Vigorous Gut Immunity: Respecting the Microbiome

by on February 1, 2014

Vigorous Gut Immunity: Respecting the Microbiome

We are in the midst of a revolution against our own inhabiting ecosystem. For hundreds of thousands of years our ancestors have paved the way for numerous colonies of microorganisms to take home on and inside of us. In the last century we have waged warfare on these microorganisms, thanks to Louis Pasteur and his “germ theory” of disease and invention of pasteurization. Modern day antibiotic over usage, processed/pasteurized foods, and our craze with antibacterial soaps and cleaners have made our human ecosystem very inhospitable. Fortunately, thanks to the rapidly declining cost of gene sequencing and the initiative of the Human Microbiome Project, we are finding out that the human body is completely saturated with microorganisms and many of them are beneficial to our survival and everyday health.

When I say saturated, microbiologists actually consider us more microbial than mammal. We are a microbial dominated planet and the microbes eat at the table first! Humans consist of about 10 trillion cells. The microbes that colonize our bodies contain about 10 times that or 100 trillion cells. If we look at the genetic level, the human body consists of 23,000 genes. In your gut alone, you carry 3.3 million genes of microbes. There is actually more genetic material from microbes in your nose than your own genetic makeup! Over 8 million genes makeup the human microbiome. And why is this important you ask?? Well, environment dictates the expression of these genes. The genes of microbes and humans are living organisms with cells composed of DNA and mitochondria. The mitochondria are the powerhouse of the cell converting chemical energy from food into a form the cells can use. Mitochondria number from 2 to 2500 per cell. On a genetic level, we are less than 1/3 of 1% of who we think we are! We are a massive ecosystem dependent upon a healthy environment.(1)

Immunity essentially takes place in the gut. Numbers vary, but at least 70% up to 80% of your immunity is in your gut. Microbes live in colonies. I like to think of them as gangs. Gangs compete for space inside your gut and wage war against each other. When colonies such as E. Coli win the war you might end up with symptoms such as diarrhea and high fever. If colonies such as Lactobacillus win the war then you stay healthy. I make this sound very simple, but we are really only scratching the surface identifying good and bad gangs and how they interact with our gut environment. The altering of beneficial bacteria in the digestive tract can weaken the immune system.

Variations in the makeup of microbial communities are even being linked to chronic health conditions such as diabetes, asthma, obesity, and many digestive disorders such as Crohns and IBS. This means that people with chronic conditions harbor different gangs of microorganisms. In a recent study, “Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice” published in Science Magazine, they were able to alter body composition of mice through fecal microbiota transplantation. FMT means they transplant the poop of the donor into the colon of the recipient. As gross as it sounds, FMT is a very successful way to colonize the gut since the colon is teaming with microbes. The obese mice fecal material was transplanted into germ free mice. The germ free mice then showed significant increases in body mass and got fat. When they took fecal material from the lean mice and implanted into the obese mice, the obese mice lost weight. But, when they implanted fecal material from obese mice into lean mice they did not get fat. The obese mice were invaded by members of the Bacteroidales microbial community but the lean mice resisted invasion by the obese microbiota. Like I state before, we are really in the infancy of fully understanding our microbiota, but it is giving us new tools to combat health and mental issues. There exists a gut microbiota-muscle axis but the only relevant studies I could find dealt with the role of muscle wasting in cancer and malnutrition. The gut muscle axis are influencers of amino acid bioavailability, bile acids, and modulators of pro-imflammatory cytokines, so future studies will probably have benefit for muscle bound freaks!(2) Your gut microbiota works in relationship with many of your internal systems.(3)

