I recently made a post on gut bacteria as it relates to food intolerance. I shared the literature I’d found with some members on Crohn’s Forum and was asked what I would recommend to a patient if I was to suggest a therapy targeted at repopulating gut bacteria?
This is highly theoretical, and my knowledge is not perfectly well rounded on this topic, and I will admit that as I go! If you can expand on any of the topics I discuss here, or find issues, I implore you to contact me at email@example.com my goal is to get the population THINKING about these topics, not to become a first rate source of primary medical advice.
My digging into this topic is still fairly new to me, but given what I’ve already read I have formulated an early dietary strategy which I intend to apply. Here’s how my post was detailed:
Therapeutic Diet for Managing and Improving IBD Related Symptoms and Food Intolerance
I’m still building on it with self experimentation. The problem would be that I would need to create a different diet for each patient based on their digestive capabilities.
It seems evident that our food intolerances are based on both the level of dysbiosis and the specific imbalances. For example the reason that some patients can have lactose but others cannot is likely due to either insufficient bacteria of the kind that consume it in the lower GI tract, or overgrowth of harmful bacteria that consume it in the upper GI tract. I think we need testing on the specific bacteria loads of healthy individuals vs. ones with specific food intolerances to see what those differences are so we can better understand what needs to be taken out or put back in.
Mine are VERY limited right now, IDEALLY I would include a higher balance of prebiotic foods in my diet but I cannot tolerate the ones I want to, while many other Crohn’s patients can.
I can tell you a rough idea of an approach I would use based on the chart I found describing bacterial growth as relates to diet.
Summary of diet-induced dysbiosis
Diet Bacteria Altered Effect on Bacteria References
Bifidobacteria spp. Decreased (absent) 
High-fat and high-sugar
Clostridium innocuum, Catenibacterium mitsuokai and Enterococcus spp. Increased 
Bacteroides spp. Decreased 
Bacteroidetes Increased 
Clostridium coccoides, Lactobacillus spp. and Bifidobacteria spp. Decreased (growth prevented) 
Mycobacterium avium subspecies paratuberculosis and Enterobacteriaceae Decreased 
B. longum subspecies longum, B.breve and B. thetaiotaomicron Increased 
C. difficile and C. perfringens Increased [54,55]
E. coli Decreased 
High n-6 PUFA from safflower oil
Bacteroidetes Decreased [59,60]
Firmicutes, Actinobacteria and Proteobacteria Increased [59,60]
δ-Proteobacteria Increased 
Animal milk fat
δ-Proteobacteria Increased 
Stage 1 diet
My first step would be to test for SIBO and the prevalance of harmful / invasive species like MAP, C. Diff, and Klebsiella because if those are a problem it limits your dietary options further. Simple sugars would DEFINITELY be off the table. Klebsiella also limits your use of standard prebiotics like RS, FOS and inulin because it’s capable of breaking the complex molecular bonds that divides them from simple sugars.
So my first treatment for those with SIBO would be one of a few things. The safe approach would be a mixture of complete carb restriction and intermittent fasting, which risks further imbalancing the gut flora in favor of bacteroidetes, but unfortunately the only other choice is powerful antibiotics which will have the same result, but with a possibly more dramatic die-off of good bacteria. It might require several antibiotics taken at the same time with bad side effects to kill off these bacteria without dietary changes.
I would restrict the diet initially to meats, broths and tolerable oils focused on safflower and coconut oil, basically a fully ketogenic diet until they see a decrease in invasive bacteria. Due to extreme restriction of diet I would also put them on a multi vitamin. I would say this approach should be completely safe, supplementing with probiotics would be optional but not necessarily effective due to the chances you’d simply be starving them out anyway. Caprylic acid supplementation is also an option that I would consider safe but not sure if it’s effective. You’d already be getting some in coconut oil.
For a more pseudo-science approach, I would say it’s -possible- but not yet tested to the point of recommendation to supplement with eugenol and carvacrol containing oils like thyme, oregano and cloves, black wallnut,wormwood, cinnamon, basil and bay leaf which have been shown to kill harmful bacteria while feeding Firmicutes strains. Until I can find further evidence on the safety and effectiveness of this therapy I would file it under a ‘maybe.’ I would like to further look into if taking them with an enteric coating to deliver them as food to the large intestines + fight off harmful bacteria there would be effective / optimal. So far search results on the topic have been no help.
Stage 2 diet
After the invasive bacteria is under control I would introduce complex carbs starting with low dose resistant starches like psyllium husks, potato starch (if tolerable), green bananas or plantains along with supplementation of FOS and inulin since foods containing it will likely be hard to digest for a patient with advanced dysbiosis due to high fiber content.
Initially they would likely experience flatulence, bloating and possibly diarrhea or constipation, so moderation and gradual increase based on personal comfort level would be necessary. Continued testing would be important to see that levels of harmful bacteria remain low and aren’t feeding on the prebiotics.
As you begin to introduce prebiotics, over the next week or so I’d say start introducing probiotics targeted at bringing up the shortcomings in their bowel diversity. Unfortunately it doesn’t seem like there are capsules or anything for Clostridia, but it’s likely Bifido bacteria would be the first choice which is a protective bacteria many Crohn’s patients are deficient in.
