Showing posts with label flora. Show all posts
Showing posts with label flora. Show all posts
Monday, March 16, 2015
Gut Flora Risk and Repair
….All 190 posts here….
The two most important contributors to health are diet and gut flora. All of the other contributors, such as exercise, genetics, environmental toxins, hygiene, etc. are of minor importance. A healthy diet, such as The Anti-Inflammatory Diet that I recommend on this blog, is simple and relatively easy to follow after weaning from the Standard American Diet. One version of the healthy diet is just eating meat, fish, eggs, dairy and plenty of vegetables, but avoiding vegetable oils and grains. Most people will be healthy with that general diet, but if and only if, they also have a healthy gut flora that is adapted to the food they eat.
Nothing comes from nothing… For bacteria to come out, bacteria must go in. You have to eat bacteria to extrude them by the pound. Each day a single bacterium growing and dividing in your gut once per hour will produce a million daughter bacteria (24 doublings, estimate that doubling two, ten times is about a thousand, and 1000X1000= million.) So if you mixed a milligram (about the size of the period at the end of this sentence) of gut bacteria with ample food, you would have a kilogram (pounds) of bacteria by the end of the day. Similarly, it takes about a day for a single bacterium applied to a petri dish of nutrient agar to produce a colony weighing about 10 milligrams. The point here, is that a single bacterium that makes it through the acid bath of the stomach can be a major player in your colon in a couple of days. This is a very good thing. We want to kiss babies, because babies systematically vacuum up bacteria from the darkest of corners and with shameless generosity present them in an irresistible pucker. We need those bacteria, and so do the babies. Hygiene, e.g. antibacterial hand soap, bleaching surfaces or closing toilet lids isolates people from potential sources of beneficial gut bacteria.
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The two most important contributors to health are diet and gut flora. All of the other contributors, such as exercise, genetics, environmental toxins, hygiene, etc. are of minor importance. A healthy diet, such as The Anti-Inflammatory Diet that I recommend on this blog, is simple and relatively easy to follow after weaning from the Standard American Diet. One version of the healthy diet is just eating meat, fish, eggs, dairy and plenty of vegetables, but avoiding vegetable oils and grains. Most people will be healthy with that general diet, but if and only if, they also have a healthy gut flora that is adapted to the food they eat.Most people make themselves sick by not matching their gut bacteria to what they eat, so let me repeat the main point of this article:
You will get sick if the bacteria in your colon can’t digest your food.
And sick means allergies, autoimmunity, cancer, etc.
Read and Heed or Dead
What Killed American Gut Flora?
There are hundreds of different species of bacteria growing on partially digested food (soluble fiber) in your colon. Americans are sick, not because they are too poor to buy food, but because they have the worst, i.e. least diverse, gut flora in the world.
Do: We pick up, recruit, eat new bacteria and repair our gut flora by:
- touching surfaces, people, pets, etc. and putting our fingers near our mouths,
- eating live fermented food, or semi-clean vegetables,
- not cooking/killing/sanitizing all of the bacteria around us,
- eating probiotics and transferring some of their genes to our gut flora.
Don’t: We wipe out or reduce the diversity of our gut flora by:
- using inappropriate hygiene that kills the bacteria we need for health,
- taking antibiotics that kill gut flora and compromise our immune system,
- trying to eat a wide variety of foods, which is counterproductive and only permits a few varieties of bacteria to survive.
Hygiene Kills Beneficial Bacteria
Nothing comes from nothing… For bacteria to come out, bacteria must go in. You have to eat bacteria to extrude them by the pound. Each day a single bacterium growing and dividing in your gut once per hour will produce a million daughter bacteria (24 doublings, estimate that doubling two, ten times is about a thousand, and 1000X1000= million.) So if you mixed a milligram (about the size of the period at the end of this sentence) of gut bacteria with ample food, you would have a kilogram (pounds) of bacteria by the end of the day. Similarly, it takes about a day for a single bacterium applied to a petri dish of nutrient agar to produce a colony weighing about 10 milligrams. The point here, is that a single bacterium that makes it through the acid bath of the stomach can be a major player in your colon in a couple of days. This is a very good thing. We want to kiss babies, because babies systematically vacuum up bacteria from the darkest of corners and with shameless generosity present them in an irresistible pucker. We need those bacteria, and so do the babies. Hygiene, e.g. antibacterial hand soap, bleaching surfaces or closing toilet lids isolates people from potential sources of beneficial gut bacteria. Traditional Food is Fermented (with Live Bacteria)
In most cultures, extra food is mixed with something like salt or spices to kill local problem microbes and then bacteria are permitted to grow. The result is fermentation of the sugars available in the food with production of organic acids, e.g. vinegar, that stop the growth of other bacteria that might grow on protein and cause objectionable flavors. Homemade fermented veggies contain a wide variety of happenstantial bacteria that can adapt to productive gut growth.
