Gut Dysbiosis: Starving our Microbial Self

Gut Dysbiosis: Starving our Microbial Self
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Inadequate consumption of prebiotics—the fiber and resistant starch concentrated in unprocessed plant foods—can cause a disease-promoting imbalance in our gut microbiome.

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For many years, it was believed that the main function of the large intestine was just to absorb water, and dispose of waste. But nowadays, it is clear that the complex microbial ecosystem in our intestines should be considered as a separate organ within the body. And that organ runs on MAC, Microbiota-Accessible Carbohydrates. In other words, primarily fiber.

One reason we can get an increase of nearly two grams of stool for every one gram of fiber is that the fiber fermentation process in our colon promotes bacterial growth. The bulk of our stool by weight is pure bacteria, trillions and trillions of bacteria, and that was on a wimpy, fiber-deficient British diet. People who take fiber supplements know this—a few spoonfuls of fiber can lead to a massive bowel movement, because fiber is what our good gut bacteria thrive on. When we eat a whole plant food like fruit, we’re telling our gut flora to be fruitful, and multiply.

And from fiber, our gut flora produce short-chain fatty acids, which are an important energy source for the cells lining our colon. So, we feed our flora with fiber, and then they turn around and feed us right back. These short-chain fatty acids also function to suppress inflammation and cancer.

That’s why eating fiber may be so good for us. But when we don’t eat enough whole plant foods, we are, in effect, starving our microbial selves. On traditional plant-based diets, like Dr. Burkitt described—lots of fiber, lots of short-chain fatty acids, and lots of protection from Western diseases like colon cancer. Whereas on a standard American diet, where we’re eating highly processed food, there’s nothing left over for our gut flora. Not only may this mean loss of beneficial microbial metabolites, but also a loss in beneficial microbes themselves.

The biggest issue presented by a Western diet is that not leaving anything for our bacteria to eat results in dysbiosis, an imbalance where bad bacteria can take over, and increase our susceptibility to inflammatory diseases, or colon cancer, or metabolic syndrome, or type 2 diabetes, or cardiovascular disease.

It’s like when astronauts return from space flights, having lost most of their good bacteria because they had no access to real food. Well, too many of us are leading an “astronaut-type lifestyle,” not eating fresh fruits and vegetables. For example, the astronauts lost nearly 100% of their Lactobacillus plantarum, which is one of the good guys. But most Americans don’t have any to begin with—though those that eat more plant-based are doing better.

Use it or lose it. If you feed people resistant starch, a type of fiber found in beans, within days, the bacteria that eat resistant starch shoot up, and then die back off when you stop it. Eating just a half can of chickpeas every day may modulate the intestinal microbial composition to promote intestinal health, by increasing potentially good bacteria, and decreasing pathogenic and putrefactive bacteria. Unfortunately, most Americans don’t eat beans every day, or whole grains, or enough fruits and vegetables; so, the gut flora, the gut microbiota of a seemingly healthy person, may not be equivalent to a healthy gut flora. It’s possible that the Western microbiota are actually dysbiotic in the first place, just because we’re eating such fiber-deficient diets compared to populations that may eat five times more fiber, and end up with like 50 times less colon cancer.

To see any graphs, charts, graphics, images, and quotes to which Dr. Greger may be referring, watch the above video. This is just an approximation of the audio contributed by Katie Schloer.

Please consider volunteering to help out on the site.

Image thanks to Hey Paul Studios via Flickr

For many years, it was believed that the main function of the large intestine was just to absorb water, and dispose of waste. But nowadays, it is clear that the complex microbial ecosystem in our intestines should be considered as a separate organ within the body. And that organ runs on MAC, Microbiota-Accessible Carbohydrates. In other words, primarily fiber.

One reason we can get an increase of nearly two grams of stool for every one gram of fiber is that the fiber fermentation process in our colon promotes bacterial growth. The bulk of our stool by weight is pure bacteria, trillions and trillions of bacteria, and that was on a wimpy, fiber-deficient British diet. People who take fiber supplements know this—a few spoonfuls of fiber can lead to a massive bowel movement, because fiber is what our good gut bacteria thrive on. When we eat a whole plant food like fruit, we’re telling our gut flora to be fruitful, and multiply.

And from fiber, our gut flora produce short-chain fatty acids, which are an important energy source for the cells lining our colon. So, we feed our flora with fiber, and then they turn around and feed us right back. These short-chain fatty acids also function to suppress inflammation and cancer.

That’s why eating fiber may be so good for us. But when we don’t eat enough whole plant foods, we are, in effect, starving our microbial selves. On traditional plant-based diets, like Dr. Burkitt described—lots of fiber, lots of short-chain fatty acids, and lots of protection from Western diseases like colon cancer. Whereas on a standard American diet, where we’re eating highly processed food, there’s nothing left over for our gut flora. Not only may this mean loss of beneficial microbial metabolites, but also a loss in beneficial microbes themselves.

The biggest issue presented by a Western diet is that not leaving anything for our bacteria to eat results in dysbiosis, an imbalance where bad bacteria can take over, and increase our susceptibility to inflammatory diseases, or colon cancer, or metabolic syndrome, or type 2 diabetes, or cardiovascular disease.

It’s like when astronauts return from space flights, having lost most of their good bacteria because they had no access to real food. Well, too many of us are leading an “astronaut-type lifestyle,” not eating fresh fruits and vegetables. For example, the astronauts lost nearly 100% of their Lactobacillus plantarum, which is one of the good guys. But most Americans don’t have any to begin with—though those that eat more plant-based are doing better.

Use it or lose it. If you feed people resistant starch, a type of fiber found in beans, within days, the bacteria that eat resistant starch shoot up, and then die back off when you stop it. Eating just a half can of chickpeas every day may modulate the intestinal microbial composition to promote intestinal health, by increasing potentially good bacteria, and decreasing pathogenic and putrefactive bacteria. Unfortunately, most Americans don’t eat beans every day, or whole grains, or enough fruits and vegetables; so, the gut flora, the gut microbiota of a seemingly healthy person, may not be equivalent to a healthy gut flora. It’s possible that the Western microbiota are actually dysbiotic in the first place, just because we’re eating such fiber-deficient diets compared to populations that may eat five times more fiber, and end up with like 50 times less colon cancer.