This is another area I need more research in. When do you introduce probioitics / prebiotics? If you introduce the prebiotics first with nothing to feed you could be feeding the already over represented bacteroidetes. If you introduce probiotics without prebiotics as food for them they may starve. Will both at the same time simply cause too much gastric upset (flatulence, diarrhea etc.) for the comfort of the patient? How long will it take to subside? This is another area I need to find hard information on.
I would look really hard at supplementing L. acidophilus in those with lactose inolerance and possibly colostrum supplementation which acts as another natural prebiotic. I need further research to confirm effectiveness of both.
Stage 3 diet
Ideally the patient’s food tolerances should continue to improve until they are able to move onto a diet rich in raw fruits and vegetables from which they can get their vitamins and prebiotics, along with meats, animal fats and healthy oils like safflower, and extra virgin coconut and olive oil. This would be the end goal for long term maintenance of healthy gut bacteria.
For those with complications of Crohn’s like having had resections it could complicate the effectiveness because bacterial populations are regional to the intestines and I have no evidence of whether those populations can migrate and what effect that has on the ecosystem of the gut.
I would look at raw, organic honey and royal jelly as a prebiotic for those in the advanced dietary stages with no signs of SIBO. I think regular testing for SIBO until dietary effectiveness is established would be best. I have reservations about honey though because some say harmful bacteria cannot digest it due to its chemical structure, while others say it can. I’d really like a confirmation on this but it doesn’t seem that many find it scientifically relevant.
Long term maintenance, comparison with obesity etc.
Over the long term, it looks like a diet rich in complex carbs and fats with moderate protein will lead to the ideal balance that we’re looking for. We basically want to be eating what obese people eat – because they have an overgrowth of Firmicutes where we have the opposite. We’re unfortunately prevented from the large intake of simple sugars typically associated with obesity because it promotes SIBO.
So what do we have to learn from this? Well unfortunately both the bacteria that we want, and the one we want to reduce depend on carbohydrates to an extent. Firmicutes seems to love fat and sugar – but bad bacteria also love sugar, so sugar binge eating is not an option to us!
Firmicutes is much less resilient to starvation than Bacteroidetes. If an obese person combined fasting with increase of resistant starches, they’d see a reduction in firmicutes and an increase of bacteroidetes.
Fasting and how it relates to this
For this reason I support the continual small meals through the day approach for Crohn’s. In the past I’ve spoken in favor of fasting for Crohn’s so let me clarify why I believe it’s not the OPTIMAL approach, and will advise against it except as a SIBO therapy until I can further investigate its effects on Bacteroidetes and intestinal flora.
During a fast we see a loss of firmicutes as well as harmful bacteria, an increase of gut-based serotonin production, and increased catecholamine production, increased cortisol production. All this is beneficial to Crohn’s healing EXCEPT the loss of firmicutes.
We also see the Bacteroidetes begins to consume intestinal mucins to avoid starvation, as a biproduct is creates butyric acid which promotes mucosal healing. So we see healing of the mucosa, balancing of the neurotransmitters, and bowel rest, great stuff really.
But we also see death of Firmicutes which leads to furthering of food intolerance. I don’t have the resources to prove if one can maintain / grow their firmicutes population during the 8 hour feeding window of an Intermittent Fasting diet, so until I sure, I deem fasting to be counter-productive to the goals of expanding dietary food tolerance.
Dairy and MAP
I’d like to make a fleeting mention of dairy. I’m starting to believe that MAP bacteria is not the primary cause of Crohn’s, and that it’s simply a result of the dysbiosis we see, and a marker of the loss of protective bacteria and overgrowth of harmful bacteria. It’s likely that the high prevalence in Crohn’s patients is a sign of overall bad gut health, and it’s possible that it DOES cause symptoms, however we also find it in healthy, asymptomatic individuals. I think in advanced dietary recovery with L acidophilus supplementation I would consider dairy to be SAFE and that the MAP should be manageable if you can restore a healthy balance of gut bacteria to protect you from it. I think monitoring of symptoms and levels of MAP in a patient in the advanced stages of the recovery diet would be very interesting to give us a better perspective on the role of dairy consumption and MAP growth.
My opinion on dairy is, perhaps, biased because I’ve NEVER seen correlation between dairy and my symptoms except when consuming it at ABSURD levels (1 gallon whole milk a day). The one time I experienced problems with dairy, I supplemented Kefir for a couple weeks and the problems subsided.
I’d like to post-edit this section to include a link to this article
With more information on gut dysbiosis as a cause of lactose intolerance.
Thoughts on another promising dietary supplement:
I just found this, I read about it before but forgot to mention it because there’s just so much stuff I’ve read lately I forget some things.
Polydextrose seems extremely promising in its ability to rebalance gut bacteria.
[QUOTE] Short-chain fatty acid production—notably that of butyrate, isobutyrate, and acetate—increased with polydextrose ingestion. There were substantial changes in fecal anaerobes after polydextrose intake. Bacteroides species (B. fragilis, B. vulgatus, and B. intermedius) decreased, whereas Lactobacillus and Bifidobacterium species increased. [/QUOTE]
[QUOTE]Conclusion: Polydextrose ingestion had significant dietary fiber–like effects with no laxative problems.[/QUOTE]
This is EXACTLY what we want.
I will definitely be looking into polydextrose, possible adverse effects, and seeing if I want to try it myself in the near future.