Mucosal microbiota transplant, clearing the gut mucosa prior to FMT Enhancing

[Michael Harrop]

I posted about this a few years ago elsewhere [1][2][3] and I'm copying all the info here for easy discussion.


"While fecal microbiota is partially normalized by extended co-housing, mucosal communities associated with the proximal colon and terminal ileum remain stable and distinct". Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models (May 2019). https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30488-7

For the people who don't know, mice eat each other's poop, thus naturally do FMT when co-housed.

This study seems to show that FMT is not enough to change the mucosal microbiome. Thus it seems like something like this would be necessary to enhance FMT:

By destroying the mucous membrane in the small intestine and causing a new one to develop, scientists stabilized the blood sugar levels of people with type 2 diabetes. https://www.theguardian.com/society/2018/oct/24/spectacular-diabetes-treatment-could-end-daily-insulin-injections

Duodenal Mucosal Resurfacing Elicits Improvement in Glycemic and Hepatic Parameters in Type 2 Diabetes—One-Year Multicenter Study Results (2018): https://diabetesjournals.org/diabetes/article/67/Supplement_1/1137-P/54118/Duodenal-Mucosal-Resurfacing-Elicits-Improvement

When destroying the membrane you're basically clearing the forest, which includes pathogens which may be responsible for diabetes. It's likely that if their method actually clears and replaces it without significant damage (unlike antibiotics) it could help many more conditions than diabetes.

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Previously I emailed a bunch of IBS & CFS researchers asking them to test that mucosal clearing either by itself or in conjunction with FMT, but it didn't seem like any were willing/able.

Someone should also test (in vitro then in mouse models) various substances that degrade/clear the gut mucosa to see if you can find one that safely boosts the ability of FMT to replace the mucus microbiota. Basically a chemical version of the method above. N-acetyl cysteine (NAC) might be one. Try while liquid fasting too.

Someone suggested:

Utilizing proteolytic enzymes may be interesting. Even to go as far as doing a retention enema to allow the enzymes to break down biofilms and the mucosal layers.

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And relevant to the "in vitro" part: GuMI: New In Vitro Platforms to Parse the Human Gut Epithelial-Microbiome-Immune Axis https://grantome.com/grant/NIH/R01-EB021908-02

My worry is that the fecal microbiome isn't adequate, and a gut microbiome transfer will require harvesting the mucosal microbiome. But an experiment like this should help to further our understanding of this.

I'm thinking there might be some type of layers. Like the microbes transferred by FMT are only able to occupy some top layer or small niches where they're able to feed on the food coming through, but unable to penetrate further down into the mucus.

This is very much inline with my own current FMT experience where the donor microbes seem to be very easily lost - such as by using iodized salt (iodine is an antimicrobial) - and I have to keep adding them.

Mucosal microbiota transplant?​

I was thinking more about "while fecal microbiota is partially normalized by extended co-housing, mucosal communities associated with the proximal colon and terminal ileum remain stable and distinct".

It should be possible to do a mucosal microbiota transplant by swabbing/collecting mucosa samples from the colon, immediately submerging them in saline to protect anaerobes, and then feeding that liquid to other mice and see how it compares to FMT/co-housing. I would also compare feeding the mucosa liquid while the recipient mouse was fasting vs not fasting.

I did a google scholar search for "mucus microbiota transplant" and didn't see anything on it.

We could even do it in humans, it would just be slightly more invasive for the donor than FMT. I've had a colonoscopy done while I was not sedated. It was painful as the object made its way through the turns especially, but perhaps we don't need to use such a large object, making it less painful.

