Pre & Probiotics: The Role of Fiber and Diet on Microbial Health in an Age of Antibiotics

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

Knowledge about microbiome topics continues to expand, even explode. There is always new research, and with each new discovery, a new fad, new products, new foods. Although there is a great deal of information out there already, there is still plenty yet to be discovered about the microbiome and the usefulness of pre- and probiotics.  

Here’s what we know

Although the past century of medicine has focused on pathogens, humans have coevolved with many more beneficial microbial species (mostly bacterial, but some fungi and worms as well) for millions of years. Stepping back before the human line began, all animals, invertebrates included, have some form of GI tract. You are probably most familiar with the “two hole” approach, in which animals eat and excrete from different ends of the body. But the original model, preserved in creatures such as jellyfish, eat and excrete from the same hole–gross but interesting, we know!

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source: Azula

Whether one hole or two, this means that for more than 630 million years (1), there has been a coevolving, beneficial relationship between animals and the microbes that call their GI tracts home.

Advances in human development

Until very recently, it was quite common to die of a bacterial or viral infection. Pneumonia, tuberculosis and influenza dominated the CDC top causes of death for the first quarter of the Twentieth Century (2). Although clean water and improved nutrition were already reducing the burden of infectious disease, the discovery of penicillin in 1928 by Alexander Fleming was a pivotal moment for mankind. Even then, penicillin didn’t become widespread until after World War II, where it’s key role in the war encouraged manufacture at scale (2). With the success of penicillin, other antibiotics derived from fungus and bacteria began hitting the market. Thus launched the age of antibiotics, which revolutionized medicine and health (how many people do you know would have died without antibiotic treatment?), but has also led to some serious consequences.  

In addition to the prominent use of antibiotics by doctors, American farmers quickly realized that antibiotics not only kept their animals healthy, but also dramatically increased their size with less feed! The result being that by the end of the 20th Century antibiotics are everywhere! Unfortunately, the vast majority of antibiotics are broad-spectrum, that is, they kill many species of microbes. By killing beneficial as well as pathogenic organisms, antibiotic exposure disrupts our beneficial microbial composition. This dysbiosis, defined as an unbalanced microbiome, can trigger many symptoms. Severe dysbiosis underlies the explosive epidemic of C. difficile overgrowth infections and antibiotic-resistant pneumonia in hospitalized patients. Microbial dysbiosis has also been linked to obesity, autoimmune diseases, and other chronic health problems. Our improved understanding of the importance of the microbiome has raised awareness that dysbiosis is a pervasive public health problem.

The discovery of the microbiome as an ecosystem and its importance in one’s overall health (as well as growing awareness of dysbiosis) has sparked a new age of pre- and probiotic products.  

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source: OptiBac

So what are pre and probiotics?

Prebiotics are insoluble ingredients that promote the activity and simulate the growth of beneficial microbes. In other words, they are the “food” for the probiotics, which are the beneficial microbes themselves (4). Some companies package a supplement that contains both pre- and probiotics (often called a synbiotic), while others keep these products separate. Either way, it is logical that in order to keep your microbiome happy you need to feed it!  

Back in the day, we used to get both our pre- and probiotics from the environment and the food we ate. Now, in an age where antibiotics are everywhere, food is sterile and food and beverage fermentation is no longer the most popular method of preservation, so it seems that we need to play catch up by using supplements to keep our microbiomes healthy!  

What’s the role of prebiotics and fiber?

So what is the prebiotic “food” you might ask? Well it turns out prebiotics are made up of different food ingredients, mostly fibers (5). While our antibiotic usage and consumption has skyrocketed, our dietary intake of both digestible and indigestible fiber has steadily decreased. We aren’t getting enough fiber in our diets, especially the insoluble (indigestible) fiber that our bacterial buddies crave. Although not all fibrous foods are considered prebiotics, these different food fibers are what feed our beneficial microbes (5).

Where has the fiber gone?

As most of you know, fiber is key in digestion and excretion, but in food products high fiber means a shorter shelf life. This resulted in the removal of fiber in virtually all processed foods in order to keep food unspoiled longer. Furthermore, the prestige, color and texture of refined grains led to their mass production in commercial bread, cereals, rice and corn. This led to many problems, such as vitamin deficiency (it was actually the emergence of deficiency diseases such as scurvy and pellagra that led medical scientists to the discovery of vitamins).

While fiber speeds intestinal motility, it also helps slow the conversion of long-chain carbohydrates to simple sugars, especially those fibers that we do not digest ourselves, but that feed our intestinal microbes. When fiber is removed from food, glucose rushes into our bloodstream in potentially harmful amounts. Our body acts quickly and efficiently, secreting insulin to remove this excess glucose, unfortunately resulting in converting most of this energy into fat. 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? It’s because the lack of fiber leads to a fast surge of energy as calories that instead of being used to fuel your body, mostly get stored as fat. Fiber can also assists in improving your feeling of satiety by signaling important chemicals (leptin/ghrelin) that promote these hunger and satiety pathways.

Our Recommendation

Besides the obvious avoidance of processed foods, consuming pre- and probiotics in some form could help maintain a healthy microbiome as well as alleviate GI and other autoimmune disease symptoms. There are many ways to do this and many products to choose from! Whether you love a certain brand of Kombucha, or find it upsets your stomach, and would rather take a supplemental pill, there is no one right way.  

Some of our favorites

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Food: Punk Rawk Labs is a small company focussing on holistic, wholesome, and delicious products. They offer a wide variety of dairy-free, nut based cheese products, as well as a Shishito Gold mustard that are also infused with probiotics.

Supplemental Pills: Seed is a combined pre- and probiotic supplement (synbiotic) company that is based on sex (not gender) promoting microbial health to improve human as well as planetary health. Hyperbiotics is a company that provides pre and probiotics differentially designed for women, children, immune support, weight, oral and gut health.  

Supplemental Powder: Hyperbiotics makes a prebiotic powder that is easy to add into your daily routine.

Having just gotten our box of Hyperbiotics, we were 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!Screen Shot 2018-07-11 at 4.46.49 PM.png

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 as well as our microbes!

Our smoothie was made with bananas, cherries, strawberries and almond milk, garnished with granola, flax seeds, cherries, banana and pear slices, sprinkled with honey.

The falafel comes as a premixed dry bag. All that is needed is an addition of water and rest for 30-60 minutes. We then mixed in our Prebiotic powder before forming and pan searing our falafel balls.  

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


  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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