Research Finds Gut Microbiome Alters the Way You Lose Weight

Research Finds Gut Microbiome Alters the Way You Lose Weight

Diet and exercise will help you lose weight.

We’ve heard it on repeat for years.

But what if there’s more to it than that?

A lot of research has suggested our gut microbiome can influence our ability to lose weight, especially if we are choosing the right foods.

Our microbiome makes up healthy colonies of good bacteria that help us to digest and absorb nutrients, often referred to as our gut flora.

These beneficial gut bacteria are made up of different species of bacteria, fungi, viruses, and other microorganisms and vary from person to person in composition.

Colonies of these commensal bacteria are located in our digestive tract.

They act as a part of our innate immune system.

Our immune system is our body’s defense against the invasion of harmful pathogens.

These microorganisms can reduce the inflammatory response, improve metabolism, and decrease the risk of disease and obesity among many other benefits.

They’ve been described as our body’s second brain because it relies on the same type of neurotransmitters as our central nervous system for communication.

There are numerous bacterial species, each performing a different role but working together synergistically.

A good gut microbiota composition can help to improve certain medical conditions such as arthritis (specifically rheumatoid arthritis), allergies, constipation, diarrhea, abdominal pain, and atherosclerosis.

It can even decrease the risk for small intestinal bacterial overgrowth (SIBO), a condition that causes disturbance in the small intestine.

Previous studies have suggested that our gut microbiota may also play a role in the gut-brain axis in autism spectrum disorder (1).

This gut-brain axis is the pathway for communication between our GI tract and our central nervous system.

Benefits of the human gut microbiota heavily rely on the composition of the microbiota, the presence of more good bacteria than bad.

As you can see, these tiny organisms can have a huge impact on our health and wellbeing.

So much so that there is a whole study dedicated to learning more about it, known as metagenomics.

Metagenomics is the study of the human genome and it’s the relationship to our gut microbiota.

So how can these good bacteria benefit weight loss?

Weight Loss Takes Guts?

Weight loss easier - gut bacteria

Our microbiome is found in the human gut, or gastrointestinal tract (GI tract).

Our gut is made up of our stomach, small intestine, large intestines, known as our colon, and other digestive organs such as our mouth and esophagus.

Our gut bacteria, also referred to as gut flora, feed off of prebiotics present in our digestive tract.

Prebiotics are compounds such as soluble fibers found in foods that promote their growth or activity in the human body.

You can improve your gut, immunity, and overall health by increasing these microorganisms.

You can do this by consuming more probiotic and prebiotic foods.

Probiotics play an important role in maintaining a healthy balance within the gut flora.

Certain conditions or treatments can reduce our flora, putting us at risk for infection.

One example is antibiotic use.

Antibiotics not only kill harmful bacteria but also kill healthy bacteria, disturbing the balance of our microbiota, resulting in dysbiosis.

Something important to consider next time you take a course of antibiotics.

Microbiome dysbiosis results when there is a lack of diversity of the microbiome, resulting in an imbalance that can render higher susceptibility to disease pathogenesis. 

The most beneficial types of probiotics include lactobacillus and bifidobacterium strains however, many other beneficial bacteria strains are being researched.

You can find good sources of probiotics in fermented foods such as kimchi, yogurt, kefir, tempeh (fermented soybeans), miso, and sauerkraut.

Good prebiotic foods include:

  • garlic
  • onions
  • leeks
  • asparagus
  • bananas
  • legumes
  • Jerusalem artichokes
  • chicory root
  • beets
  • dandelion greens
  • yeast
  • whole grains
  • oats and other complex carbohydrates and resistant starches.

Disruption of healthy bacteria in the colon can result in inflammation and troublesome conditions.

It can also affect peristalsis in the colon, the contraction of muscles that moves food along for nutrient absorption by intestinal cells.

These conditions include clostridium difficile infection, inflammatory bowel disease, ulcerative colitis, diarrhea, and even increased risk for colon cancer.

When we are low on good bacteria in our gut, our microbiome is unbalanced.

This leaves space for pathogens to disrupt the flora and cause illness.

Aside from antibiotic use, other health conditions can disrupt our gut flora including metabolic syndrome, autoimmune diseases, and viruses.

A poor diet can also disrupt our gut flora.

It is also linked to increased risk for obesity and other chronic diseases.

However, research has shown promise with improvement in weight loss by improving our gut health.

In a systematic review and meta-analysis of 21 different studies on prebiotics, probiotics, and synbiotics on body weight, probiotics were associated with a significant improvement in body mass index (BMI), fat mass, and body weight (2). 

Let’s take a look at some of the key players in our gut health

Gut Bacteria: Good vs Bad Players

A number of studies have shown specific gut bacteria may play a key role in weight loss, such as the genus Prevotella (3).

This genus of bacteria was found to be some of the fastest-growing microbes.

It’s believed that bacteria that grow faster take more nutrients in food for their growth, leaving less for us to cause weight gain. 

Those bacteria that produce enzymes that rapidly break down starches or fiber into sugar had the opposite effect on weight.

The main functions of the microbiota are digestion, vitamin synthesis for Vitamin B12, Vitamin K, thiamine and riboflavin, and metabolism (4).

Some forms are believed to increase energy production from food and cause inflammation that may be linked with threats of obesity.

Obese individuals tend to have a greater amount of Firmicutes.

These bacterial taxa are shown to negatively affect our resting energy expenditure, a.k.a the calories we burn at rest.

Bacteroidetes, on the other hand, show a positive correlation with body weight.

A higher ratio of Firmicutes to members of the phylum Bacteroidetes is believed to disrupt our metabolism and put us at risk for weight gain (4).

Akkermansia muciniphila is another bacteria present in the intestinal tract shown to improve human host health.

This strain of bacteria has been linked to lower fasting glucose, subcutaneous fat measurements, and inflammation in mice.

Faecalibacterium prausnitzii, an anaerobic bacteria, is one of the main components of the gut microbiota and one of the most important butyrate-producing bacteria.

Butyrate, a short-chain fatty acid, is a metabolite produced from the breakdown of fiber made by certain types of bacteria.

Butyrate is said to have anti-cancer and anti-inflammatory functions that could help decrease the risk of diseases such as heart disease and other inflammatory diseases (5). 

Some microbes are downright harmful to our gut bacteria, such as pathogenic bacteria strains Escherichia Coli, Clostridium Perfringens, and staphylococcus microbial cells.

These are pathogenic bacteria that can cause illness in healthy people by attacking host cells.

How to Improve your Gut Microbiota

Now that we know what a critical role our gut health plays, how can we improve our body chemistry to support it?

There are some environmental factors that can affect our gut health including age, gender, stress, medication, lifestyle, and presence of GI disorders.

The human gut microbiome is established in early life.

Gut health is heavily influenced by the microbial composition of our mother and how we were delivered (through birth canal or cesarean).

These gut microbes are a result of the vaginal microbiota of our mother.

It’s also influenced by the presence of breast milk as an infant.

Being fed breast milk during infancy over formula increases the diversity and strength of the microbiome.

Aside from genetic factors, our lifestyle can largely impact the presence of microorganisms in our gut.

Numerous studies conducted on germ-free mice suggest that a high-fat diet and a high-sugar diet results in a decrease in immune function as a result of dysbiosis.

The first step to increasing the good bacteria in our digestive tract is diet.

Let’s take a look at some foods that heal the gut and cut down on body fat.

Gut Bacteria – Gut Healing Foods

A diet high in fat and meat is associated with a higher risk for the development of conditions such as Crohn’s disease, Inflammatory Bowel Disease (IBD), and ulcerative colitis (UC).

High intakes of these types of foods result in inflammation that can wreak havoc on our good bacteria.

Choosing a vegetarian diet or a high-fiber diet can help to reduce this inflammation. 

It can also help to boost Prevotella bacteria (6). 

Those who struggle to get enough probiotic foods in their diet can also utilize probiotic supplements however, further research is still needed on their effects.

Supplements should contain a number of bacteria and they should be live bacteria for health benefits.

Prebiotics are another important factor in improving microbiome diversity.

Most are able to get adequate prebiotics in their diet by choosing high-fiber foods such as fruits, vegetables, and whole grains.

The recommended intake of fiber is 25 grams of fiber a day for women and 38 grams a day for men.

However, the average intake of fiber for adults in the United States is about 15 grams of fiber a day.

Not only do these help to promote the growth of beneficial bacteria, but it also provides many other health benefits.

Prebiotic foods can help reduce the risk for heart disease, diabetes, obesity, and other chronic diseases.

Studies have shown dietary polyphenols can also help.

Polyphenols act similar to prebiotics and can exert antimicrobial activities to increase immune response and prevent pathogens (7).