For reference, the mucosal microbiota seems to be significantly different from the fecal microbiota:

Mucus: A Special Home of Our Microbes (2018): https://www.karger.com/Article/FullText/495115#scrollNav-4 "So far, we know that the mucus of surface epithelia seems to be one of the most important habitats for host-associated bacteria"

Differential clustering of fecal and mucosa-associated microbiota in ‘healthy’ individuals (2018): https://onlinelibrary.wiley.com/doi/10.1111/1751-2980.12688 "Analysis of faecal samples that have been transported at ambient temperature does not adequately reflect the colonic mucosa-associated microbiota in healthy individuals"

Gut mucosal-associated microbiota better discloses Inflammatory Bowel Disease differential patterns than faecal microbiota (2018): https://www.dldjournalonline.com/article/S1590-8658(18)31260-X/abstract

Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria (Mar 2019): https://journals.asm.org/doi/10.1128/mbio.01984-19

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals (June 2019) https://www.gastrojournal.org/article/S0016-5085(19)40986-4/fulltext "In an analysis of saliva, mucosal, and fecal samples from 21 healthy adults, we found each individual, and each GI region, to have a different bacterial community. The fecal microbiome is not representative of the mucosal microbiome."

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals (May 2019) https://journals.sagepub.com/doi/10.1177/2050640619852255 "gastrointestinal location is a larger determinant of mucosal microbial diversity than inter-person differences. The bacterial load of mucosal samples decreased from oesophagus to proximal ileum, but drastically increased again in the lower GI tract. The composition of the microbiota markedly changes along the GI tract with larger diversity in the lower GI tract than the upper GI tract."

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Conflicting data:

Fecal samples and rectal swabs adequately reflect the human colonic luminal microbiota (Oct 2024, n=10)

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Maybe the ultimate end game will be clearing the mucosa in the recipient and using mucosa microbiota from the donor, but for now, maybe whichever one is easier could be a significant improvement on its own compared to standard FMT.

 

[Michael Harrop]

Related threads:

• Improve FMT effectiveness with mucus and biofilm dissolver? N-acetyl cysteine (NAC)
• FMT engraftment
• Strategies To Increase The Effectiveness Of FMT

 

[Otto Kretschmer]

Any specific ways to clear/destroy the mucus membrane? Would a colon cleanse before FMT do it?

 

[Michael Harrop]

The OP covered a unique method that one study used for diabetes patients. The next comment covers the possibility of using NAC. A colon cleanse doesn't seem sufficient https://humanmicrobiome.info/fmt/#before-the-procedure.

 

[Otto Kretschmer]

By the way all of this shows just how little we know about the human microbiome... A long way ahead.

 

[Asclepius]

By destroying the mucous membrane in the small intestine and causing a new one to develop, scientists stabilized the blood sugar levels of people with type 2 diabetes. https://www.theguardian.com/society/2018/oct/24/spectacular-diabetes-treatment-could-end-daily-insulin-injections

Duodenal Mucosal Resurfacing Elicits Improvement in Glycemic and Hepatic Parameters in Type 2 Diabetes—One-Year Multicenter Study Results (2018): https://diabetesjournals.org/diabetes/article/67/Supplement_1/1137-P/54118/Duodenal-Mucosal-Resurfacing-Elicits-Improvement

When destroying the membrane you're basically clearing the forest, which includes pathogens which may be responsible for diabetes. It's likely that if their method actually clears and replaces it without significant damage (unlike antibiotics) it could help many more conditions than diabetes.

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Unfortunate that they didn't seem to test the microbiota of the mucus before and after treatment. If it fully changes the mucus membrane then surely it must have a huge impact on the microbes living there. Maybe most of the microbes will be lost with it, which makes me wonder what microbes will end up in the new membrane and the risks of performing it on a larger part of the intestine than just the duodenum.

Maybe the ultimate end game will be clearing the mucosa in the recipient and using mucosa microbiota from the donor, but for now, maybe whichever one is easier could be a significant improvement on its own compared to standard FMT.

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The problem with using Duodenal Mucosal Resurfacing though is that you won't be able to treat most of the small intestine since it relies on using an endoscope. In the article it also said that it took 1 hour to just treat the duodenum, so the feasibility of doing this to the entire small and/or large intestine seems rather low.

Ingesting something that can affect the mucosal layer is probably going to be the easiest method of altering the mucosa if this is important for the success of FMT.