To see any graphs, charts, graphics, images, and quotes to which Dr. Greger may be referring, watch the above video. This is just an approximation of the audio contributed by Katie Schloer.

Please consider volunteering to help out on the site.

Image thanks to Hey Paul Studios via Flickr

97 responses to “Gut Dysbiosis: Starving our Microbial Self

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  1. One way to seed the gut with the missing L. plantarum (and many other beneficial bacteria presumably in short supply among SAD eaters) is by eating fermented foods, including sauerkraut, kimchi & kombucha. If you make your own, as I do, you can regulate quality, taste, and sodium content–and perhaps forestall some of the problems that Dr G has mentioned in previous videos in which he’s voiced strong (and to my mind overstated) reservations about kimchi & kombucha. Taken regularly and in moderation, I believe fermented foods can play a crucial role in optimizing immunity and prevention dysbiosis. And others agree: http://www.ncbi.nlm.nih.gov/pubmed/25343046




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      1. Koreans have the highest sodium consumption of any nation, 5,280 mg/day, 19% of which comes from kimchi, and global epidemiology implicates sodium in gastric cancer risk.

        Fermented food advocates don’t have much support in the literature. Bacterial RNA from fermented foods can be detected in feces, but the food fermenters are different strains than those specialized for the colon environment. There’s also the problem common to probiotics: they change fecal bacterial composition while being taken, but there’s little evidence that they effectively compete with established populations. The colon microbiota revert to that seen before probiotics, defined primarily by one’s personal microbiota and habitual diet, when probiotics are discontinued. The greatest effect of fermented foods may be antimicrobial, as bacteria and yeast compete in a state of constant chemical warfare.




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        1. I question your strictly adversarial/competitive characterization of the microbial environment. There are many examples of symbiosis in nature, and we see so many references to “beneficial” probiotic strains in the literature. Can you cite some scholarly support for the idea that fermented foods are antimicrobial?

          The fact that the microbiota reverts to the pre-treatment state without replenishment by probiotic strains is not an argument for not eating probiotic foods. As the video points out, not eating fiber also returns the gut to a depleted state.

          But I agree that the sodium in kimchi is extremely worrisome. I was shocked when the recipe I planned to try called for soaking the cabbage in a brine containing literally pounds of salt, even though most of this would eventually be washed away.




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          1. Find another recipe. I never use more than 1/4 cup salt if I’m brining a head of cabbage–and most of that gets rinsed away. Kimchi used to be heavily salted to preserve it through the winter, and I suppose many Koreans still prefer it that way, but it’s possible to make much healthier versions with very little sodium.




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            1. I agree KnowBeans, . . find another recipe. I made my own kimchee as well. For an entire huge head or two smaller heads of chinese cabbage I use 1, sometimes a little more, or 2 Tbs of kosher salt. I sprinkle it on the cleaned, cut cabbage and let it ferment overnight. Rinse the next day and finish the recipe. So, I agree, kimchee can be made with much less salt. And gosh, I can’t stop eating it!!




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              1. I did not know that you could only leave the salt on overnight. Doesn’t it go mouldy when you rinse the salt off? Post your recipe for low salt Kimchi please :) ?




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          2. They’re not singing Kumbaya in the fermentation vats. Fungal antibiotics are well known, but bacterial fermenters have also been producing bacteriocins and nisins, often targeting closely related strains, since early Life’s history. As these antimicrobial compounds are potential alternatives to synthetic preservatives, this list of work in the field is very abbreviated.

            kimchi: 1, 2, 3, 4
            kombucha: 5, 6
            sauerkraut: 7
            tempeh: 8

            Yes, symbiosis is important in nature. But it occurs when organisms requires synthetic pathways or a habitat that it can’t provide for itself, not between organisms competing for the same resource.




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              1. I know anecdotal evidence is inconsequential….unless you are the one who experiences it. Just like a WFPB diet, I gave fermented foods a month trial to see what might happen, and I was not disappointed with both physical and mental effects. Eating fermented foods is to me in the same class as fiber… keep eating it! I also make my own low salt ferments.




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                1. Just a quick question, have you ever tried salt free sauerkraut ?
                  What are your fav vegetables?
                  Have you ever tried using a canning jar ,filling it up and just closing the lid real tight?
                  I was worried the jar was going to explode…lol but it didn’t. Very different kraut .We just started eating some a week old. The unpasteurized kimchee in the store is 6.99 per 250ml.
                  cheers!




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                  1. I haven’t tried salt free, just low salt, and use lots of herbs to compensate.
                    I don’t know if I have a favorite actually, whatever is on sale or growing in the garden I guess! One of my favorite ferments is salsa using our foraged local nopale cactus instead of tomatillos, and lotsa cilantro.
                    Some people use special jars for fermenting, but I just use canning jars or even recycled glass jars, I just make sure to burp and shake them at least daily once fermentation begins, to release the gasses and mix up the contents. Works for me!




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                    1. salsa ! why didn’t I think of that.
                      Somebody told me once to jusr seal the jar and not let the gas escape that there would be more bacteria in it, just curious.
                      in the garden this week the pumpkin vines grew 42 inches …stand back!




