The Microbiome and the Influence of Nutrition


Flip through most health and nutrition-focused magazines these days and you’ll likely come across an article on the microbiome. In addition, multiple research studies are being conducted to further develop our understanding and appreciation for the microbiome, how it functions, and how we me may be able to influence it. 

So, what is the microbiome? Simply put, it is the collection of all microbes, such as bacteria, fungi, and viruses that naturally live on our bodies and inside of us. There are trillions of such micro-organisms in the human body, a staggering number that exceeds that of human cells by approximately 10 to 1 (or more, depending on who you read). 

When we break down the word, we see that “micro” means small, while “biome” relates to a community occupying space. Hence, the microbiome is a microscopic community of organisms that serve multiple functions within the body. Most notably, the microbes help us digest food in order to produce energy and contribute significantly to our overall health and wellness—likely by protecting us against pathogens and helping to develop our immune system. This latter effect on immunity has been the focus on much recent attention given to the microbiome. Interestingly, when in balance, the microbiome may actually help to control bloating, mood, depression, anxiety, and binge eating. 

While microbes inhabit all parts of our body that are exposed to the environment, including our skin, mouth, eyes, and urinary tract, the majority reside in the gut where they have a constant supply of nutrients. Therefore, the recent attention on the microbiome has been largely focused on the “gut microbiome.” Studies show that the human gastrointestinal tract houses a vast collection of bacteria that play an important role in maintaining the health of the gastrointestinal system. In fact, there are from three to 100 times more bacteria in the gut than there are cells in the human body. Some common forms include the following: Lactobacillus reuteri, Lactobacillus acidophilus, Bifidobacterium longum

Research and Testing the Microbiome

Unlike other popular topics within the health field for which people make claims within substantial evidence in support of such claims, the microbiome has been well-researched. In fact, a substantial amount of time and money has been allocated to investigations into the microbiome, with a particular focus on the link between the microbiome and human health. The National Institutes of Health funded the Human Microbiome Project, spanning over 10 years, in an effort to provide discoveries that link interactions between humans and their microbiomes to health-related outcomes. A search on the medical database Pubmed using the term “microbiome” returned 138,175 hits—clearly indicating extreme interest in this field of study. 

With all the talk about this exciting area, many individuals have asked how they can have their microbiome tested. It should be understood that microbiome testing measures the amount and types of microbes, such as bacteria and viruses, in your gut and uses a small stool sample for the analysis. While such tests can be conducted in a doctor’s office, there exist many companies that now offer the testing via an at-home test kit. The test procedures are rather simple; collect a small stool sample onto a cotton swap; place inside a collection tube; seal within an envelope; and mail for analysis. The company typically returns a full report, along with recommendations for how the microbiome can be improved. One word of caution: do not compare your results to those of someone else. The weight of evidence to date indicates that a high level of interindividual variability exists in the human microbiome, so individuals should only focus on where they are now and how they might improve. 

Influences on the Microbiome

It has been noted that a variety of factors can influence the microbiome, including conditions surrounding birth (delivery method—vaginal birth preferred) and early phase development (feeding methods—breastfeeding preferred), as well as the use of antibiotics, and age. Related to the present article, a great deal of attention has been focused on the role of nutritional intake, as this is something most people have direct control over. 


The relationship between nutrition and the gut microbiome has been well-described, with multiple studies focused on this area of research. That said, this continues to be an area of ongoing investigation, with new information becoming available regularly. What we know from studies to date is that the diet is a source of fuel for the microbiota and a good indicator of the composition of the gut microbiome, as there exists a direct relationship between diet and the abundance of certain gut microbial communities. The overall dietary goal is to consume a highly diverse variety of plant-based foods, those of different colors (e.g., 5 or more servings of fruits and vegetables each day). 

Much of the nutrition research has focused on the ingestion of carbohydrates in the form of dietary fiber, which serve as fuel for the gut microbiota. Beyond this, intake of fermented foods is widely suggested, including sauerkraut, kimchi, kefir, and yogurt. Diets high in fermentable carbohydrates support the relative abundance of Bifidobacterium, Ruminococcus, Dorea and Roseburia, among others. Collectively, intake of the above foods on a regular basis should ensure that you are building a diverse community of bacteria within the gut—one that will promote health and well-being. 

At the same time, there are certain things that should be avoided. First, a diet that is low in dietary fiber is not helpful. Men should aim for at least 30 grams of fiber per day, while women should aim for at least 25 grams per day. In addition, simple sugars should be avoided, as well as artificial sweeteners, additives, and preservatives—as these can negatively impact the microbiome (or have negative consequences in terms of glucose tolerance). Finally, limiting or eliminating processed foods and fast foods should be a goal if a healthy gut microbiome is desired. 

While whole food nutrition is likely most influential on the gut microbiome, dietary supplements are often recommended as well. Most common are the pre- and pro-biotics. While a lot has been shared regarding both of these, probiotics represent the “good bacteria” that appear to aid overall health, while prebiotics serve as a “food” that is used by the probiotics. The two certainly work together to create a healthy bacterial environment in the gut—one that fosters stronger immunity and a more capable defense system. 


The microbiome is the collection of trillions of microbes that influence our health, with the majority contained within our gut. While the microbiome is influenced by many factors, whole food nutritional intake appears to be the most important. If the goal is to bolster the microbiome and related immune system, consuming a variety of plant-based foods appears most important. Beyond this, the use of prebiotic and probiotic dietary supplements may complement the ingestion of a microbiome-smart diet.

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