by Bill Roberts T-Nation
Here’s what you need to know…
- The bacteria in your gut affects your ability to be lean and healthy.
- Your GI tract has more than 1000 kinds of bacteria, weighing two pounds total. They’re your gut microbiome and they’re important.
- Those with low microbial diversity have higher rates of obesity. They also feel like crap.
- Studies show some bacteria causes obesity and other bacteria protects against it. “Bad” gut bacteria can cause cravings that wreck your diet.
- Taking probiotics is useless for most people. And taking antibiotics can kill off the good gut bacteria.
- You can optimize your gut bacteria through certain foods, supplements, and diet strategies.
Gut Bacteria: Where You Get It, What it Does
Bacteria begins to colonize your gut the moment you’re born. If you were delivered naturally, breast fed, given raw fruits and vegetables, and allowed to play in microbe-rich dirt, then chances are you started life with a healthy, diverse microbiome.
But what if you were delivered via Caesarian section, formula-fed, and grew up in the city?
Well, you may have a higher rate of allergic and immune-related diseases, and of developing metabolic disorder and becoming obese. You also have a higher chance of getting diabetes and have higher systemic inflammation.
Luckily, the choices you make as an adult can fix or prevent these problems.
Fat Gain and Gut Bugs
What happens if you cause mice to be born completely free of bacteria, and continue raising them in a bacteria-free environment?
They enjoy one surprising benefit: They don’t get fat, even when given diets that make ordinary mice obese: high fat, high fructose, or high sucrose.
Let’s take it further. Take some gut bacteria from obese mice and administer it to the bacteria-free mice. They now become obese themselves, even on a healthy diet.
Now as a final step, take gut bacteria from lean mice and administer them to the above mice while keeping them on the healthy diet. They become lean again.
In other experiments, four sets of human identical twins were found where one twin was obese and the other lean. Germ-free mice were colonized with the colon bacteria of the twins. The mice colonized with bacteria from the lean twins remained lean.
But the mice colonized with bacteria from the obese twins became obese.
After this, the resulting lean and obese mice were allowed to live together and thus swap bacteria to some extent. On being exposed to the lean mice with their lean-human bacteria, the obese mice became lean too.
These experiments show that some bacteria can cause obesity, and others can protect against it.
The Surprising Result of Gastric Bypass Surgery
It turns out that while eating is reduced by the these surgeries, the beneficial effects far exceed those which occur from identical reduced eating without surgery.
Researchers found that with gastric bypass surgery, bacterial populations of the GI tract shift radically. A result is reversal or major improvement of Type II diabetes. This reversal occurs prior to weight loss, rather than being a consequence of it.
Another benefit is increased energy expenditure relative to caloric intake. In researchers’ comparisons, the food intake is the same and absorption is the same. The key difference appears to be bacterial population of the gut.
Can Antibiotics Trigger Obesity?
On the flip side, taking the antibiotic vancomycin often triggers obesity in previously non-obese patients.
Stool samples show they have greatly depleted levels of beneficial bacteria, and increased levels of bacteria known to have obesogenic effects.
Further, different GI tract bacteria are associated with obese people than with lean people, even where diets are the same. Additionally, those with diabetes have markedly different bacterial populations than the non-diabetic.
There are also proven biochemical mechanisms for causation. It therefore becomes likely that these bacteria are contributors to elevated body fat, metabolic impairment, insulin resistance, and adipose inflammation when not counterbalanced sufficiently by beneficial bacteria.
How Does Bacteria Make You Fat?
Scientists now believe both excessive gain of body fat and difficulty losing body fat are largely a consequence of adipose inflammation.
The inflammation causes fat cells to be more prone to enlarge further, and to send hormonal signals which cause metabolic impairment and reduced insulin sensitivity in muscle.
One way in which this occurs is that gram-negative bacteria such as Enterobacter, Shigella, Klebsiella, Desulfovibrionaceae,and Escherichia (including E. coli) can release the endotoxin LPS, which powerfully promotes systemic inflammation and can promote obesity.
Another mechanism contributing to fat gain: Some gut bacteria activate the endocannabinoidsystem.
By doing this, they cause the host (that’s you) to feel the “munchies” and thus the bacteria get more food for themselves. This endocannabinoid system signaling also negatively affects muscle cells, fat cells, and insulin sensitivity.
