“Microbiome” – it’s a popular buzzword these days, but this word means different things to different people.  What is the microbiome, really? How does it affect your body? Does it help you or does it hurt you?

When we think of microbes, most of us immediately think of getting sick, right?  Get out your Lysol, your bleach, your antibacterial soap! Scrub until everything is spotlessly clean or risk a deadly infection…right!?!

Well, not exactly.

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Is this what you picture when you hear the word “bacteria?” Most people do, but the truth is, they’re not all bad.

Microbes have a bad rap that they don’t deserve!  While some species can make you sick, most microbes coexist with you and actually help your body function properly in an elaborate, microscopic ecosystem called your microbiome.  The microbiome is made up of bacteria, fungi, protozoa, and even viruses that live on the surface of and inside different parts of your body and are absolutely essential to your well-being.  

Each region of your microbiome (e.g. on your skin, inside your ears) is different and immensely complex, but here we’ll be focusing on the many species of bacteria that live in your stomach and intestines.  Throughout your entire life, these bacteria work with you, helping you digest food, regulating your stress levels, supporting your immune system, and even producing the chemicals your nervous system and muscles need to work properly!  

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Your gut microbiome is like a forest; many microbial species live together in harmony.

The microbiome is a dynamic ecosystem

The microbiome, like any ecosystem, is healthiest and most stable when a diverse population of species live there in specific proportions.  In general, when an ecosystem has reached a healthy, biodiverse balance, no single species can dominate over the rest and monopolize access to resources like food, water, and shelter.  In such an ecosystem, competition for resources is in a sort of equilibrium, and all species can exist in relative harmony with one another because every species has access to enough resources to support a stable population of individuals.  

This all may sound like an idyllic, even utopian hidden world reserved for bacteria, but when it comes to the ecosystem that houses your microbiome, this balance is important for you, too.  Depending on the unique composition of your microbiome (how many different kinds of microbes live there and in what proportions), each microbial species that lives there contributes to the way your body works in its own way.  Strike the perfect balance and your microbiome will help you feel happy and healthy; but, if the microbial species in your microbiome are out of balance, or if a microbe has taken up residence in a place or concentration that affects your body negatively, you may not feel very well at all.

When the balance is tipped

When disaster strikes, even the healthiest microbial ecosystem may be left in complete ruin.  A nasty case of food poisoning, a course of antibiotics, or other drastic physiological changes dramatically alter the levels of biodiversity within your gut, and when you experience any of these, you may suffer a short period of intense digestive upset.  However, with rest and recuperation after such an illness, your microbiome will also recover, leaving you as good as new.

In contrast to the kind of catastrophic ecological collapse in your gut that makes you violently ill, there is a second kind of ecological upset that can occur in the gut that is less drastic but more persistent.  These prolonged imbalances in our gut microbial ecosystem are associated with chronic illnesses that we associate with our lower digestive system, including Irritable Bowel Syndrome and Type 2 Diabetes, as well as some conditions that seem to have nothing to do with the digestive system, such as depression, Parkinson’s disease, and autism.  Each of these diseases is associated with distinct changes in the proportions of microbial species within person’s microbiome, changes that are often resistant to intervention.  Furthermore, it is worth noting that research so far has not established an answer to the natural follow-up question: does this stubborn, unhealthy microbiome composition (where less beneficial species dominate the ecosystem) cause illness, or does the illness cause and perpetuate an unhealthy microbiome?

The microbiome in your daily life

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E. Coli, one of the many bacteria species that lives in your intestines.

You may find it bizarre to be told to think of your microbiome as a complex, dynamic community, but it is important to understand and cultivate this tiny ecosystem, because it is essential to your well-being.  The physical environment of the microbiome is as important to preserve as a forest is for larger plants and animals. While it is true that microbes may not live in trees, or burrows; drink from streams or lakes; or munch on vegetation or other animals, these bacteria do still share some of same basic needs as larger lifeforms.

