Low gut microbiota diversity goes with higher rates of obesity, insulin resistance, fatty liver disease and low-grade inflammation, so the goal is a diverse gut. Long-term eating habits shape that diversity. Above all, a fiber-rich diet shapes it. Prebiotics and probiotics reduce low-grade inflammation in the gut. They also improve gut barrier integrity (how well the gut lining holds together).
If Hippocrates, the father of modern medicine, is to be believed, “All disease begins in the gut”. The gut and its microbiota form a complex, open, and linked ecosystem. It is widely accepted that healthy gut microbiota is essential for good health. An imbalance in the gut flora could leave one open to a wide range of diseases, both infectious and non-communicable, including diabetes and obesity. We urgently need good ways to prevent and treat metabolic disorders such as diabetes and obesity. In this article, we look at the role of gut microbiota in diabesity (diabetes plus obesity). We also review ways to reach the best metabolic health.
- What is Gut Microbiota and Gut Microbiome?
The gut microbiota is the term for the whole community of microbes in the gut. The gut microbiome is the full set of genes those microbes carry. The gut microbiota is known to be associated with metabolic syndrome and the diseases that come with it. These associated diseases, including obesity, T2D, and fatty liver disease (NAFLD/NASH), all seem to be linked to changes in which microbes are present. However, causality has not been proven yet. For this reason, the potential causal and personal role of the human gut microbiota in obesity and T2D is a high research priority. The gut microbiome holds a huge variety of microorganisms. They range from bacteria to viruses, fungi, phages, protozoa, and archaea, and all of them live in our adult bodies. One proposed view is that our microbiota is a microbial (endocrine) organ living in partnership inside our gut. This has led to a new view. It suggests that many lines of microbes can talk to each other and shape the host’s immune system and metabolism in several ways. Some of the abilities of this “organ” are:
- The degradation of otherwise indigestible components of our diet
- harvesting of energy and nutrients
- shaping of the host immune system
- maintaining the integrity of the gut mucosal barrier
- xenobiotic metabolism
In this way, gut microbiota add to our biology in ways that help both sides. Current research data on precision (personalized) nutrition suggest that diet changes should be tailored to each person to prevent chronic diseases. That includes giving pre-, pro-, and syn-biotics, as well as antibiotic treatment. The tailoring would be based on genes, food and drink intake, and nutrient intake. It would also be based on the microbiome, metabolome, and other omic profiles (detailed lab profiles of the body).
- The gut and diet….
Diet is essential to what lives in the gut and how it works. The microbiota changes quickly when the diet changes in big, fast ways. Short-term changes can change the human gut microbiota in function and makeup significantly in 48 hours. Examples are switching between plant- and meat-based diets, or adding more than 30 grams of fiber per day, or following a diet with a different fat/fiber mix. Fiber-rich diets have been shown to improve insulin resistance in lean and in obese subjects with diabetes. However, only long-term eating habits shape the makeup of the gut microbiota. That is because short-term diet changes failed to change the major features and classification of the microbiota.
- What is the impact of Gut Microbiome in Insulin Resistance and Type 2 Diabetes?
When the gut microbiome has low diversity, there are higher rates of obesity, insulin resistance, non-alcoholic fatty liver disease (NAFLD), and low-grade inflammation. Low bacterial diversity also had pro-inflammatory traits. Two signs suggested this. There were fewer butyrate-producing bacteria. There were more mucin-degrading bacteria, which break down the gut’s mucus layer. These traits potentially weaken the gut lining. That causes low-grade inflammation through endotoxemia (bacterial toxins getting into the blood). This low-grade inflammation of visceral adipose tissue (the fat packed around your organs) may provide a link between obesity and insulin resistance. Ethnic differences between human populations may also affect which microbes are present. Karlsson et al. compared T2D-associated metagenomes (gut gene data) between Chinese and Swedish subjects with T2D. The data pointed to different gut bacterial species doing similar metabolic jobs. The authors could also tell subjects with T2D apart from healthy subjects. Their predictive power was better than that of body mass index (BMI).
- What is the effect of Gut Microbiota in Lipid Metabolism?
