[dropcap] Y [/dropcap] your gut is the tropical rainforest of your body, at least in terms of bacterial diversity.


Strange as it may seem, there are actually supposed to be certain sorts of beasties in your bowel. Intestinal bacteria of all sorts make their home in the colon, helping to break down wastes and contributing to the fermentation of undigested foodstuffs. They are not a problem so long as they stay in the colon and so long as one sort doesn’t outbreed another sort and create an imbalance causing Gut Dysbiosis.


A new study, detailed online Nov. 18 in the journal Public Library of Science-Biology, found that the bacterial community in the human bowel is 10 times more diverse than previously thought.


In sheer numbers, the mammalian colon harbors one of the densest microbial communities found on Earth. For every human cell in your body, there are roughly 10 single-celled microbes, most of which live in your digestive tract.


Previous estimates of the number of distinct kinds of microbes in the human colon ranged upwards of 500. These older estimates were made by growing the bacteria that dwelled in the lower gut in a Petri dish, but this method often left rarer species out of the count, only capturing their more common brethren.


David Relman of the Stanford University School of Medicine and his colleagues used a technique known as pyrosequencing to get a more complete count of the different varieties of bacteria colonizing the human colon (see list of some).


Pyrosequencing has been used before to assess the richness of bacterial ecosystems in marine environments and soil, Relman said. “But this was one of the first times it has been employed to look inward at the ecosystems within our own bodies,” he added.


Pyrosequencing generates extremely large numbers of small DNA “tags” copied from the genes of organisms being examined. Species can be sorted out from each other by looking at variations in DNA sequences that code for a molecule universal among all living cells.


“The new gene-sequencing technology lets us check far more ‘bacterial ID cards’ than the older methods did,” said Les Dethlefsen, a postdoctoral researcher in the Relman laboratory and the primary author of the study.

The new study found that the bacteria community of the colon was even more diverse than ever imagined, turning up at least 5,600 separate species or strains. The work was funded by the Doris Duke Charitable Trust, National Institutes of Health and National Science Foundation.


While intestinal microbes by and large mind their own business, feeding off the food we send to our stomachs, they also perform critical functions, such as fine-tuning our immune systems and producing nutrients such as vitamin K. And just by occupying intestinal real estate and eating up our waste, they prevent pathogens from gaining a foothold.


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Taking antibiotics can reduce the number and diversity of the resident bacterial population. Many scientists worry about the large-scale effects of over-prescribing antibiotics, particularly the potential to create more antibiotic-resistant strains of harmful bacteria. Relman and Dethlefsen hope that pyrosequencing will help better suss out the effects of antibiotics on beneficial bacteria and their human hosts. (extract from Live Science 2008)


Some thoughts on the use of enemas.
One of the natural alternative medicine treatments that some people like to use is an enema (also known as a clyster, high colonic, colonics, colonic irrigation, colon hydrotherapy, and colon cleansing). Judging from many testimonials people do feel better for a day or two after doing one. Especially those people suffering from chronic constipation. However, there is no scientific evidence that enemas help any medical condition other than a bowel obstruction and temporary relief from constipation. In fact there is quite a bit of research on the harms and risks associated with enemas, especially from frequent use.


Electrolyte imbalances from frequent use of colon cleansing is common, especially from coffee enemas. This can lead to dehydration, heart attack and even death.


More commonly people can develop a dependency to enemas and are unable to defecate normally without them. This can lead to complications and withdrawal symptoms when one stops using enemas to defecate.


Even worse many people self-medicate with enemas for problems that have little, or nothing, to do with the colon, such as: problems in the stomach from an ulcer or an h.pylori infection, Small Intestinal Bacterial Overgrowth (SIBO), or a small intestinal candida overgrowth will not be helped by an enema. The ileocecal valve, located between the small intestine and the colon, will block enema fluids from reaching the small intestine (which is a very good thing, otherwise you will simply be washing fecal matter and colonic bacteria in the small intestine).


The use of probiotics in an enema sounds useful on the surface. After all the goal should be to restore the intestinal microbiota to a healthy state and what could be better than a direct application of probiotics. However, this is a misguided approach.


“Humans evolved in the presence of numerous microbial communities that preceded the appearance of mammals on planet Earth. The role of these microbial communities in our evolution is a matter of considerable interest. Indeed, comparative studies with germfree and conventional animals have established that the intestinal microflora is essential for the development and function of the mucosal immune system during early life, a process that is now known to be important to overall immunity in adults. An absence of intestinal bacteria is associated with reductions in mucosal cell turnover, vascularity, muscle wall thickness, motility, baseline cytokine production, and digestive enzyme activity and with defective cell-mediated immunity (83).


Furthermore, the intestinal microflora makes important metabolic contributions to vitamin K, folate, and short-chain fatty acids, such as butyrate, a major energy source for enterocytes, and also mediates the breakdown of dietary carcinogens… Resident bacteria serve a central line of resistance to colonization by exogenous microbes and thus assist in preventing the potential invasion of the intestinal mucosa by an incoming pathogen.” — From the journal American Society for Microbiology


Here is a list of the most common bacteria normally found in the colon, see how many of these are listed on your bottle of probiotics before you decide to use them in an enema. The reason for taking probiotics orally is to create an environment for your normal microbiota to flourish, they can not directly replace your native flora. This is done in large part by the lactic acid (and other compounds) these transient strains produce as a by product.