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| Shockey |
Cooking Kills
We cook to dissolve and soften foods. Meat can be eaten whole and our stomach enzymes will easily digest the protein and fat to provide all of our nutritional needs. The only plant material that can be digested by our enzymes is starch. The rest of the plant requires cooking to make the protein available and the remaining carbohydrates, soluble fiber, require digestion by hundreds of different enzymes produced only by microorganisms. Cooking will release soluble fiber to feed gut flora, but it also kills bacteria, so some raw foods must be eaten to make sure that the gut is always supplied with fresh bacterial recruits. Cooked or pasteurized foods do not contain live bacteria and are not useful as sources to repair gut flora.
Probiotics are not Gut Flora
Commercial probiotics are made from bacteria used in dairy products (dairy probiotics) or bacteria used to make enzymes in other products, such as laundry detergents.
These bacteria can be repackaged and sold as probiotics, because they have already been tested for toxicity. These bacteria don’t normally grow in the gut and if you swallow them, they just pass through. These “probiotics” can temporarily provide some of the functions of gut flora, because they are bacteria, but they don’t grow in the gut.
Gut Flora are Bacteria Created in the Gut
Gut bacteria produce chemical signals that coordinate the metabolism of food by hundreds of different species of bacteria. We call these chemical signals vitamins, because humans extract the vitamins from the bacterial biofilms that always line the gut, so humans don’t need to produce their own vitamins. Gut flora can produce all of the vitamins that we need, so it is not surprising that multivitamins do not provide any health benefit and concentrated vitamins my be harmful by disrupting normal metabolism of gut flora. Biofilms also promote the exchange of genes between different species of bacteria, so the concept of species does not actually apply to gut flora, where new species are rapidly being created. A common example of this process is the curing of lactose intolerance by simply eating small amounts of live yogurt for a couple of weeks. The cure results from the transfer of a gene that produces an enzyme to digest lactose from the yogurt probiotic bacteria to the regular gut bacteria. The new species, a natural GMO, continues to grow in the gut, digest lactose, and cure lactose intolerance. The yogurt probiotics just get flushed away and that is why dairy probiotics must be eaten continuously to provide some of the benefits of healthy gut flora.
Antibiotics Kill Gut Flora, Compromise the Immune System and Cause Disease
Antibiotics are a huge benefit in curing and avoiding infectious disease. Unfortunately, antibiotics can cause lasting damage by killing beneficial species of bacteria of the gut flora. Loss of essential bacteria is commonly seen as food intolerances (true food allergies are rare) or constipation. Since gut flora are needed for development of both the aggressive and suppressive parts of the immune system, which occurs in the lining of the gut, then antibiotics slowly lead to loss of function of the immune system that leads to autoimmunity or allergies. Probiotics typically administered following antibiotic treatments do not repair the gut flora and leave the immune system damaged and prone to autoimmune diseases and allergies.
Variety in Foods Leads to Loss of Diversity in Gut Flora
It may be more entertaining to eat a new cuisine at each meal, but it confuses your gut flora. Your gut is a river that endlessly moves food from mouth portal to pottie. Bacteria divide and eddies cast some of the bacteria back to mix with food upstream before inevitably moving with the masses down and out. Bacteria that don’t multiply as quickly as others eventually become extinct. Bacteria that grow well on broccoli may wither with onions. If you continue to eat some broccoli and some onions, then your gut flora will adapt, but if the type of polysaccharides, the soluble fiber, changes continuously, then you will end up with the stunted gut flora of Americans. Diversity of gut flora is reduced by too much variety in food.
