Why Bacteria Can Protect Your “Second Brain” and Boost Your Immune System Naturally


You may be looking for ways to boost your immune system naturally. So let me ask a question: Have you ever felt “butterflies in your stomach” when you were nervous? Or had a “gut feeling” about something?

Well, this most likely means you’re getting signals or messages from a source that might surprise you: your second brain.

This second brain is technically known as your enteric nervous system (ENS). The ENS is comprised of over 100 million nerve cells that line the 30 feet of your gastrointestinal tract from the esophagus all the way to the rectum.

As you might expect, the ENS in your gut plays a big role in controlling digestion in multiple ways. Releasing enzymes necessary to break down the food you eat, controlling blood flow to assist with nutrient absorption, the process of elimination — these are all functions of your ENS.

Unlike the brain in your skull, the ENS can’t write a grocery list or multiply numbers.  But the two brains do communicate with each other in some ways that researchers are only now beginning to understand.

Scientists have discovered that the ENS can actually be responsible for triggering emotional responses. For example, bowel irritation can send signals to your skull’s brain leading to mood changes, even anxious or depressed feelings.

But one of the most fascinating things researchers are investigating is how your second brain can affect your immune response and promote a healthy immune system.


Your Second Brain and a Healthy Immune System

When you think of your immune system, your GI tract is probably not what comes to mind.

However, approximately 70% of your immune system is actually located in your gut. Scientists call this the GALT, or gut-associated lymphatic tissue.

A number of different immune cells live in the GALT, including activated T cells, macrophages, mast cells, and many others. Since many pathogens gain entry to the body via the gut mucosa, it’s vital to have a healthy community of immune cells to provide healthy immune system defense.

But in addition to the different types of immune cells, your gut also contains something else critical to good health. The GI tract is home to about 500 different types of bacteria — about 100 trillion organisms.

In fact, you have so many bacteria and other organisms in your gut, scientists now consider them to comprise a type of organ — the ‘microbial organ’ or microbiome.

Your Unique Gut Microbiome Serves Many Purposes

Every person’s body has a an entirely unique network of microorganisms, as these colonies have developed and multiplied since birth.

Approximately 85% of the bacteria in your gut should ideally be so-called friendly bacteria. These include species such as Lactobacillus or Bifidobacteria.

Far too often, however, non-beneficial bacteria start to crowd out the friendly strains. This imbalanced situation is known as dysbiosis. It can be the cause of common bathroom complaints, such as constipation or diarrhea, gas, bloating, and abdominal discomfort.

But as you’ve seen, your gut is also a big part of maintaining a healthy immune system. That’s another big reason to keep your gut health in top shape.

Unfortunately, a number of things can lead to dysbiosis or intestinal imbalance:

  1. Increasing age. The aging process leads to a decline in numbers of friendly gut bacteria, and an increase in the numbers of non-beneficial bacteria.
  1. Overuse of antibiotics. The CDC estimates that at least 30% of antibiotics prescribed during outpatient visits are actually unnecessary. Since they basically function to kill bacteria, their indiscriminate use can reduce the abundance and diversity of intestinal bacteria, including those important in immunity.
  1. Medications other than antibiotics.
  1. Excessive stress.
  1. Fatigue, and lack of quality sleep.
  1. Toxins in the environment.
  1. Nutritional deficiencies and poor diet.

The good news is that there are some positive steps you can take to balance your digestive system and boost your immune system naturally.

You can reduce your intake of processed foods and sugar. It’s also important to get more fiber into your diet. Most Americans do not get the 20-35 grams of fiber they need for good health. You can make positive lifestyle choices to reduce stress, avoid toxic products, and sleep better. You can also take probiotics after a course of antibiotics.

But one of the most important steps you can take for a healthy immune system is to add a high-quality probiotic supplement to your daily health regimen.

Most people think of yogurt when hearing about probiotics. But yogurt is usually highly processed and full of sugar, making supplementation a better plan.


Probiotics for Better Digestion and Boosting Immune System Health

The word probiotic actually means “for life.” Probiotics have been scientifically shown to help with numerous health concerns, particularly conditions of the digestive and immune systems.

John DiBaise, MD, a gastroenterologist at the Mayo Clinic , reports that “Probiotics seem to change how your immune system reacts to an invading microorganism and whether your digestive tract becomes inflamed as a result.”

Researchers continue to find more and more health benefits for taking daily probiotics, even beyond boosting your immune system naturally.