Polyphenols are natural compounds found in fruits, vegetables, cereals, tea, coffee, dark chocolate, and red wine, among others.

Studies have shown polyphenols to help increase commensal bacteria and decrease risk factors for various diseases (7).

Fecal Microbiota Transplants?

The standard recommendation for those with alterations in their gut microbiome is to eat more fiber-rich, plant-based probiotic and prebiotic foods.

It is also suggested to reduced highly processed foods and red meats. 

For those who require more than just a dietary adjustment to improve their gastrointestinal tract flora, fecal microbiota transplant procedures have been created to help increase intestinal microbiota.

A recent study suggests fecal transplants from a healthy adult with high Prevotella bacteria may be able to help increase recipients who have low amounts of this bacteria (8).

A fecal microbiota transplant, or a stool transplant, is when you take stool from a healthy donor and transplant it to another to help improve their digestive system’s microenvironment.

It is an effective treatment for those suffering from Clostridium difficile infection and is more successful at treating than with the use of antibiotics.

Conclusion on Gut Bacteria and Weight Loss

A diverse microbiome can not only have a great impact on the health of our GI tract and reduce exposure to pathogenic organisms, but it can also improve the human metabolism and decrease the risk for obesity.

Choosing food sources rich in dietary fiber, polyphenols and probiotics can improve the human microbiome by improving the composition of the microbiota.

Probiotic-rich foods include fermented foods, such as yogurt, and are easily accessible to most individuals. 

These live microorganisms can provide a positive impact and support a healthy body and weight.

Further investigation is needed on the effects of probiotic and prebiotic supplements however, reducing red meat, processed foods, and high-fat foods can improve the composition of the gut microbiota.

With so many different strains of microbes, further study is needed to fully understand their function and effect on human health.

Because of this, the National Institute of Health has created the Human Microbiome Project for metagenomic analysis on the various species levels

Metagenomes are the study of genetic material from a mixed community of organisms.

This can hopefully help us better understand and utilize these microorganisms for the betterment of the human body.

Avoiding an unhealthy diet and choosing more plant foods may be the microbiome solution.

A high intake of fruits, vegetables, and whole grains can help to limit bad bacteria and create a healthy microbiome for the long run.

Because of the connection between gut health and weight loss, these microbes may be a beneficial treatment for those with obesity or who struggle to lose weight.


  1. Srikantha, Piranavie, and M. Hasan Mohajeri. “The possible role of the microbiota-gut-brain-axis in autism spectrum disorder. (Xanax) ” International Journal of molecular sciences 20.9 (2019): 2115.
  2. John, George Kunnackal et al. “Dietary Alteration of the Gut Microbiome and Its Impact on Weight and Fat Mass: A Systematic Review and Meta-Analysis.” Genes vol. 9,3 167. 16 Mar. 2018, doi:10.3390/genes9030167
  3. Hjorth, M.F., Blædel, T., Bendtsen, L.Q. et al. Prevotella-to-Bacteroides ratio predicts body weight and fat loss success on 24-week diets varying in macronutrient composition and dietary fiber: results from a post-hoc analysis. Int J Obes 43, 149–157 (2019).
  4. Aoun, Antoine et al. “The Influence of the Gut Microbiome on Obesity in Adults and the Role of Probiotics, Prebiotics, and Synbiotics for Weight Loss.” Preventive nutrition and food science vol. 25,2 (2020): 113-123. doi:10.3746/pnf.2020.25.2.113
  5. Ferreira-Halder, Carmen Veríssima et al. “Action and function of Faecalibacterium prausnitzii in health and disease.” Best practice & research. Clinical gastroenterology vol. 31,6 (2017): 643-648. doi:10.1016/j.bpg.2017.09.011
  6. Gagliardi, Antonella et al. “Rebuilding the Gut Microbiota Ecosystem.” International journal of environmental research and public health vol. 15,8 1679. 7 Aug. 2018, doi:10.3390/ijerph15081679
  7. Kumar Singh, Amit et al. “Beneficial Effects of Dietary Polyphenols on Gut Microbiota and Strategies to Improve Delivery Efficiency.” Nutrients vol. 11,9 2216. 13 Sep. 2019, doi:10.3390/nu11092216
  8. Wilson, B.C., Vatanen, T., Jayasinghe, T.N. et al. Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity. Microbiome 9, 107 (2021).

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