Pre- & Probiotics for Our Bacterial Buddies
Reversing the Damage of Antibiotics

We all love good food, and it turns out that our bacterial buddies are no different. But while the food we eat might be yummy to us, it often lacks what our bacteria love most: fiber. Here's a list of some of our favorite pro- and prebiotics.

So you’re walking around the grocery store, and you come to the dairy aisle. You look past the heavy whipping cream and milk. What do you see? There it is, right next to the sour cream and butter: Greek yogurt. The component that elevates your breakfast from “basic” to “bad and boujee.” The product that might bring you a few extra likes on your Instagram brunch post. Slapped on the side of this magical container is a single word: “probiotic.” If you couldn’t tell already, we’re big fans of Greek yogurt. But beyond its ability to add class to an otherwise mundane breakfast, we’re more interested in its probiotic performance. So, what are probiotics? And while we’re at it, what are prebiotics? Just how do they purport to support the bacterial buddies that live in our guts?

The antibiotic age

To get a better idea of what probiotics are, we’re going to take a look at antibiotics. Until quite recently, it was pretty common to die of bacterial infections. In fact, tuberculosis (TB)–a bacterial infection that is uncommon today–was still one of the CDC’s top causes of death in the early 20th century (2). Bacterial pneumonia still is! The discovery of penicillin by Alexander Fleming in 1928 led to mass, effective antibiotics for humankind. Replacing the older sulfa drugs as a “magic bullet,” penicillin (and WWII) launched us into a new age of antibiotics.

Farmers soon realized the benefits of antibiotics in agriculture and added them to cattle and chicken diets. This is because they not only reduced the incidence of disease, but also dramatically increased growth with less feed! The result is what you might expect. Because of their usefulness in health and agriculture, antibiotics were everywhere by the end of the twentieth century.

The dark side of antibiotics

However, antibiotic use isn’t all sunshine and rainbows. Because of how they were discovered, the vast majority of antibiotics are broad-spectrum. The prevailing belief was that the only good bacteria were dead bacteria. That meant that killing as many bacterial species as possible was a feature, not a bug. So, the first generations of antibiotics not only killed harmful strains of bacteria, but also the good strains. Remember, this was before the dawning realization that there ARE good strains of bacteria.

Because of their kill-em-all mode of action, antibiotics often disrupt the balance of our microbiomes. This leads to a state of imbalance known as “dysbiosis”. Dysbiosis makes our bodies weaker and more prone to other diseases. For example, broad-spectrum antibiotic treatment leaves the gut at risk of overgrowth by pathogens like C. difficile. Even worse, oral and gut dysbiosis have been linked to obesity, autoimmune diseases and other chronic health problems.

Clearly, we want to keep our microbiomes healthy. In other words, that means keeping our bacterial buddies in balance. Thankfully, pre- and probiotics products and foods are here for that reason.

probiotics help promote bacterial health, while broad-spectrum antibiotics disrupt microbial balance. it is important to incorportate preobiotics into the diet to maintain overall health
source: OptiBac

What’s the difference between pre- and probiotics?

Prebiotics are foods that promote the activity and growth of beneficial microbes in our gut. In other words, they are the “food” for the bacteria. Probiotics, on the other hand, are the beneficial bacteria themselves (4)! Some companies package supplements that contain both pre- and probiotics (often called a synbiotic), while others keep these products separate. Some yogurts and cheeses contain live bacteria. Kombucha and other probiotic beverages do too. While yeast make beer and wine, they are dead by the time we drink it.

Back in the day (i.e., thousands of years ago), our ancestors’ diets were rich in pre- and probiotics. Before refrigeration, fermentation was a major way to preserve food. Beer, wine, bread, cheese and of course, yogurt are all made by letting our microbe buddies (bacteria or yeast) pre-digest porridge, grape juice or milk. But in the modern age, we refrigerate, freeze and fast ship fresh food. Even worse, processed food is sterilized and low in fiber. As a result, we often lack the pre- and probiotics that were common in our ancestors’ diets.

What do prebiotics have to do with fiber?

So what is the prebiotic “food”? Well, it turns out that prebiotics are primarily made up of fiber (aka roughage or indigestible long-chain carbohydrates) (5). While our antibiotic use has skyrocketed, our dietary intake of both digestible and indigestible fiber has steadily decreased. In other words, we aren’t eating enough fiber in our diets, especially the insoluble (indigestible to us) fiber that our bacterial buddies crave. Although not all fibrous foods are considered prebiotics, certain fibers are yummy food for our beneficial microbes (5).