Here is a list of some researched strains of probiotic bacteria you may want to consider when making your best choice of an effective daily probiotic supplement:

  • Bifidobacterium bifidum. This strain of probiotic bacteria is the most prominent one found in the large intestine and female vaginal tract. Like all probiotics, B. bifidum assists the body in producing and absorbing vitamins. Plus, it boosts immune system function and improves digestive function. B. bifidum may also offer benefits against the overgrowth of yeast and provide help for occasional diarrhea.
  • Bifidobacterium longum. This bacterial strain is also found predominantly in the colon, and is considered by researchers to be one of the most important probiotic strains. B. longum produces lactic acid. This increases gut acidity to help discourage the growth of non-beneficial microbes. Studies suggest this strain promotes overall digestive health and immune support.
  • Lactobacillus acidophilus. The public is most familiar with this strain of probiotic bacteria, because it is commonly used in yogurt. Lactobacillus acidophilus works primarily in the small intestine, but also has the potential to support vaginal and urinary tract health. Additionally, L. acidophilus probiotic can reduce antibiotic side effects, including diarrhea. It can also help with common digestive concerns, including constipation.
  • Lactobacillus rhamnosus. This probiotic species resides primarily in the small intestine and vaginal tract. One feature is its resistance to stomach acid, which makes it a valuable addition to a daily probiotic supplement formula. It functions to optimize both the GI and genito-urinary tracts. Studies show that Lactobacillus rhamnosus can reduce occasional diarrhea, and even help with lactose intolerance.
  • Lactobacillus casei. This species of probiotic bacteria is located in the mouth and small intestine, where it has a wide temperature and pH range. This helps it survive the journey through the GI tract for better effectiveness. Research demonstrates that Lactobacillus casei provides immune support.
  • Lactobacillus sporogenes. Also known as Bacillus coagulans, this probiotic bacterial strain can produce spores, which helps resist destruction as they pass through the gut. Just a few of the benefits seen in studies with this Bacillus coagulans strain include improvement of diarrhea, simple constipation, and other digestive health concerns.


Choosing a High Quality, Effective Daily Probiotic Supplement for Boosting Immune and Gut Health

When you decide to shop for probiotic supplements, there are some things you should keep in mind.

As you’ve seen above, some probiotic bacteria strains are more resistant to surviving the harsh conditions of the GI tract. So it’s often best practice to choose a multi-strain probiotic formula for the most comprehensive support.

Some quality products also contain prebiotics, which essentially comprises a natural food source for the probiotic bacteria. This is a good feature to look out for when choosing a top probiotic.

Some products tout their numbers of colony forming units (CFU’s), which indicate the numbers of viable cells. However, as the National Institutes of Health notes, higher CFU counts do not necessarily translate to a product with more health benefits, as they can be misleading. Consumers should look for products labeled with CFU numbers at the end of the product’s shelf life, rather than numbers at the time of manufacture.

There are plenty of probiotic supplements on the market that are of dubious quality and provide no benefit. The last thing you want to do is waste your money on a product you think will make you healthy when it actually provides no benefit.

In searching for probiotics, you will find plenty of companies advertising their daily probiotic supplements for extremely low prices. The phrase “you get what you pay for” holds true in the case of probiotic supplements. When something seems too good to be true, it usually is.

Companies advertising cheap probiotic supplements do so by cutting corners in order to save money. This could mean using lower quality ingredients and inferior strains. The result is a probiotic supplement that will not help you, and in some cases, could make you worse. Take your time to consider the quality of the supplements, not just the bottom line price.

When you go to buy probiotic supplements, spending a little more money for high quality products will pay dividends in good digestive and immune system health.



As you’ve seen, using probiotic supplements can help you achieve better gut health, along with many other benefits. They provide benefits in both prevention and treatment when it comes to health concerns.

So whether you suffer from health issues presently or just want to stay healthy as you grow older, taking probiotics daily can help you maintain better overall health and boost immune system health naturally.


Note: This article is not intended to constitute medical advice. Any actions should be done in consultation with your physician.


Sources for This Article Include:

Yan F, Polk DB. Probiotics and immune health. Curr Opin Gastroenterol. 2011;27(6):496-501. doi:10.1097/MOG.0b013e32834baa4d

Johns Hopkins Medicine.

Scientific American. Feb 2010. Think Twice: How the Gut’s “Second Brain” Influences Mood and Well-Being

Andrew Platt. Immunity in the Gut. British Society for Immunology.


Harvard T.H. Chan School of Public Health. The Microbiome.

Centers for Disease Control and Prevention. Antibiotic Prescribing and Use in Doctor’s Offices.

Markowiak P, Śliżewska K. Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients. 2017;9(9):1021. Published 2017 Sep 15. doi:10.3390/nu9091021

Brown AC, Valiere A. Probiotics and medical nutrition therapy. Nutr Clin Care. 2004;7(2):56-68.

National Institutes of Health. Probiotics.

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