think.

Probiotics can be harmful in a subset of people, for example suffering acute pancreatitis. Consider the bacteria that we used to get in contact with when living in a more natural environment. So get your hands a bit dirty, only use soap occasionally etc.

Not sure if I have posted this before, but you should definitely watch it.
https://www.youtube.com/watch?v=M4p3JI7s1dw

PS you're definitely onto something narouz, but I don't think antibiotics nor probiotics are going to be your answer.

 

[narouz]

Suik-
That was an interesting video. Thanks!

Many things to talk about, but
one takeaway for me involved Alms' point late in the video
where--after a Salmonella bout--he shows how his microbiome recolonized
(with, he says, "just bacteria that happened to be around at the time"),
and then remained quite stable like that for a while.

That would seem to support one simple scenario I've been interrogating:
1. someone takes antibiotics
2. a disturbance occurs in the balance of microflora
3. that new balance (or imbalance) continues, fairly stable, for a while.

So, simply:
If our gut microflora get disturbed (antibiotics, say) and unbalanced,
might be reasonable to try to rebalance it by other intentional intervention.

(Oh: in my previous post I meant to write microbiome where I wrote macrobiome.
As to "favorable bacteria": I don't think I'm ready to attempt a definition at this point.
But I just mean the ones, for instance, that Peat mentions as being "generally favorable."
The goal would simply be a counter-intervention, hoping to nudge back toward healthy balance,
see above.)

 

[lindsay]

I just wrote a whole response and it didn't post - bummer.

But I was going to say that I had a lot of trouble post antibiotics and I'm still dealing with it. All I wanted to eat was cheese for months (a probiotic in it's own sense).

I have used Kefir and potato starch with honey post salmonella poisoning in the past - the effects were rapid and profound.

Also, we don't live in a germ free world. Might as well learn to live with them.

 

[narouz]

I just wrote a whole response and it didn't post - bummer.

But I was going to say that I had a lot of trouble post antibiotics and I'm still dealing with it. All I wanted to eat was cheese for months (a probiotic in it's own sense).

I have used Kefir and potato starch with honey post salmonella poisoning in the past - the effects were rapid and profound.

Also, we don't live in a germ free world. Might as well learn to live with them.

lindsay-
Sorry your first post didn't make it!
(I've lost many a post because I hit "Preview," thought I was done, then clicked to another site.)

Also, we don't live in a germ free world. Might as well learn to live with them.

This is just what Peat says.
It wouldn't seem weird to me to think that
if we can knock our germ balance out of whack with antibiotics
we might try knocking it back into balance with probiotics....

 

[tara]

Hi narouz, I've read your posts, but not gone off to read others of Jorge's etc.
Jorge seems convinced that 'favourable' microbes will not colonise permanently, but I wonder if in the evidence he relies on there is any serious control for and experiment with the terrain? If the terrain favours pathological microbes, and you add more benign ones, perhaps one would expect the pathological population to soon re-establish dominance?
I don't have a set opinion on whether there may sometimes be a case for attempts to add more benign populations, but even if it could sometimes be helpful, it isn't clear which ones one would want, or how best to supplement them. It could be that the desirable additions are a complex set of many species. It could be that having a wide range together is part of what helps them persist.

 

[narouz]

It's a new idea for me, tara.
I'd always just assumed the "favorable" bacteria
just reproduced themselves endlessly--indeed overpopulating
in the Peat view.

Peat mentioned one or two intestinal bacteria in an interview which he said
on balance
were favorable.
He wasn't attempting to be exhaustive--just fleshing out the general idea
that, yes, there is such a think a favorable bacteria.

Maybe food history re fermented foods should not so easily be cast aside.
We've evolved to co-exist with dogs and cats over the millennia,
seemingly with good results.
Maybe we've likewise developed a mutually agreeable relationship with certain intestinal bacteria.

I did have "a set view" about probiotics until recently--a Peat view, against them.
So...I don't know. I'm opening it up for review.

 

[Zachs]

What makes probiotics, "favorable"? Seems like if they are unable to permanently colonize that they are useless at best.

A few have talked about traditional cultures and fermentation. Remember that these peoples did not ferment foods for the "health benefits" that people talk about today. They only did this as a way of preserving food. This has only been a practice in our very recent past so saying that traditional healthy cultures were healthy from consuming fermented foods is speculation at best.

 

[narouz]

What makes probiotics, "favorable"? Seems like if they are unable to permanently colonize that they are useless at best.

Zachs-
Just because a girlfriend can not be permanent,
are they "useless at best"...?

Kidding aside...
Peat says our gut health depends upon a balance of bacteria vs bacteria.
He says some are, on balance, favorable.
Well...okay.
If we agree...
1. a balance is desirable
2. favorable bacteria do not permanently recolonize
...then this would seem to point to...
periodically replenishing favorable bacteria,
probably as an intentional tactic.

