How Can I Improve My Microbiome?

When you read about that inventive simile—the one which paints your microbiome like the galaxy--it’s a fairly accurate comparison. There are about one billion trillion stars up there, according to astronomers, and multiple trillions of bacteria are working hard in our bodies to keep us healthy. This vast number of organisms is carried within you and everyone you see. Your microbiome is also as distinctive as you are; the exact population of bacteria, genes and related biocompounds is never found to be duplicated in anyone else—even twins.

Microbiome researcher Peter Belenky, PhD of Brown University describes the gut microbiome as home to literally trillions of bacteria that “have specifically coevolved with its host. This community helps the host in many ways such as breaking down dietary fiber and assisting in the maintenance of overall intestinal health -- by ensuring the intestinal cells form a tight barrier and competing for resources with harmful bacteria.”

History of Microbiome Research

Unlike knowledge of other biological structures and functions in the human body (eg, cardiovascular, joints, liver, etc.), the existence, structure and function of the gut microbiome is largely relatively new. According to a scientific analysis about the history of microbiome research, pioneering studies in this realm weren’t published until the early 2000s.

Despite its late entry into the scientific consciousness, this early research was so compelling that the US National Institutes of Health (NIH) launched the massive Human Microbiome Project in 2007. As of the end of 2017, according to the NIH, HMP researchers published more than 650 studies in this area.

The new second phase, called the Integrative Human Microbiome Project (iHMP), goes further. For example, in May of 2019, researchers from the iHMP published a series of papers investigating host and microbiome interactions in pregnancy and pre-term birth, inflammatory bowel disease and pre-diabetes.

Research on the microbiome is still an energetic, lively work in progress. This is important as the information yielded by vigorous studies informs probiotic/prebiotic, as well as symbiotic product development to be more precise and easier for you to use.

New Research Milestones

Microbiome research today is largely focusing on what affects the system’s health status and what can improve it.

A meta-analysis of metagenomic studies using a collective 3,655 samples from the oral and gut microbiomes revealed what the researchers called “staggering microbial gene diversity.”

The team of microbiologists and bioinformaticians wanted to find out how many genes are there in the human microbiome, and discovered that there may be more in the collective human microbiome than stars in the visible universe—and that up to 50% of these genes are unique to the individual (like a fingerprint; these genes are called “singletons”). Prior to this study, the scale of the human collective microbiome’s genetic diversity has not been quantified; such diversity, they said is “fundamental to deciphering human-microbe interactions.”

This groundbreaking work marks the gateway of future efforts to analyze the entire genome of the human microbiome, according to the researchers. Prior to this meta-analysis, most research efforts focused on identifying the types of bacteria comprising the microbiota (bacteria-only environment) and how each impacted health or disease; studying bacteria alone reveals only part of the microbiome story. Genetic content varies greatly between the same strains—much like siblings are not identical in their DNA. Future efforts will look at how genetic compositions of strains and species can impact homeostasis.

The microbiome—bacteria and genes—are directly impacted by diet, and can thus be remodeled. Like your weight and cholesterol, you can improve the quality and therefore, health, of your microbiome.

Research has shown that harmful changes in the microbiome can generate increased risk of illnesses such as cardiovascular disease, obesity and some cancers. But new research has identified certain molecules that can remodel an imbalanced/unhealthy microbiome into a more healthy one. The research utilized a class of molecules called self-assembling cyclic D, L-alpha-peptides created in a laboratory originally to kill pathogenic bacteria. This can potentially augment the use of probiotics, prebiotics and synbiotics in the future, especially in disease states.

The authors of this recent project state, “Our hypothesis was that instead of killing bacteria, if we could selectively modulate the growth of certain bacteria species in the gut microbiome using our peptides, more beneficial bacteria would grow to fill the niche, and the gut would be 'remodeled' into a healthful gut. Our theory was that process would prevent the onset or progression of certain chronic diseases."

Your gut microbiome is also highly affected by antibiotic therapy – and we do not recommend eschewing an antibiotic course if deemed necessary. But antibiotics, besides inducing stomach cramps and other GI woes, can also disrupt the healthy balance of the microbiome. A mouse study showed how a course of antibiotics changed the composition and metabolism of their gut microbiomes.

The research team’s goal is to find new ways to protect the inhabitants of the microbiome during and after a course of antibiotic therapy, also potentially alleviating some of the side effects of antibiotics. For example, they found that the mice given amoxicillin, an antibiotic commonly used to treat ear infections and strep throat, had drastically reduced certain bacteria normally present in the gut as well as changed the genes used by the remaining bacteria.

Meanwhile, diet can help shape a desirable microbiota, the bacterial population of the microbiome. Scientific authors of a new review assert, “Reshaping host–microbiota interactions through personalized nutrition is a new therapeutic avenue for both disease control and prevention.”

When seeking a diet that will improve the composition of your microbiome, you often find that it’s the same type of diet for all other aspects of health: high in fiber, abundant in fruits and vegetables, and to avoid processed, nutrient-stripped foods. For the microbiome boosting, fermented foods, which are making a huge splash in supermarkets (and on menus), is highly recommended, as are foods containing polyphenols (green tea, olive oil, seeds, nuts, red wine, grapes).

It is important to try to modify your diet for the long-term. Another recent study revealed a strong link between diet quality and the microbiome in the colonic mucosa; a high-quality diet was linked to more beneficial bacteria while a low-quality diet was associated with more potentially pathogenic bacteria and reduced beneficial microbes. A “good-quality diet” the authors used as a reference is that which is recommended by the Dietary Guidelines for America: high in fruits, vegetables, and whole grains, and low in added sugars, alcoholic beverages and solid fats.


It is not difficult to eat for a healthy microbiome—it’s the same as targeting any other area of health and overall well-being. If you are a person not inclined to consume yogurt or fermented foods (as these are not attractive to many), simply take good-quality probiotics and prebiotics to supplement and support the colonies of good bacteria in your microbiome. Even their genes will be nourished and happy!

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