Vigorous Gut Immunity: Respecting the Microbiome

If FMT of a healthy donor is not your cup of tea, then your best bet is to colonize your own gut accordingly. We need a fully functional and well operating digestive system to ward off chronic inflammation. Most people perceive an acidic environment with poor health, but in reality, the crappy processed foods, rancid vegetable oils, abuse of antibiotics, fluoridated and/or chlorinated water, and toxins/pollutants are making our stomachs more alkaline. The ideal pH of the colon is between 6.7 and 6.9. Acetic acid and lactic acid are some of the by-products that help do this. The acid environment inhibits the growth of harmful bacteria like those in the Phylum Proteobacteria, which includes a host of bad guys like strains of E. Coli, Salmonella, Vibrio, and Helicobacter.(4) Good bacteria also produce a volatile fatty acid, which along with the other acids, make it difficult for fungus and yeast (candida) to survive.(5)

The good news is that it is fairly easy and cheap to test your own PH. At any local drug store or aquarium store you can pickup some PH strips. The following chart should give you a good indication of your gut environment.

Source PH Level
Saliva 6.2-6.4 early morning over 7 by night
Urine over 6 but under 7
Stool 6.7-6.9

To keep a nice pH status, you need to properly feed the microbe communities. You need to activate the fermentation tank inside your gut. Your gut microbes are feeders of fermentable substrates. The byproducts of fermentation include short chain fatty acids (primarily acetate, butyrate, and propionate), organic acids, and gases like hydrogen. (4) These byproducts influence the PH of the colonic environment. Most Americans are starving their gut bugs because we consume foods that contain very little if any indigestible substrates better known as fiber. The Oligosaccharides family of fiber substrates is poorly digested by human enzymes and in turn provides a great food source for our gut bacteria.(13) Other indigestible oligosaccharides with prebiotic effects include fiber gums, fructooligosaccharides (FOS), inulins, isomalto-oligosaccharides, lactilol, lactosucrose, lactulose, pyrodextrins, soy oligosaccharides, and xylooligosaccharides.(6) Inulin is a long chain prebiotic fiber; long chain prebiotics contain 9-64 links per saccharide molecule and are digested more slowly, providing food for bacteria in the left side of the colon. Oligofructose is a short chain prebiotic, containing 2-8 links per saccharide molecule and fermenting in the right side of the colon, considerably faster.(7) Inulin and Oligofructose stand out for their ability to ferment the short-chain fatty acids (SFCA’s). A full spectrum prebiotic supplement would be something like oligofructose-enriched inulin (OEI), which contains all possible saccharide links.(8)
Our hunter gatherer ancestors ate upwards of thousands of species of plants and consumed enormous amounts of fiber from plant materials. The mean daily dietary fiber intake for 2007-2008 was 15.9 g/day.(9) A meager attempt compared to modern day hunter/gatherers, Hadza children, who get anywhere from 30-100g/day.(4) 100g of fiber seems like a daunting task for any modern American who doesn’t spend his days roaming outdoors and grazing. So we can spend our time focusing on some of the most common produce that gives us the most prebiotic fiber. There are numerous plants that provide good sources of prebiotic fiber, but I have listed the most common and available ones below.


Top Prebiotic Foods:

In parentheses is the prebiotic fiber content by weight, followed by the amount of food required to obtain 6 g prebiotic fiber:

  • Raw chicory root (64.6%) – 1/3 oz
  • Raw Jerusalem artichoke (31.5%) – 3/4 oz

(NOTE: Jerusalem artichoke is NOT the green globe artichoke you see at the store. It’s a totally different plant.)

  • Raw dandelion greens (24.3%) – 1 oz
  • Raw garlic (17.5%) – 1.2 oz
  • Raw leek (11.7%) – 1.8 oz
  • Raw onion (8.6%) – 2.5 oz
  • Cooked onion (5%) – 1/4 lb, or 4 oz
  • Raw banana (1%) – 1.3 lb

Besides munching down on a bunch of raw veggies you have another option that has recently been getting a lot of attention. Resistant starch (RS) is a fermentable insoluble fiber able to avoid digestion and pass along into the large intestine where it produces the same healthy gases and acids that soluble fiber does. The result of its fermentation is the SCFA butyrate. The Butyrate produced by the beneficial bacteria are food for colon cells. Without butyrate the colon cells starve and die. Butyrate producers (Roseburia and Eubacterium for example) are also known to be cross feeders and feed off of other activities so you run the risk of starving out multiple species of bacterium.(10) In addition to its benefit on the colon, RS can provide better quality of sleep, digestion, mineral and nutrition uptake, and most notably its effect on lowering blood glucose levels. RS seems to have an immediate response to lowering blood glucose in follow up meals and even with overall fasted glucose levels. RS could be promising for Type 2 diabetics.