Where has all the fiber gone?

As most of you know, fiber is key to healthy digestion and comfortable excretion. What you might not know, however, is that food products high in fiber have shorter shelf lives. As a result, food producers remove fiber in most processed foods to keep them fresh for longer. Furthermore, they sterilize processed foods to prevent microbial decay at every step from the ingredients to the manufacturing process. That’s to get rid of pathogens and prevent rot, which are good things. But maybe sterile food is too much of a good thing!

While fiber helps our guts do their jobs, it also slows the conversion of long-chain carbohydrates to simple sugars. We see this most in fibers that that feed our intestinal microbes. When we don’t get enough fiber in our food, we digest quickly and glucose rushes into our bloodstreams in potentially harmful amounts. Our bodies respond by secreting insulin to remove this excess glucose. Unfortunately, this converts these sugars into fats. Have you ever wondered why you can eat an entire bag of processed snacks, or why you are hungry an hour after you eat a meal at McDonalds? Well, it’s because the lack of fiber in these processed foods causes the calories to be stored as fat instead of being used for energy.

Recommended prebiotics and probiotics for your bacterial buddies.

Besides avoiding processed foods, you should also be mindful of consuming pre- and probiotics to maintain a healthy microbiome. In balancing the bacteria in your body, you can alleviate GI and other autoimmune disease symptoms. With that said, we’re pleased to inform you that there are many ways to increase your intake of pre-/pro- biotics! Whether you’re a fan of Kombucha and yogurt or would rather take a supplemental pill, there are many products you can use to keep the balance in the bacteria.

Some of our favorite probiotic and prebiotic products

Punk-Rawk Lab's probiotics products help promote bacterial balance in the microbiome
  • Food: Punk Rawk Labs is a small company focusing on holistic and delicious products. They offer a wide variety of dairy-free, nut-based cheese products, as well as a Shishito Gold mustard infused with probiotics.
  • Supplemental Pills: Seed is a combined pre- and probiotic supplement company that aims to improve human as well as environmental health. Hyperbiotics is a company that provides pre and probiotics designed for women and children. Their products also support weight, immunity, and oral and gut health.
  • Supplemental Powder: Hyperbiotics also makes a prebiotic powder that you can easily add into your routine.
Hyperbiotics have a variety of pre and probiotics products that promote microbiome health

Having just gotten our box of Hyperbiotics, we here at Your Autoimmunity Connection are especially excited to try out the Prebiotic powder! With virtually no flavor, one small scoop of powder is incredibly easy to add into many foods.

We ended up making a delicious smoothie bowl and Trader Joe’s pre-mixed falafel by combining ingredients with our Prebiotic powder. Both of these dishes are gluten-free, dairy-free, easy to make, and packed with nutrients for our bodies and our microbes! We made our smoothie with bananas, cherries, strawberries and almond milk. Then we garnished it with granola, flax seeds, cherries, banana and pear slices, sprinkled with honey.

The falafel comes as a premixed dry bag. Just add water and rest for 30-60 minutes. We then mixed in our Prebiotic powder before forming and pan searing our falafel balls.  

Using hyperbiotics prebiotics powder to make falafel and smoothies!

Click here to learn more about the microbiome in our microbiome blog series and comment below with any questions or additional ideas about pre- and probiotics!

Written by: Becca Malizia, BS, Bonnie Feldman, DDS, MBA, Ellen M. Martin


  1. “Timeline: The Evolution of Life.” New Scientist, Accessed 13 July 2018.
  2. “Leading Causes of Death, 1900-1998.” Diabetes Mellitus, 1975,p. 67.
  3. “Alexander Fleming Discovery and Development of Penicillin- Landmark.” American Chemical Society, Accessed 13 July 2018.
  4. Roberfroid, Marcel B. “Prebiotics and Probiotics: Are They Functional Foods?” The American Journal of Clinical Nutrition, vol. 71, no. 6, June 2000, pp. 1682S-1687S., doi:10.1093/ajcn/71.6.1682S.
  5. Blaut, Michael. “Relationship of Prebiotics and Food to Intestinal Microflora.” European Journal of Nutrition, vol. 41, no. 1, Oct. 2002, pp. I11-16., doi:10.1007/s00394-002-1102-7.


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