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Refractory Gut and Probiotics - Part 2

The breakdown of foodstuffs into fuels and repair pathway components is fundamental to health. Based on extensive surveying, some levels of gut dysbiosis are epidemic in the United States. The problem appears to be less pervasive in other developed nations but is still staggering. The current standard of care medical system does little to detect, measure, and remediate gut issues except for the most severe conditions, including irritable bowel syndrome and diverticulitis. However, the treatments do not address fundamental root-cause issues.

The Mayo Clinic treats Diverticulitis with antibiotics, clear liquids, pain-relieving medications, and a low-fiber diet. This treatment regiment contribute sto the loss of microbiome integrity. Poor Charles Mayo - rolling in his grave!. The Mayo Clinic suggests the following treatments: avoid foods that trigger symptoms, eat high-fiber foods, drink plenty of fluids, exercise regularly, and get enough sleep. None of these treatments reflect the highly complex gut domains. Nor is that what the implement across various gut problems.

The gut is an open system extending from the mouth to the anus. The oral and saliva microbiomes in healthy subjects contain millions of microbes swallowed daily with food. Still, their persistence in the gut is impeded by many factors, including the acidity of the stomach, the production of bile acids (BAs), digestive enzymes, and other lesser-understood components of that ecosystem. Antimicrobial proteins in the stomach, duodenum and further downstream protect the host against harmful or pathogen organisms. They may recognize commencal and beneficial organisms but further study is required.

Many other major variables affect further downstream microbial colonization, such as chemical parameters like pH, oxygen concentrations, redox potential, the biological production of mucus, bile, and antibodies, and physical aspects, including gut architecture, peristalsis and transit times. Hence, a concentration gradient of microbes is found along the small intestine, as microbial abundance in duodenal aspirates were found to be a 1000-fold lower than that of oral samples, although consisting of somewhat similar microbial taxa.1

1. Barlow JT , Leite G , Romano AE , et al . Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome. Microbiome 2021;9:214.doi:10.1186/s40168-021-01162-2 pmid:

The small intestine contains an increasing number of thousands to several hundred million of cells per gram of content with partly oxygen-tolerant Firmicutes and Proteobacteria as major phyla.2,3 This all culminates in the lower gut where climax communities of up to 100 billion cells per gram reside for up to a few days, since transit in the colon is over a dozen times longer than that in the small intestine. Hence, the colonic microbiome is dominated by mainly anaerobic bacteria, including thousands of species and millions of genes, distributed among the major phyla of Firmicutes (predominantly Ruminococcaceae and Lachnospiraceae), Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia (Akkermansia)4-7.

2. Seekatz AM , Schnizlein MK , Koenigsknecht MJ , et al . Spatial and temporal analysis of the stomach and small-intestinal microbiota in fasted healthy humans. mSphere 2019;4:e00126–19.doi:10.1128/mSphere.00126-19 pmid:

3. Leite GGS , Weitsman S , Parodi G , et al . Mapping the segmental Microbiomes in the human small bowel in comparison with stool: a REIMAGINE study. Dig Dis Sci 2020;65:2595–604.doi:10.1007/s10620-020-06173-x pmid:

4. Zoetendal EG , Rajilic-Stojanovic M , de Vos WM . High-Throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 2008;57:1605–15.doi:10.1136/gut.2007.133603 pmid:

5. Qin J , Li R , Raes J , et al . A human gut microbial gene Catalogue established by metagenomic sequencing. Nature 2010;464:59–65.doi:10.1038/nature08821 pmid:

6. Rajilić-Stojanović M , de Vos WM . The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014;38:996–1047.doi:10.1111/1574-6976.12075 pmid:

7. Li J , Jia H , Cai X , et al . An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 2014;32:834–41.doi:10.1038/nbt.2942 pmid:

Excreted as feces, it is this biomass that makes up what is usually termed the gut microbiome but is more appropriately called the "gut ecology," the integrity of which is associated with either good health or many diseases and is highly modifiable by diet, supplements, toxins (from water, air, and foods), and drugs. It provides the starting material for fecal microbiota transplantation (FMT) that has been shown to cure patients with recurrent Clostridioides difficile infections and other diseases.8 Both probiotics and an optimal gut ecology provide a strong deterrent to pathogens.

