Paleo Gut Flora Repair

….All 190 posts here….

I was shocked to learn that there were some paleo (meat and veggie) eaters who were getting cured with resistant starch.  I didn’t know that some were sick and, as I said in a previous post, I would not have guessed that starch was good for anything, but spikes in blood sugar.  I was rudely awakened by the shouts of Richard Nikoley on Free the Animal, though I suspect the sanity behind the argument came from Tim and Dr. BG (though she has now modified her position)  He presented a kind of Second Coming of Paleo with resistant starch to feed the gut flora as soluble fiber.  How could I question food for flora?  (How could I question Nikoley without my karate gi?)

Paleo is not Paleo

It took me a while to realize that paleo is not the same for everyone.  I thought my Anti-Inflammatory Diet (meat/fish/eggs/dairy and veggies, without vegetable oils or sugars or grains) was paleo.  The way that I used this AID, it was high in saturated fat, low in polyunsaturated fat, high in protein, low in high glycemic carbs and ample in prebiotic, soluble fiber.  Some would say it is low carb.  Judging from comments on Free the Animal, I think I would be cast out by some of the more carnivorous (LC and VLC) in the paleo community for including prebiotic fiber.  Some people don’t want to feed their flora, microbiota.  It is a kind of “Let them eat meat,” mentality.

Gut Flora/Microbiota are Friends

I think of my gut flora as fellow travelers on my life journey and what’s good for them is good for me.  I don’t intentionally abuse them, but I also forget that they might not enjoy bourbon or the phytoalexins in herbs and spices.  I don’t begrudge them the soluble fiber that they need, and I think that they are a little happier with each apple (pectin) I feed them.  I simply forget that most people haven’t taught micro, DNA sequencing and the biochemistry of plant cell wall polysaccharides.  My wife starts to roll her eyes at any sentence containing “flora”, “antioxidant”, “inflam-“, “omega-“, “carb”, “paleo”, or even “microbiobiota.”  And the list gets longer.  I think that I'm out of touch, until I read Nikoley.

Paleo Diet without Prebiotic Fiber is Hard on Gut Flora

People get sick on paleo, because they don't feed their flora.  Gut flora are needed to supply vitamins, short chain fatty acids and immune system stimulants.  If you don’t feed your flora you get vitamin deficiencies, gut inflammation and autoimmune diseases (Treg deficiency).  It is very important to remember that feeding your flora means matching the soluble fiber with the existing flora.  Most people make the mistake of assuming that if they change their diet, then their flora will also change.  Their flora will adapt with each of their hundred different species of gut bacteria increasing or decreasing in numbers, but no new genes will be present to digest new soluble fiber.  Eating a meat diet will eventually eliminate gut bacteria needed to digest some plant materials and produce intolerances.  The missing bacteria will not be regained upon return to eating plants again.

Changing Diet Does Not Repair Gut Flora

Many people lose species of gut flora as they change from diet to diet, eat processed foods lacking soluble fiber or use antibiotics.  The loss may be permanent, but need not be.  Food intolerance and most “allergies” merely reflect missing species of bacteria, and introducing new bacteria fix the problem.  Lactose intolerance, for example, can be cured by eating live yogurt.  Similarly, many immunological problems, such as autoimmune diseases, result from species of gut bacteria that are needed for the development of the immune system, which takes place in the lining of the gut in response to gut bacteria.  New bacteria need to be introduced to fix the deficiency and diet alone is not enough.  Just to be clear;  meat-exclusive paleo can lead to autoimmune diseases, because of deficiencies in gut flora diversity/species and adding back soluble fiber can only cure the diseases, if the bacteria needed to digest the fiber polysaccharides are still present or are reintroduced.  Also note that there is soluble fiber polysaccharide sufficient in a carnivorous diet to support properly adapted gut flora.

Dairy Probiotics Do Not Repair Gut Flora Destroyed by Antibiotics

Don’t expect dairy probiotics to cure diseases caused by deficient gut flora.  Bacteria that grow on dairy cannot survive in the gut.  I know that physicians, including Dr. Oz, recommend that patients treated with antibiotics eat yogurt to repair their gut flora.  It ain’t  gonna happen.  That treatment is just for the doctor’s benefit (and provide some temporary functionality), to make her feel like she is addressing the problem responsibly.  I suggest that the antibiotic-damaged gut flora will screw up the immune system and bring the patient back to the doctor’s office even sicker.  Antibiotics are very good for business.

Health in a Crock

So, here comes the part that was missing from Nikolay’s Paleo plus RS.  He left out the missing gut flora.  RS is a panacea for those with some gut bacteria that can digest RS, but for those with profoundly crippled gut flora, e.g. some of those with autoimmune symptoms, RS is just inert fiber, not flora food.  

Fermented Vegetables Repair Gut Flora

New bacteria must be eaten, and I think that the cure, short of the real deal fecal transplant, is still available in the original, paleo form of naturally fermented, live foods.  The answer (and please forgive the fervor, because I think health can be this simple) is Fermented Vegetables, by Kirsten and Christopher Shockey.  Their book, right, is coming out in September, and I think that the most important part of this cure is that it looks and tastes fantastic.  This is not canned, dead sauerkraut.  These are culinary delights from simple recipes in which the natural bacteria do all the work.  Since they are long time friends of mine, I have coerced Kirsten into giving me some advance access to some of her recipes.  She has also tentatively agreed to share on my blog some of her personal fermentations on happy bellies.  So check back for future posts.

