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Lifestyle and the Microbiome: Simple Steps

A basic overview.

by Malay Nanavaty

Big Modulators of the Microbiome

We have covered many aspects of the microbiome over the course of the last few blog posts. We have learned about what kinds of bacteria live inside your gut, as well as how they adapt to external challenges. It is clear the microbiome is a dynamic community that is able to tolerate rapid changes in the environment. The genetic diversity present in a healthy microbiome enables it to live in harmony with its host, during both periods of stability and during periods of acute crisis.

This blog post is going to take a broader perspective on the topic of microbiome regulation. We will try to track how different nutrients affect the microbiome as a whole. Additionally, we will take a look at the important changes in microbiome populations that occur over the course of one’s life.

The Macronutrients and the Microbiome

Of course, the biggest factor that modulates your microbiome is the food you eat. This food essentially determines what kinds of bacteria need to exist in the gut to help you break down, detoxify, and absorb it. This dependence of the microbiome on diet is the reason that microbiomes across the world differ so much. Generally speaking, the healthiest people across the world are those who have the most diverse microbiomes. This diversity is essential for preserving the ability to process unique molecules in food as well as regulating immune function. There seems to be one major macronutrient that helps sustain this diversity: carbohydrates.

Carbohydrates: The Jeckel and Hyde Macromolecule

The food group of “carbohydrate” is one surrounded by insane amounts of controversy. No one can seem to agree on whether these molecules are good for you or not. When it comes to their impact on the microbiome, the topic becomes much more complicated. For the sake of sanity, I will keep my discussion of carbohydrates as basic and direct as possible.

The most important carbohydrates for your microbiome is fiber. Fiber is important because your body is unable to digest it by itself. As a result, fibers are the only major source of energy that your microbiome has access to. Additionally, fibers are very complex molecules that require a lot of processing for energy extraction. Because of this, your microbiome needs a lot of different bacterial species to come together for fiber processing.

When processing is complete, many of the fiber molecules are converted into a molecule called “short chain fatty acids (SCFAs)”. These molecules are important as a source of energy for colon cells. In addition to that, SCFAs signal to the gut tissue to maintain its structure. Without this signal, the gut would start to degrade and generate inflammation. Finally, due to the acidic nature of these SCFAs, they make sure that the colon remains acidic enough to stop any pathogens from colonizing the surfaces.

Protein, Exercise, and More: Non-Carbohydrate Contributors

There are a few minor contributors to the nutrition of the microbiome. Protein for example, can reach the colon and stimulate the growth of different kinds of bacteria. These bacteria are able to break down the protein but also generate toxic compounds such as ammonia and hydrogen sulphide as byproducts. These molecules can be absorbed into the bloodstream or directly damage colon cells.

Chronic stress also has a major impact on the microbiome. When a person is stressed, the contraction frequency of the gut changes. This change enables pathogenic bacteria to compete for space with resident microbiome members. On the flipside, regular exercise has been shown to promote diversity retention in the microbiome, although it is unknown how or why this occurs.

A Healthy Diet for the Microbiome

The general advice for maintaining a diverse microbiome is simple. Basically, make sure that you eat plenty of fiber along with energy dense foods. This additional fiber will maintain microbiome diversity as well as negate the detrimental effects of protein fermentation. Undigested fiber absorbs water, which means it will also absorb the toxic fermentation products made during protein breakdown. Additionally, high fiber will slow food transit through the gut, allowing the body to digest more protein before it gets to the putrefactive bacteria.

Age and Changes in the Microbiome

Unsurprisingly, the microbiome does not remain the same throughout your life. Different phases in your development are associated with different microbes living in your gut. For example, during gut colonization, one’s microbiome looks radically different than in its final form. However, the changes that happen in the microbiome during early infancy can have lifelong impacts on health.

Babies that are breastfed have been shown to have microbiomes almost entirely composed of Lactobacillus and Bifidobacterium. These bacteria help regulate healthy immune system development, reducing the prevalence of chronic autoimmune conditions such as asthma and eczema. Improper colonization at this early stage has also been shown to affect neural development, increasing the chances of developing disorders such as autism.

As you get older and start eating solid foods, your microbiome dramatically changes. The levels of Lactobacillus and Bifidobacterium drop dramatically as different Bacteroidetes and Firmicutes bacteria begin to dominate. As we discussed in a previous post, adults have few to none Lactobacilli colonizing their guts. Initially most people have many more Bacteroidetes in their microbiome than Firmicutes. However, this ratio slowly reverses as adults age. We do not know why this occurs, but it may be associated with age-related nutrient deficiencies and frailty.


The microbiome is an essential part of your digestive, developmental, and immune health. In return for this service, the only thing the microbiome asks for is food and shelter. Although we classify the microbiome as a community that is separate from your body, it should be thought of as any other organ. You are just as incomplete without a healthy microbiome as you are without a healthy heart. If you provide for the basic needs these bacteria require, your microbiome will remain healthy and so will you. Hopefully this post has provided you with a better picture of the basic functions of your

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