8. van Nood E , Vrieze A , Nieuwdorp M , et al . Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013;368:407–15.doi:10.1056/NEJMoa1205037 pmid:

A current and worthy focus on human health is the gut microbiome. The gut microbiome, or gut microbiota, is a complex network of microorganisms living in the intestines, including bacteria, viruses, fungi, parasites, and protozoa. The gut microbiome is unique to each person and interacts with many of the body's systems to help with many of its functions. The three main constituents of the gut microbiome are the bacteriome, virome, and mycobiome.

Food intake profoundly affects the organisms found in the gut, most likely by providing differing macro and micronutrient profiles.

  • Infants from rural Africa, with a diet dominated by starch, fiber, and plant polysaccharides, harbor a microbiota abundant in the Actinobacteria (10.1%) and Bacteroidetes (57.7%) phyla.

  • In contrast, in European children, whose diet is rich in sugar, starch, and animal protein, the abundance of these groups is reduced to just 6.7 and 22.4%.

  • Some short-chain fatty acid (SCFA) producers, such as Prevotella, were exclusive to the microbiota of African children.

  • This trend was also apparent in healthy individuals consuming high amounts of carbohydrates and simple sugars.

  • A decreased SCFA output is also evident in individuals consuming a low microbiota-accessible carbohydrates (MAC) diet, a notable effect since SCFAs play an important role in host health via, for example, anti-inflammatory mechanisms. The abundance of MACs is substantially reduced in the Western diet. 9

9. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017 May 16;474(11):1823-1836. doi: 10.1042/BCJ20160510. PMID: 28512250; PMCID: PMC5433529

Understanding the relationship between the human gut microbiota composition and the ecological forces shaping the biogeographical and ecological relationships between physically interacting taxa is limited. Interbacterial antagonism may play an important role in gut community dynamics (competition). Yet, the conditions under which antagonistic behavior is favored or disfavored by selection in the gut are not well understood.

Great physiological and ecological variations occur across the gut. The intraluminal pH rapidly changes from highly acidic in the stomach, optimally 1.5-2.5, to about pH 6 in the duodenum. The pH gradually increases in the small intestine from pH 6 to about pH 7.4 in the terminal ileum. The pH drops to 5.7 in the caecum but again gradually increases, reaching pH 6.7 in the rectum. 10.

10. Fallingborg J. Intraluminal pH of the human gastrointestinal tract. Danish Medical Bulletin. 1999 Jun;46(3):183-196. PMID: 10421978.

Image above from:

The gut does NOT just contain a dozen or so microbiome organisms. This small number is what is found in most probiotics. That's why I recommend equilibrium and Bravo products. They have vast numbers of strains and do NOT focus on "CFUs" - colony forming units.

Here is a link to an article discussing stool composition:

Here are greater details on the case study presented in Part 1.

Patient/Client (23 yo) suffered from lower-level quadrant gut pain and thinning hair. She had tried normal gut treatment, including probiotics, prebiotics, digestive support supplements, and treatment for H. pylori and other infectious species. She had seen many doctors, including Dr. Minkoff. Nothing seemed to work.

Patient/Client came to us with her grandmother's help. She had dropped out of college and was frequently bedridden due to debilitating pain. Her stomach was constantly Distended and always in pain. She is extremely knowledgeable about health, much of which she learned to help her on her path to restoring her own health. She was willing to try anything. Dr Lewis had her Labs drawn and met with her several times, giving her protocols. The main protocol was probiotic therapy with probiotic / gut ecology support to help re-seed and heal the gut.

Patient/Client was willing to try anything to get rid of the pain and get back to her normal life. The probiotic protocols included different probiotics on different days and supplementing with fermented food every other day. Other gut support supplements, including bile salts, digestive enzymes, and stomach acid support, are included in the protocol. After about one week, Patient/Client complained that it was giving her more grief than good, so she quit the probiotic regimen. Patient/Client also tried LDN, oregano oil therapy, and many other things suggested by others.