Matching Food to Gut Flora Takes Time
All of the gut problems that people complain about, gas, bloating, diarrhea, constipation, food intolerances/allergies (except gluten and a couple of others), etc. are due to a mismatch between food and the digestive enzymes of gut flora. Modern food processing retains protein, fat and starch and removes the polysaccharides/soluble fiber that reaches the colon, feeds gut bacteria and produces short chain fatty acids (acetic acid, butyric acid, propionic acid) that feed the colon and reduce inflammation. It takes time for gut bacteria to adapt to new soluble fiber in new foods by recruiting or creating new bacteria, and this is only possible, if inappropriate hygiene is avoided or if homemade fermented foods are eaten.
Sunday, March 15, 2015
Health in Diagrams I — Gut Flora and Diet
---All 200 posts here---
This is the first of three posts to summarize my thoughts on diet, inflammation and disease mediated by gut flora. I decided that I needed to make my points as explicit as possible by putting them down in diagrams and making references to my other posts. By the time I finish, I will reach my 200th blog post at Cooling Inflammation.
Health in Diagrams II -- Curing Autoimmunity and Allergies
Health in Diagrams III -- Inflammation from Cell to Tissue
Everyone Leaves Out Gut Flora
I want to first explain and diagram my current understanding of the relationship between gut flora (the complex community of hundreds of different types of bacteria and fungi in the intestines) and diet. My impression is that many people have health problems based on diet, but when they try to heal their health, they fix their diet and see only limited benefits. Medicine provides only a temporary treatment using dairy probiotics. The problem is that they failed to fix their gut flora, which was also damaged by their unhealthy diet.
Health Requires a Match between Diet and Gut Flora
It is a myth that gut flora will just adjust to diet and a healthy diet leads to a healthy gut flora.
A damaged gut flora lacks necessary species of bacteria. Antibiotics, for example, can permanently delete dozens of particular bacterial species of gut flora that can only be replaced by reintroducing the missing bacteria by eating those bacteria again. The missing bacteria may be needed to digest particular foods and the result is food intolerances, commonly mistaken for food allergies. Antibiotic use frequently leads to autoimmune diseases, that are caused by deficient regulatory T cells of the immune system that develop in the lining of the intestines in response to particular gut bacteria. The natural source of gut bacteria is eating the bacteria clinging to raw or fermented vegetables.
Antibiotics and Autoimmunity
Diagram Showing the Interaction of Food, Gut Flora and the Immune System
Food is just Protein, Fat and Soluble Fiber
The human body produces enzymes to fully digest proteins, fats and one polysaccharide, starch. All other parts of plants and animals are edible (fermented by gut flora) soluble fiber polysaccharides or insoluble, undigestible fiber consisting of cellulose or lignin, which together also make up the undigested organic matter, humus, of soil. Grains are problematical for health, because their starch is readily converted to sugar, i.e. high glycemic, and their fiber is insoluble (not fermented by gut flora) and high in phytate. Phytochemicals, plant polyphenolics, are of questionable value as antioxidants and are of unexplored importance for their antimicrobial impact on gut flora.
Phytochemicals, Natural Antibiotics and Antioxidants
Polymers (Protein, Starch) are Hydrolyzed by Enzymes to Oligomers and then Monomers (Amino Acids, Glucose)
The stomach mixes protein digesting enzymes, proteases, and starch digesting amylase, with food protein and starch. Proteases convert the long chains polypeptides, polymers of protein amino acids, into shorter fragments, oligopeptides. The specific nature of the stomach proteases leaves groups of basic amino acids (lysine, arginine), heparin-binding domains, intact. These peptides, similar to the defensins of the microvilli crypts, are anti-microbial and work with residual acidity to reduce bacterial growth in the first part of the small intestines. Pancreatic enzymes then digest the peptides further and the small peptides are ultimately digested by enzymes on the surface of intestinal epithelial cells just prior to absorption. Similarly, starch is degraded to oligosaccharide amylodextrins, which are then hydrolyzed to glucose at the intestinal surface prior to absorption. Amino acids and glucose are not normally available to bacteria in the intestines.