In recent decades, it has become clear that lipids (fats) from the diet also coordinate many metabolic, inflammatory, and innate immune processes. The role of dietary fats in nutrition is beyond doubt. Fat buildup together with low-grade inflammation is a hallmark of atherosclerosis (hardening of the arteries). There is emerging evidence that how atherosclerosis develops is related to gut microbiome differences from person to person. Atherosclerosis seems to be related to TMAO. TMAO is a new marker associated with higher risk of atherosclerosis and coronary artery disease. Bile acids are other key gut regulators of fat and cholesterol metabolism. They help the gut absorb and move nutrients, vitamins, and fats from food. Bile is made in the liver (helped by products from fat breakdown). Then 95% of all bile acids are reabsorbed in the terminal ileum (the end of the small intestine) and taken back up by the liver. This loop is called the enterohepatic circulation. The gut microbiota turns primary bile salts into secondary bile salts. It does this through bile acid de-hydroxylation. Short courses of oral antibiotics affect which gut microbes are present and how bile acids are handled in humans. Even so, researchers found differing effects on glucose metabolism.
- What effect does the Gut Microbiome have on Appetite?
Obesity is defined as an imbalance between energy intake (usually food intake) and energy use. The brain is a key regulator that detects changes in energy balance. It triggers behavioral and metabolic responses to correct them. The hypothalamus plays an important role in controlling both food intake and energy balance. It receives hormone and (vagal) neuronal signals from the rest of the body. Changing the gut microbiome with prebiotics has also been shown to affect portal vein levels of other hormones, including GLP-1. That in turn affected food intake, followed by a drop in body weight and fat mass.
- What are the Microbial Signatures in T2DM and Obesity?
Dysbiosis is the disruption of the normal microbiota. It has been described as involved in a wide range of diseases, including diabetes, obesity, and insulin resistance. It does this by upsetting the energy balance. So it has been suggested that changing the microbiota may help treat these diseases. This could be done directly (by antimicrobials, diet, prebiotics and/or probiotics, stool transplant, microbial-derived signaling molecules or metabolites) or indirectly (e.g., immunotherapy).
- What is the Influence of Diet on Gut Microbiota in Diabetes and Obesity?
Diet is one of the major lifestyle factors in the start, prevention and control of diabetes, obesity and other cardiometabolic (heart and metabolic) diseases. It is also strongly linked to changes in microbiota. Many reports have shown that a genetic risk for obesity may have interacted with an obesogenic (obesity-promoting) setting. Together they may have driven the obesity epidemic. That setting includes a major shift in how people eat, which affects the gut microbiota. It also includes a sedentary lifestyle and physical inactivity. To date, there are many popular diets, including Mediterranean, gluten-free, vegan, Western, omnivore, and vegetarian. Most of these diets have been clearly linked to different microbiome profiles. After the industrial revolution, Western countries moved from the traditional diet to a diet rich in heavily processed foods, fats, sugars, proteins, and additives. That diet stayed low in micronutrients and dietary fibers. It is also called the Western diet. These diets lacked dietary fibers. Fibers are essential for gut health because they spur the growth and/or activity of certain helpful microorganisms. In contrast, people in traditional societies with a fiber intake of almost 50–120 g/day carry a much more diverse gut microbiota, which indicates good health. SCFAs (short-chain fatty acids) are found in lower amounts in people eating a Western diet. The Western diet was correlated with a drop in total bacteria and in helpful resident bacteria. Vegan and vegetarian diets are rich in plant foods that gut bacteria can ferment. Subjects eating them were reported to have a microbiota with a lower abundance of Bacteroides sp. and Bifidobacterium sp. The Mediterranean diet (vegetables, moderate consumption of poultry, olive oil, cereals, legumes, wine, nuts, fish and a low amount of red meat, dairy products, and refined sugars) provides benefits. They come from its high content of mono-unsaturated and poly-unsaturated fatty acids. They also come from its high levels of antioxidants, fibers and vegetable protein. People on a Mediterranean diet have a gut microbiota with high levels of Lactobacillus sp., Bifidobacterium sp., and Prevotella sp., and low levels of Clostridium sp. These species are associated with weight loss, a better lipid profile and decreased inflammation. Proteins in the diet have also been reported to help shape the microbiota. People eating a diet rich in beef had high levels of Bacteroides sp. and Clostridia. They were low in Bifidobacterium adolescentis, unlike people eating a meatless diet. Several recent studies have shown that some diets are linked with microbial diversity. These include vegetarian whey/pea protein and animal protein (meats, eggs, and cheese). Eating animal-based protein was positively associated with more bile-tolerant anaerobes (bacteria that live without oxygen). These include Alistipes sp., Bilophila sp., and Bacteroides sp.