 

[Michael Harrop]

I wonder how risky removing the mucosal layer is. Perhaps something like this could be a part of the remove & restore procedure:

The bile acid tauroursodeoxycholic acid (TUDCA) can increase mucus secretion rates. TUDCA treatment reversed the mucus secretion defect caused by vancomycin treatment, restoring a proper mucus barrier (2024)

 

[indigo34]

This is a literature review I did evaluating the above-cited evidence that there is a significant difference between the mucosal and fecal microbiomes in humans. My conclusion is that there is insufficent evidence due to two issues with the research: 1) the use of mouse studies and 2) the use of bowel prep prior to endoscopic collection of mucosal samples in humans. The GI tracts of mice are different from that of humans on a structural and cellular level so we should be careful when attempting to translate scientific conclusions from one to the other that may be affected by these differences. More info at the end of the post. Osmotic laxative bowel prep prior to colonoscopy entails consuming large amounts of laxatives that flood the mucosa with water and clear out huge amounts of bacteria. Expecting the mucosal microbiota to look similar before and after this type of prep is a poor assumption that should have been cited as a limitation in these studies.

1) Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models

• Mouse study. Unlikely to be directly translatable to humans.
• See pictures attached.

2) Mucus: A Special Home of Our Microbes (2018)

• The evidence seems to be in citations 9 and 10: "Structure and metabolic function differ greatly between bacteria residing in the lumen and the outer layer, which is rich in mucus-related sugars [9, 10]"
• Citation #9. Mouse data, likely not directly translatable. Even the supporting evidence referenced within the article is based on mouse data.
• Citation #10. Does not demonstrate that the bacterial communities in mucus are significantly different from those in the lumen. In fact it potentially suggests the opposite:
• "Previous studies on mucus utilization by B. thetaiotaomicron and A. muciniphila have suggested that mucus utilization is reserved for a subset of the intestinal microbiota (Derrien et al., 2004; Sonnenburg et al., 2005; Tailford et al., 2015a). However, we found that 64% of the tested strains belonging to the Clostridiales order were capable of growing on mucin as a sole carbon source. These findings suggest that the mucin-utilizing capacity of the intestinal microbiome has been underappreciated."

3) Differential clustering of fecal and mucosa-associated microbiota in ‘healthy’ individuals (2018)
- Sampling technique: Endoscopy, meaning osmotic laxative bowel prep.

4) Gut mucosal-associated microbiota better discloses Inflammatory Bowel Disease differential patterns than faecal microbiota (2018)
- Sampling technique: Not specified in free version but probably colonoscopy due to the use of the terms "biopsy" and "regardless of disease location." Emailed the author.

5) Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria (Mar 2019)
- Does not provide evidence that mucosal microbiome different from fecal, just that "mucin exposure modifies the physiology of bacteria." All or most bacteria in the colon are likely exposed to mucins due to the constant shedding of the outer mucus layer.

6) Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals (June 2019)
- Sampling technique: Lower endoscopy, osmotic laxative bowel prep.

7) Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals (May 2019)
- Sampling technique: Double balloon enteroscopy through the mouth and anus. Osmotic laxative bowel prep.


Discussion
1) I did not find convincing evidence in the above studies that the human microbiota are significantly different from each other in the mucus layer versus in the lumen.
2) This belief may have stemmed from the inappropriate application of mouse data to humans and the under-appreciated effects that laxatives have on the microbiota in the mucosa.
3) There was one human study that did not replicate these findings, and they did not use bowel prep.
Fecal samples and rectal swabs adequately reflect the human colonic luminal microbiota
https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2416912
4) It's plausible a thicker mucus layer as opposed to an absent one would result in better FMT engraftment in humans by providing nourishment for the incoming bacteria, and an over-abundance of mucus degrading bacteria in a person with a particularly unhealthy gut might result in excessive colonization resistance to FMT.

"IBD patients also have a thinner inner mucus layer and reduced glycosylation of MUC2 (Fyderek et al., 2009; Larsson et al., 2011). These alterations in mucus production likely contribute to reduced commensal fitness, driving the microbial dysbiosis in IBD patients. Together, these observations suggest the relevance of intestinal mucins in establishing bacterial colonization and maintaining health-promoting functions of the microbiome, such as tryptophan metabolism."

5) Bacteriophages seem to live within the mucus layer (see paper #5 of the lit review) so a thicker mucus layer would also hypothetically facilitate their engraftment via FMT.


Mouse versus Human GI Systems

I found this article enlightening.
How informative is the mouse for human gut microbiota research? (2015)
https://pmc.ncbi.nlm.nih.gov/articles/PMC4283646/
"Although these differences do not mean that the murine model is not valuable to study host-microbiota interactions, care must be taken in making direct parallels between murine and human gut with regard to microbiota composition, because host-microbiota co-evolution could have been influenced by these anatomical divergences."

Some notes from the article:

• Cross-sections of mouse and human colons appear markedly different (see 2nd attached picture).
• The murine colon is relatively smooth whereas the human colon has pouches called haustra and more transverse folds.
• Fermentation occurs in the large intestine in humans, not the vestigial cecum, but the cecum is relatively large in the mouse with fermentation capacity.
• Goblet cells (which generate mucins) are abundant throughout the human colon but significantly less so in the distal colon and rectum of mice.
• The distribution of antimicrobial-producing Paneth cells is also different.
• Disturbingly the article indicates, "most human gut microbiome studies use stool samples, whereas cecal contents are usually used in mouse gut microbiome studies." The murine cecum does not even have a good direct parallel in the human GI tract, particularly on a microscopic level.

 

[indigo34]

"While fecal microbiota is partially normalized by extended co-housing, mucosal communities associated with the proximal colon and terminal ileum remain stable and distinct". Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models (May 2019). https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30488-7

For the people who don't know, mice eat each other's poop, thus naturally do FMT when co-housed.

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There are several factors to consider when translating the conclusions of this and other FMT mouse studies to humans that I did not elucidate in my previous post.

• Mouse FMTs do not bypass any of their GI tract while human FMTs seek to bypass the acid-producing stomach and antimicrobial-compound producing Paneth cells in the small intestine. The murine small intestine is also lined with Paneth cells.
• There is likely a meaningful dosage difference in mouse FMTs versus the human FMTs typically studied: small amounts over time versus a single high dose.
• The comparatively small dose of mouse FMTs means we should, at a minimum, be considering how the antimicrobial effects of the murine Paneth cells may be affecting the results. (We should be thinking about this regardless of dose size, really.)
• Paneth cells are located on the epithelial, and likely have a larger effect on mucosal microbiota than the microbiota in the lumen, although they are known to affect both. (Particularly relevant for this discussion.)
• Proximal colon: One location cited in the article. It follows the small intestine and cecum where Paneth cells are located, which have antimicrobial effects.
• Terminal ileum: Another location cited in the article. The murine small intestine lacks the mucosal folds seen in humans (see picture #1 in above post) which possibly makes it harder for bacteria to penetrate the small intestinal mucus layer in mice as compared to humans. There are also numerous Paneth cells here in contrast to the colonic mucosa of humans and mice.

 

[Michael Harrop]

human FMTs seek to bypass the acid-producing stomach and antimicrobial-compound producing Paneth cells in the small intestine

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This is not correct. https://humanmicrobiome.info/fmt/#upper-vs-lower-routes

In the ASU study they drank the liquid straight.

The comparatively small dose of mouse FMTs

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Why do you say this? They're chowing down on whole stools pooped out by the other mice. That seems like a larger dose if anything. But certainly a longer dosing period compared to most human FMT studies.

 

[indigo34]

This is not correct. https://humanmicrobiome.info/fmt/#upper-vs-lower-routes

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Well it's at least partially correct i.e. lower route which obviously bypasses those things. We certainly should not be assuming mouse FMT is directly comparable to lower route human FMT, especially considering the differences sometimes seen between human upper and lower route FMT. Or do you disagree?

My understanding was that capsules were double encapsulated as opposed to single encapsulated to open later in the small intestine or at least to bypass stomach acid. If that's not the case what is the point of double versus single encapsulation for FMT? I take a type of prescription enzyme that's supposed to open in the small intestine and I assumed it was similar.