Washing out your native bacteria and replacing it with relatively very small amounts of lactic acid bacteria is not helpful. You would be far better off consuming a serving or two of sauerkraut each day (one 3 ounce serving has more bacteria than your whole bottle of probiotic pills), it would also benefit your small intestine. (extract from John Herron)


Another area undervalued, is feeding the existing bacteria with Pre-biotics is as important as re-seeding. There are strains of bacteria within us which are simply not available in any capsule, they have been passed on from our mothers at birth and from soils and other methods we know little about yet, but can be wiped out with a long course of antibiotics, our loss of these bacteria is why people can feel completely messed up and out-of-sorts after a serious course of them.


What Are Prebiotics?
Prebiotics are quite simply, indigestible food ingredients that stimulate the growth and maintenance of beneficial gut microbiota. Or ‘indigestible by humans’ is more accurate, because they are being digested – just not by our host digestive system (about 90% of prebiotic fiber makes it through the small intestine intact). Instead, it’s those oft-thankless, microbial workhorses of our colons doing all the work while we reap the benefits. They are getting free meals, so don’t feel too bad about putting them to work. Note: Prebiotics should be avoided if healing the gut of SIBO and during the first 2 phases of The Heal Ur Gut PLAN.


So you could say that prebiotics are food for your flora, those living organisms that contribute to our health and well being. For our intents and purposes, prebiotics are classified as soluble fiber. Conversely, insoluble fiber is the stuff that the human digestive system – neither host cells nor gut flora – cannot process nor digest, instead acting as a lubricant stimulant for our bowels (literally tearing our insides up, prompting the release of natural lubricant to speed up processing and limit damage). When most people discuss the so-called benefits of dietary fiber, they’re talking about insoluble fiber’s effect on stool passage and volume.


It speeds up the process and makes for bigger toilet paper bills. But we’re not interested in mere bulking agents here. We’re interested in soluble fiber, in the type of fiber that our gut flora can actually consume and ferment. That would be inulin and oligofructose, along with fructooligosaccharides (FOS), galactooligosaccharides (GOS), and other oligosaccharides. Pectin, too, appears to have some prebiotic potential, but inulin and oligofructose are the big ones. Of course, all of these can be obtained by adhering to the Primal Blueprint Food Pyramid and eating a few servings of vegetables and fruits each day.


Researchers distinguish between long chain, short chain, and full spectrum prebiotics. 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. A full spectrum prebiotic supplement would be something like oligofructose-enriched inulin (OEI), which contains all possible saccharide links.


Historical Precedent
Prebiotic foods were certainly consumed by our ancestors, when and where they were available. The strongest evidence consists of cave deposits in North America in which remains of inulin-and-oligofructose-rich agave, sotol, wild onion, and camas bulbs have been found, along with massive cooking stones and vast (around twelve feet in diameter) ovens. Since similar cooking pits have been found the world over, from Australia to Europe, with some dating as far back as 30,000 years ago, it seems likely that these disparate sites were also used to roast the occasional fibrous tuber. None come with hard evidence of fibrous root or tuber remains, but that’s to be expected. Vegetable matter doesn’t last that long. We do know that wild roots, tubers, and other fibrous foods are available almost everywhere and that they are eaten where available by local populations.


Take this account (PDF) of the Hadza of Central Tanzania, where the “tubers are continuously available throughout the year” and “all of their tubers have high fiber content.” Or there’s the Maori, who used nearly every part of the cabbage tree, prized for its inulin content (which partially converts into fructose when steamed) and touted as a natural cure for colic, diarrhea, and other gastrointestinal disorders (maybe they were on to something?). If these types of fibrous, wild foods were widely eaten – and it seems likely that they were – early humans got a fair amount of prebiotic fiber in their diets.


One of the most compelling arguments for the importance of prebiotics in the human diet is the presence of galactooligosaccharides in human breast milk. Even the most ardent detractor of the viability of Paleolithic nutrition couldn’t deny that the macronutrients and micronutrients present in the only food specifically and expressly ‘designed’ for human consumption – breast milk – are necessarily suitable for human consumption (unless there’s some creepy, nutty vegan extremist offshoot claiming breast milk promotes the suffering/subjugation of women and the consumption of too much dangerous saturated fat that I don’t know about). Breast milk contains both probiotics (bifidobacterium, mostly) and prebiotics for the bacteria to feed on. Since it’s in breast milk, there is a precedent for prebiotics in the human diet by design.


What About the Health Benefits?

It’s all well and good to establish that prebiotic fiber was available to and even regularly consumed by many early human populations, but to build a case for inclusion in our modern diet requires some more recent evidence.


Dietary inulin and oligofructose increase fecal bifidobacteria.


Dietary inulin and oligofructose increase magnesium and calcium absorption. Most interestingly was the fact that calcium uptake apparently increases with inulin intake only when calcium intake is low or calcium requirement is high, suggesting a modulating (rather than blind) effect.

Prebiotics (inulin, oligofructose, and xylooligosaccharides) exhibited inhibitory effects on precancerous colon lesions in rats. Xylooligosaccharides increased gastrointestinal flora more than inulin and oligofructose, indicating possibly greater effectiveness.


An eight week regimen of 4g daily xylooligosaccharides Effects of Xylooligosaccharides in Type 2 Diabetes Mellitus reduced fasting glucose, HbA1c, oxLDL, LDL, and apolipoprotein B levels in Type 2 diabetes patients.


Prebiotics increase the production of short chain fatty acids in the human colon, including the supremely beneficial butyric acid, given a great summary by Stephan .


Galactooligosaccharides improved symptoms in patients with Irritable Bowel Syndrome.


Prebiotics combined with probiotics (called synbiotics) was more effective at gut modulation than either alone.


Matt Metzgar guesses that the supposed health benefits of whole grains stem from their prebiotic content, and that it was the widespread consumption of refined flour free of soluble fiber that made an already poor grain-based diet even more damaging. Sure, you could eat whole grains and get a bit of prebiotic fiber (along with loads of insoluble fiber, lectins, gluten, phytic acid and starch), but why go through the trouble when you could get even more from some crisp jicama sticks, Jerusalem artichoke, garlic, onion, or leeks with less effort, less roughage, and fewer antinutrients? To get the recommended six grams of inulin from chicory root, you’d have to eat a third of an ounce; to get the same six grams from whole wheat flour, you’d have to consume a quarter of a pound!


How Much Should We Be Consuming?
Jeff Leach, of PaleoBiotics Lab, recommends upwards of 135 g per day of prebiotic fiber, based on research into archaeological evidence from the Northern Mexican desert. That seems really extreme to me. I guess extreme conditions (“semi-arid region” with “limited rainfall and poor soil conditions”) necessitate extreme diets (“plant-based diet”). Those northern Chihuahans weren’t getting much dietary fat, so they probably had to rely on their gut flora to convert the prebiotic fiber into short chain fatty acids. That’s how the gorillas do it: they end up with a high-fat, moderate-protein, low-carb diet simply by consuming and fermenting an incredible amount of indigestible fibrous plant matter. We moderns have access to real animal fat and protein, so I doubt we need anywhere near 135 g of inulin and oligofructose.


Prebiotics are important, all the research on gut flora and probiotics points to prebiotic fiber (as opposed to insoluble fiber, the stuff seniors pop like candy, bran muffins, etc.) is actually quite important. Gut health is much more than just the small intestine. It’s almost as if there’s an entirely different digestive system playing out in the colon. The human colon may not be as robust and expansive as the gorilla colon, but it has the potential to do some damn fine work all the same – provided it gets the prebiotic fuel it needs. I suggest you provide that fuel by eating several servings of Primal prebiotic-rich foods each week, if only as a short experiment. Give it a couple weeks, at least until the sometimes explosive (but totally normal and expected) gaseous reactions subside, and monitor your digestive health.


What Foods Contain Prebiotics?
Let’s take a look at some more examples. 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
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


Inulin/oligofructose content (per 100g raw)


Chicory root – 41.6 g/22.9 g
Jerusalem artichoke – 18 g/13.5 g
Dandelion greens – 13.5 g/10.8 g
Garlic – 12.5 g/5 g
Leek – 6.5 g/5.2 g
Asparagus – 2.5 g/2.5 g
Banana – 0.5 g/0.5 g


Inulin content is altered by cooking, but not a lot; some of it is even converted into fructose (that’s how agave nectar is made, in fact). As Jeff Leach shows, traditional-style oven roasted chicory root (356 degrees F) lost about 10-20% of its inulin content, while cooked/fried onions lost only 10%. It’s safe to assume that cooking will preserve most of the prebiotic fiber in other foods too.


As for getting all the other prebiotics, researchers are beginning to explore through whole foods and it isn’t yet clear how available, say, xylooligosaccharides are in the context of a normal Primal eating plan. From we can see, most of the newer, more obscure prebiotic supplements are obtained by processing oats or corn or some other cheap, readily available food source. They undoubtedly occur in other veggies, too, but it probably doesn’t make financial sense to reduce several dozen tons of broccoli or asparagus when you could just as easily process a bunch of cheap grains such as with rice bran.


Supplementation seems pretty safe all around, especially in the context of a probiotic-rich diet. On the other hand, sticking with the Primal Blueprint Food Pyramid and eating a variety of fresh vegetables (leafy greens like kale, chard, and spinach, as well as broccoli, cauliflower, and any other vegetable that contains soluble fiber) will get you plenty of soluble, prebiotic fiber in all its forms and is definitely safe. (extract from Mark Sisson)


If you would like to understand more about Gut health or suspect you may benefit from some focussed attention on your concerns, download our free Heal Ur Gut (HUG) Booklet below.


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