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                    2. Well, lacto fermentation is an anaerobic process, but since it takes place in the liquid and solids, people often just used covered crocks. (not sealed, just lidded to keep debris and buggies out). Since we’ve been doing this for ages, I don’t really think a lot of the rigid do’s and don’ts are necessary, it just works…it’s use was preservation in far less than sanitary conditions, so pretty straightforward! Once fermentation gets going, the gasses tend to push the solids above the liquid, so for me shaking and burping both keep the kahm yeast (or mold, which I’ve never personally seen) from getting established on the surface of the solids, mixes any layering, and allows the gas to vent so the jars don’t blow (hasn’t happened YET in 5+ years of almost daily ferments, even using recycled pickle jars and the like)…plus offers an opportunity to taste and see where things are!
                      Some things (like salsa) I like best after only a few days of active fermenting, (once you see bubbles/bottom liquid) and others a couple weeks or longer. (I live in a warm climate so your milage may vary, and taste is the best guide! Some people fill a zip-lock bag with water, squeeze out the air, and lay that on top of their ferments, which works too, but I’m not crazy about the plastic). They also recommend a boiled rock or broken crock to lay on top to keep solids submerged, and I sometimes do this with a gallon container because it’s hard to shake, but generally the shake and burp works great. There is no one way to have success, it’s whatever works for you, good ole trial and error!
                      Ah some busy vines you have! I have all kinds intermingling, I’m not going to know what they are until they fruit! Spaghetti squash, seminole pumpkins, watermelon, butternut, saved seeds from some yummy squash, and a ton of sweet ‘taters in all different hues, which grow like mad here! A real mess of vines! I love gardening, every day is a new adventure! I think everyone should plant and grow something, even if it’s just in a pot or a jar of sprouts!




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                    3. Good comment. I agree. Humans have been fermenting vegetables and grains for a very long time. There a lots of different ways to do so. I also tried it to find out if it would help solve my chronic yeast problems and leaky gut syndrome. Commercial probiotics work as long as you take them but the $$$ involved can be considerable. Fermented foods seem to do an even better job over all. Not as easy as popping a pill but so what. I have an antique crock–about 4 gallons and use it to ferment cabbage, make pickles, and such. Does a great job.
                      For a while I make my kraut in canning jars but it reduces so much I end up with multiple jars, half full. Now I make it in the crock and transfer to sterilized canning jars.
                      I’m busy on my mini farm and the crock seems to be the easiest for large batches. I have a porcelain saucer weighted down by a jar full of brine to keep the contents under the brine. And a lid to keep out the dust, wild yeasts (mostly) and such. The brine is about 4 teaspoons for 2 large heads of cabbage. Commercial cabbage is often too dry to create enough of its own brine so I add some 2% brine i needed. Home-grown cabbage produces tons of its own brine. No additions needed.




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                    4. Great that you have a nice crock! I wanted one but they were so pricey I ended up repurposing a cast off 3 gallon glass “bottle” with a maybe 4 inch wide neck, which was meant to be decorative, but I put it to work. Since it had no accommodation for any kind of lid or seal, and a short neck but a fat belly, standard options didn’t really work, so I ended up stretching a rubber glove over and into the opening! lol It looks hilarious once fermentation gets going, like some mutant blue cow, but it not only keeps the baddies out, but allows the gasses to expand without sacrificing the integrity of the bottle. Not as practical as a crock, but sure an interesting centerpiece!
                      I totally agree about ferments being a better alternative to pills, for several reasons. Expense for me is the big one, but the fact is that in having a variety of people doing the active microbes test across brands by adding it to milk, the majority of them showed little to no activity, so are not only expensive but pointless. I can’t prove it but I also think consuming the food with the microbes must help shelter them from digestive processes and shuttle them to their destination because of the various obvious and dramatic benefits I and others have happily noted. Plus the prebiotics are already available for the probiotics. Fermenting is cheap, easy, safe, practical, tasty, effective, and on and on! Options are endless and I get to control and eat my experiments like the mad scientist I am! Another interesting thing is I used to dislike tart/sour flavors before I started fermenting, but now I actually crave them! I don’t think it would be worth the effort, however minimal, if the positive feedback wasn’t dramatic! Adding fermented foods to a good diet has taken it to the next level for me because I was already sick, but the many benefits were blatantly obvious. I love Dr G but I think ferments need a lot more research beyond a few extreme and complicated examples. The biggest surprise for me was the boost in mental health! Who would have thought one could find joy in soured food filled with microbes that most of us were taught to fear and obliterate!
                      In fact, one of my favorite cultured food sites covered that last topic recently… https://www.culturedfoodlife.com/can-cultured-foods-hurt-me/
                      (If you do visit, check out “My Story” from her website on the upper right of the page, amazing.)




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                    5. I totally agree with everything you said. Plus, the culturedfoodie.com site is awesome. Thanks! As for my crock, I lucked out and bought it an antiques and collectible store in Pomona, After searching the web, ebay, and more, I found this one by accident. It was obvious that the store owner had no clue about how much they were selling for elsewhere. I treasure it and make sure I treat it with kid gloves.

                      We make our Kombucha, however, in straight-sided 2-gallon glass jars that we bought at–of all places–Walmart. They have lids and work great for the Kombucha.




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                    6. Funny, I found a sun tea gallon jar with a built in spigot for four bucks at Walmart, that ended up getting utilized for my continuous brew jasmine tea kombucha! I tap that daily and when it gets low just add more tea. My other gallon jar is a lesser grade of plain green tea for second fermenting for more fizz and flavors. I’m wondering if I’m the only one who actually likes it better at room temp than cold most of the time? I grow roselle (hibiscus tea) and use that a lot to second ferment, but did you know you can also use hibiscus tea in place of regular tea to make an awesome kombucha? Love it!
                      Thanks for the link, going to check it out now.




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                    7. Did not know that about the hisbiscus. We are also growing rosell to make our on Jamaica drink. They aren’t big enough yet to yield much, though. I’ve never tried the continuous brew kombucha. We generally bottle ours and set aside for a while to let the fizzy develop. Our favorite flavoring is pomegranate juice. Before we moved to the country, we had two gigantic pomegranate trees that gave is gallons of juice. I like kombucha both cold and at room temp.




