6 Steps to Rebuild Gut Flora Metabolism

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gut flora metabolism

6 Steps to Rebuild Gut Flora Metabolism 

Gut flora is a term used to describe the trillions of microbes that live in our intestines.  The most up to date research has revealed that the balance of our gut bacteria plays a large role in our metabolism.  Many studies are even showing that changes in our gut flora are highly correlating with obesity and other metabolic disorders (4).

Remember that girl that seemed to be able to eat EVERYTHING and not gain a pound? We always assumed that she just had a rock star metabolism.  How many people do you know (you may be one of them) who has “done everything right” and still not lost weight? This weight loss resistance is becoming more and more common.

gut flora

Gut Flora and Your Weight

Did you know that science says your gut bacteria is largely responsible for how fast or slow your metabolism is? Even better, what if I told you that we can manipulate your gut flora in order to enhance your metabolism?  Of course, there are many lifestyle and diet factors that you can incorporate to lose weight and change your metabolism to a degree.

Science is showing that if we can balance our microbiome, we can significantly change our metabolism and quit counting calories. The counting calorie method eventually turns into an exhausting and ineffective way to lose weight.

As a matter of fact, caloric restriction typically leads to the body going into starvation mode and storing all of our intake as fat the best that it possibly can. This is not very effective for long term health and weight loss.  This article will answer why the gut microbiome impacts our metabolism and how to correct the balance in order to speed up our metabolism.  Discover how to rebuild gut flora metabolism.

gut Microbiome, 10 Ways To Improve The Gut Microbiome, gut flora

Function of The Gut Bacteria

The type and the amount of each species present plays a large role in how lean or obese we are as well as our risk factors for developing diabetes amongst other related metabolic disorders.  Your gut bacteria does the following:

  1. Controls the amount of calories you extract from foods
  2. Causes cravings
  3. Extracts nutrients such as B12 from our foods.
  4. Produces short chain fatty acids

It should be noted that the only way to properly extract these fatty acids is by having the appropriate bacteria present in the gut.  If we are lacking these bacteria, we will lack the ability to produce these short chain fatty acids and get the benefits that were mentioned above.

Conversion Gone Wrong

Different bacterial species will convert the same foods into different end products.  This means that if we have a harmful balance of gut bacteria, they can take foods, even healthy foods, and convert them into compounds that lead to fat storage, insulin resistance, gas production, and inflammatory compounds.

On the other hand, a healthy balance of gut bacteria can create compounds that lead to fat burning, fat storage prevention, inflammation reduction, improved satiety, improved gas production, and increased insulin sensitivity.

Our original gut flora has a set metabolism and is highly responsible for our ability to lose or gain weight. It is also heavily influenced by our lifestyle and diet.  Big influential factors include: antibiotics, chemical, processed foods, pesticides, herbicides, heavy metals, toxins, pathogens, medications, supplements, and anything else that enters into our digestive tract.

Thankfully, this can be adjusted by introducing the proper bacteria into the digestive tract and feeding them the right foods to help them flourish and maintain a healthy metabolism (11).

Short Chain Fatty Acids

The gut flora breaks food down into nutrients. It can extract and create nutrients, but it can also rob us of nutrients when an imbalance is present.  A healthy gut flora will extract short chain fatty acids, which have been proven to protect against diet induced obesity (4).

The main short chain fatty acids found in the colon include butyrate, propionate, and acetate. Butyrate and propionate protect against obesity by stimulating the production of satiety hormones and reducing cravings, therefore decreasing the amount of foods ingested by the host.  Acetate inhibits weight gain regardless of food intake and does not affect the gut hormones like butyrate and propionate do (4).

gut flora


Butyrate, a short chain fatty acid, has been shown to enhance adaptive thermogenesis and fatty acid oxidation (burning of fat). It has also been shown to improve mitochondrial function, increase insulin sensitivity, and reduce fat production (1).

Butyric acid becomes sodium butyrate after coming into contact with sodium. Sodium butyrate is a common compound found in foods such as grass fed cheese, butter, and ghee.  When these foods are consumed, sodium butyrate is then broken down into butyric acid in the body, which makes them a great source for this fat burning molecule.

Butyrate is also produced from the fermentation process of foods high in dietary fiber in the large intestine. This process depends heavily on the types of microbes present in the large intestine as well as the dietary food sources.

