Prebiotics, Probiotics, and Digestive Enzymes: Which Should You Choose?

Ding-ding-ding. That sound marks the start of a grueling championship match between prebiotics, probiotics, and digestive enzymes for the “Most Beneficial for Gut Health” title. For now, each contestant is holding their ground well. But, of course, only five minutes have passed. So here comes the golden question: which will you put money on (figuratively, of course) in this face-off reminiscent of an electrifying, adrenaline-pumping WWE Triple Threat match? And how would you know if you got it right?

You’ll have to stick around till the end of this article to find out.  

What are prebiotics? Probiotics? And what about digestive enzymes? 

Clear on which you’re feeling good about? Or alternating between choices? Whether the former or latter (or anything in between), that might all change once you gain a deeper understanding of what prebiotics, probiotics, and digestive enzymes really are, plus what they bring to the table:

  • Prebiotics: Indigestible fibers that occur naturally in many vegetables (e.g., garlic and asparagus), fruits (e.g., banana and apple), and whole grains (whole wheat and whole oat) (1, 2). 
  • Probiotics: Live bacteria and yeasts found naturally in foods such as yogurt, kimchi, sauerkraut, miso, and kefir (3). Also known as "good" gut bacteria. 
  • Digestive enzymes: Special proteins that help break down larger food molecules, like fats, proteins, and carbs, into smaller molecules that your body can absorb and use (4). 

How, exactly, can each improve gut health?

To understand how each of the above could improve gut health, you'll need to understand the gut microbiome and its role in health. So, first things first: your gut microbiome (aka "gut microbiota" and "gut flora") refers to the bustling community of trillions of bacteria, archaea, fungi, and viruses found in your — yep, you guessed it — gut (5, 6, 7). Each person has a unique network of gut flora, thanks to genetic and environmental factors. Meaning? Your gut microbiome can look wildly different from your mom's, partner's, and colleague's. 

And, in most cases, that's perfectly okay because a universal "blueprint" for a healthy gut microbiome detailing which microorganisms and how much of those you should have doesn’t exist. Instead, scientists agree that a healthy gut is one that:

  • Contains a diverse array of microbes, and 
  • Maintains a balance between “good” gut bacteria that have a symbiotic relationship with the body and “bad” gut bacteria that are pathogenic (i.e., could lead to disease and illness)

So, how does an unhealthy gut impact your health? Well, the question here should really be: how does it not? A large body of evidence has now found that gut health also plays a role in immune functioning, chronic disease development, and emotional well-being beyond affecting the digestive system (8, 9, 10, 11). This underscores the importance of keeping your gut health in tip-top condition. And that, in turn, brings back to mind our three contestants: prebiotics, probiotics, and digestive enzymes. 

As they continue to battle it out in the ring, let’s look at how each of them could contribute to better gut health. 

Prebiotics nourish “good” gut bacteria 

Here is a quick recap. Prebiotics are specialized, indigestible plant fibers. If your eyes snagged on “indigestible”, that’s understandable — because, after all, how beneficial can these fibers be if your body cannot even break them down?

Okay, let's clear this up quickly. Unlike other carbohydrates like simple sugars and starches, your body cannot break prebiotics down into single-unit sugars (e.g., glucose, fructose, and galactose) that are absorbed into your bloodstream and used as energy. But they are for the “good” gut bacteria in your microbiome. As it turns out, your “good” gut bacteria can metabolize and ferment the prebiotics for energy (12, 13). Confused? A simpler way of thinking about this is: prebiotics are not food for you, but, instead, food for your “good” gut bacteria. 

This means they help nourish and promote the growth of “good” gut bacteria, encouraging a healthy balance between the “good” and “bad” in your microbiome. Sweeter still, the fermentation of prebiotics also produces short-chain fatty acids (SCFAs), including butyrate, that are tremendously beneficial for gut health. More specifically, these compounds could help:

  • Lower the pH in the gut, creating a more hostile environment for “bad” gut bacteria (14)
  • Enhance the gut’s ability to absorb nutrients from food (15)
  • Improve gut motility (i.e., how quickly food moves through the digestive system), which in turn, helps with alleviating constipation and reducing uncomfortable symptoms associated with gastrointestinal disorders (16, 17, 18, 19, 20)

Probiotics “top up” your tank of good gut bacteria 

Prebiotics sound impressive. So how do probiotics stack up? As mentioned earlier, these are live "good" gut bacteria. How they work is quite straightforward: they act as a "top-up" for the "good" gut bacteria, potentially crowding out unwanted and harmful microbes in your microbiome — nudging you back to a happy, healthy, balanced gut. That said, while all probiotics will typically increase the concentration of “good” gut bacteria, not all will exert the same health benefits. 