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              2. Bacteriocins and nisins are proteins, so little would survive the stomach. Antimicrobial fermentation waste products like vinegar and alcohol are rapidly absorbed. I haven’t encountered research on whether these microbes might also produce small-molecule antibiotics like those of medicine that might reach the colon. So I suspect fermented food consumers might have better oral health.

                I’ve repeatedly encountered unwarranted assumptions about fermented foods and the gut microbiota in discussions elsewhere, much of which centering around probiotic misconceptions. For a decade quantitative PCR has revealed that more easily cultured fermenters like those in probiotics and fermented foods (Lactobaccilus) are relatively minor constituents of the gut population, but due to the streetlight effect, those species dominated earlier literature. More recent research has focused on better markers of microbiota health (A. muciniphila, F. prausnitzii, Roseburia sp.) which are too difficult to culture for commercial probiotics and aren’t used in food fermentation. Species like these are the reason the microbially accessible fraction of dietary fiber is more important that any amount of active culture yogurt.




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                1. I really appreciate all the clarification, Darryl. Probiotics have probably been hyped far beyond their proven worth. Diet (i.e., WFPB vs SAD) is undoubtedly the most important factor in determining the health and make up of our microbiome. As Dr. G pointed out in “How to Change Your Enterotype” (http://nutritionfacts.org/video/how-to-change-your-enterotype/), the gut of a lifelong vegetarian will look like that of a meat-eater within a day or so (and vice versa) after switching diets.




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          3. Yes, all good points, thanks.

            However, the link makes the point that salt is not the only risk factor with kimchi etc. The role of nitrate/nitrits is also relevant.




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            1. I’ll find the study sometime soon, but a Korean study showed that besides the heavy traditional salting, it was the addition of animal products to the diet that caused the issues for kimchi in relation to nitrate/nitrites.




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      2. As is so often the case, the dose makes the poison. I eat a few tablespoons of kimchi a week, whereas many Koreans eat that much for breakfast–and even more at lunch & dinner. Plus, “kimchi” is a generic term that may (or may not) include various kinds of cabbage, radish, & other vegetables, plus various mix-ins. I make a lightly salted vegan version that leaves out the fish sauce, fermented shrimp, and other ingredients commonly used in Korea. It may be very different from the ones featured in the study you cite–and no, I’m not worried about its giving me gastric cancer. The individual ingredients–Napa cabbage, daikon, carrot, garlic, ginger, wakame & Korean red pepper, plus a very little sea salt–are so healthy alone that it’s difficult to see how they might turn poisonous after undergoing lactofermentation.




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        1. See my comment to Tom above. The traditional kimchi is literally cured and steeped in salt and fish sauce, making it at home eliminates the issues and like you said, how can the other ingredients that are so healthy become otherwise after beneficial low salt fermentation? I just know how beneficial it’s been for so many health issues for me, so I have to question these generalizations that would prevent others from healing.




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      3. Germans eat sauerkraut with pork products, I wonder if Koreans do too? I see they have the seventh highest pork consumption in the world.




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      1. Yeah because of a few cases of acidosis? I know kombucha can get pretty vinegary when it ferments for a long time, but still don’t see how it can be any worse than vinegar, (which he recommends), unless you are chugging it like water! I love the stuff and always have some jasmine kombucha going.




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        1. I agree that Kombucha needs to not be chugged like water and that it IS a healthful food if made right. It should not be vinegary and needs skill to ferment correctly. I make my own and it has proven to be something my body benefits from. We use organic Rooibos tea as a base instead of black tea. Maybe that makes a difference?




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    1. Animals feed large amounts of fermented feed, like 50 % of their diet , have much shorter life spans than animals not fed fermented feeds at least on the farm I used to work on. Thats pretty extreme amount of ferments in their diet though, also it wasn’t the salt that caused the shorter life span, because there was no salt in their ferments.
      Myself am trying a small amount of sauerkraut in my diet for better digestion and it seems to be working well.
      I have been on a McDougall type WFPB diet for about 8 months now, lost 30 lbs, blood pressure from 180/120 to 118/79 and even though my doctor said I wasn’t pre diabetic, I had diabetic type pain in both feet and ankles, burning pain , best describes it , is gone as well. cheers!




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  2. Starving our microbial self is a wonderful perspective article, but the author’s emphasis was on how inadequate the term “fiber” is, and the need for a more descriptive term.

    Dietary fiber is a problematic term commonly employed for lack of a better option. Current use of this term is complicated by multiple definitions associated with different official organizations. In addition, multiple laboratory tests may be used to determine ‘‘dietary fiber’’ content specified on nutritional labels, none of which provides an accurate measure of what the definitions specify. The most standard method of quantifying dietary fiber content neglects many types of carbohydrates that are destined for microbiota fermentation in the colon, like inulin, but includes noncarbohydrate entities like lignin. In addition, the term dietary fiber encompasses the carbohydrates that are fermentable by an individual’s microbiota plus those that remain unfermented and serve a bulking role…Much of the cellulose humans consume is not metabolized by gut microbes and does not qualify as a microbially accessable carbohydrate

    So if we’re looking for microbially accessable carbohydrates and not roughage, where are they?

    • fructoligosaccharides: all Allium vegetables (garlic, leeks, onion, shallot, scallion), particularly raw or lightly cooked, some Brassicaceae (broccoli, Brussels sprouts, cabbage), raddichio, snow peas, nectarine, longon, blueberry, asparagus, chili, beets, raspberry, okra, watermelon
    • inulin (a longer chain fructoligosaccharide): chicory, jerusalem artichoke
    • galactooligosaccharides: beans, some in onions, beets, broccoli, raddiccio, fennel bulb
    • arabinoxylans: wheat, barley, and rye bran, and grain products made with these
    • resistant starch: a high fraction in some raw starches (potato starch or green banana), moderate amounts in some unleavened flatbreads (maize tortillas), as well as starches that have undergone retrogradation (eg, cooked then slowly cooled potatoes and pasta)




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    1. Darryl, thank you for providing the link to the article, which is extremely interesting to read carefully. Also, thank you for listing what plant sources can provide the various types of “MACs”. I was fascinated by the idea presented in the article that a diverse population of gut microbes was important, in our gatherer-hunter ancestors, to be able to adapt to different foods being available at different times. The authors also raise the issue of whether we modern humans may have permanently lost some strains of beneficial gut bacteria; they end by speaking of the need to “re-wild” the Western microbiota.




