Microbiome Myths You Really Need To Know

Feb 22 / Kristina Mitts

1) Germs are bad and if it’s a pathogen it’s REALLY bad!​​

Let me first shock you by saying: “there is no such thing as a bad bug and you cannot blame your microbes for all of your problems!” Our microbes are kind of like children; (or pets if you are a fur parent) a microbe is only as good as the home you create for it and the directions you give it. 

With the exception of a select few, our microbes will only behave badly, or overgrow to the point of being problematic, if they are encouraged to do so. They take their cues from pH and inflammation levels, what types of food are available to them, how balanced your circadian rhythm is, and who they keep company with. And because our focus is the gut microbiome, we’ll need to consider other aspects of digestion, such as bile, enzyme and stomach acid secretion.

A good example of this is E-Coli. There are many species of E-Coli that we naturally carry with us in our gut microbiome. E-Coli is commonly thought of as a “bad bug,” but even the ones with greater capacity to cause damage to produce Vitamin K and B12, metabolize lactose, and can prevent overgrowth by other pathogenic species. 

If we do end up having one of these species grow out of control within us, we really want to try to understand why it was able to in the first place. 

2) All prebiotic fibres are the same

If you went to your GP when you first started having gut issues, it’s likely that they recommended taking something like Metamucil, Prunes, Flax, or Psyllium Husk.  And if you were compliant enough to follow through on those recommendations, you were more than likely scared off from taking fiber when you found that they made your gut issues worse than before!

There are two problems with this:
  • Your doctor likely prescribed the wrong type of fiber for your condition.
  • Your doctor did not prescribe fibre at the right time in relation to your treatment plan

It is true that fiber is a prebiotic and acts as food for gut bacteria, but as I mentioned not all fibre is the same. A common misconception our clients have is that all fibre feeds all bacteria (including bad ones), and thus, should be avoided. This isn’t true. Some types of fibre will feed mostly Bifidobacteria species while others might feed more Roseburia species. Some types of fibre have antimicrobial activities against certain microbes and some can even reduce endotoxemia!

For many people with gut issues, you’ll want to address the root cause of your issues before introducing fibre. Otherwise, you might end up with a whole lot more gas, bloating, and brain fog!

3) 7-10 Day parasite, Candida or other gut cleanses from the Health Food Store will solve your gut problems

Marketing for quick and easy cleanses is everywhere these days: its sexy, its fun, its clean… you know, you’ve seen them on the shelves at your local health food store. But if you truly have IBS or some other form of chronic digestive imbalance, these kits will be inadequate when it comes to resolving your problems.

First, a 10-day course of herbs isn’t long enough to change the terrain. It takes at least 4-6 weeks to make changes that are beyond the surface level. It can take years to establish a new baseline.

And if it’s a Parasite cleanse? Most parasites have cyclic life-cycles from egg or cyst form, into larvae, and then into full-grown organism. Not all stages are vulnerable to herbs (or even antibiotics). Not to mention, some Parasites are considered commensal and important players within the microbiome. Those in the microbiome field are starting to voice the idea that the enactment of scorched earth policy upon our microbiome has likely deprived us of important immune modulation from certain parasites.

Third, without knowing which organisms you have, it’s hard to know that the herbs you are taking are the correct ones for your specific issues. I hear all the time that people have been blaming symptoms on Candida and using Candida cleanses without knowing if Candida is even the problem. It’s easy to blame Candida for fatigue, skin issues or sinus problems; which could just as easily be due to SIBO, histamine intolerance or some other issue entirely.

And finally, these kits typically focus on “killing” microbes, without any mention of restoring the environment or commensal microbes. So, better to know which pathogens are present, so that an experienced professional can help guide you to the right combination of products, for the right amount of time.

But even if you don’t do that, please never again think that 10 days of grocery store herbs is going to restore your microbiome.
Created with