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The Microbiome’s Effect on Metabolism

  • By Sara Vance, your Golden Door Nutritionist & Author of The Perfect Metabolism Plan

Is Bacteria the Solution to the Battle of the Bulge?

This is the third article in Sara’s series on metabolism. The first article explains how blood sugar stability is critical for a healthy metabolism, the second article covers the role that stress plays in weight gain and disease. This article points to the role of the Microbiome.

We are told that if we want to lose weight, we just need to create a calorie deficit – so basically just eat less calories (energy in) than we expend (energy out). Makes perfect sense – so why doesn’t it work? It doesn’t work because our bodies aren’t calculators!

The human body just is not that simple – far from it.  Stress, hormones like insulin, our activity level, and a number other factors – all impact how our body is processing those calories – including our microbiome.

Micro – bio – what? 

Our microbiome is the collection of microorganisms that reside within and on our body.  The human body is host to trillions of bacterial cells – in fact, it has more bacterial cells than human cells! A large percentage of these bacteria live in our digestive tract – often referred to as “our gut.”  These bacteria are living organisms that interact with and impact our weight, immune system, digestion, disease risk, inflammation, brain health, mood, and more.

Just a mention of the word bacteria, might have you reaching for the antibacterial soaps, wipes, and sprays. We typically think about bacteria as causing disease. And yes, many bacteria are dangerous – especially antibiotic-resistant strains of bacteria like MRSA (Methicillin-resistant Staphylococcus Aureus). But we also need to realize that not all bacteria are bad, in fact – there are beneficial bacteria – the word probiotic literally translated means “for life.”

Gut Bacteria. It’s all About Balance – “Symbiosis”

When it comes to microbiome – it’s all about balance and diversity. Some of our bacteria are “good guys,” some are the “bad guys” (pathogens), while others are “neutral”.

Probiotics, Prebiotics and Post-biotics

  • Probiotics are beneficial bacteria strains which are created naturally during the fermentation process, found in our microbiome, and in supplements.
  • Prebiotics are fibers that bacteria feed on. Found naturally in fiber-rich foods and some fiber supplements.
  • Post-biotics are the byproducts of probiotic metabolism, and play important roles in digestion, assimilation of nutrients, immune system, and even disease prevention.

Bacteria & Our Weight

Our weight is closely connected to type of bacteria in our guts.  According to this New York Time article, “the bacterial makeup of the intestines may help determine whether people gain weight or lose it, according to two new studies.”  Bacteria in our gut is closely tied to metabolic hormones like insulin and leptin, which affect our body’s ability to process sugars, regulate appetite, and our energy. Research has identified two types of anaerobic bacteria in our digestive system that appear to affect our weight:

  • Bacteroidetes– associated with leanness, and satiety.
  • Firmicutes– associated with obesity, and hunger; found in higher proportions in obese mice and humans

So what this means is – if you have more firmicutes – and you eat a piece of cake, you could extract more of the fat and calories than someone who has more bacteriodetes. 

The Microbiome is Unique & Dynamic

Our microbiome is unique to each of us – kind of like a fingerprint. But unlike a fingerprint, our microbiome is not static – it can change/shift.  So if the our bacterial balance gets disturbed (say by taking a round of antibiotics, overuse of antibacterial agents, a diet high in processed foods or sugar, or a stressful event), this can cause the pathogenic bacteria (and yeasts) to grow and take over, which research shows can create a cascade of issues – including weight gain.

Researchers have found that just 3-7 days of a low fiber “western” diet can negatively impact the diversity and number of beneficial bacterial strains in our gut. Research shows that immigrants experience a significant bacterial shift within weeks of moving to the United States, which affects their weight and disease risk. A study out of Kings college in London found that eating a predominantly fast food diet for 10 days resulted in a loss of 1,300 species, shifting the balance of bacteria from predominantly bacteriodetes to firmicutes. Studies have even revealed that some of the weight loss that occurs with gastric bypass may be due to a shift in gut bacteria, perhaps even more so than the physiological change in the anatomy!

