Bacteria and the Microbiome: Why Bacteria is Crucial to Our Health

February 8, 2024 Posted by AHW Endowment

A hand holds an illustrated depiction of the human digestive tract

The term bacteria isn’t always thought of positively, as it can sometimes be the driving factor behind infection, illness, and disease. However, in our bodies and the world around us, many bacteria are good and work to keep us and our environment healthy.

Nita Salzman_Academic ProfileIn our recent episode of Coffee Conversations with Scientists, Dr. Nita Salzman, MD, PhD, professor, Pediatrics and Microbiology & Immunology; director, Medical Scientist Training Program; founding director, Center for Microbiome Research at the Medical College of Wisconsin, discussed the role bacteria play in our bodies and the importance of the microbiome communities that are crucial for our good health.

The Role of Bacteria and the Microbiome in Our Health

Trillions of microorganisms make up our microbiome, living in and on our bodies. These include bacteria, viruses, fungi, and parasites that mostly reside in the gut. Dr. Salzman shared that while humans have 30 trillion human cells and 20,000 human gene cells, our microbiomes have 39 trillion microbial cells and between two and 20 million microbial genes, meaning our microbes are a very significant component of our being. Microbes are essential to many of our body’s processes, though the existence of microbiomes isn’t exclusive to human bodies: almost everything in our environment has a microbiome.

Bacteria are the best-studied component of the human microbiome and the one we understand the most. In the digestive tract, or gut, bacteria ferment non-digestible dietary fiber, extracting and providing the body with energy and nutrition. This bacteria’s byproducts support the development and function of the immune system, synthesize vitamins, and even produce serotonin.


Different types of bacteria in the digestive tract form communities and depend on each other for nutrition and survival. Together, these groups of microorganisms interact with the human body to maintain a balance of our metabolism and our immune systems.

Good Bacteria vs. Bad Bacteria

It might be tempting to label bacteria as good or bad, since some bacteria help us stay healthy, and other bacteria can make us sick or create problems in our bodies. However, Dr. Salzman doesn’t label bacteria as one or the other. “There are relatively few truly bad bacteria that almost always cause human disease, and we would call them pathogens or pathogenic bacteria,” she notes. “Pathogenic bacteria aren’t pathogenic to all species. Bacteria that can live perfectly okay in a chicken, like salmonella, which doesn’t make the chicken sick but would make us very sick. It’s all about how bacteria communicate with a particular host.”

Dr. Salzman further explains that in the gut ecosystem, there is a combination of different bacteria microbes that are kept in balance by our immune system. When the system is in balance, the bacteria help our digestive and immune systems function. However, when not in balance, it can lead to infections, digestive problems, and obesity, among other health problems.

Bacteria, Diet, and Weight Gain

The bacteria in the gut ecosystem that supports metabolism is responsible for extracting nutrients from foods and giving the body energy and nutrition. When there are disruptions to those bacteria populations, it can affect the body’s metabolism and change our resting metabolic rate (the rate at which our bodies burn calories), potentially leading to obesity. Antibiotics and medications play a role in such disruptions to the bacteria populations.


The health of our gut microbiomes and our immune systems depend heavily on what we feed our bodies. As Dr. Salzman explained, if we eat and feed our gut bacteria good foods that help them produce optimal byproducts (nutrition and energy) for our bodies, we experience better health outcomes.

When our diets consist of non-healthy foods that don’t give gut bacteria what they need to do their jobs, those bacteria will decrease in numbers as will their byproducts, which impacts our metabolism and our immune system function. Dr. Salzman shared this example: If we don’t eat enough fibrous foods, the bacteria that eat fiber might, instead, eat our digestive tract’s protective mucus layer, making it thinner. This would allow bacteria to get closer to our bodies and potentially cause disease and disrupt our health.

Gut Bacteria and Digestive Supplements

As gut health becomes a better-known health topic, more dietary supplements are hitting the market with promises to support your digestive system, such as kombucha, prebiotics, and probiotics. But do these products really help enhance your gut microbiome?

According to Dr. Salzman, “A probiotic is a live bacterial product that is thought to have a beneficial effect… With probiotics, it’s not that they aren’t beneficial, but there is not a lot of research on their effects, and any you ingest will only last a day or two in your system. They will not change your gut bacteria colonization.”

Prebiotics are essentially food that feed bacteria, and they will change the ratios of bacteria that are fiber fermenters vs. fibers that just eat sugar, for example. Prebiotics will enhance the beneficial bacteria or limit the bacteria that’s beneficial. As Dr. Salzman says, you’re not eating live bacteria, you’re feeding the bacteria you have.

Though these products may be beneficial, it’s important to provide your body with whole and healthy foods as a primary source of nutrition.

Learn More About the Microbiome

Want to learn more about Dr. Salzman’s research about the human microbiome and the importance of it in our overall health? Click here to read about the exciting research underway with her project, The Human Holobiont: Enhancing Health and Preventing Disease.

Watch the full episode of Coffee Conversations with Scientists featuring Dr. Salzman: