How Your Gut Microbiome Can Transform Your Metabolic Health

Kristina Mitts in butyrate leaky gut metabolic health 06 Aug 2025 • 3 min read

Author Bio

Kristina Mitts | Registered Nutritionist

Kristina is a Registered Nutritionist with experience working in the fields of Functional/Integrative Medicine and Microbiome Restoration. She began her career working in microbiome-focused clinics and realized that the clinics were missing an opportunity to improve outcomes for patients by not assessing the microbiome through the lens of 16s rRNA testing like Biomesight. In the last few years she branched more into functional medicine. Kristina loves to teach clients how to harness their microbiota to reduce bloating, brain fog, histamine and food/chemical intolerance, and other chronic or autoimmune health issues.

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Feeling sluggish? Struggling with blood sugar or weight? It might be time to check in with the trillions of tiny tenants living in your gut. Your gut microbiome—the community of bacteria, fungi, and other microbes in your digestive system—plays a starring role in your metabolic health. When this microbial city is thriving, it helps your body process nutrients efficiently. When things are out of whack, it can contribute to weight gain, insulin resistance, and other metabolic issues.

 The Gut-Metabolism Connection: It's Complicated

Think of your gut as a bustling city. Good microbes break down food, extract energy, and produce helpful compounds. Less desirable microbes can cause inflammation and disrupt key metabolic processes. It’s a constant balancing act, and the state of your microbiome can influence your metabolic health. The relationship is complex, and it's a two-way street, meaning the dysbiosis can cause metabolic dysfunction or metabolic problems can cause dysbiosis.

Potential "Good Guys": 

Certain bacteria are associated with better metabolic profiles. For example, Akkermansia muciniphila, a mucus-loving microbe, tends to be more abundant in lean individuals with good insulin sensitivity. Similarly, bacteria that produce butyrate, a short-chain fatty acid (SCFA), like Faecalibacterium prausnitzii and Roseburia intestinalis, may help regulate blood sugar and reduce inflammation. Those with more Bifidobacterium and subsequent acetate production are less likely to over-eat as acetate helps with fullness signalling.

Potential "Bad Guys": 

On the flip side, an overgrowth of certain bacteria could spell trouble. Low SCFA producers are linked to insulin resistance and a higher risk of type 2 diabetes. An unbalanced microbiome may contribute to "leaky gut," where toxins, such as lipopolysaccharide, enter the bloodstream, triggering inflammation and potentially disrupting metabolic processes.

How Might Your Microbiome Be Influencing Your Metabolism?

Researchers are still teasing out the exact mechanisms, but here are a few possibilities:

Blood Sugar Regulation: 

The microbiome can influence how your body processes sugar. SCFAs like butyrate may improve insulin signaling, helping maintain stable blood sugar levels after meals.

Appetite Hormones: 

Your gut bugs talk to your brain! The microbiome communicates via the gut-brain axis, potentially influencing hormones like leptin and ghrelin, which play a role in hunger and fullness. To assess your “microbial appetite” look at the section of your results titled “Short-Chain Fatty Acids.”

Gut Barrier Integrity: 

A healthy microbiome helps maintain the integrity of the gut lining, preventing harmful substances from entering the bloodstream and triggering inflammation. When you look at your biomesight results, you’ll want to look at both the “Gut Permeability” section as well as the “Toxins” section to assess this.

Fat Metabolism: 

Microbes play a role in processing bile acids, which are essential for fat digestion. An imbalanced microbiome may disrupt this process, potentially impacting blood fat levels.

Tips for Leveraging Your Microbiome to Boost Metabolic Health

Eat More Prebiotics:

Think of fiber and polyphenols as fuel for your beneficial bacteria. Foods like whole grains, legumes, fruits, green tea and vegetables promote the growth of SCFA-producing microbes. It may feel impossible at first, but if you introduce select prebiotics slowly and intentionally you will soon realize the benefit.

Examples: Oats, lentils, apples, broccoli, wild rice, tea and spices

Include Polyphenol-Rich Foods:

Polyphenols in colorful fruits and vegetables feed beneficial species like Akkermansia muciniphila and discourage unwanted overgrowth such as C. difficile.

Examples: Berries, spinach, dark chocolate.

Avoid Ultra-Processed Foods:

Ultra-processed foods can promote dysbiosis by feeding harmful bacteria while starving beneficial ones. Prioritize shopping for whole fruits, vegetables - even frozen ones as they too provide beneficial prebiotics for your microbiome.

Try Intermittent Fasting:

Giving your gut a break allows mucus-loving bacteria like Akkermansia to thrive, improving gut integrity and metabolic health. Intermittent fasting can look like an 8 hour fasting window or a 4 hour fasting window or 12 hours! The length of time depends on your personal tolerance.

Consider Probiotics:

Probiotics (live beneficial bacteria) can improve your microbial terrain and help encourage balance. In regards to commercially available products, Akkermansia muciniphila and Veillonella probiotics stand out for the ongoing research as to their impact on metabolic health. Lactobacillus gasseri, Bifidobacterium animalis, Lactobacillus rhamnosus, and others show promise for improving metabolic health by targeting inflammation, insulin resistance, and lipid profiles. However, strain-specific effects vary significantly, and further research is needed to optimize their therapeutic potential for individual needs.

Probiotic-rich foods are a welcome option as well: Yogurt, kefir, natto, kimchi.

Stay Active:

Regular exercise promotes microbial diversity and boosts SCFA production. Active people will tend to have more of a microbe called Veillonella in their microbiome. This microbe helps to degrade lactic acid and may improve physical performance.

Avoid over-supplementation or unnecessary supplements:

Many compounds are effective at specific dosages and may be problematic at higher dosages. Take butyrate for example; research is exploring high levels of butyrate as being able to dysregulate blood sugar and other aspects of metabolic health. Not to mention, certain supplements can reduce beneficial microbes. Grapefruit seed extract is a good example of a popular supplement that may harm the microbiome with over-use.

Disclaimer: this information is for educational purposes only

References: 

The role of short-chain fatty acids on insulin sensitivity: a systematic review and meta-analysis, Nhan H.T. Pham, Mugdha V. Joglekar, Wilson K.M. Wong, Najah T. Nassif, Ann M. Simpson, Anandwardhan A. Hardikar, medRxiv 2022.11.22.22282645; doi: https://doi.org/10.1101/2022.11.22.22282645

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Gao Z, Yin J, Zhang J, Ward RE, Martin RJ, Lefevre M, Cefalu WT, Ye J. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes. 2009 Jul;58(7):1509-17. doi: 10.2337/db08-1637. Epub 2009 Apr 14. PMID: 19366864; PMCID: PMC2699871. 

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Pham NHT, Joglekar MV, Wong WKM, Nassif NT, Simpson AM, Hardikar AA. Short-chain fatty acids and insulin sensitivity: a systematic review and meta-analysis. Nutr Rev. 2024 Jan 10;82(2):193-209. doi: 10.1093/nutrit/nuad042. PMID: 37290429; PMCID: PMC10777678.

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Reza Ghotaslou, Edris Nabizadeh, Mohammad Yousef Memar, Wahid Mina Hama Law, Mahdi Asghari Ozma, Milad Abdi, Mina Yekani, Hiva Kadkhoda, Rasoul hosseinpour, Soleyman Bafadam, Anahita Ghotaslou, Hamed Ebrahimzadeh Leylabadlo, Javad Nezhadi,

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