Antimicrobial Heparin-binding Domains
Fats are Dissolved by Bile, Digested by Lipase and Absorbed
Fats are triglycerides, i.e. three fatty acids attached to the three hydroxyl groups of glycerol. Fats are hard to digest, because they form oily droplets. The droplets are dissolved in the intestines with bile, which is an acidic form of cholesterol, that is produced in the liver and stored in the gall bladder. Fat in a meal triggers bile release from the gall bladder into the small intestines. The bile represents a huge reservoir of the cholesterol that is synthesized by the body and dwarfs the cholesterol content of any meal. Statins decrease body production of cholesterol, interfere with bile/fat digestion and lower lipid cholesterol levels. (Unfortunately, lowering lipid cholesterol levels has minimal impact on heart disease and the only impact of statins on cardiovascular disease is through weak anti-inflammatory side effects.) Pancreatic lipase removes two of the fatty acids from each triglyceride. The fatty acids (a.k.a. soap) and monoglyceride are absorbed by the intestinal cells and reformed into triglycerides that make their way to lymphatic lacteals and are dumped into the blood, where they circulate as chylomicrons surrounded in lipoprotein. Lipoprotein lipase binds to heparan sulfate on the surface of blood vessels and gradually removes fatty acids, until the diminished chylomicron is absorbed by the liver and exits as a VLDL. (Note that this is another connection between lipid metabolism and inflammation, since inflammation decreases heparan sulfate on cell surfaces. Heparan sulfate also mediates LDL binding to cells and amyloid stacking.)
Heparin-binding Domains
Plant Polysaccharides are Soluble Fiber and Food for Gut Flora
All that remains of food after the protein, fat and glycemic starch (glycogen) have been removed in the small intestines are plant cell wall polysaccharides, resistant starch, storage polysaccharides, e.g. inulin, plant beta-glucan, animal glycans, e.g. chondroitin sulfate and heparan sulfate, and insoluble fiber. The insoluble fiber passes on to be a minor contributor to the bulk of stools and the rest of the polysaccharide is potentially fermentable by gut flora into short chain fatty acids (formic, acetic, propionic, butyric acids). Some of the polysaccharides are simple repeating units of one or two sugars in long chains, but others are made of five to ten different sugars in complex branched structures. Simple repeating polysaccharides require just a few different enzymes for their initial synthesis and a few for their digestion. Thus, resistant starch can be digested by a couple of enzymes into glucose that can be used by most gut flora. Arabinogalactan, on the other hand, requires a dozen enzymes for plant synthesis and an equal number of hydrolytic enzymes to produce arabinose and galactose, which require further enzymes for metabolism in a select few of species of gut flora bacteria.
Resistant Starch as a Panacea
Food Intolerance/“Allergy” Indicates Missing Bacteria
Gut flora in general can produce several hundred different enzymes for digestion of diverse soluble fiber, but most soluble fiber polysaccharides can only be digested by certain bacteria and those bacteria increase, if the complementary fiber is present in the diet. If a fiber is absent from the diet, bacteria that specialize in digesting that polysaccharide will be eliminated. People living on diets limited to just a few types of soluble fiber can only digest those fibers and a shift in diet to other types of soluble fiber will lead to symptoms of dietary upset, such as bloating, gas production and food intolerance. Food intolerances reflect inadequate diversity in gut flora and a mismatch between bacteria and food. Food intolerances can be eliminated by repairing gut flora and the typical repair solution is eating homegrown fermented vegetables that provide the missing species of bacteria.
Paleo Gut Flora Repair
Immune Cells Develop in Response to Gut Bacteria
Most of the body’s immune cells are in the intestines. Cells of the immune system are constantly dividing in bones and the thymus gland, developing in the lining of the intestines and migrating to other tissues. Filamentous bacteria of the gut flora stimulate the development of aggressive immune cells that kill other cells that are infected with pathogens or viruses or are cancerous. Furrows perpendicular to the flow of food cultivate the growth of Clostridium species that ferment soluble fiber, e.g. resistant starch, and release butyric acid that stimulates the development of regulatory T cells, Tregs. It is the Tregs that control the aggressive immune cells and prevent attack on self (autoimmunity) or innocuous antigens (allergy). It appears that merely eating resistant starch, e.g. potato starch, with probiotics that contain butyric acid producing Clostridium bacteria may provide a cure for many autoimmune diseases.
Free the Animal: A Resistant Starch Primer for Newbies
Gut Biofilms Release Vitamins as Quorum Sensing Signals
The gut flora lines the intestines in numerous biofilm communities, which form from dozens of different species of bacteria that communicate by exchanging molecules called quorum sensing signals. These signals from the biofilms intimately attached to the lining of the intestines are vitamins. Thus, healthy gut flora are the major source of vitamins and other sources, such as fruits and vegetables are only needed, if the gut flora is damaged, e.g. by antibiotics.