If upper-route FMT in fact does not bypass stomach acid then it is still very dissimilar to mouse FMT. Mice have a stomach pH of 3-4 and human stomach pH is 1-2. In other words the human stomach is much more deadly to bacteria, although the effect depends on the type of bacteria. For example, my understanding is Bacteroides species would not survive human stomach acid without the person first taking a PPI or acid suppressor. What is your take on that?

Why do you say this? They're chowing down on whole stools pooped out by the other mice.

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I just didn't think mice are eating the equivalent of a human consuming a 50 gram stool in one sitting but maybe they are. Do you know the amount of stool they consume per kg body weight over time? I assumed it would take up a small portion of their diet but did not look up the numbers.

The reason I brought up dosage is because it is a major factor in FMT effectiveness. 5g per day for 10 days may not have the same effect as 50g at a single time, or 50g for 10 days, etc. I think we should try to figure out the approximate dose used in mice relative to humans, and use that information when trying to draw conclusions. While keeping in mind the other mouse-to-human limitations too.

 

[Michael Harrop]

My understanding was that capsules were double encapsulated

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It's done, it's just not necessarily needed.

If that's not the case what is the point of double versus single encapsulation for FMT?

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I've seen occasional complaints about "poop burps". Some people have also not wanted to see poop in the capsules at all due to personal revulsion. So there are a few additional reasons.

PPI or acid suppressor. What is your take on that?

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It is still up for debate I think, but at the end of the "Before the procedure" section (https://humanmicrobiome.info/fmt/#before-the-procedure) there's a citation against it.

Do you know the amount of stool they consume per kg body weight over time?

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I don't recall ever seeing that mentioned, but it would certainly be interesting to know. I just did a search for "mice coprophagy" but don't see anything on the amount they eat.

 

[indigo34]

Not sure if this is the right thread to post this in, but I have a few questions about the details of the "clearing existing microbiome" clinical trials we are asking the NIH to do. If all these questions have been answered elsewhere feel free to delete.

• Are these human trials, animal trials or both? What animal(s) would be used?
• If done in humans would this be examined as an "FMT prep" type of trial? As in, the outcomes of people with and without their microbiome cleared would be compared following FMT from a high-quality donor?
• If so, wouldn't we first need clinical trials to demonstrate the safety and efficacy of the donor in question?
• If the clearing of the microbiome would not be immediately followed by FMT, what is the mechanism for safety that is suspected for removing the microbiome which is essentially a vital organ? Like why do we think this would not do harm and potentially kill someone?
• Edit: Even if FMT would immediately follow the microbiome clearing, would it be safer to look at the effectiveness of FMT routes and dosing as a way of improving outcomes instead? Or has that been studied sufficiently already?

 

[Michael Harrop]

• Both. There are already studies in both. Probably mice then humans.
• You could and should, but as noted in the OP, a study showed that clearing the mucosa alone was enough for major improvement. I currently think it's the #1 priority, and the most promising, impactful intervention, with FMT being a close #2.
• Yes, probably. I'd do them concurrently. Test donor quality while clearing the mucosa in mice, then proceed as indicated.
• As noted, there is a study in the OP already. Similarly, many patients report temporary relief from colonics, colonoscopy prep, fasting, liquid diets, etc. The goal is to make that long-lasting. Safety would largely depend on the method used to clear the mucosa.
• I think there is sufficient evidence to say that FMT routes & dosing are quite limited factors that do not need major attention.

 

[indigo34]

As noted, there is a study in the OP already. Similarly, many patients report temporary relief from colonics, colonoscopy prep, fasting, liquid diets, etc. The goal is to make that long-lasting. Safety would largely depend on the method used to clear the mucosa.

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Yeah I don't think you can draw many conclusions about what it would take to clear the microbiome in the colon, and what the result would be, from the mucosa-destroying study in the duodenum. That's my opinion. The colon and duodenum are very different, especially with respect to the concentration of bacteria.