Still further, gut bacteria increase adipocyte fat storage by suppressing FIAF (fasting-induced adipocyte factor).
All these actions work towards moving an individual further along the path of adipose inflammation and metabolic impairment. They can even lead to obesity and/or diabetes.
When their balance in the GI tract is unfavorable, gut bacteria have the tools to work powerfully against fat loss or towards fat gain and to advance metabolic impairment. That’s bad news to the individual with an unfavorable balance who’s aiming for a lean, muscular physique.
Gut Bacteria Can Control You Like A Puppet
Metabolically-unfavorable gut bacteria can cause cravings of the junk foods that best feeds them. They can also cause you to feel dysphoric (bad) feelings when they’re deprived of their favorite foods.
This is accomplished not only by the endocannabinoid system, but by their ability to exert strong influence on the vagus nerve and the enteric nervous system.
It’s not funny stuff. The cravings and bad feelings can be powerful motivators to break a diet plan.
The good news is, you can break their control fairly quickly by not giving in. When you consistently don’t give in, these bacterial populations reduce, you become metabolically healthier, and you start feeling better than ever. No cravings, no dysphoria.
One of the reasons, I believe, for success of diet plans such as the Velocity Diet or paleo diets is the breaking of this cycle and the resulting improvements in metabolic health.
How Does Good Gut Bacteria Help Body Composition?
Beneficial gut bacteria help body composition and metabolic health by suppressing other bacteria which have the above adverse effects, by enhancing gut lining integrity, and by producing short-chain fatty acids (SCFA).
SCFA’s decrease systemic inflammation, provide satiety, upregulate gene expression of leptin, reduce stress-induced corticosteroid levels, improve insulin sensitivity in muscle, and decrease insulin sensitivity in adipose tissue via activation of FFAR2 (free fatty acid receptor 2.)
That’s a great combination to have going for you.
How Do I Improve My Gut Bacteria?
There’s a very strong correlation between the diversity of your gut’s bacteria and metabolic health. The more bacterial types you have the better, at least with regard to bacteria acquired in natural ways.
So, one mode of improvement is to acquire greater diversity of bacteria. Another is to change your diet in a manner which supports the function of beneficial bacteria, and shifts balance to their and your favor.
You can also take nutritional supplementation which works towards improving bacterial balance and/or to increase SCFA production.
Skip the Yogurt and Eat Some “Dirty” Veggies
As convenient as it would be to just go buy some capsules or a container of yogurt, these won’t do much to increase your microbial diversity.
First, how many strains of bacteria will be in the product? Six, perhaps?
But you probably have a thousand or more types of bacteria colonizing your GI tract already. Six more would be a pretty tiny increase, percentage-wise.
No, to increase microbial diversity, the only way to do it is the natural way that humans have been doing essentially forever. Acquire them from your food and environment!
As a species we’re adapted to very substantial microbial exposure from plant foods and from the dirt, and particularly dirt in which the food plants grow.
It’s historically abnormal for nearly all vegetables to be boiled, baked, fried, or cleaned to the point of near sterilization as occurs with commercial produce today.
By increasing consumption of locally grown vegetables, for example purchased at farmer’s markets, and eating much of it raw, your exposure to natural bacteria will be closer to what man is adapted to.
Home fermentation of such vegetables can increase their value even further. (Commercially fermented foods often have no useful bacteria.)
And don’t fear a little dirt from a good source. Vegetables from a trusted farm don’t have to be scrubbed to death, if at all. A light rinse will do.
Our ancestors had a little dirt on their food, and native peoples around the world today aren’t afraid of eating their food in a pretty natural state. Studies show their microbiomes are more diverse than ours.
Beneficial Diet Strategies
Additionally, some dietary techniques are likely to increase your number of bacterial types present, or types that are present in large number:
Improve the quality of your carbohydrate intake.
Try replacing products containing refined wheat with any of slow-cooked oatmeal, buckwheat, sweet potatoes, parsnips, carrots, turnips, squash, potatoes, rye berries, barley, brown rice, or parboiled rice.
There’s a wealth of choices, and you’ll experience real benefits from switching.
Have variety in your macronutrient composition rather than similar balance in every meal.
By having some meals which are protein/fat and low carb and others which are protein/carb and low fat, differing bacteria with differing nutritional preferences and differing bile tolerance will all get their opportunities.
