Will You Actually Catch More Microbial Health with Honey?

As divisive an argument as any in the Western health sphere, the benefits and pitfalls of bees’ gift to Pharaohs and your evening tea are complex and intricate.

Simply put? We know honey is a natural whole food with centuries of documented holistic use… but we can’t seem to decide if it’s a good idea to snack on it like it’s sauerkraut.

Especially from the perspective of your microbiome, its effects can be wide-ranging. 

There’s so much to consider – was the honey wild-harvested? Organic? Raw? Processed? What kind of bees created this honey? Is it even ethical to buy honey, knowing that the process of cultivating honey can harm bees and their precipitously declining population? Even though it’s good sugar, is it still too much? Does heating it matter, or are you supposed to eat it raw in order for it to have any benefits?


We don’t have to have all the answers to all of those questions right at this minute. 

But we can parse through the available literature on the effect honey has on your microbiome and determine how to best use it as a digestive aid, and how to avoid it messing with your digestive system.

First things first: you need raw, or unpasteurized, honey. Your garden variety grocery-store-honey has likely been pasteurized in order to extend its shelf life, prevent crystallization (which is actually fine), and kill yeast.

But… we know that any process responsible for changing dthe structure of any product that much is a double-edged sword. The pasteurization process kills a lot of the beneficial nutrients in honey.

Let’s examine where raw honey can help feed beneficial bacteria, and what kind of interactions it might have with harmful bacteria…

The Sour Sides of Honey

We know the effect that antibiotics can have on the microbial diversity of the gut biome – they tend to indiscriminately wipe out bacteria. 

Which is, of course, a problem when your gut thrives on the presence of beneficial bacteria.

While honey is considered antibacterial, it also contains hydrogen peroxide naturally, which is an antiseptic. In many cases, its antiseptic properties are responsible for its classification as antibacterial. 

Antiseptic isn’t exactly the same as antibacterial. Antibacterials can only target bacteria, for example, and can only kill them. Antiseptics can target bacteria and other microbes, and not kill them… just slow them down.

(That’s why Manuka honey is often used to treat wounds in hospitals and on the battlefield, in addition to the fact that the thickness of honey helps maintain moisture during the healing process. Medical grade and sterilized, but still.)

However, its high sugar content can feed Candida and other harmful bacteria in the gut. Fructose doesn’t only disrupt the balance of the microbiome – it also isn’t absorbed well in the gut, and so can ferment and lead to gas, bloating, and other digestive discomforts.

It’s still better for you than table sugar, but too much fructose is still the gut’s enemy. 

But on the bright side…

Honey’s Sweet Benefits

Honey is considered to be an excellent prebiotic. 

Prebiotics are different from probiotics. For something to be considered a prebiotic, it must meet these standards:

  • It must be able to resist digestion from human enzymes and thus reach the large intestine still whole.
  • It must be able to be fermented by the probiotics living in your gut.
  • It must hold up against gastric acidity.
  • It must aid in the growth of bacteria associated with well-being.

Raw honey meets all of those qualifications! 

It contains oligosaccharides, which are not digestible by the small intestine and thus are able to make it to the large intestines. Once the oligosaccharides reach their destination, they feed the good bacteria and help them create nutrients we need.

Specifically, honey tends to nurture bifidobacteria and lactobacilli, which we know are some of the main bacteria responsible for our positive gut health and for crowding out harmful bacteria that cause digestive and other issues.

And remember – not all honey is harvested the same way, or comes from the same nectar source. 

Most honey produced in the world is flower honey, produced by bees removing the nectar from flowers. 

But other, more specialized forms of honey might be more effective for the purposes of gut rejuvenation and nourishment. Pine, acacia, and chestnut honeys, for example, have all been used to help build a healthy gut and soothe digestive issues.

When consuming honey on a daily basis, putting it in your tea or coffee, over granola, in your marinades, or any other way is a fine way to reap its benefits. 

If you want it to have a concentrated impact, consider simply swallowing a spoonful of it raw! But keep in mind the quality of the honey you’re eating, its high sugar content, and the kind of honey it is for the best gut benefits.

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NY Times Best Selling author and film maker. Taoist Abbot and Qigong master. Husband and dad. I’m here to help you find your way and be healthy and happy. I don’t want to be your guru…just someone who’ll help point the way. If you’re looking for a real person who’s done the work, I’m your guy. I can light the path and walk along it with you but can’t walk for you.