Thank you for the clarification. Did not realize you were referring to those types of interventions (like laxatives). I don't think having zero microbiome is the same as what happens from those interventions since of course it does grow back in those cases. In contrast, the microbiome doesn't "grow back" in a germ-free mouse. I think microbiome suppression more accurately describes what is happening from those interventions.

I don't think eliminating the microbiome 100% is a necessarily a realistic goal. There are bacteria in the air, water, food, another person's saliva, your own skin. I think it would be pretty hard to ensure nothing will start growing in the small or large intestine eventually. Even in the duodenum study that was not achieved long-term.

 

[Michael Harrop]

I'm not sure where you're getting "zero microbiome" from. I don't think 100% elimination is a goal at all. I agree that it doesn't seem possible.

I described the problem in my most recent experience report:

It seems very clear to me that there are layers. FMT is basically "You have bad poop on your hand so you smear good poop on your hand". You're not getting rid of the bad poop; you're just adding some good stuff to the surface layer. You have a diseased microbiome deeply embedded in the gut mucosal lining, and you're lightly pouring a healthy microbiome over it and hoping some of it takes hold. We need to remove that diseased mucosa.

Another appropriate example seems to be a thin layer painted over magma. As soon as you adequately disturb the magma, your top layer cracks and everything goes to hell.

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So the goal is to remove as much of the bottom layer as possible, including biofilm, and then rebuild it with healthier microbes.

I don't think you can draw many conclusions about what it would take to clear the microbiome in the colon

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This is why mice are experimented on first.

Did not realize you were referring to those types of interventions (like laxatives). I don't think having zero microbiome is the same as what happens from those interventions since of course it does grow back in those cases. In contrast, the microbiome doesn't "grow back" in a germ-free mouse. I think microbiome suppression more accurately describes what is happening from those interventions.

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There are essentially two main forms of dysbiosis:

1. Missing microbes. Eg: you lack the microbes needed to metabolize bile acids, so the unmetabolized acids burn your intestine, resulting in permeability, etc.
2. Problematic microbes. Sometimes you can suppress them with FMT, but it can be difficult, can be highly dependent on donor quality, etc.

All of the interventions I mentioned essentially put a pause on the results of the dysbiosis, either by not feeding problematic microbes, or not triggering harmful bile acids, etc. As mentioned, they are only temporary and don't fundamentally change the gut microbiome. What they do is provide evidence that stopping the activity of the existing microbiome can result in major relief. So we need to find a way to do it in a more permanent manner.

Most likely, you're going to want to follow up any of these interventions with FMT from a high-quality donor.

The early life of an infant may be a near comparison. They most likely get their mucosa, microbiome, and immune system slowly fed, built, and trained, via breastmilk, etc.


Here's another example:
Mucin-driven ecological interactions in an in vitro synthetic community of human gut microbes (2024)

Author Maryse Berkhout said on social media:
"We developed a synthetic community of human gut microbes that completely degrades mucin glycans"

I asked her:
"Do you think this could be used to clear the gut mucosa prior to FMT to enhance the effect of FMT? My initial thought is that it wouldn't work fast enough, but perhaps the patient could take this probiotic mix daily for some weeks prior to FMT. Maybe along with a special diet."

 

[indigo34]

I'm not sure where you're getting "zero microbiome" from. I don't think 100% elimination is a goal at all. I agree that it doesn't seem possible.

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That's how I interpreted "clearing the microbiome," I'm glad that isn't your goal. If you had said partially clearing or suppressing the microbiome I would have gotten your meaning sooner. Apologies for the misunderstanding on my part.

It seems very clear to me that there are layers. FMT is basically "You have bad poop on your hand so you smear good poop on your hand". You're not getting rid of the bad poop; you're just adding some good stuff to the surface layer. You have a diseased microbiome deeply embedded in the gut mucosal lining, and you're lightly pouring a healthy microbiome over it and hoping some of it takes hold. We need to remove that diseased mucosa.