Allow periods of no or little new nutritional flow, such as a 10 or 12 hour break between the last meal of the day and breakfast, or occasional days of reduced calories.
One reason to do this is that certain beneficial bacterial prosper relative to other bacteria during these times.
How Do I Feed My Good Bacteria?
Eating for good GI tract health doesn’t require particular macronutrient ratios. Peoples around the world have eaten the foods available to them and been healthy. Humans, and their gut microbiomes, are flexible and can be healthy with a wide range of diets.
Most reasonable macronutrient ratios can be fine — anything but high carb combined with high fat — if the carbs are from traditional sources and the fats are not high in linoleic acid.
To feed beneficial bacteria better, “fiber” from vegetables, fruits, tubers, and whole grains have excellent effect in improving their numbers and supporting SCFA production. I used quotes for “fiber” because preferred substances are not fibrous and can even be water soluble.
Polyphenols, phenolic acids, and anthocyanins from fruits and vegetables are also very beneficial for GI tract health.
What About Probiotics and Fermented Foods?
Currently available probiotic products don’t have enough total bacteria, or enough types of bacteria, to make much difference compared to what you already have.
In addition, the products also typically only provide bacteria potentially suited to the proximal small intestine, even though colonic bacteria are of key importance.
Further, studies have found that the administered bacteria typically fail to colonize and are undetectable within three hours.
Still another consideration is that if the bacteria were able to colonize your GI tract and you’d been previously exposed, then they’d already be present, in natural balance according to your diet. So why administer more, unless having a reason to create an unnatural balance?
All that sounds dismal, but explains why probiotics do little for the average person and I don’t generally recommend them.
There can be exceptions. Some probiotic bacterial strains help with diarrhea, constipation, irritable bowel syndrome, pouchitis, urogenital infections, Clostridium difficile infections, enterocolitis, and eczema. If you have one of these conditions, a suitable product could be of help.
If considering a product for such a condition, be sure it uses the same strain of bacteria as any cited study. If the species is the same but the strain different, the study is irrelevant.
Unfortunately, probiotic manufacturers routinely cite irrelevant studies.
Prebiotics, Anthocyanins, and Other Supplements
The first category of supplementation we’ll consider is prebiotics, or fiber which supports beneficial bacteria.
Very briefly, if you consume plenty of vegetables and tubers (like potatoes) and some fruits, there would no point to the consumption of prebiotics. Your beneficial bacteria are already getting all they need.
But if your consumption of these is less than humans traditionally have eaten, then supplementation makes sense. I recommend combining inulin with arabinogalactose to give a total of 6 grams per dose, and/or using Bob’s Red Mill potato starch at about 10 grams per dose.
If combining both methods, then cut amounts of each in half. These can be taken one to several times per day, usually with a meal.
I want to make clear that prebiotic supplementation, alone, generally doesn’t make a profound difference. It should be part of an overall plan, rather than the entirety.
Another way is anthocyanin supplementation, such as with Indigo-3G®. Modulating your gut bacteria isn’t the main purpose of Indigo-3G, but anthocyanins in general do have this positive effect.
Superfood does an excellent job of providing polyphenols and phenolic acids. Superfood has positive effects on the microbiome, which may be a partial explanation of the benefits people experience.
If wishing to use a specific polyphenol rather than a combination of extracts, quercetin is an excellent choice. Red wine polyphenols are also effective.
Resveratrol doesn’t have much effect on gut bacteria, but when taken before a meal with substantial fat and calories it acts to block the inflammatory TLR-4 signaling produced by some bacteria in response to such meals.
We haven’t yet tested using Rez-V™ this way versus dosing at other times, but research supports that it will reduce inflammatory signaling when used before such meals.
I suggest taking the three capsule dosing with or shortly before the largest meal of the day which has substantial fat.
Berberine, a plant extract, has some outstanding properties in modulating the gut microbiome. It works principally by inhibiting inflammation-promoting bacteria and shifting balance towards beneficial bacteria.
It works so well that marked reductions in blood sugar are often seen among those with impaired insulin sensitivity, and substantial fat loss often occurs.
Lastly, magnesium deficiency impairs bacterial balance in the GI tract. If you need help in this area, Elitepro™ Minerals or ZMA® provide all the magnesium needed.
- Bäckhed F1, Ding H, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15718-23.