Dr Lewis, Jodi Laird, and Patient/Client met with Novel Biome, discussing doing a fecal matter transplant. The capsules were expensive; ultimately, she decided it was too much money. Dr. Lewis enlisted help from other doctors, including Dr. Sabine Hazan and Dr. Dallas Hack. Each indicated that colon recolonization is critical to individuals similar to Patient/Client and that rectal inoculation has the best chance of improving her condition. At the time, fecal transplants were believed to be the best way to go because of the rectal administration and the ecology supporting the organisms supported by the fecal material. But this was not financially viable.

Patient/Client decided to try some things on her own. She did not do well taking probiotics orally, so she took them internally as an enema. She used a variety of different probiotics.

Here are Patient/Clients own words explaining what she did.

I should let you know that the pain disappeared as well as bloating with me doing the probiotic enemas at home, making them myself.

I initially sought a fecal transplant donor. I know of people who do fecal transplants within families. I couldn’t find any donor for fecal transplants. However, continuing to take probiotics was not an option. I was having trouble with the probiotics orally as I was experiencing some nausea and other adverse symptoms. So here is what I did. I took 5-6 capsules each of :

• Physician’s Choice 60 billion CFU

Taken orally before this enema formula:

1. Poured the powder into a little fleet enema bottle & added water only about 1/3-1/2 way full.

2. Did not refrigerate,

3. Manually agitated / shook it up,

4. Inserted after a bowel movement or before bed.

5. Did this every 3rd day for a month.

Orally, I also took the Heme plus one with B-12 & folate as co-factors.

I should mention I took a product called Digestacure as well, but I did this for about 6 weeks prior & I didn’t notice any positive changes until the formula for the enema above.

There are no adverse side effects from doing them rectally.

Patients can calculate the dosage for nonheme or heme iron with this chart I have from an iron group on Facebook.

My max dose is 100 mg of heme iron & I am trying to get my ferritin from 54 to above 125.

I should also mention I have fulvic acid here, the ion biome brand, butyrate, l glutamine, LDN, and gut peptides, but I have yet to notice help with those. It was 100% the probiotics & I never went through the colonoscopy.

Dr. Lewis's comment: I would incorporate many of the 4R / 8R programs. One supplement that might be considered for inclusion in the enema is.

Ingredients include: L-Glutamine, N-Acetyl-D-Glucosamine, (shellfish free), Citrus Pectin, Deglycyrrrhizinated Licorice, (DGL)(Glycyrrhiza glabra)(root), Aloe Vera Extract, (Aloe barbadensis)(leaf), Slippery Elm, (Ulmus rubra)(bark), Mucin, Marshmallow, (Althea officinalis)(root), Chamomile , (Matricaria chamomilla)(flower), Okra Extract, (Abelmoschus esculentus)(fruit), Cats Claw , (Uncaria tomentosa)(bark), Methylsulfonylmethane, (MSM), Quercetin, Prune Powder, Zinc Carnosine


Refractory Gut - Part 1 Reproduced

Microbiome Labs is arguably the top company supplying gut-optimizing supplements. Their flagship product is Megaspore. Spore is emphasized because they realize that organisms do not always make it through the strong acid of the stomach. Thus, they encapsulate the organisms in a spore that is resistant to the acid. I assume - but have not studied - that the spore is capable of releasing the organisms in the colon. What I can state is that people with real problematic guts do not see the benefit expected from oral probiotics, including Megaspore.

Within the last year, 5 different people asserted that rectal administration is a necessary delivery method for probiotics to be most effective. These folds are:

  1. Sabin Hasan: She asserts that oral fecal capsules are not that effective, although they were developed by her collaborator and father of fecal transplants, Dr. Thomas Borody.

  2. Dr. Dallas Hack: He is one of the most prestigious doctors no one knows. As a colonel in the military, he funded over 1,400 projects in brain health.

  3. Novel Biome - a fecal transplant company: I cannot find the name of the company, but I talked to two of its scientists, and they indicated that rectal administration is preferred.

  4. Dr. Gamble: She was (and still is to some degree) a colon hydrotherapist. She told me that members of this profession routinely make probiotic suppositories with cocoa butter, then freeze them and deliver rectally.

  5. A client of mine - and Dr. Minkoff's - and neither of us to solve her long-term gut issues that were so severe that she left college. Below is her story of how she amalgamated a lot of information and treated herself. We encouraged her to get rectal fecal transplants but the cost was prohibitive. The process described below solved 4 years of misery.