- What are the Future Perspectives on the Gut Microbiome?
Growing evidence suggests that gut microbiota plays a significant role in the start and progression of metabolic syndrome (MS). The gut microbiota was proven to modulate plasma glucose, appetite, serum lipids and pro-inflammation. Prebiotics or probiotics are widely used to change the microbiota. They can reduce low-grade intestinal inflammation. They can also improve gut barrier integrity. That can reduce plasma glucose and serum lipid levels, induce weight loss and decrease insulin resistance. Based on these results so far, the gut microbiota may be a potential treatment target for MS. However, clinical trials addressing how well current or potential treatments work in metabolic syndrome are needed. Also, people who are obese are likely to have an imbalance in gut microbiota makeup. This possibility is an exciting path for more research and possible new treatment targets. However, because most studies have been done in animals, direct translation of the findings to humans is limited. Prebiotics or other newly found helpful bacterial strains are potential interventions that will be used for treatment in the near future. It will be important to test how well they work. Likewise, studies will test metabolites (by-products) of the microbiota, including SCFA butyrate supplements. They will check if this compound has similar effects on food intake, energy use, and metabolic health in humans. The human gut microbiota affects whether metabolic syndrome develops, and those effects can be changed. That makes managing it a promising treatment approach. Mapping each person’s microbes at the metagenomic (gene) level gives insight into specific treatment targets. It also supports personalized treatment.
Frequently asked questions
What is the difference between gut microbiota and the gut microbiome?
The gut microbiota is the community of microbes living in the gut: bacteria, viruses, fungi, phages, protozoa and archaea. The gut microbiome is the full set of genes those microbes carry. Together they work like an organ. They break down food we cannot digest, harvest energy and nutrients, shape the immune system and keep the gut barrier intact.
How does the gut microbiome affect insulin resistance?
Low diversity in the gut goes with more obesity, insulin resistance, fatty liver disease and low-grade inflammation. A low-diversity gut has fewer butyrate-producing bacteria and more mucin-degrading bacteria. That mix can weaken the gut barrier. It can cause low-grade inflammation through endotoxemia. Inflammation of visceral fat (the fat packed around your organs) may be the link between obesity and insulin resistance.
How quickly does diet change your gut bacteria?
Fast, but not for long. Big diet shifts can change the gut microbiota’s makeup and function within 48 hours. Examples are switching between plant- and meat-based diets or adding more than 30 grams of fiber a day. Only long-term eating habits reshape its major features, so a short diet change is not enough.
Do probiotics and prebiotics help metabolic health?
Yes. Prebiotics and probiotics are the most widely used ways to adjust the gut microbiota. They can reduce low-grade intestinal inflammation and improve gut barrier integrity. That lowers plasma glucose and serum lipids, supports weight loss and decreases insulin resistance. Prebiotics have also been shown to change GLP-1 levels, which affected food intake, body weight and fat mass.
What diet is best for gut bacteria?
A fiber-rich one. People in traditional societies eating 50 to 120 grams of fiber a day carry a far more diverse gut microbiota. The Western diet of heavily processed foods, fats and sugars lowers helpful bacteria. The Mediterranean diet brings more Lactobacillus, Bifidobacterium and Prevotella. These species are associated with weight loss, better lipids and less inflammation.
Related reading
References
- Frontiers in Nutrition: Gut Microbiota, Host Organism, and Diet Trialogue in Diabetes and Obesity. Retrieved from https://www.frontiersin.org/articles/10.3389/fnut.2019.00021/full
- NCBI (2018): The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013535/
- NCBI (2017): Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5655955/
Medically reviewed by Dr. Gurpreet Singh Padda, MD, MBA, MHP
Interventional pain physician, addiction medicine specialist and obesity medicine diplomate.
Licensed in Missouri and Illinois.
Last reviewed June 18, 2026