- Cani PD, Osto M, et al. Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity. Gut Microbes. 2012 Jul-Aug;3(4):279-88.
- Cani PD, Amar J, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes. 2007 Jul;56(7):1761-72.
- Geurts L, Neyrinck AM, et al. Gut microbiota controls adipose tissue expansion, gut barrier and glucose metabolism: novel insights into molecular targets and interventions using prebiotics. Benef Microbes. 2014 Mar;5(1):3-17.
- Cox LM, Blaser MJ. Pathways in microbe-induced obesity. Cell Metab. 2013 Jun 4;17(6):883-94.
- Puddu A, Sanguineti R, et al. Evidence for the gut microbiota short-chain fatty acids as key pathophysiological molecules improving diabetes. Mediators Inflamm. 2014;2014:162021.
- Larsen N, Vogensen FK, et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One. 2010 Feb 5;5(2):e9085.
- Underwood MA. Intestinal dysbiosis: novel mechanisms by which gut microbes trigger and prevent disease. Prev Med. 2014 Aug;65:133-7.
- Cotillard A, Kennedy SP, et al. Dietary intervention impact on gut microbial gene richness. Nature. 2013 Aug 29;500(7464):585-8.
- David LA, Maurice CF. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559-63.
- Xiao S, Fei N, et al. A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome. FEMS Microbiol Ecol. 2014 Feb;87(2):357-67.
- Lakhan SE, Kirchgessner A. Gut microbiota and sirtuins in obesity-related inflammation and bowel dysfunction. J Transl Med. 2011; 9: 202
- Fei N, Zhao L. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J. 2013 Apr;7(4):880-4.
- Ridaura VK, Faith JJ, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013 Sep 6;341(6150):1241214.
- Parnell JA, Reimer RA. Weight loss during oligofructose supplementation is associated with decreased ghrelin and increased peptide YY in overweight and obese adults. Am J Clin Nutr. 2009 Jun;89(6):1751-9.
- Turroni F, Ribbera A, et al. Human gut microbiota and bifidobacteria: from composition to functionality. Antonie Van Leeuwenhoek. 2008 Jun;94(1):35-50.
- Scher JU, Sczesnak A. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife. 2013;2:e01202
- De Filippo C, Cavalieri D, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA. 2010 Aug 17;107(33):14691-6.
- Wu GD, Chen J, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011 Oct 7;334(6052):105-8.
- Ho JTK, Chan GCF, Li JCB. Systemic effects of gut microbiota and its relationship with disease and modulation. BMC Immunol. 2015; 16: 21.
- Keenan MJ, Zhou J, et al. Role of resistant starch in improving gut health, adiposity, and insulin resistance. Adv Nutr. 2015 Mar 13;6(2):198-205.
- Alcock J, Maley CC, Aktipis CA. Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. Bioessays. 2014 Oct;36(10):940-9.
- Mayer EA. Gut feelings: the emerging biology of gut-brain communication. Nat Rev Neurosci. 2011 Jul 13;12(8):453-66.
- Li JV, Ashrafian H. Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut. 2011 Sep;60(9):1214-23.
- Trasande L, Blustein J, et al. Infant antibiotic exposures and early-life body mass. Int J Obes (Lond). 2013 Jan;37(1):16-23.
- Fanaro S, Chierici R, et al. Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl. 2003 Sep;91(441):48-55.
- Blustein J, Attina T, et al. Association of caesarean delivery with child adiposity from age 6 weeks to 15 years. Int J Obes (Lond). 2013 Jul;37(7):900-6.
- Liou AP, Paziuk M. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med. 2013 Mar 27;5(178):178ra41.
- Muccioli GG, Naslain D, et al. The endocannabinoid system links gut microbiota to adipogenesis. Mol Syst Biol. 2010 Jul;6:392.
- Harris K, Kassis A, et al. Is the gut microbiota a new factor contributing to obesity and its metabolic disorders? J Obes. 2012;2012:879151.
- Parkar SG, Trower TM, et al. Fecal microbial metabolism of polyphenols and its effects on human gut microbiota. Anaerobe. 2013 Oct;23:12-9.
- Martínez I, Lattimer JM, et al. Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J. 2013 Feb;7(2):269-80.
- Kim KA, Gu W, et al. High fat diet-induced gut microbiota exacerbates inflammation and obesity in mice via the TLR4 signaling pathway. PLoS One. 2012;7(10):e47713.
- Zhang X, Zhao Y, et al. Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats. PLoSOne. 2012;7(8):e42529.
- Cani PD, Bibiloni R, et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes. 2008 Jun;57(6):1470-81.
- Cani PD, Neyrinck AM, et al. Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia. 2007 Nov;50(11):2374-83.
- Zhang Y, Li X, et al.Treatment of type 2 diabetes and dyslipidemia with the natural plant alkaloid berberine. J Clin Endocrinol Metab. 2008 Jul;93(7):2559-65.
- Ding S, Chi MM, et al. High-fat diet: bacteria interactions promote intestinal inflammation which precedes and correlates with obesity and insulin resistance in mouse. PLoS One. 2010 Aug 16;5(8):e12191.
- Parnell JA, Reimer RA. Prebiotic fiber modulation of the gut microbiota improves risk factors for obesity and the metabolic syndrome. Gut Microbes. 2012 Jan-Feb;3(1):29-34.
- Ramirez-Farias C, Slezak K. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii.Br J Nutr. 2009 Feb;101(4):541-50
- De Palma G, Nadal I, et al. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. Br J Nutr. 2009 Oct;102(8):1154-60.
- Miyazaki K, Masuoka N, et al. Bifidobacterium fermented milk and galacto-oligosaccharides lead to improved skin health by decreasing phenols production by gut microbiota. Benef Microbes. 2014 Jun 1;5(2):121-8.
- Kim SW, Suda W, et al. Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res. 2013 Jun;20(3):241-53.
- Jernberg C, Lofmark S, et al. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology. 2010 Nov;156(Pt 11):3216-23.
- Walter J, Martínez I, Rose DJ. Holobiont nutrition: considering the role of the gastrointestinal microbiota in the health benefits of whole grains. Gut Microbes. 2013 Jul-Aug;4(4):340-6.
- Hidalgo M, Oruna-Concha MJ, et al. Metabolism of anthocyanins by human gut microflora and their influence on gut bacterial growth. J Agric Food Chem. 2012 Apr 18;60(15):3882-90.
- Bushman FD, Lewis JD, Wu GD. Diet, gut enterotypes and health: is there a link? Nestle Nutr Inst Workshop Ser. 2013;77:65-73.
- Queipo-Ortuño MI, Seoane LM, et al. Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels. PLoS One. 2013 May 28;8(5):e65465.
- Turnbaugh PJ, Bäckhed F, et al. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008 Apr 17;3(4):213-23.
- Van den Abbeele P, Gérard P, et al. Arabinoxylans and inulin differentially modulate the mucosal and luminal gut microbiota and mucin-degradation in humanized rats. Environ Microbiol. 2011 Oct;13(10):2667-80.
- Nielsen TS, Laerke HN. Diets high in resistant starch and arabinoxylan modulate digestion processes and SCFA pool size in the large intestine and faecal microbial composition in pigs. Br J Nutr. 2014 Dec 14;112(11):1837-49.
- Terpend K, Possemiers S. Arabinogalactan and fructo-oligosaccharides have a different fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME ®). Environ Microbiol Rep. 2013 Aug;5(4):595-603.
- Lopez-Siles M, Khan TM. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol. 2012 Jan;78(2):420-8.
- Pachikian BD, Neyrinck AM, et al. Changes in intestinal bifidobacteria levels are associated with the inflammatory response in magnesium-deficient mice. J Nutr. 2010 Mar;140(3):509-14.
- Han J, Lin H, Huang W. Modulating gut microbiota as an anti-diabetic mechanism of berberine. Med Sci Monit. 2011 Jul;17(7):RA164-7.
- Yin J, Xing H, Ye J. Efficacy of berberine in patients with type 2 diabetes mellitus. Metabolism. 2008 May;57(5):712-7.
- Qiao Y, Sun J, et al. Effects of resveratrol on gut microbiota and fat storage in a mouse model with high-fat-induced obesity. Food Funct. 2014 Jun;5(6):1241-9.
- Etxeberria U, Arias N. Reshaping faecal gut microbiota composition by the intake of trans-resveratrol and quercetin in high-fat sucrose diet-fed rats. J Nutr Biochem. 2015 Jun;26(6):651-60.