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Obesity, Chronic Disease, Toxins, and the Biome

Over the last decade, there has been increasing research on the correlation between the microbiota in the body and chronic disease. We already know that obesity is a risk factor for comorbidities such as cardiovascular diseases, diabetes, and various cancers. While a high calorie diet had previously been thought to be linked to obesity, we now know that is an very indirect link. Over-consumption of calories is typically due to the body sending a message that it is starved of nutritionally dense foods. This is more directly linked to the microbiota in the digestive process. When the biome is balanced and we consume nutrient dense foods, caloric intake is rarely a problem for people.

We hold 10 to the 14th power of bacteria and archaea of more than 1000 species in the human gastrointestinal tract. All together the biome organisms weigh about SIX pounds. We are just on the verge of naming the biome a separate 6lb organ! Those organisms should create an environment of diversity with a balance of workers who can do all the jobs that are needed to be done. The job of the biome is to break down food matter, process nutrients, enzymes, and hormones for the cells to use in creating the biochemistry needed for homeostasis (balance), to regulate all metabolic processed, and to neutralize microbes that are harmful.

Non-beneficial organisms (NBO’s) consume, create, and thrive in a landfill like environment. They love the garbage and they produce more garbage, toxic gases such as hydrogen sulfide, methane, and ethanol. However, we do not want to wipe them out completely because they serve a purpose. We need to change the power structure to allow beneficial organisms (BO’s) to do their jobs. BO’s utilize foods taken in to turn nutrients into a usable form for the cells. When we have a diet high in foods that are not nutrient dense, these BO’s die off and the NBO’s become predominant. Some major issues with overgrowth of NBO’s is high inflammation, malnutrition, increased gut wall permeability, and SIBO (small intestinal bacterial overgrowth). It has long been understood that inflammation is correlated with obesity. We also know that permeability, know as leaky gut, underlies arthralgias, poor immune function, and autoimmune diagnoses.

A paper that can be found at links the gut microbiota to obesity. Another study on mice found that obese mice are missing Bacteriodes thetaiotaomicrom, which is an organism that protects against adiposity, development of fat cells.

While there are organisms involved with obesity and metabolism, we cannot discuss this without discussing the cell since the organisms and the cells work in tandem so, there is another consideration; toxins and the body’s mechanisms for protecting the vital organs! Where do toxins come from? Well, anything that is put on, in, or around the body that has an adverse impact on cellular function and health is considered a toxin. These can be general toxins, mostly synthetic products, materials, and foods. They can also be heavy metals and a few of them are more prominent such as aluminum from food storage and deodorants. And toxins can be produced by any NBO such as in case of infection, root canal teeth or cavitations of extraction site, or the body biome. Most people grasp the concept of more toxins coming in that going out. However, it is often exceedingly difficult for people to wrap their heads around the idea that they have made many changes to eating cleaner and avoiding incoming toxins but they are still challenged by chronic symptoms. What if it is not all toxins coming in? What if there is an overload of these NBO’s to the point that they are creating a toxic environment that has been competing with all the work you have done! Biotoxins have a very detrimental impact on the entire body if we do not have the organisms needed to regulate these gram-negative toxin producing buggers!

Whether the toxins are exogenous or endogenous, they behave the same way. The circulating toxins are harmful to the vital organs because they damage the cells that make up the organ systems and they disrupt the biochemical process needed for those organ systems to do their jobs They also alter our DNA, turning on genetic switches that hold our POTENTIAL for disease. MTHFR is just one example of a genetic SNP that gets turned on and it’s a common one because toxins turn it on and the biochemical hiccups in the methylation cycle become so pronounced that the body’s’ ability to run toxins through the liver and out via the detox pathways become impaired! So, the body will pack these toxins away in fat cells. If someone has excess adipose tissue, that is usually the first line of defense to keep the toxins out of the brain and nervous system. The toxins cause the fat cells to balloon up and increase in size and quantity. Calories have very little to do with this and that is why some people are doing everything right but cannot lose weight. This is also why many people say they cannot do a specific kind of diet because they feel awful when they are losing weight. It’s usually not the diet. It is usually that the diet is working, but the toxins are being released from the fat cells. If this is the case, weight loss attempts should be done with an awareness of toxin levels and consideration of a cellular repair and downstream/upstream detox in order to help move those toxins out.