Pay close attention, because some of these recipes may cure what ails you.  They have the potential to repair your gut and are the healthful fix for a sickening faux “paleo” diet.  Note that homemade, live fermented veggies contain 1) fermenting bacteria responsible for acidifying the brined veggies for storage, 2) additional bacteria of the species missing from your gut flora and are just along for the ride, and 3) veggies that have their soluble fiber intact and ready to feed your gut flora.  Cooking, pasteurizing or otherwise harming the live, working bacteria in fermented vegetables destroys their benefit in contributing to your gut flora.  It only takes a few of the bacteria that do survive passage through your acid stomach to fix your gut flora.

Major Points of a Healthy Paleo Diet

• Meat/fish/eggs and veggies, without dairy, grains, vegetable oils and processed foods.
• Nikoley and others pointed out that a healthy paleo diet has soluble fiber, e.g. RS, to feed gut flora.
• Resistant starch is a unique category of soluble fiber with health benefits.  (Other types of soluble fiber may also be needed.)
• Diet alone is not enough for health, add gut flora.
• Diet and gut flora need to match.
• The natural paleo source of gut flora bacteria is homemade fermented vegetables.

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.

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)

Shockey

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.

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.

Dr. Oz on Gut Flora Repair

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Where is the hippo? Trying to repair a complex community of a couple of hundred different species of bacteria by just changing diet, is like a zoo trying to add hippos by building a new enclosure and supplying it with fodder. You can wait and wait, but you can't add new species without adding new species. Hippos don't appear by spontaneous generation and neither does E. coli or other gut bacteria. You have to ship in hippos from other zoos and after antibiotic-induced extinction of gut bacteria, you have to introduce or eat missing species of bacteria. Also just adding probiotics will not provide a lasting fix for damaged gut flora any better than adding more elephants or giraffes will improve the diversity of a zoo lacking hippos.

I am amazed that Dr. Oz and the medical industry can encounter symptoms of dysfunctional gut flora, e.g. constipation, food intolerance, autoimmunity, allergy, that are preceded by antibiotic treatment and not address the compromised species diversity of the gut. The involvement of gut bacteria in immune system function is documented in the biomedical literature. The lasting impact of antibiotics on gut bacteria is known. Then why do Dr. Oz and the rest of the medical industry just recommend probiotics, a half dozen different species of bacteria found in fermenting dairy products (think elephants and giraffes), to repair a decimated gut bacterial community? They seem to be perplexed and ask, "Where is the hippo?"

Generalizations about Gut Bacteria

Each healthy human maintains a subset of a couple of hundred of the couple of thousand different species of bacteria found in humans around the globe. The diverse community in each individual may differ in species, but has approximately the same complement of genes in people sharing the same diet.

• 1-200 different species of bacteria per person
• 1-2000 different species of human gut bacteria
• 1 million different genes among the different bacteria
• Most genes are involved in digesting plant carbohydrates, i.e. soluble fiber: inulin, pectin, fructans, algal sulfated polysaccharides, etc.
• Diet diversity, e.g. the Modern American Diet, reduces the diversity of the gut bacterial community, presumably because the rapid change in foods permits survival of only generalist bacteria that can digest many different foods.
• Simple diets produce gut flora diversity, but only if there is access to diverse bacteria.
• Health may result from diverse gut flora developed from a simplified diet and ample bacterial resources.
• Obesity and other diseases may result from simplified gut flora developed from a changing, complex diet and a sterile environment/isolation.
• Vegan and paleo extremes can lead to healthy gut flora diversity, if the gut bacterial community is permitted to adjust to the diet composition by avoiding rapid changes and providing diverse bacterial sources.
• Meat contains complex polysaccharides, e.g. glycosaminoglycans, such as chondroitin sulfate and heparan sulfate proteoglycans, which are bacterial fodder equivalent to soluble fiber.
• Probiotics are unique bacterial species that do not persist in the gut of adults, but dominate the gut of milk eating babies and stimulate development of the gut and immune system.
• Probiotic bacteria can temporarily provide developmental signals for immune system development that are normally provided by a healthy gut flora.
• Antibiotics cripple gut flora needed for development of the immune system.
• Common medicines have significant antibiotic activity and modify gut flora.

Damage to Gut Flora is Not Repaired by Diet Alone
There is little or no effort being made by the medical industry to develop approaches to repair gut flora damaged by disease, unhealthy diets or medical procedures. This is similar to a surgeon stepping away from removal of a diseased organ without closing the wound. Antibiotics leave a gut flora that will remain permanently damaged without systematic, monitored repair. It might also be suspected that disruption of gut flora by antibiotics and the introduction of large amounts of new foods, such as high fructose corn syrup and vegetable oils may contribute to or cause the modern prominence of obesity. After all, gain or loss of weight changes gut flora, obese individuals have damaged gut flora, and trading gut flora between fat and lean animals, trades weight gain/loss behaviors.

Sources of Bacteria to Repair Damaged Gut Flora

• We must eat new bacteria in order to replace bacterial species lost by antibiotics or unhealthy diets.
• Probiotics -- bacteria that aide gut function, commercially from dairy fermentation
• Fresh vegetables -- bacteria are on the surfaces of plants unless the vegetables are cleaned or cooked
• Fermented foods -- Bacterial growth leading to acid or alcohol production has beed used in the preparation and storage of many foods and provides a rich bacterial resource.
• Environment -- Bacteria are transferred to our hands and face from other people, pets and surfaces, unless hands and the body are continually washed. Sanitizers and frequent washing of hands and surfaces eliminate acquisition of environmental bacteria to repair damaged gut flora. Social isolation and hygiene block repair of gut flora.
• Replacement -- experimental replacement of damaged with healthy gut flora (fecal transplant) has been very effective in curing many diseases without significant risks, but is restricted by the medical industry.