That's because probiotics can exert health effects through genus, species, and strain-specific mechanisms (21, 22, 23). Don’t worry; we’ll start from the beginning. Here’s what you need to know: probiotics have three different qualifiers. Let’s take Bacillus subtilis HU58, a probiotic strain found in Dr. Danielle’s Gut Assist Probiotic, for instance:

  • Bacillus” is the genus. This is the broadest identifier. It covers several different types of bacteria under the same general category but with many different characteristics and health benefits. 
  • Subtilis” is the species. This term gets a little more specific now. All the bacterial strains within a species are similar, but, of course, with some subtle differences between them. 
  • “HU58” is the strain. The most detailed level of identification. A specific strain is one type of bacteria. 

Without diving into the nitty-gritty (and risk boring you), here’s what three different genera (the plural form of genus) do:

  • Lactobacillus: Supports the digestion of lactose, healthy digestion, bowel regularity, and promotes better sleep (24, 25, 26). 
  • Bacillus: A special type of sporulating probiotic resistant to harsh conditions, like exposure to gastric acid. Nourishes the intestinal lining and may relieve symptoms of irritable bowel syndrome, rheumatoid arthritis, constipation, and intestinal gas (27, 28, 29, 30). 
  • Bifidobacteria: Promotes normal inflammatory processes in the gut, healthy immune function, better physiological response to stressors, and mood regulation (31, 32, 33, 34).

Digestive enzymes pick up the slack for breaking down food

Ah, finally, our final contender: digestive enzymes. If you’ve been thinking, “Wait, don’t our bodies naturally make digestive enzymes?”, you’re right. Kind of. See: under normal circumstances, your body is more than capable of producing enough of the following:

  • Amylases help break carbohydrates into single-unit sugars
  • Proteases help break down proteins into amino acids
  • Lipases help break down fats into fatty acids 

But there are also off-cases where you may run into digestive enzyme deficiencies, which could cause symptoms like bloating, gas, nausea, abdominal pain, heartburn, diarrhea, oily stools, fatigue, and loss of appetite. And, of course, let's not forget malnutrition — which could, in turn, cause many issues, like osteoporosis, anemia, and blood clotting disorders. So, what are some examples of these "off-cases" (35, 36, 37, 38)?

  • Exocrine pancreatic insufficiency (EPI): EPI occurs when your pancreas stops producing digestive enzymes. It can happen in pancreas diseases, including diabetes, pancreatic cancer, cystic fibrosis, and chronic pancreatitis. 
  • Achlorhydria: A lack of stomach acid. Causes of this condition include stomach cancer, antacid medications, and hypothyroidism. 
  • Genetic disorders: Sometimes, individuals may be born without pancreatic or salivary amylase. 
  • Surgical procedures: Certain medical procedures can lead to digestive enzyme deficiencies. One good example is gastric bypass surgery for obesity, which makes the stomach smaller to promote satiety.  

At the risk of stating the painfully obvious, in these cases, supplementing digestive enzymes (like Dr. Danielle’s Gut Assist Digestive Enzymes) is often necessary to relieve uncomfortable gastrointestinal symptoms and prevent malnutrition. 

Prebiotics, probiotics, and digestive enzymes: who won?

If we were to hold an actual championship match between prebiotics, probiotics, and digestive enzymes, it'd be a really close match. And … to be honest, there might not even be a clear winner (sorry if you were genuinely vested in the results!) That's because each benefits your gut health differently. 

Still, while it's easy to say, "You know what? Take all three!" the truth is that it might not make financial sense for you, align with your preferences, or be realistic. So, here are three questions you could ask yourself to prioritize your supplementation needs:

  • Do you have a condition that necessitates digestive enzymes? If not, you could go ahead and skip them.  
  • Can you realistically ramp up your prebiotic intake through your diet? Prebiotics are naturally found in many common fruits and vegetables, like chicory root, leeks, asparagus, barley, and seaweed. Do you foresee yourself building your diet around these foods? If yes, you could skip prebiotics if you like. 
  • How tolerant are you of fermented foods? You can find probiotics in yogurt, kefir, non-heated kimchi, sauerkraut, and miso. Are you a big fan of these foods, or do you usually go, “No, thank you,” when presented with them? If it’s the former (and you eat plenty of these probiotic-rich foods), you could skip probiotics if you like.

To your health and happiness, Doctor Danielle

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