Dr. Oz, Vitamins, Biofilms
Volume of Stools Reflects Gut Flora Fermenting Soluble Fiber
The bulk of bowel movements, stools, is bacteria, the compressed gut flora that accumulated in the colon while fermenting soluble fiber. We always hear that we need to eat fiber for regularity, but since insoluble fiber is only a minor contributor to stool volume and it is associated with anti-nutritive attributes, such as the binding and removal of zinc and iron by phytate, the fiber that counts for regularity is soluble fiber. Regularity results from the fermentation of soluble fiber polysaccharides producing short chain fatty acids, such as butyrate, that are the major source of energy for colon cells. And the growing bacteria in the colon provide most of the bulk of the hydrated stools. Inadequate dietary soluble fiber or damaged gut flora, dysbiosis, leave only dehydrated insoluble fiber and compact stools of constipation. Constipation can result from dehydration or excessive retention, but chronic constipation, even in the presence of adequate dietary soluble fiber, is an indication of damaged gut flora and an increased risk for diseases resulting from deficiencies of Treg production: autoimmune diseases and allergies. Constipation and associated autoimmune diseases can be cured by repairing gut flora and supplying adequate dietary soluble fiber.
Milk, Kefir and Gut Flora
Gut Flora Disease and Obesity
---the other 200 posts---
The health of your gut flora (the interacting trillions of bacteria of a couple of hundred different species that make up the pound of bacteria that you carry primarily in your large intestines) is more important than your genetics to your overall health. Thus, your health is a result of diet, gut flora adapted to your diet and exercise. Everything else, your genetic risks, environmental toxins, etc. are of only minor impact.
I am trying to paint the big picture of how the food that you eat and your gut flora interact to determine your health, by which I mean whether you get sick, become obese and/or bloat with gas.
Health Depends on Gut Flora
If you are healthy, you have a couple of hundred different species of bacteria that help you to digest the protein, fats and carbs that you eat in meat and vegetables. Your body easily digests protein and fats in meat, fish, eggs and dairy, because enzymes to digest them are present in your stomach and small intestines. The only carbs that your body can digest are some simple sugars and starch. The rest of the polysaccharides present in plants cannot be digested without the help of bacteria. The polysaccharides that your gut flora can digest are fermentable, soluble fiber, e.g. resistant starch, pectin, inulin, arabinogalactan, xylans, beta-glucan, etc. If you can’t digest soluble fiber, because you have damaged gut flora, dysbiosis, and are missing essential bacterial species normally found in a healthy gut, then the soluble fiber just passes through as insoluble fiber and readily dehydrates into hard, constipated stools. Partial digestion due to just a few missing bacterial species produces the symptoms of food intolerances.
Constipation Results from Dysbiosis
The bottom line is that the volume of healthy, soft, firm stools is made up of gut flora that digested dietary soluble fiber and converted it into more bacteria. If you eat more soluble fiber, this food for your gut flora, will produce proportionately more bowel movements.
Gut Flora Guide Immune System Development
Most of cells of your immune system are in the lining of your gut and there are particular species of gut bacteria directly involved in the development of immune cells that have different functions as they spread throughout your body. Some of these cells are aggressive and attack pathogens, while others make sure that the aggression doesn’t get out of control and cause autoimmune diseases or allergies.
Gut Flora Divided into Groups to Show Involvement in Disease
Recent studies have demonstrated the role of gut bacteria in producing nutrients, vitamins and neurotransmitters. To highlight the essential role of gut flora in disease, I have divided the hundreds of species of gut bacteria into groups to illustrate their direct involvement in development of the immune system and regulation of the flow of dietary nutrients involved in obesity. A recent study shows that an infection can produce a change in gut flora associated with marshaling additional fatty acid nutrients for the host instead of just producing more gut flora. Chronic change of gut flora in this way leads to obesity. Other types of dysbiosis contribute to infections, cancer, autoimmune disease, allergies, food intolerances, gas and bloating.
Group A Bacteria Provide Aggressive Immunity
There are several dozen species of bacteria in healthy gut flora, including the filamentous bacteria, that trigger the development of the aggressive part of your immune system that attacks pathogens, and kills cells of your body that are infected with viruses or are cancerous. Most antibiotics don’t permanently damage this group of bacteria, so after a course of antibiotics you can usually still stop infections. Excessive suppression of aggressive immunity contributes to cancer.