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I get that this is what you think is happening but I do not agree that this is what the scientific evidence demonstrates. I did a review of the evidence you provided on there being a fundamental and important difference among the layers and it was flawed and incomplete, mostly due to sampling methodology. In contrast I think the evidence may point to significant uniformity among the layers.
https://forum.humanmicrobiome.info/threads/mucosal-microbiota-transplant-clearing-the-gut-mucosa-prior-to-fmt.393/post-2078
https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2416912

I think your goal may be more accurately described as overcoming colonization resistance in FMT recipients. Suppressing or "clearing" the recipient microbiome is one strategy, but there are others, some you have talked about. For example, multiple FMTs as opposed to one. That's what I was trying to get at with my last question about dosing earlier but I didn't use the right words. Multiple FMTs would give incoming microbes more time and more opportunities to fight for biological niches, and their metabolites may also reduce inflammation during the treatment, both of which may improve the chances of a successful outcome. Clearing the existing microbiome is not necessary for this strategy to work.

As far as the mucus layer is concerned I think a thicker one is more likely to improve outcomes as opposed to an absent one. Part of my reasoning comes from the patients who need the least versus the most FMTs for a cure: C. diff versus ulcerative colitis. C. diff can be cured in a majority of cases with a single FMT. From the archived powerofpoop website, IBD patients require as many as 50+ for a cure. In ulcerative colitis, the mucosa is diseased precisely because it is too thin, not the opposite. There is not a super thick mucus layer harboring lots of bad microbes but an extremely thin one. In C. diff though, the infection is constantly triggering the intestines to secrete more mucus in an attempt to protect the body and eliminate the pathogen.

Mucus provides a source of nutrition for microbes, and not just the microbes found within the mucus layer. https://pmc.ncbi.nlm.nih.gov/articles/PMC5672633/ It makes sense that a thicker mucosa would enhance the effects of FMT and not the opposite. If the mucosa were completely absent, microbes would have less to subsist on and competition would be fiercer, giving the original, adapted recipient microbes even more of an advantage.

There are essentially two main forms of dysbiosis:

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This is incomplete. There is definitely a third type of dysbiosis which is an imbalance of the existing microbes. This is why so many people cure themselves of various illnesses simply with diet, despite the presence of problematic microbes. Even healthy people with healthy microbiomes have "problematic" microbes, their growth is just kept in check due to population dynamics and they do not cause inflammation for that reason. (I recently read something you posted a long time ago about low-abundence keystone bacteria having this effect https://news.uoregon.edu/content/oregon-study-suggests-some-gut-microbes-may-be-keystones-health from https://maximiliankohler.medium.com/do-not-eat-dirt-63b5d04bf4c. Which points to the missing microbes cause of dysbiosis, but I found useful for thinking about population dynamics. It's also probable that restoring missing microbes would be insufficient for restoring health if not combined with a healthy diet.) Basically if those were the only two forms of dysbiosis, I do not believe dietary changes could have such dramatic, positive effects in some people, and they would instead require FMT.

Most likely, you're going to want to follow up any of these interventions with FMT from a high-quality donor

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I agree that this is the safest option.

 

[Michael Harrop]

I did a review of the evidence you provided on there being a fundamental and important difference among the layers and it was flawed and incomplete

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From what I understood, your review of the evidence looked at the fecal microbiome vs the mucosal microbiome, which is a different matter. Your linked analysis did not look at layers of the mucosa. I don't recall any studies that have done that either. I think you're confusing two different things.

Regarding your IBD vs C. diff comparison, that is interesting but unconvincing. It is certainly not enough to warrant skipping such experiments. Your statements are also missing supporting citations. They also fail to address the body of evidence supporting the need & benefit of clearing the existing microbiome/mucosa. The suggestion that longer treatment could suffice is uninformed, and I already commented on that. I'm a little surprised by your post.

In ulcerative colitis, the mucosa is diseased precisely because it is too thin

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If that were so, something like this should cure UC then: https://forum.humanmicrobiome.info/threads/mucosal-microbiota-transplant-clearing-the-gut-mucosa-prior-to-fmt.393/post-1507

I doubt you're right. More likely, it is a dysbiotic gut microbiome resulting in a thin mucosa. Even though the mucosa is thin, you still need to, or will benefit from, removing the problematic microbes. If the cause of the thin mucosa is missing microbes, then you may have higher success with FMT alone.