Thousands of different species of bacteria find shelter within your digestive system, and some anchor themselves to the gut walls (prime real estate for a bacterial cell that doesn’t want to get swept away with this afternoon’s lunch).  Having taken up residence in your gut, bacteria and other microbes can get the other basic resources that they need: food and water. As you eat and drink, your microbiome eats and drinks, absorbing water and breaking down the food that you consume for its own nourishment.  But instead of only benefiting the bacteria, the bacteria’s feeding is beneficial to you, too. Without the aid of the bacteria in your microbiome, you are not capable of fully digesting the food you eat. And so, in this elegant system, industrious microbes work within you, breaking down food for their own sustenance, an at the same time, ensuring that you also get all of the nutrients you need to survive.  

But wait, there’s more – your microbiome does so much for you beyond helping you get the most out of your food.  When you are healthy and your body is working properly, the microbiome of your gut produces chemicals that support your immune system to prevent you from getting sick.  Your gut microbiome is also responsible for producing over 90% of the serotonin in your body (your brain produces the other 10%).  This huge bacterial pool of serotonin keeps your digestive system running like a well-oiled machine.  Finally, your microbiome helps to regulate levels of cortisol, a chemical responsible for activating the stress system.  Through stress levels and other indirect pathways, your gut microbiome can influence your mood, and vice versa. This brings whole new meaning to the idea that a person can have a “gut feeling” about something, doesn’t it?  

Your microbiome helps you every day, so what can YOU do to help your microbiome?

A healthy microbiome is typically made of thousands of species of microbes that do not make humans sick, but rather make them feel great.  However, when pathogenic microbes get into your gut and wreak havoc, or when the balance of bacterial ecosystem in your gut is subtly thrown off, it can make you sick.  Ironically, antibiotics can make your gut microbiome turn against you. Antibiotics kill off both good and bad bacteria, and as you recover, bacteria that grow the fastest dominate the new ecological landscape – and sometimes the winners are not so good for your health.  It is for this reason that it is so important to consume prebiotic and probiotic foods when recovering from illness or after you take a course of antibiotics.  Prebiotic foods promote the growth of “good” bacteria in your gut, while probiotics actually contain live microbes that help repopulate your gut with the species of bacteria it needs to function properly. They also help your microbiome regain its biodiversity.  

gut microbiome blog illinois science councilOur gut microbiome may as well be a distinct organ in our bodies: with major roles in our health and well-being, it’s important to take good care of it.  While it might be useful to consume probiotics after a course of antibiotic treatment to restore your microbiome, taking a daily pill may not be the most reliable way to maintain a healthy gut microbiome in the long-term.  The composition of microbes within supplements is not always well-controlled, is not regulated by the FDA, and varies greatly from brand to brand.  Additionally, many of the claims that companies make about probiotics’ effectiveness are not clinically supported and need to be tested in controlled, clinical trials to be trusted.  

On the other hand, there is strong evidence suggesting that you can effectively manage the health of your microbiome simply by improving your diet.  You can do this by eating foods high in healthy bacteria, including, but not limited to, yogurt, kefir, kombucha, sauerkraut, kimchi, pickles, and cottage cheese (depending what dietary needs you may have, of course).  Also be sure to compliment these probiotic foods with wide variety of fruits, veggies, grains, proteins, and fats to support the many different kinds of bacterial species in your gut. And finally, be sure that your diet is LOW in preservatives and refined sugar (which the bad bacteria love), and HIGH in fiber.  A diet like this may sound complicated, but eating these tasty foods will create a healthy and biodiverse ecosystem in your digestive tract where good bacteria can flourish and will make you feel great, too!


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Kate Proudfoot is a post-doctoral scholar at the University of Chicago, where she received her Ph.D. in cell and molecular biology. Kate is also an organizer for Expanding Your Horizons Chicago, a one-day symposium aimed at engaging middle school girls in science.


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Total Solar Eclipse on April 8, 2024

Total Solar Eclipse on April 8, 2024

On April 8th, 2024, a total solar eclipse will sweep across North America, from Mexico to the Maine-Canadian border. For those who experienced the spectacular solar eclipse of 2017, this one will be similar, crossing the United States from west to east and passing through or near several major metropolitan areas. And while its path is quite different this time, Carbondale, Illinois, a reasonable destination for Chicago-area residents, will once again be on the line of totality.    

Just a little background on eclipses:  Lunar and solar eclipses are not uncommon – they each occur about twice a year when the moon is crossing the ecliptic, the path of the sun in the sky.

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