Group B Bacteria Provide Suppressive Immunity
There are dozens of other species of bacteria, including Clostridia, that control the development of the suppressive half of your immune system that produces immune cells, such as regulatory T cells, Tregs, that stop the aggressive cells of your immune system from attacking your own cells and innocuous things such as food and pollen. Many common antibiotics damage these species of bacteria and are thought to contribute to the development of autoimmune diseases and allergies. Inflammatory bowel disease is characterized by a simplified gut flora with only half the healthy number of bacterial species. Resistant starch preferentially feeds these bacteria to enhance suppressive immunity and in some individuals cure autoimmune disease.
Group C Bacteria Convert Soluble Fiber to Short Chain Fatty Acids (SCFA)
The fermentable soluble fiber in your diet is typically from vegetables and it is converted by the largest and most diverse group of bacterial species into short chain fatty acids. Each different plant polysaccharide, and there are hundreds, requires many enzymes for complete digestion to the simple molecules used by the bacteria to make its own proteins, fats and polysaccharides. Absence of bacteria that are specialized for the digestion of particular polysaccharides or other dietary components can disrupt gut flora and cause digestive disturbances that are experienced as food intolerances (also confused with food allergies that are rare.) Some of the bacterial species convert polysaccharides into butyric acid and other short chain fatty acids that are the major source of energy for cells that form the lining of the intestines. These SCFAs are also a major food source for other gut bacteria.
Group D Bacteria Convert SCFAs to Fecal Bacteria to Produce Bulk of Bowel Movements
In healthy people, the SCFAs produced by gut flora feed the intestines and the remainder produced in the large bowel is converted into more gut bacteria, which forms soft stools. Antibiotics typically damage these bacteria and result in constipation. These bacteria are typically more sensitive to antibiotics than those that digest the soluble fiber and produce SCFAs, so the excess SCFAs pass into the blood stream and contribute to obesity instead of stools. Lean mice with gut flora exchanged from obese mice, become obese. Cattle are fed antibiotics to enhance the conversion of corn polysaccharides into SCFAs and body fat prior to slaughter.
Group E Bacteria convert Soluble Fiber to Methane and Hydrogen, Bloat
Increased volume of the intestines, bloating, results from conversion of soluble fiber into methane, hydrogen and carbon dioxide gases. Some of this gas is absorbed into the blood and can pass from the large intestines, through the blood, and back to the stomach and small intestines. Helicobacter pylori, the cause of stomach ulcers and gastric cancer, can utilize hydrogen from the blood as an energy source.
In Summary:
A+B+C+D = healthy, normal weight
A+C+D = normal weight, autoimmunity and allergies
B+C+D = normal weight, susceptibility to cancer, chronic Lyme disease, food poisoning
A+B = normal weight, constipated
A+B+C = obese, constipated
A+B+D = normal weight, food intolerances
A+B+C+E = obese, constipated, bloated
Cure for Dysbiosis and Associated Diseases is Repair of Gut Flora
The excitement about the use of resistant starch (RS) and probiotics with Clostridia and other soil bacteria to reverse the symptoms of autoimmune diseases is based on the ability to repair gut flora damaged by poor nutrition and antibiotics. Low carbohydrate diets that do not provide soluble fiber to feed gut flora lead to dysbiosis and chronic diseases. Resistant starch, as the name suggests, passes on to the colon by avoiding digestion with amylases in the small intestines and acts as a soluble fiber to feed gut flora in the colon. Clostridia convert the RS to sugars and SCFAs usable by other gut flora. Note that some species of Clostridia produce toxins and it is these pathogens that take over in hospitals after the healthy species are killed off with antibiotics. Fecal transplants are the best treatment for these hospital acquired infections.
I have discussed the role of hygiene, muddy veggies, fermented foods, etc. in several other posts on repair of gut flora.
Complete repair of gut dysbiosis is possible, but it requires more than just changes in diet and dairy probiotics, as typically recommended erroneously by the medical industry.
Health is dependent on:
- an Anti-Inflammatory Diet,
- gut flora adapted to your diet
- exercise and
- adequate sleep
The rest (genetics, vegan vs. paleo, environmental toxins, organic veggies, GMOs, etc.) are minor contributors, less than 10% in aggregate, to overall health.
ref.
Gut microbiota composition correlates with changes in body fat content due to weightloss
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