A few have talked about traditional cultures and fermentation. Remember that these peoples did not ferment foods for the "health benefits" that people talk about today. They only did this as a way of preserving food. This has only been a practice in our very recent past so saying that traditional healthy cultures were healthy from consuming fermented foods is speculation at best.

I'll go along with that.
We don't know either way.
It would not seem far-fetched to me to find
that we evolved healthy guts over time by, in some cases,
developing a symbiotic relationship with certain "friendly" bacteria.
This would seem to be somewhat mainstream thinking.
It is only us Peatians who regard it as radical/wrong.

 

[Zachs]

But whats wrong with our already permenant favorable flora that we are given at birth through delivery and breast milk? What exactly does probiotic supplementation accomplish in those short (or long) bouts of supplementation? If they arent able to colonize, wouldnt that mean that they are ether inferior to our already colonized flora or that they are not receiving their preferred food source and also therefor not a favorable choice?

I guess my question is, what will supplementation accomplish?

 

[narouz]

But whats wrong with our already permenant favorable flora that we are given at birth through delivery and breast milk? What exactly does probiotic supplementation accomplish in those short (or long) bouts of supplementation? If they arent able to colonize, wouldnt that mean that they are ether inferior to our already colonized flora or that they are not receiving their preferred food source and also therefor not a favorable choice?

I guess my question is, what will supplementation accomplish?

Many unknowns here, and this is a new area of investigation for me.
That said:

-I'm not at all sure that you "already" have a "permanent favorable flora" given to you at birth.
Some probably do have an excellent microflora from birth.
Permanent?
There does seem to be science arguing that flavorable gut flora does not automatically
and permanently reproduce and repopulate.
If this is true, then it would seem to be a matter of maintaining a favorable balance of microflora,
either intentionally or willynilly.

-Even if one does have a favorably balanced gut microflora--even from birth--
what about the effects of powerful pharma antibiotics?
Or, as you bring up, what about periods where our favorable microflora
do not, for whatever reason, "receive their preferred food source"...?

-From what I've been reading lately,
it seems at least arguable that
our "already colonized flora" are not permanent.
They may be fairly stable, but apparently that is not because they auto-reproduce
without any replenishment from the outside.

 

[Zachs]

Where would one have gotten outside sources of bacteria before fermentation was utilized? Sure we would have eaten bacteria from soil and other organic sources, maybe even the odd fermented fruit here and there but certainly nowhere near the amount given in a probiotic supplement. Would that be enough to keep gut flora populated and balanced?

I agree on the unknown of what antibiotics and ingestion of other chemicals play in our digestive health but it also seems that taken a random supplement of the most easily flourishing microbes is kind of a ahot in the dark on whether it will have a favorable effect if any.

 

[narouz]

Where would one have gotten outside sources of bacteria before fermentation was utilized? Sure we would have eaten bacteria from soil and other organic sources, maybe even the odd fermented fruit here and there but certainly nowhere near the amount given in a probiotic supplement. Would that be enough to keep gut flora populated and balanced?

Maybe.
There are other variables to be considered.
As you noted in your last post: what about favorable food for favorable bacteria?
(or, favorable food for unfavorable bacteria?)

I agree on the unknown of what antibiotics and ingestion of other chemicals play in our digestive health but it also seems that taken a random supplement of the most easily flourishing microbes is kind of a ahot in the dark on whether it will have a favorable effect if any.

It wouldn't seem random at all to me.
It seems like an intentional effort to repopulate targeted "friendly" microflora.

 

[Zachs]

What i mean is, there are something like 1000 species of bacteria in the digestive tract alone, what makes you think the the 5-10 strains in a supplement will have any positive effect in such a competitive environment?

On a personal note, i went through several phases on eating large amounts of ferments and taling supplements. Every time i got major digestive issues, mostly pain in my upper right abdoman and systemic chronic inflammation.

 

[narouz]

What i mean is, there are something like 1000 species of bacteria in the digestive tract alone, what makes you think the the 5-10 strains in a supplement will have any positive effect in such a competitive environment?

There does seem to be science about which species are "healthy" or "favorable."
And while there are many different strains as you say,
there also seems to be science about what strains dominate, and dominate with a favorable result.
The opposite also.

On a personal note, i went through several phases on eating large amounts of ferments and taling supplements. Every time i got major digestive issues, mostly pain in my upper right abdoman and systemic chronic inflammation.

Are you saying you got the abdomen pain because you ate fermented foods...?
Over in my Candida thread,
I relate the observations of a poster named Jorge
on a Candida forum.
He argues that the upper right abdomen pain is more often coming from
the cecum/ascending colon/transverse colon--
the places where--according to him--Candida yeast/fungus builds a fortress.

 

[Zachs]

So are you saying that the dominate strains in our gut are the same strains found in fermented foods?

Yes from things such as kefir, yogart, kombucha and probiotics. The inflammation and pain was exaccerbated by a diet high in animal products but still came on when following a almost fat free/animal product free diet so im sure it was the ferments. This could be endotoxin load from ferments or maybe the lactic acid feeding other bacteria/yeasts? Im not sure.