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    2. Within the fiber research community, it is well recognized that there are three types of dietary fiber: (1) bulking, like ) cellulose and soy fiber (2) viscosous, like psyllium, beta-glucan from barley and oats and (3) fermentable like resistant starch and inulin. Dr. Dan Gallaher from the University of Minnesota first proposed these classifications in 2006 in “Present Knowledge in Nutrition” published by ILSI, 9th edition, chapter 8 “Dietary Fiber”. Unfortunately, I don’t think this chapter is available online. It has been proposed that we should replace the insoluble vs. soluble descriptions of fiber with “bulking, viscous and fermentable” as these more accurately describe the benefits of different types of dietary fibers.

      It is really important to distinguish between different types of dietary fibers and emphasize the value of fermentable fibers such as those described above. I hate articles that talk about the benefits of fermentable fibers and then recommend that people increase their overall fiber in their diet. At best, it is misleading and at worst, it is outright fraud. It is not true that all fibers have the benefits of fermentable fibers!

      It is really important to know that fermentable fibers are available as supplements. The clinical studies showing the benefits are not generally done with foods – they’re done with supplements! For instance, a huge study was published last year switching the diet of South Africans with African Americans living in the Pittsburgh area (http://dx.doi.org/10.1038/ncomms7342). They used Hi-maize resistant starch to boost the resistant starch content in the African American diet. I doubt they could get African Americans to actually eat the foods that South Africans eat every day. Supplements are the easiest way for people to boost their fermentable fiber intake if you know which ones to take!

      I am very excited about the health claim petition to the FDA that resistant starch helps to reduce the risk of type 2 diabetes. ALL of the clinical studies were done with supplements or foods with added resistant starch. If people want to reliably boost their microbiota diversity, supplementing with fermentable fibers is the best option. And yes, eat foods rich in fermentable fibers as well.




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    1. Waiterbyrd: The three short-chain fatty acids are acetic acid, propionic acid, and butyric acid. You can get acetic acid by including vinegar in the diet and the other two by eating foods rich in soluble fiber, the ones Julie has mentioned. (Butter has butyric acid but also has a lot of bad things.)




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    2. The short answer is fermentable fiber! Fibers, like cellulose, soy fiber, psyllium, hemicellulose and many other fibers containing cell walls, are not fermented or are minimally fermented and will not increase short-chain fatty acids.




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        1. Beans, peas and other legumes, under-ripe or green bananas, and intact whole grains (not processed whole grains) are great sources of resistant starch, while cooked and cooled starchy foods, i.e., potato salad, sushi rice, etc. have a little bit – perhaps a gram or so. See http://www.resistantstarch.us/posts/rs-in-foods/ for more information.

          Legumes, bananas and intact whole grains also have small quantities of inulin and FOS (i.e., bananas have 0.3% and wheat has 1 or 2%). Onions, garlic, jerusalem artichokes, leeks and chicory are probably the best sources of inulin and fructo-oligosaccharides. Lots of vegetables will have minor quantities, but I don’t have a handy source for how much. One reference reported that onions have between 1-7 % inulin”, chicory has 14-17% inulin, garlic has about 13-16% and leeks can have as high as 10% inulin if it is consumed within one month of harvesting and artichokes had 2.5%. Source “On the presence of inulin and oligofructose as natural ingredients in the Western Diet” by Dr. Jan Van Loo et al. Critical Reviews in Food Science and Nutrition 1995.

          In short, it can be hard to get higher levels of fermentable fibers from food sources alone.




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  3. My wife is a type 1 diabetic who has gastroparesis. Has anyone successfully treated this condition or heard of a way to lessen the symptoms? She is mostly wfpb.




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    1. Longstanding T1D can lead to this disorder. Make sure she has good blood sugar control. Look at all her medications, many have anticholinergic effects or opioid effects that slow gastric emptying. Even some diabetic medications can slow emptying via their effect on gastrointestinal hormones. It is hard to be on a WFPB diet, as Raw fruits and veggies can stay in the stomach for hours-causing increased nausea, occassional vomiting. Nature’s natural prokinetic (accelerates emptying) is ginger. This may help but I advise my patients with this disorder to get a good Vita-Mix or similar product in order to continue on a WFPB diet. This diet is better tolerated in a more liquid or cooked form. Good Luck.
      Dr. K




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  4. What about intermittent fasting? I have heard that it has a wide array of health benefits, but is it not just starving one’s microbes of fiber and other essential nutrients?




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    1. I do not thin that the period of dietary restriction on IF is long enough to eliminate your good microbes although I have not seen any literature on this.




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    2. Not at all. I have been doing a type of intermittent fasting for years by simply confining all of my food intake to a window between noon and 8 or 9 PM. Neither our cells nor our bacteria require a continuous food supply. Check out Dr. Greger’s excellent videos on hormesis.




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      1. I was doing exactly that for a while too but stopped when I followed up a few references eg (TRF = time restricted feeding)

        “Thus, far, relatively few RCTs of IER and TRF have been performed in human subjects, with the results of several studies of alternate-day and twice weekly energy restriction demonstrating weight loss and abdominal fat reduction and suggesting improvements in indicators of energy and lipid metabolism and inflammation (44⇓–46, 51, 61). On the other hand, a study of TRF in which healthy normal weight subjects consumed a balanced daily food intake within a 4-h or 12-h time period each day revealed no improvement (79, 80), which is similar to the lack of any short-term benefit of TRF in mice when the animals are fed a balanced diet (23). This finding suggests that the short-term benefits of TRF might depend on the diet and body composition.”
        http://www.pnas.org/content/111/47/16647.full

        “There were no significant effects of meal frequency on heart rate, body temperature, or most of the blood variables measured. However, when consuming 1 meal/d, subjects had a significant increase in hunger; a significant modification of body composition, including reductions in fat mass; significant increases in blood pressure and in total, LDL-, and HDL-cholesterol concentrations; and a significant decrease in concentrations of cortisol.”
        http://ajcn.nutrition.org/content/85/4/981.full

        The increases in BP and total and LDL cholesterol were concerning (to me at least). What is your take on this?