Resistant starch can be obtained through food or food supplement. The most popular foods for highest levels of resistant starch seem to be parboiled white rice, potatoes, plantain chips, and legumes (beans). Potatoes and rice must be cooked first, then cooled. The starches become gelatinized then retrograded after cooling. The cooling packs the substance resulting in the formation of type 3-resistant starch. I think bodybuilders make out nicely in this category since they tote around pre-cooked meals all day and probably have had their share of eating them cold! The two food supplements most commonly used for RS are potato starch and plantain flour. They can be easily added to water, shakes, soups, etc. Recommendations have been to get 20g/day of RS.(11) 4 TBSP of potato starch and you are already at 30-35g of RS, whereas 1 cup of cooled rice yields 5g or a medium potato will yield you about 8g. If you are daring enough, an average-sized raw potato contains about 50g RS.(12) I know some individuals that will eat a couple of raw potato slices per day. RS could provide very beneficial for the low carbohydrate population. With a low carbohydrate diet, it is very difficult to provide your gut enough prebiotic material. Many low carb diets are gut starving diets, so some type of RS supplementation or prebiotic fibers to keep your gut bugs happy would be advised.

If you are unfamiliar to these prebiotic foods then you might experience some rumbling and tumbling in the belly and some light gas! When I began introducing the leeks and unions into the diet (and I did them raw), I had light belly rumbling for a couple of days, but as my gut got associated, it went away. I already eat numerous raw foods so it wasn’t that much of an adjustment for me. Like anything, I would recommend slowly adding in some raw prebiotic veggies. I would recommend them raw or slightly cooked since cooking destroys the prebiotic enzymes. You can easily add them raw to salads, tuna fish with paleo mayo, on top of meats like grass fed burgers, and my favorite, guacamole. I personally am not a fan of much supplementation. I tried to get all my nutrition from the most nutrient dense foods so I have not given the potato starch a try. People who have type 2 diabetes and are extremely sensitive to glucose and have poor blood sugar control and insulin resistance, leptin resistant, and don’t do well with starch and foods that contain a lot of fermentable fiber would probably benefit from supplementing potato starch or plantain starch.(10) I already eat cold rice and potatoes. IF I am cooking or baking some potatoes I will usually cut one up and eat a couple of slices raw. I have been eating reheated rice and potatoes for years so I’m glad it has been a benefit on my gut microbes!

As I stated earlier, the relationship between our health and our human microbiome is at an infant stage, but microbiologists are finding correlations between human microbiota and human health on almost a daily basis. It is hard to piece out correlation with causation. I think this quote by Chris Kesser states it perfectly.

“The genes that we inherit from our parents of origin are set, and certainly there are environmental triggers and epigenetics to consider, but the genes that we have in our microbiota are somewhat mutable. We don’t really know how much yet, of course, but as a case in point, what they found is that the bacteria that ferment the fiber and produce butyrate, which causes epigenetic changes that regulate the expression of genes that are responsible for the differentiation of T cells. And so, it’s the gut microbiota effecting epigenetic changes in gene expression in our body, which have real and lasting effects on our health.”(10)

Besides enriching your gut with prebiotic material it would probably do you some benefit to walk around barefoot outside more often, get your hands dirty and while you’re at it grow some of your own produce, open up some windows and let in some fresh air, limit your intake of antibiotics, avoid chlorinated/fluorinated water, and bond with your dog more often. If you are interested in mapping out your own personal microbiome then you are in luck. The Human Food Project is looking for US citizens to participate and to compare the microbes in your gut to those in the guts of thousands of other people in the US and around the world. for more info.
















Tony Cotroneo