In short, butyrate can treat and prevent diet-induced insulin resistance by promoting energy production and enhancing mitochondrial function (1). In other words, butyrate is great for increasing metabolism and energy.

The take away about butyrate is this:

  1. It helps the body produce energy and reduce oxidative stress.
  2. Great food sources include grass fed cheese, butter, and ghee
  3. Our gut flora creates a large amount of butyrate from foods high in fiber. Sources include produce such as broccoli, carrots, Brussel sprouts, green peas, apples, oranges, and grapefruit (2).
  4. We must have balanced gut flora to reap the benefits of butyrate (1).


Acetic acid is a naturally occurring acid found in produce such as strawberries, apples, grapes, pineapples, and oranges. This organic acid gives vinegar its distinct flavor and smell. It can also be found in fermented vegetables, grass fed cheese, and vinegars that are used for preparing foods.

Studies have shown that acetic acid actually inhibits the accumulation of body fat and hepatic lipids.  This is done without altering food consumption. It suppresses body fat accumulation by upregulating genes necessary for fatty-acid oxidation and mitochondrial processing (5).

Acetate has also been found to have an inhibitory effect on the conversion of glucose to fatty acids in the liver. Treatment with acetate has shown a reduction in fat accumulation in adipose tissue, protection against fat accumulation in the liver, and improved glucose utilization.

Based on these findings, research is suggesting that acetate is a promising compound for improving obesity and obesity linked type 2 diabetes (6).  Another study found that not only did the intake of vinegar reduce obesity, but it also reduced serum triglyceride levels.

This same study also saw that when the individuals stopped ingesting vinegar, their waste line and measurements went back to where they had initially began. This indicates that the intake of vinegar on a daily basis is necessary in order to maintain the anti-obesity effects (7).


Propionate is produced by microorganisms such as megashpaera, veillonella, and selenomonas and without these organisms we will struggle to produce an adequate amount.

Propionate is vital for utilizing glucose for energy in red blood cells.  The presence of propionate has been shown to increase satiety and decrease the desire for sugar and overeating (4).


How Do We Rebuild our Gut Metabolism?

There are two forms of bacteria that have gained the most attention when it comes to burning fat.  These two species include bacteriodetes and firmicutes.  First, we need to address the ratio of these two species in the gut flora.

A higher ratio of firmicutes has been directly associated with obesity, diabetes, inflammation, and metabolic syndrome. A higher ratio of bacteriodetes has been associated with healthier and leaner individuals (11).

Here are 6 ways to improve your gut flora and favor the development of bacteriodetes over firmicutes.  These steps will also create a healthier, anti-inflammatory environment in your gut and improve your nutrient assimilation.


Increase Fibrous Vegetables and Good Fats

We can increase bacteriodete proliferation by feeding them foods high in fiber and eliminating sources of sugar. The key is to increase good quality fats, non starchy vegetables, and good quality protein.

These foods should replace grains and sugars which are both high in glycemic index and feed candida yeast and harmful bacterial overgrowth. Artificial sweeteners should also be avoided due to their toxic effects.

Prebiotic, The Top 33 Prebiotic Foods for Your Digestive System

Eliminate Sugars and Simple Carbohydrates

Firmicutes feed off of sugar and simple carbohydrates. These species are extremely powerful and can actually manipulate neurotransmitter production, which then cause your brain to crave sugar.

We must eliminate their food source in order to starve them out of our system.  This diet plan can still be satisfying and delicious when done correctly.  Our focus should be on regulating blood sugar and having a good amount of satisfying fats and proteins with our vegetables and low glycemic fruit.

Sugar Cravings, 7 Ways To Stop Sugar Cravings

Practice Intermittent Fasting

Intermittent fasting is also beneficial for balancing the gut flora by increasing beneficial bacteria levels such as the bacteriodetes species we have discussed. It also increases human growth hormone levels which prevent fat storage.  Begin by consuming all of your food in a 12 hour window. Keep 12 hours between your dinner and breakfast. You can then increase this to a 14-16 hour fast.

The goal is to consume all of your calories within an 8-10 hour window because the microbes in our gut go through a cycle similar to our circadian rhythm. When we remain in a fed state, we prevent the recycling of beneficial gut flora.  During the fasting period, be sure to super hydrate your system with water and organic herbal teas. Using lemon water and apple cider vinegar are also great for restoring gut microbiome balance.