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    3. I would speculate that as the food source for gut bacteria is reduced that the populations of all species drastically fall in number, but when eating resumes the numbers rapidly swell back.

      This does suggest a potential strategy for accelerating a transition from gut populations high levels of the “bad” bacteria to one dominated by the “good” gut bacteria when abruptly transitioning from a high fat/high protein diet to a whole food diet high in fiber. A short fast between the last carnist meal and the first WPBF meal would shrink the number of all gut bacteria, but only the health promoting ones that survive off of fiber would return back to normal numbers.

      After all there a significant percentage of people who dive in head first and transition overnight. Taking a fasting day to allow your system to “cleans”, though I hate that word, might have some merit.




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    4. Dr. Mercola is an advocate of intermittent fasting. He is also against being a vegetarian and promotes organic meats, eggs, and dairy. Both Mercola and Dr. Gregor have multitudes of supporting study and facts to promote their mostly opposing views of how to be as healthy as possible They both seem to be healthy even though their ideologies are diametrically opposed. So maybe, like the sages of yore taught–moderation in all things. I am not a vegetarian although I was one for more than ten years. I am now about 90% vegetarian, a 99% whole foods, organic, and home grown advocate. If I eat a strip of bacon ever couple of weeks, I don’t think it’s going to throw me into dysbiosis.




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  5. In the video and others, Dr. Gregor stresses the benefit of “fresh fruits and vegetables”. But also talks about eating “half a can of chickpeas”. My question is: Are canned vegetables less healthy for you and your gut bacteria than fresh vegetables? I haven’t seen any videos or articles that address this. I grow most of my own vegetables but live in a cold climate and rely on canned vegetables for about 3-4 months of the year.




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      1. Thanks. Looks like canned beans are just as good for you as dried. I’d like to see a comparison using some vegetables other than beans though. Maybe we’ll get one in the future.




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    1. This was a big surprise for me. I just googled the question. Every website I looked at said that in general, canned (and frozen) vegetables were as or more nutritious than fresh. These aren’t NutritionFacts videos, but I’m satisfied and will continue to eat my home grown/ home canned veggies.
      http://www.webmd.com/food-recipes/20070316/canned-fruits-veggies-healthy-too?page=2
      http://well.blogs.nytimes.com/2013/05/27/really-the-claim-fresh-produce-has-more-nutrients-than-canned/?_r=1




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  6. When I began eating more fiber daily–legumes and a powder supplement, etc.–I suddenly began remembering my dreamsupon waking. There were anecdotal reports on Internet attributing dream recall to buytrate produced by well-fed microbiome, but apparently no studies yet?




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    1. Annetha: That’s such an interesting idea. I think it would be an awfully difficult thing to test, but it sure would be interesting to try!

      I hadn’t heard that idea before. Thanks for sharing.




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    2. My dream recall frequency and intensity is directly correlated to how long I’ve been sleeping. Maybe eating better gives you more restful/effective sleep?




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  7. What would happen if someone doesn’t have a colon? Would the small intestine begin acting microbially like the large intestine over time?




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  8. Dear doctor l have 2 girls with elkodis colidis what to recomendend for her one wich is 23 years old she is allergik for all medisen the other is 17 she take salofalk is posible to treadment please is very difecalt for me the problem is about 12cm




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    1. Elkodis Colidis- or ulcerative colitis in English, is thought of as an autoimmune disease. It might be helpful do an elimination diet to see if there are any foods that your daughters are allergic to. I had inflammatory bowel syndrome, which although is a bit different, it cleared up within a year of going vegan. I have also read that mushrooms, celery and parsley can help ulcerative colitis- but there are contradictory statements about this in the literature.




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    2. Maria: A couple of articles that might interest you and your children: Influence of dietary factors on the clinical course of ulcerative colitis: a prospective cohort study and The value of an elimination diet in the management of patients with ulcerative colitis.. The second study actually addressed an elimination diet. Though a small study, it suggests that different people’s response to UC is different with different foods. Hope this helps some.




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  9. I read on some “health” website that the probiotic species you find in probiotic supplements, like lactobacillus, are all aerobic bacteria and don’t help much because most mutralistic bacteria that we really need is anaerobic. I also read that the bacteria in probiotic supplements are like not “colonizer” strands or something and can’t actually reproduce and recolonize your gut (so you have to keep buying the supplement). Any truth to these claims?




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  10. Koreans have the one of the highest stomach cancers in the world do to consumption of sodium from eating kimchi .,, kimchi contains a lot of sodium .




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    1. Thanks for your comment!

      The difference lies in native Africans (high fibre) vs modern African (typically low-fibre). And in the video you mention, Dr Greger clearly states that despite African-Americans having a low fibre diet, they also appear to have a low meat & low saturated fat diet + their cholesterol is much lower, which helps them to preserve their health in terms of risk of colon cancer.

      Hope this answer helps!




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      1. Thank for your response!

        African Americans don’t have low colon cancer incidence, and they don’t have a low meat diet, as far as i know. perhaps you mean modern Africans rather than African Americans?

        So if i understood it correctly , there are actually 3 groups of Africans, which are, African Americans, native Africans, and modern Africans, is that right?

        Does modern Africans are recent immigrants of Africans to USA?or are they the people living in SSA today?




