Is Gut Bacteria Making You Fat?

by Bill Roberts

Control Gut Bacteria, Control Body Composition

Can't seem to lose fat and keep it off? Have crazy cravings? It could be caused by a problem with your natural gut bacteria. Here's why and how you can fix it.

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 (Buy at Amazon). Modulating your gut bacteria isn’t the main purpose of Indigo-3G, but anthocyanins in general do have this positive effect.


Superfood (Buy at Amazon) 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 (Buy at Amazon) 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 (Buy at Amazon) provides all the magnesium needed.

ElitePro Minerals



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