Our Gut & Disease

Hippocrates, the father of modern medicine, famously said “All disease begins in the gut.” Research is revealing that he was one to something. Our gut bacteria affects our immunity (80% of our immune system resides in our gut), our mental health (the gut is often referred to as the second brain and produces most of our serotonin), and may play a role in the development of heart disease, diabetes, multiple sclerosis, certain cancers, Parkinson’s disease, susceptibility to infection, and even dementia and Alzheimer’s disease.

10 Tips for Taking Care of Your Gut Bugs

So now that you know the importance of taking care of our gut bacteria, here are some tips to put into action. Just remember, when increasing fiber intake or adding in fermented foods – do so slowly and gradually to allow the digestive system to adjust. Also make sure to stay properly hydrated in order for the fiber to work.


  1. Gradually increase your fiber intake, especially prebiotic fibers.* – Fiber is the food for our good gut bugs, allowing it to thrive and proliferate.
  2. Strictly limit added sugars – we all know sugar is empty calories and causes us to pack on the pounds, but it also has a negative effect on our microbiome, and promotes inflammation
  3. Replace artificial sweeteners with a more natural alternative like monk fruita study published in the journal Molecules found chemical sweeteners reduced beneficial bacteria.
  4. Consume fermented foods with good bacteria* – like kefir, yogurt, kimchi, traditional sauerkraut, kombucha, and miso.
  5. Avoid antibiotics unless absolutely necessary – if you do need to take them, make sure to consume a healthy fiber-rich, low sugar diet during and afterwards
  6. If you consume animal proteins, choose organicconventionally raised livestock are regularly given antibiotics, which could be contributing to the rise of resistant bacteria, as well as affecting our microbiome.
  7. Avoid foods treated with pesticides and herbicidesas studies show that they may cause bacterial shifts which could contribute to obesity, increased disease risk, and antibiotic resistance
  8. Use plain soap, instead of antibacterial soaps antibacterial chemicals in soaps and gels could create resistant bacteria, according to Scientific American
  9. Exercise regularly – in addition to helping reduce stress, improve blood flow, exercise is known to improve our bacterial make up
  10. Manage Stressstudies show that high levels of stress can negatively impact the way our microbiome functions.

Talk to your health provider about supplementing. A probiotic supplement may be helpful for improving the balance of bacteria in the gut. Another option is to supplement with prebiotic fibers*, and there are some postbiotic supplements as well. Probiotics may be contraindicated in those with an overgrowth of bacteria (SIBO), or an immune deficiency. Talk to your health practitioner to determine if supplementation is appropriate, and which probiotic strains are best suited to your needs.

The Key to Reaching Your Ideal Weight

If you are struggling with your weight – just know, you are not alone – an estimated 70% of the population is overweight or obese today. In order to reach a healthy weight, the metabolism needs to be reset. When we focus on optimizing the metabolism – not only can our weight come back into balance, but it can help to lower our disease risk, and improve many other aspects of health too. The gut is just one factor in a healthy metabolism. Learn about the 10 keys to optimizing your metabolism in ‘The Perfect Metabolism Plan’.

Find more information & recipes about metabolism & health at

*please make dietary changes such as adding fiber and fermented foods gradually. If bloating or other digestive issues occur, back off and contact your doctor if extreme.


A Nutritionist & the Author of the book The Perfect Metabolism Plan, Sara Vance has been in the fitness and health industry for over 25 years.

Sara believes that healing the metabolism is the real secret to reaching our ideal weight and achieving vibrant health.

Sara empowers people how to use nutrition and natural lifestyle changes to live their very best life. Sara shares her knowledge for nutritional approaches to health in blogs, recipes, videos, and as a speaker – she has been a regular guest on San Diego morning shows for over 7 years. Find her articles, videos, and more information at:

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