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    2. Native Africans eat a lot of resistant starch (now recognized as a type of dietary fiber, but this was a relatively recently development). Here is the link to a major clinical study that actually measured the fiber content of South Africans and then fed a high resistant starch and low fat diet to African Americans in Pittsburgh. http://dx.doi.org/10.1038/ncomms7342 The South Africans ate 28 grams/day of fiber PLUS 38 grams/day of resistant starch. the African Americans in Pittsburgh ate an average of 14 grams/day of total fiber (including resistant starch). When their diets were switched, the microbiome diversity was dramatically increased and inflammatory biomarkers were dramatically decreased in African Americans, while the opposite was true in South Africans.

      Here is another study that focuses on the topic. http://dx.doi.org/10.1111/j.1572-0241.2000.01848.x According to this study, the fiber intake of urban Blacks in south Africa decreased from 25-30 grams/day when they were eating a traditional diet, to 15-20 grams (not including resistant starch). However, starch and resistant starch content is very high.




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  11. Hello Dr. Greger,
    I’m a vegan, and have been for the past 4.5 months. A concerned meat-eater friend of mine sent me this article: http://mbe.oxfordjournals.org/content/early/2016/04/04/molbev.msw049 Kothapalli et al., 2016.

    It suggests that multi-generational vegans maintain higher arachidonic acid and that they must also have greater inflammatory potential and higher rates of chronic diseas related to inflammation.

    This seems counter to everything else I’ve ever read. It’s the only article on the matter I could find. It seems like a large leap, and also seems that they are not taking into consideration the fact that we have far less inflammation due to diet. I was really hoping you could do a video on this !

    Thank you!-Claire




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    1. This article has been misunderstood, perhaps deliberately, by militant anti-vegetarians and pro fat advocates.

      The study is about a particular genetic mutation in Indian populations. It is not relevant to all vegetarians. The actual article also describes this mutation as an advantage not a disadvantage. The speculation about inflammatory potential is just that : speculation. Presumably by people with an agenda to discredit vegetarian diets. The abstract quite clearly states:

      “This study is consistent with previous in vitro data suggesting that the insertion allele enhances n-6 LCPUFA synthesis and may confer an adaptive advantage in South Asians because of the traditional plant-based diet practice.”
      http://mbe.oxfordjournals.org/content/early/2016/04/04/molbev.msw049




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      1. “by militant anti-vegetarians and pro fat advocates” I got a chuckle from those descriptors. truly sad that anyone could qualify for such.




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    2. before.the.fall: Tom gave an excellent reply. I’ll be adding this reply to my list of good ones. Here is my standard reply before now: ​

      Below are links to a whole host of excellent responses to the interpretation of the study you are talking about. Bottom line: Basically, your quote is criminally misleading “journalism”–not an understanding of the actual study.
      .
      Dr. Greger: http://nutritionfacts.org/video/plant-based-treatment-for-angina/#comment-2597611517
      Dr Katz: https://www.linkedin.com/pulse/vegetarianism-nutrition-science-meets-media-nonsense-davidDr
      Garth Davis: https://www.facebook.com/drgarth/posts/1126374594050114?hc_location=ufi
      NF Moderator Dr. Jon: http://nutritionfacts.org/video/plant-based-diets-and-artery-function/#comment-2596819840
      NF Moderator Renae: http://nutritionfacts.org/video/almonds-for-osteoporosis/#comment-2601476959
      NF Moderator Dr. Jen: http://nutritionfacts.org/2016/03/31/dr-gregers-new-google-talk/#comment-2599942486 and http://nutritionfacts.org/2016/03/31/dr-gregers-new-google-talk/#comment-2601267177
      NF Moderator Dr. Alex: http://nutritionfacts.org/video/plant-based-treatment-for-angina/#comment-2597863794
      .
      Here’s how I put it all into perspective in my head: *Suppose* someone found out that descendants of *some* healthy people have developed an adaptation where consuming table sugar is even more unhealthy than it already is for everyone else. Thus, future generations might be even more sensitive to the negative health impact of eating Twinkies than we are today. Does that mean we should all eat a bunch of Twinkies today so that our ancestors aren’t worse off eating Twinkies? Of course not. That would be absurd. And that’s essentially (as I understand it) what the article you are quoting is saying in regards to eating meat. What’s more, that claim is a complete twist of what the actual study is actually saying.
      .
      Does that help?




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    3. To add to what Tom and Thea said. The study is a genetic study looking at a genetic variation in the genes that control and build the enzyme that converts the omega-3 alpha linolenic acid (ALA) to the longer chain EPA and DHA, but also converts linoleic acid (LA) to arachidonic acid (AA). The hypothesis being tested was that populations whose ancestors ate a largely plant-based diet would have had little if any preformed EPA, DHA or AA in their diet and so would have had a evolutionary pressure to retain mutations in the genes responsible for regulation of the creation of the upconverting enzyme. On the flip side populations like the Inuit, who consumed large amounts of animal products would have all the preformed long chain polyunsaturated fatty acids they needed and so would show a preference for mutations that downregulated the production of the enzyme. And that is indeed what they found. Yay!

      The authors went on to say the implication of this is that these traits evolved during a time these populations ate a traditional plant-based diet, that is a whole-food, plant based diet with little or no refined vegetable oils and so had an LA/ALA ratio from 4:1 to 1:1. Thus the amount of EPA and DHA and AA created from the precursors would have been well balanced. Remember that AA isn’t evil, and in fact is an essential nutrient that your body absolutely has to have, but just in the right ratio to EPA and DHA.

      However the genetic variants that allowed these folks to do better on a diet without any preformed LCPUFA would place them at increased risk from diets where the LA/ALA diet is out of whack as it is in industrial countries where consumption of diets with large amounts of refined fats with very high percentages of LA is common. So the mutations that adapted these populations to a more plant-based diet made them even more vulnerable to eating our crappy western diet.