I was just having trouble with the probiotics orally as I was experiencing some nausea. I just took 5-6 capsules each of Megaspore, Megagenesis, Restore Flora, Seed, Primal Defense, Megaprebiotic, Akkermansia, & Physician’s choice 60 billion… I think that’s all of them… & poured the powder into a little fleet enema bottle & added water only about 1/3-1/2 way full, did not refrigerate, shook it up, & inserted after a bowel movement or before bed. did this like every 3rd day for a month.

I should mention I took a product called Digestacure as well, but I did this for about 6 wks prior & I didn’t notice any positive changes until the probiotics. No adverse side effects doing them rectally.

I should also mention that I have fulvic acid here, the ion biome brand, butyrate, L glutamine, LDN, and gut peptides, but I never noticed any help with those. It was 100% the probiotics, and I never went through with the colonoscopy.


Here is information from different sources on the problems with oral administration and the benefits of rectal administration for gut issues.

While you can consume probiotics orally, using an enema places them directly into your colon. This prevents them from encountering stomach acid, which can kill 60 percent of probiotics.

Rectal administration of Lactobacillus casei DG modifies flora composition and Toll-like receptor expression in colonic mucosa of patients with mild ulcerative colitis.

Conclusions: Manipulation of mucosal microbiota by L. casei DG and its effects on the mucosal immune system seem to be required to mediate the beneficial activities of probiotics in UC patients.

Probiotic Gastrointestinal Transit and Colonization After Oral Administration: A Long Journey

Orally administered probiotics encounter various challenges on their journey through the mouth, stomach, intestine and colon. The health benefits of probiotics are diminished mainly due to the substantial reduction of viable probiotic bacteria under the harsh conditions in the gastrointestinal tract and the colonization resistance caused by commensal bacteria. In this review, we illustrate the factors affecting probiotic viability and their mucoadhesive properties through their journey in the gastrointestinal tract, including a discussion on various mucosadhesion-related proteins on the probiotic cell surface which facilitate colonization.

A new mode of probiotic therapy: Specific targeting


• Luminal bacteria are inducers of inflammatory bowel disease.

• Rectal probiotics in colitis altered mucin and TLR mRNA expression close to control.

• Rectal probiotics almost eradicated tissue damage and were superior to oral route.

• Targeted introduction can increase the effect of probiotics.


1. How long does it take for the probiotic to start working?

If taken rectally verses orally for some individuals they may notice a change in their presenting symptoms such as bloating, normality of bowel movements and less flatus ( gas) within a few days ( particularly if given rectally) . For others symptom relief can take longer even up to 3-4 weeks. Over time you may notice a change in your mood with less anxiety symptoms occurring if that was a concern for you.

The key is to make sure you are supporting your body with the daily intake of a oral probiotic and ensuring your daily diet contains prebiotic such as fermented foods, as prebiotics feed the good bacteria in your intestine. It also depends on what symptoms you have and if you have any underlying medical conditions and your general health.

2. How long does the effect of rectal probiotics for?

This can partially depend on the amount and species of bacteria you are given. It also depends on why you had the probiotic, if for general health then you can generally expect if you also implement supportive practices such as balanced diet and management of stress response that the body should colonised the bacteria given and keep exerting it’s effect for several months.

Everyone’s Large intestines is so different in its responses so it is a very individual measure.

You are may be able to tell that you need a top-up of probiotics if the symptoms you were originally using for a start appearing again. So some a dose of probiotic is a rapid fix for others with chronic condition it can take along time and patience but worth it in the end when you finally feel full of energy and happier in your mindset.

3. Should l take my oral probiotic after a rectal infusion?

It is best to let you body over the next week or so after rectal probiotics settle. More is not necessarily better. You may get some responses such as some bloating after a probiotic so it is better not to exacerbate your symptoms by taking more.

Moderation is always the best approach . If too much in frequency or volume is administered, some people may experience increased flatus, nausea, and bloating for a short time.


How Probiotics Affect the Microbiota

In the next blog on this topic, I will provide a complementary overview of compositions for gut health.


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