Introduce Probiotics

We must introduce the healthy bacteria into our gut in order for the species to take root and proliferate from feeding off of the healthy fibers, proteins, and fats that we are consuming.  We use natural sources such as coconut water kefir, grass fed yogurt, kombucha, and fermented vegetables in order to introduce these bacteria. These are great food sources that should be ingested daily in order to maintain a good balance.

Start with a table spoon in order to allow the gut to adjust Increase to 1-2 servings a day.  SBO Probiotics – Ultimate is the probiotic that we start our clients on and typically see the best results with. This probiotic is full of bacteriodete species that are needed to convert and reap the benefits of our healthy nutrients.

These organisms also contain natural antimicrobials that fight against parasites, fungi, viruses, and pathogenic bacteria. SBO Probiotics also has spore forming bacteria present, which enables the microbes to naturally adapt to the harsh conditions of the GI tract.  I typically start my patients on one capsule a day away from food and supplements. This can be increased up to 4 in one day but I usually see results when using 2 capsules a day.

Reduce Harmful Pathogens

In order to reduce the amount of firmicutes and other harmful pathogens, we use natural anti-microbials.  Using herbs such as oregano, thyme, basil, and rosemary are essential for fighting pathogens. Garlic, onion, lemon, and apple cider vinegar are also great foods to use for fighting pathogens.

GI Clear is a concentrated form of natural antimicrobials and we use this for patients to reduce their microbial load if bacterial or yeast overgrowth is suspected. It contains berberine, which is a plant alkaloid that has proven effective in killing pathogens.

It also contains black walnut extract which has numerous studies have found to have powerful anti-microbial, anti-parasitic properties.   This is a key parasite killing agent and it also acts as a mild laxative that helps expel the waste products of dead bacteria and parasites.

GI Clear also contains tribulus extract, barberry extract, sweet wormwood, magnesium caprylate and bearberry which all act to reduce our pathogen load and improve bowel motility.

Use Bone Broth

Bone broth is great for building healthy bones, relieving joint pain, hair and nail health, healing the gut, fighting infection, reducing swelling, and removing arterial plaque.  Liquid nutrition is more easily absorbable by the body as well meaning that we are able to extract more nutrients.

For more extreme cases, I will recommend doing a bone broth fast that lasts 3-5 days. This should be done with the support of a health care provider. This gives the gut a break from digesting complex foods, which allows the lining to heal.

It also provides nutrients to rebuild the gut lining and fight off harmful pathogens. This will significantly help fight off fermicutes and other harmful pathogens.  You can use this bone broth recipe or use premade organic grass fed or pasture raised stock bones.

Bone broth protein powder is also a great way to reap the benefits of bone broth without the hassle of making the broth itself. This is great for taking on the go and adding to unsweetened coconut milk.

gut flora

Take Away

Many people have tried eating healthy but fail to lose weight or see results. A major cause of this is that their gut flora is favorable for turning fibers into hydrogen and methane gas instead of fat burning compounds such as short chain fatty acids.

Many people have experienced eating a “super healthy” diet and only experienced gas and bloating as a result (11).  Without changing the species present in our gut, the body simply continues to suppress weight loss, increase calorie absorption, increase insulin resistance, and increase gas production.

With this approach, we are changing gene expression to favor a lean body. This approach is a much more powerful and permanent approach than the standard weight loss formulation of calculating calories in vs. calories out.

This leads to enhanced fatty acid oxidation (fat burning) in the liver and muscle tissues and decreased production of new fat.  Metabolic reconditioning is a very effective way to lose weight by changing our metabolism at the molecular level (9).

gut flora

Sources For This Article:

1. Gao Z, Yin J, Zhang J, et al. Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice.Diabetes. 2009;58(7):1509-1517. doi:10.2337/db08-1637.
2. Busch, S. (2015). What Are Nonstarch Polysaccharides? Livestrong. Online Link
3. Andrews, R. Resistant Starch. Precision Nutrition. Online Link
4. Lin HV, Frassetto A, Kowalik Jr EJ, et al. Butyrate and Propionate Protect against Diet-Induced Obesity and Regulate Gut Hormones via Free Fatty Acid Receptor 3-Independent Mechanisms. Brennan L, ed.PLoS ONE. 2012;7(4):e35240. doi:10.1371/journal.pone.0035240.
5. Tomoo Kondo, Mikiya Kishi, Takashi Fushimi, and Takayuki Kaga. Acetic Acid Upregulates the Expression of Genes for Fatty Acid Oxidation Enzymes in Liver To Suppress Body Fat Accumulation. Journal of Agricultural and Food Chemistry 2009 57 (13), 5982-5986.Online Link
6. Yamashita H, Fujisawa K, Ito E, Idei S, Kawaguchi N, Kimoto M, Hiemori M, Tsuji H. Improvement of obesity and glucose tolerance by acetate in Type 2 diabetic Otsuka Long-Evans Tokushima Fatty (OLETF) rats. Biosci Biotechnol Biochem. 2007 May;71(5):1236-43. Epub 2007 May 7.Online Link
7. Kondo T, Kishi M, Fushimi T, Ugajin S, Kaga T. Vinegar intake reduces body weight, body fat mass, and serum triglyceride levels in obese Japanese subjects. Biosci Biotechnol Biochem. 2009 Aug;73(8):1837-43. Epub 2009 Aug 7.Online Link
8. Lin J, Handschin C, Spiegelman BM. Metabolic control through the PGC-1 family of transcription coactivators. Cell Metab. 2005 Jun;1(6):361-70. Online Link
9. Caro-Quintero, A., Lizcano, F., Reyes, A., & Rodriguez-Castano, G. Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle. Frontiers in Genetics. (2016) 7: 224..doi: 10.3389/fgene.2016.00224.
10. Zhanguo Gao, Jun Yin, Jin Zhang, Robert E. Ward, Roy J. Martin, Michael Lefevre, William T. Cefalu, and Jianping Ye. Butyrate Improves Insulin Sensitivity and Increases Energy Expenditure in Mice. DIABETES, VOL. 58, JULY 2009.Online Link
11. Cardona, F., Garcia-Fuentes, E., Moreno-Indias, I., Queipo-Prtuno, M. I., Sanchez-Alcoholado, L., & Tinahonest, F. J.Insulin resistance is associated with specific gut microbiota in appendix samples from morbidly obese patients (2016). American Journal of Translational Research. 8(12): 5672–5684. Online Link

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Dr. Jockers

Dr David Jockers is passionate about seeing people reach their health potential in mind, body and spirit. He is the host of the popular “Dr Jockers Functional Nutrition” podcast and the author of the best-selling books, “The Keto Metabolic Breakthrough” and “The Fasting Transformation.”


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  1. I’ve read a LOT of articles on this subject and this is the very BEST one.
    “Completely” helpful information.
    Thank you.

  2. Great article but it has been recently shown that a low F/B ratio is highly conducive to high levels of TMAO. My personal tests (F/B ratio < 6, TMAO = 58.2) corroborate that finding.

    What would you suggest as the best way to increase fermicuties?


  3. Wonderful article! I have recently had a GI MAP stool analysis done, for some reason I can’t get any doctor to run a SIBO test on me. The stool test is showing an overgrowth of Enerococcus faecium and Morganella spp., would you recommend any herbal antimicrobial to kill the overgrowth. My Firmicutes:Bacteroidetes ratio is very low (firmicutes 4.99e10, Bacteroidetes 3.46e12). Do you think a high probiotic/prebiotic protocol is enough?

    Thank you for your time!

    1. Hey Keri, we don’t typically treat an overgrowth of commensal bacteria or even dysbiotic bacteria unless we know the individual has a lot of GI related symptoms and the gut function tests (calprotectin, sIgA, etc) are out of range. If you would like to order a SIBO test, you can off of our website here https://drjockers.com/bio-health-sibo-breath-test/

      Also, you can work with one of our functional health coaches on a plan to help you reach your health goals. They are well equipped with all the best protocols for gut issues. https://drjockers.com/long-distance-coaching/

  4. My understanding is that dry capsule probiotics are inert and cannot thrive letterland reproduce in the human gut. Is that true, and is that true of your product?

  5. Are the short chain fatty acids butyrate, propionate, and acetate available as supplements, and if so, is it a good idea to take them?

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