      In a nutshell the study says that if you come from a population where a largely plant-based diet was eaten, like most of Africa and Asia, you more than most have the genes to do better on a whole-food/plant based diet with no added oils, and on the converse are more at risk from inflammatory mediated diseases like heart disease if you eat a diet with an especially bad omega-6/omega-3 ratio.

      It said absolutely nothing about vegetarian diets as a general class causing increased levels of arachidonic acid. The dishonesty to say that this was the primary conclusion of this study is breathtaking.




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    4. Claire, I just reread your comment and my response and I can see that my last paragraph could be taken the wrong way. I can see where you could take what I wrote as saying that you personally was saying that the study conclusions were that vegetarian diets raise arachidonic acid. Hopefully you didn’t read it that way because that is not at all what I meant. I was talking about the meat-pushers in industry, their apologists in academia and stooges in the blog-sphere who will take studies like this and turn it on its head to convince the public, including vegans such as yourself, that it said exactly the opposite of what it actually does. Welcome to the fun-house hall of mirrors that is the animal food industries relationship to nutritional science where no study no matter how favorable to a plant based diet can’t be distorted, misquoted, “explained away”, or just simply lied about to make animal foods look healthy.




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  12. Great post! The good bacteria in our guts do eat indigestible contents in our food like fiber and ferment able carbohydrates. One thing that is not mentioned that I think is very misunderstood by a lot of people especially the “vegan” doctors is that the same food that feeds the good bacteria also feed dysbiosis the bad bacteria. So for people who have gut infections and switch to a vegan diet in many cases can get worse if they are eating foods high in ferment able carbs. Speciafically starchy foods and fruits high in ferment able carbs. In these cases it’s important to take an herbal formula to kill of these bad guys and also a probiotic. Once the ratio to good guys to bad guys are in the right proportion than these ferment able foods should not be a problem because you are have a higher amount of good bacteria in your gut than bad guys.




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  13. As someone with IBS, I think it’s in large, due to my terrible diet. For 15 years of my life I hated all veggies and rarely ate fruit or grains. I only liked steak and cheese and my stomach paid the ultimate price. Through a lowfodmap diet, and whole food plant based diet I’ve been able to seriously improve my gut function. I’m wondering where the studies of IBS are. If it’s food caused it seems like the meat and dairy industry would have a big interest in silencing this research. Any input?




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  14. We live in the Philippines and I am wondering if we have picked up some
    extra
    bacteria or something that isn’t supposed to be in our gut. Our stools
    are nicely formed, stay formed in the flush, and easy to pass, but messy
    to clean up after. Is this normal? We go through a lot of TP!




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  15. What’s the recommendation for people with Small Intestine Bacterial Overgrowth (SIBO)? Most of the sites I look at suggest a low-carb approach. But I just can’t see that as a healthful option, given all the dangers associated with that way of eating.




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  16. I would like it very much if Dr. G would do a video on the association of fermented plant foods and digestive system cancers. There is much research on this in Asia. As has been mentioned here, researches speculate that it could be from salt, mycotoxins, Nitrates, etc. that are created and used in fermentation. Even though it seems to be the rage to eat these foods now, I have avoided eating fermented plant foods because of the possibility of this risk.




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  17. I thought there was never going to get the cure for HIV as i was told by the doctor, over 7 moths i has be on drugs to get rid of HIV in my body, is not that easy to be taken drugs for months no cure. just last month i had some persons saying about natural herbs that cured HIV & i found out if it’s true about the herbal Dr they talked about i emailed him for question and he proved his cure to my satisfaction & more evidence. & i paid for one after taking it for 3weeks, definitely his natural herbs cured my HIV. i know some persons also need this cure you can only get the cure from Dr Sago his email:drogunrootherds@outlook.com, Dr OGUN may God bless you and your gift of nature sir. you can also call him on his cell +2349033375429




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  18. Does anyone know anything about SIBO (small intestine bacterial overgrowth?) What to do for it, that is not Toxic, like antibiotics. Also, I am a metastatic breast cancer patient, so I try to eat only plant-based, mostly legumes and cruciferous veggies and the like, and those are the very things that seemingly contribute to the whole bacterial problem. I don’t know how to effectively treat the SIBO AND address my cancer concerns. Any help would be greatly appreciated. Thank you.




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  19. Hello Christine,
    I’m sorry to hear about your breast cancer and SIBO. I looked up SIBO on PubMed (free database of medical articles) and found a couple of interesting ones. First is a good review article: http://onlinelibrary.wiley.com/doi/10.1111/apt.12456/full. Check out the Treatment section in particular: they discuss using antibiotic treatment, which I know you are understandably against, but also some discussion of probiotics. Next was one specifically about using probiotics for treatment, and has some hopeful findings: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4311312/.

    I hope this helps, some.




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      1. Dear Dr. Jon,

        Thank you for taking the time to respond to me. And for the link to the video.

        I have had a seriously-distended stomach (think 6-7 months pregnant on a 100 lb. frame) since I altered my diet to primarily follow Dr. G’s recommendations. This coincided with my MBC diagnosis. I backburnered the issue due to my focus on fighting the cancer, but lately I felt that there was definitely something “wrong” with this picture. My GI doc feels that taking prednisone for pulmonary sarcoidosis may have instigated the problem, but in any event, he believes I have SIBO. In my research to understand the nature of SIBO, everything that I have read concerning treatment to eliminate the overgrowth of bad bacteria in the SI has indicated that I need to eliminate the FODMAPS foods (many of which are the massive quantities of “offending” plants that I consume.)

        I have yet to encounter anyone who proposes otherwise. I am stumped, because I don’t know how to both rid the SI of the buildup of bad bacteria, AND feed my body what it needs to combat the cancer.

        The other confusing piece for me concerns whether to introduce probiotics or not. Additionally, I refuse to introduce pharmaceutical antibiotics into the mix, so am exploring “herbal antibiotics instead.” I’ve read both opinions. I hope I answered your question, and that you might be able to further espouse on the subject.

        Many thanks!

        christine




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