What I am trying to convey here is that cellular function and the microbiota work together to prevent chronic health issues. I think of the biome as a city. The city needs all kinds of workers, ones that produce, ones that protect, and ones that clean up messes! Here are just a few jobs of some specific organism functions:

Akkermansia muciniphila

-lower subcutaneous adipose tissue

-decreased fasting glucose ratios

-improved insulin sensitivity

-decreased inflammation

Bacteriods uniformis MS03

-generates short-chain fatty acids

-optimizes Th1/Th2 thus reducing autoimmune disorders

Bifobacterium bifidum

-usually in short supply in adult GI tract

-makes nascent B vitamins

-regulate intestinal terrain

-digests milk products

-psychobiotic species that supports normal natural inflammatory activity in intestines and brain

Lacticaseibacillus casei


-supports insulin sensitivity

-elevation of glutathione

-facial and skin flakiness may be related to low counts

Parabacteriodes destasonis

-modulate hosts metabolism

-produces secondary bile acids

-thought to exert protective effects against neurological and metabolic function

Roseburia hominis MS06

-promotes and regulate innate immunity via interaction with human genes

Streptococcus thermophilus St-21

-reduces uremic toxins

-mitigate bacterial dysbiosis in the lumen

These are just a few of trillions of organisms in the biome and they each have specific jobs and they need specific foods to survive. These are foods most people do not consume. One helpful food combination is Astaxanthin (a derivative of carotenoids which are found in orange, red, and yellow pigmented foods), combined with Antrodia cinnamomea, which supports and regulates the gut microbiota, regulates weight gain, and improve fat and glucose metabolism. Food is either healing or not. The Standard American Diet is not healing and contributes to a limited microbiome. I do not want to eat crickets but it occurs to me that while most people are watching this introduction of insects into the food chain and want nothing to do with it because it is not natural, many are very willing to consume things packaged as “foods” are known to be way more harmful that we know insects to be. To me, the idea of cockroach milk is not really that much worse than what we know that PUFA oils do to the body, for instance. I don’t want either!

Alterations to the gut biome have been found to happen with the use of Metoformin (diabetes), which increase Akkermansia municiphila (see above). Gastric bypass has shown significant increase in Bacteriodes species, which are known to regulate weight. Is it possible that changing the biome is more the key to a healthy weight than medication and surgery? Another interesting study showed that fecal transplant from a post gastric bypass mouse into a obese mouse will decrease weight and fat mass, indicating that the biome may be more important to healthy weight than the calories taken in. So, if you have struggled with weight while doing everything recommended to lose weight, have you tried hiring some more workers to do the jobs that need to be done and also to help increase the productivity of other workers?

If not, consider doing the following:

-test your transit time

-if SIBO is suspected, do a breath methane test

-do a 30 day phase of wiping NBO’s from your gut biome, bacterial, viral, fungal, and parasitic, including the NBO’s in the small intestine (SIBO)

-do a 30 day foundational reseed

-continue with 30 day reseeds with organisms specific to immune, neurological, and skin

-also available is a specific reseed for women who have hormone imbalance-can also be used internally to reseed vaginal biome

-soon an oral biome reseed will be available

-feed all organisms their preferred foods with a prebiotic for the phases

-to get the best benefit consider a cellular repair prior to the wipe phase

-to get ideal results consider following with an active downstream and then upstream detox

This will reset your gut and get the cells working. The whole goal would be to add in the foods and organisms that create the nutrients and hormones needed by the cell for every organ system to do it’s job. The body is an amazing machine with trillions of moving parts and processes. Obesity and chronic disease are a consequence of a deeper issue and all chronic issues go back to the body biome and the cellular function. If things go the way many of us hope they go, new scientific data will continue to emerge that will lead to less focus on the disease, or consequence, and more focus on the root causes that either promote health or cause disease. However, for now, we are still acting to educate about the importance of a terrain that is diverse enough to control the germs that conventional medicine is focused on. A diverse gut will help control microbes. Given that obesity was such a risk factor in COVID, it makes sense that the biome may have been the real risk factor!

All disease begins in the gut-Hippocrates

Fix the cell to get well-Dr. Dan Pompa (the gut is composed of cells)

For more details about the cellular repair, detox, and gut programs, contact me at

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