Your intestines are home to many different kinds of bacteria (and some non-bacterial organisms as well). Together they’re called the “gut microbiome.”

They come from the food you eat – and whatever else gets into your mouth. Bacteria start colonizing your gut at birth.

Your gut microbiome aids in digestion and produces vitamins and other compounds that affect your health. It seems to play a role in many other health-related functions, including metabolism, cardiac health and mood.

New evidence shows that the bacteria in our gut also interact with our immune systems, and might even influence the body’s immune reaction to vaccines.

How can bacteria in your gut interact with your immune system?

We are still learning how gut bacteria and the immune system interact. Research suggests that the interaction evolved over time to manage the balance between reacting to harmful pathogens and tolerating non-harmful organisms. You want your immune system to react to the pathogens that can make you sick, while letting the beneficial bacteria living in your gut go about their business.

We are still learning what a healthy gut microbiome looks like. Evidence suggests that a balanced and diverse microbiome might contribute to better health overall, and a less diverse or less balanced microbiome can have a negative impact on health.

A review article from 2014 suggests that the overuse of antibiotics, changes in diets and the elimination of beneficial organisms that work with bacteria (like nematodes, a kind of worm) in high income countries may have resulted in gut microbiomes that lack the resilience and diversity of functions required to establish balanced immune responses. Why does that matter?

Having less diverse gut bacteria has been linked to inflammatory bowel diseases and the increase in autoimmune diseases in developed countries.

For instance, a 2013 study found that children living in Bangladesh have more diverse gut microbiomes than children from the United States. Researchers suggest that dietary differences – with children in the US eating more animal fats and protein – are a factor.

How do vaccines work?

Let’s start at the beginning. Vaccines work by introducing dead or weakened viruses or bacteria or pieces of them (called pathogens) to your body. Your immune system finds them and generates protective antibodies and other responses to that pathogen. Because they are dead or weakened, vaccines cannot cause disease symptoms in the majority of people.

This means that your body will have the antibodies to fight the pathogen and will be ready to mount a quick immune response if it’s ever encountered again. So if you are exposed to the pathogen – the kind that can cause real symptoms – your body already knows how to fight it. You don’t need to develop immunity by actually catching that disease and suffering its real, and sometimes dangerous or deadly, symptoms. You can go your entire life without ever suffering the symptoms of that disease. This is why the word “vaccine” has become synonymous with protection.

Unhealthy gut bacteria can make vaccines less effective

Scientists have started examining the interactions between gut bacteria and responses to vaccines. A recent review article concluded that the composition of your gut microbiome can influence whether a vaccine has an effect in your body.

Unhealthy gut microbiome composition (or “dysbiosis”) can lead to inflammation. And that means more bacterial cells pass through the damaged lining of the gut, which stimulates further immune system responses. This is called “leaky gut.” Vaccines may not be as effective because the immune system is already busy dealing with these bacterial cells “leaking” through the gut.

On the other hand, having a diverse and “healthy” gut microbiome, and thus no gut inflammation and “leakiness,” might allow a person’s immune system to focus on responding to the vaccine effectively.

Recent research has also found that the effectiveness of the seasonal flu shot could be enhanced by intestinal bacteria. The immune system detects specific proteins from the bacteria, and this detection seems to increase the immune system’s response to the flu vaccine. Then your body has an easier time mounting an immune response if you are exposed to the real flu virus.

Could an unhealthy gut microbiome be the culprit in the rare cases when a person has an unexpected immune reaction to a vaccine, such as an anaphylactic reaction? We don’t know for certain yet, but it is a possibility.

Science is nowhere near being able to tell you which bacteria will always cause what immune system responses. And keep in mind that your gut bacteria are by no means the only factor affecting your immune system. Nutrition, age, sex, genetics and the kinds of pathogens you’ve been exposed to can all have an effect.

We don’t yet know exactly what a health-beneficial gut microbiome may look like, though recent research points to the fact that the specific biochemical functions that different bacteria can carry out are more important than the species present in your gut.

Keeping your microbiome in good shape

As far we know the best way to establish and maintain a healthy gut microbiome is to get enough sleep and exercise, eat healthy meals that include lots of fruits and vegetables, avoid chronic and excessive stress and not to drink too much.

You can also help maintain healthy gut bacteria by taking antibiotics only when they are necessary. Remember, antibiotics don’t help if you have a virus, such as colds or the flu.

By Elizabeth Bent, Research Associate at University of Guelph. Bent receives funding from the Ontario Ministry of Agriculture and Food, and the Natural Sciences and Engineering Research Council of Canada. She consults to her own company, Renaissance Biological Solutions, Inc. She does not work with or research vaccines, though she does work with different kinds of microbiomes, and bacteria isolated from microbiomes. This article was originally published on The Conversation. Read the original article.