Changes in Gut Bacteria Are Linked to Diet and Disease

Gut Microbiota

The human digestive system is home to trillions of bacteria and other microbes.

Collectively known as the gut microbiota or gut flora, this is one of the most active areas of research in nutrition, obesity and human physiology.

Recently, a review article discussing the role of the microbiota in the development of obesity and metabolic diseases was published in Advances in Nutrition.

Below is a summary of the review’s main points.

Gut Microbiota

Article Reviewed

Scientists at the University of Copenhagen, Denmark, reviewed the available evidence linking the gut microbiota with obesity, metabolic diseases and diet.

Can We Prevent Obesity-Related Metabolic Diseases by Dietary Modulation of the Gut Microbiota?

Beneficial Functions of the Gut Microbiota

Most of the gut microbiota lives in the colon, which may host more than 1,000 different species of bacteria.

Some of these bacteria have beneficial or even essential functions, whereas others are neutral or potentially harmful.

In healthy people, beneficial bacteria dominate the gut environment. Their most important functions are to:

  • Produce short-chain fatty acids to feed the cells that line the colon.
  • Protect the gut wall and keep harmful substances out of the blood.
  • Reduce the growth of harmful microbes by competing with them for resources.
  • Form essential vitamins, such as vitamin K.
  • Regulate the immune system.

Bottom Line: Our digestive system is home to trillions of bacteria, many of which have beneficial or even essential functions.

Imbalanced Gut Microbiota is Linked to Disease

A well-balanced gut microbiota is a sign of good health.

Unhealthy lifestyle habits and certain diseases are associated with a microbiota that is imbalanced or at least different from that of healthy people. This condition is sometimes called dysbiosis.

Adverse conditions that have been associated with changes in the gut microbiota include inflammatory bowel disease, type 2 diabetes, atherosclerosis and non-alcoholic fatty liver disease.

The gut microbiota of obese people is also different from that of normal-weight people.

However, these are all observational studies that can’t demonstrate a causal relationship, and the true explanation for these associations is currently unknown.

Yet experiments in mice and humans suggest that the microbiota may play at least some role in the development of obesity and metabolic syndrome.

This is an active area of research, and new pieces to the puzzle are gradually being discovered.

Bottom Line: Several adverse conditions, such as metabolic disorders and obesity, are associated with an imbalanced microbiota.

How Do Nutrients Affect the Gut Microbiota?

Multiple factors affect the gut microbiota, including genetics, age and how you’re born. Yet the most important factor is probably your diet — what you eat and how much.

Below is a detailed overview of how different nutrients affect the gut microbiota.

Carbs and Fiber

Carbs are usually the main component of the human diet, and for this reason, the most common types of gut bacteria feed on carbs.

Some carbs, such as resistant starch, pass to the colon undigested. There, they are fermented by beneficial bacteria that produce short-chain fatty acids (SCFAs).

SCFAs are the main sources of nutrition for the cells lining the colon, and essential for colon health.

Additionally, a high rate of carb fermentation helps maintain a slightly acidic environment within the colon, favoring the growth of beneficial bacteria.

However, certain types of fiber are better than others. These are known as prebiotics, and include fiber such as inulin, galacto-oligosaccharides, fructo-oligosaccharides,resistant starch and arabinoxylan.

By increasing the activity and growth of beneficial bacteria, prebiotics have a variety of health benefits.

Yet keep in mind that easily digested carbs, such as sugar and refined carbs, do not offer the same benefits as whole, fiber-rich carbs.

Bottom Line: Fiber is essential for many beneficial gut bacteria. The healthiest types of fiber are collectively known as prebiotics.


Animal studies indicate that very high fat consumption may lead to metabolic endotoxemia.

Metabolic endotoxemia is characterized by high circulating levels of lipopolysaccharides, triggering an inflammatory response in the body.

Lipopolysaccharides, also known as endotoxins, are found in the membranes of gram-negative bacteria, which are potentially harmful.

Scientists have suggested that metabolic endotoxemia may be associated with an imbalanced gut microbiota.

They speculate that endotoxins from harmful bacteria may somehow escape across the gut wall and into the blood stream, promoting metabolic disorders.

This idea is supported by observational studies that have associated high levels of lipopolysaccharides with obesity, type 2 diabetes and metabolic syndrome.

Interestingly, eating prebiotic fiber may counteract many of these effects.

However, more human studies are needed before any strong conclusions can be reached.

Bottom Line: Animal studies have associated high fat intake with metabolic endotoxemia. However, prebiotics may counteract these effects


Little is known about the effects of protein on the gut microbiota, but several studies indicate that a high intake of protein may be harmful for colon health.

Undigested protein may reach the colon, where it is fermented by bacteria that produce potentially harmful substances.

This may not be a concern on a well-balanced diet, since eating prebiotic fiber may counteract some of these effects.

Bottom Line: High protein intake may have adverse effects on colon health, but prebiotics may counteract some of them.


Probiotics are live bacteria that provide health benefits when consumed.

These include friendly bacteria such as Bifidobacteria and Lactobacillus, which have numerous health benefits.

Supplements that contain both probiotics and prebiotics are known as synbiotics.

Synbiotics help the friendly bacteria survive and grow in the digestive tract, and are probably more effective than taking probiotics or prebiotics separately.

Bottom Line: Numerous studies show that probiotics may have various health benefits. These benefits may be greater when probiotics are taken with prebiotics.

Treating Metabolic Conditions Through Diet

A few human trials have found that supplementing with dietary fiber, including prebiotics, may change the gut microbiota. It may also improve insulin sensitivity, systemic inflammation and lipid metabolism.

Although these findings clearly show that taking prebiotics may improve metabolic disorders, they do not prove that these disorders were caused by an imbalance in the gut microbiota.

In fact, supplementing with prebiotics might improve metabolic conditions independently from their effects on the microbiota.

Bottom Line: Human trials have shown that prebiotics may improve metabolic disorders and change the gut microbiota. However, the role of the microbiota is still unclear.

Summary and Real-Life Application

In short, this review shows that metabolic disorders, such as obesity, are associated with changes in the gut microbiota.

Additionally, studies indicate that improving the gut microbiota may help treat metabolic disorders. However, the causal role of the microbiota has yet to be proved.

Certain types of fiber, known as prebiotics, are probably the most effective dietary strategies for maintaining a healthy gut microbiota.

Written by Aline Pilani

Hey, I’m Aline Pilani. I am a certified personal trainer and nutritionist. I have spent the last 10 years of my life helping people losing weight, increase their health and confidence, and I truly want to do the same for you.