Language of the Immune System for a Healthy Microbiome

It’s a zen koan for 2020, a spin on the parable of the tree falling in the forest: if your immune system speaks and no one understands what it’s saying, does it make a sound? The answer is yes. When in distress, the immune system rings proverbial alarm bells that are accompanied by warning messages that we need to decode.

This is critical work: headed into the fall, we’re fighting off both COVID-19 and this year’s version of the seasonal flu, both of which take advantage of weakened immune systems to ravage our respiratory tracts and other key organs. (Learn more on exactly how our immune system battles the flu in this great explainer.)

Here are some of the statements that your immune system could be whispering in your ear--or shouting at the top of its lungs.

“I’ve kept you sick with this cold for over a month now. My resources are depleted.”

A virus that won’t go away indicates that your immune system is struggling to perform its regular functions. The University of Maryland shares an easy-to-understand explanation of how the body reacts to a virus:

“When viruses enter our bodies, they find a cell and inject it with their genetic material. This allows them to take control of the cell and multiply.

To battle this, the body's immune system must destroy infected cells. When the body first encounters a new viral infection, it deploys T cells, which find and kill infected cells. If the infection continues, the body then deploys B cells, which create antibodies that can better attack infected cells.”

If the B cells are successful, antibodies are created that protect us from future infections. But if the T and B cells are out of energy, or if there’s a communication issue among members of the immune system’s team, then the immune system is telling us that it’s in need of repair.

“That awful stomach pain you’ve been having? It’s because I’m stressed. And guess what? Diarrhea’s next.”

Since almost 70% of the immune system lives in our gut, this message makes sense: the gut will complain loudly when its most important resident is malfunctioning. Dr. Erica Sonnenberg, a Stanford research scientist, breaks it down:

“The gut microbiota, also referred to as the microbiome, is the collection of microorganisms that call your intestines home. A major function of this community of bacteria is to consume carbohydrates. But not just any type of carbohydrates, a specific type called microbiota-accessible carbohydrates, or MACs. MACs are complex carbohydrates: the types found in fruits, vegetables, whole grains and legumes. When our gut microbiota consumes MACs it releases compounds into our gut that help our body regulate its immune system, keep pathogenic, or bad, bacteria at bay and even contribute to whether we are lean or obese.”

But when our MAC consumption is low and our microbiome becomes imbalanced, our gut begins to gurgle, sometimes quite literally.

“Yep, that’s another sinus/ear/fungal infection. You need more antibiotics, because my defenses aren’t working.”

Recurrent infections of the same type (4 or more in a year) means that the immune system isn’t developing antibodies to what made you sick in the first place. When the B cells struggle, you’re susceptible to getting the same infections again...and again. This is a sign that you need to investigate the underlying cause of your immunodeficiency.

When your immune system works well, it runs invisibly in the background, deterring and repelling threats to safeguard your body against invading pathogens. But when the immune system malfunctions, it speaks up; there are valuable lessons to absorb if we just listen.

Continue your gut check with our microbiota infographic shared at

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