If the mucosa were completely absent

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We'll have to run animal studies to test it.

There is definitely a third type of dysbiosis which is an imbalance of the existing microbes

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Perhaps that deserves its own category, but I can see it falling under either of the two I previously mentioned. All dysbiosis is an imbalance.

This is why so many people cure themselves of various illnesses simply with diet, despite the presence of problematic microbes

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This conflicts with the previous statement. If there are problematic microbes then it falls under #2.

However, I think in most cases where there are clear symptoms and actions are taken to shift the balance to alleviate them, the underlying cause is not really eliminated, it's just made less obvious. But that's a big grey area, because you could take a really healthy person and feed them crap to make them sick and ruin their eubiotic state. The whole categorization is a big grey area really, that mostly only makes sense under specific circumstances. In most cases there will be a combination of each.

Perhaps instead of "two main forms of dysbiosis" I should have said "two main causes". But this is a bit off-topic for this thread.

 

[indigo34]

Your linked analysis did not look at layers of the mucosa. I don't recall any studies that have done that either

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If you can't provide any studies that have looked at the layers of the mucosa you speak of in your theory then I don't understand why you are so convinced you are right, to be honest. It seems to me to be based on a hunch or speculation and not scientific underpinnings. I understand why you want your theory studied but I think you may have a hard time convincing researchers to look into it, since they may think it lacks credibility. If you could provide more scientific papers that led you to this theory aside from the ones I already reviewed in the OP then that could change my mind. I'm interested to know because usually you follow the science pretty closely and perhaps I've missed something.

They also fail to address the body of evidence supporting the need to clear the existing microbiome prior to FMT

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You mean the conflicting evidence that antibiotics are helpful and that bowel prep is helpful prior to FMT? That's hardly a body of supporting evidence.

If that were so, something like this should cure UC then: https://forum.humanmicrobiome.info/threads/mucosal-microbiota-transplant-clearing-the-gut-mucosa-prior-to-fmt.393/post-1507

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I'm confused. This says antibiotics result in damage to the mucosa and can lead to ulcerative colitis which is precisely what I implied in my posts - that a thin mucus layer is bad/diseased. I never said the mucus layer should be harned, if anything I've said the opposite a few times. I did say the mucosa was diseased in UC. Saying something is diseased could mean you think it should be excised or it could mean you think it should be cured. I meant the latter. I think you misunderstood which is kind of surprising given all my hesitations around the idea of removing the mucus layer in general.

More likely, it is a dysbiotic gut microbiome resulting in a thin mucosa.

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I agree with this. I meant that the thin mucus layer is a sign of disease/illness, as opposed to the root cause of it being diseased. As in, "you can see it's diseased because it's so thin." Sorry for the poor choice of words. A thin mucus layer is more likely to result in a state of illness and dysbiosis just by being too thin though, thereby not protecting the intestines sufficiently and making damage and inflammation more likely. So it's kind of a vicious cycle, although I agree the root cause is the microbes. Sorry that was badly worded though I can understand how my meaning was misconstrued here.

But that's a big grey area, because you could take a really healthy person and feed them crap to make them sick and ruin their eubiotic state.

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100% agree and I was thinking about this exact scenario when I was thinking about the categorizations. That's why I wanted to add another category, to cover cases where FMT is not necessary to return a person to a place of good health since they exist. I agree there is significant overlap among the categories in general.

Your statements are also missing supporting citations.

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C. diff mucus production
(It alters mucin prduction to some extent, possibly a slight decrease, not nearly as significant as in UC. My original search result may not have been correct.)
https://journals.physiology.org/doi/full/10.1152/ajpgi.00091.2014

C. diff cure rate from FMT (80-90%)
https://www.health.harvard.edu/blog/stool-transplants-are-now-standard-of-care-for-recurrent-c-difficile-infections-2019050916576

UC mucosal layer abnormalities
https://www.ncbi.nlm.nih.gov/books/NBK459282/

UC remission rate from FMT (26-50%)
https://www.nature.com/articles/s41598-023-41182-6