FAQ - Frequently Asked Questions about the Human Microbiome
Find out how to maintain or develop an optimal gut microbiome, or restore a damaged one. Covering interventions like prebiotics, probiotics, and FMT (Fecal Microbiota Transplants).
How to restore the gut microbiome?
What can I do to restore my gut microbiome after taking antibiotics (or after any other type of major perturbation)?
The standard suggestions are specific probiotics and a healthy, whole foods diet (which can include prebiotics and fasting). However, FMT (fecal microbiota transplant) is the only thing that will restore host-native microbes that were killed off by antibiotics, or are lost or missing for other reasons.
The current microbiome science generally supports a diet high in a variety of fibrous whole foods, however, there is large person-to-person variation based on each person's unique gut microbiome. And thus diet may need to be personalized (via elimination diet).
Nearly everything you do/ingest (including exercise and sleep) will impact the gut microbiome. So things like herbs/supplements are of course another thing that can be experimented with. However, results will vary significantly from person to person.
FMT (fecal microbiota transplant) is the most complete option, but safe and effective donors may not be readily available to everyone. And current evidence suggests that even FMT may not be able to restore all the damage done by antibiotics. So the most important thing is to avoid unnecessary antibiotics.
What about autologous FMT?
Autologous FMT (aFMT): Freeze my stool before antibiotics then use it for FMT afterwards?
- You risk reinfection with whatever pathogen you took the antibiotics for. Or if not a specific pathogen, you are putting back microbes that were not protective and may have contributed to the condition.
- The vast majority of the population is in poor health and has dysbiotic gut microbiomes, and thus, the vast majority of the population would be better off not using their own stool for FMT, but rather FMT from someone who qualifies as a high-quality donor.
- One study showed a high rate of adverse events for autologous FMT.
A reasonable situation to use aFMT would be if you are in great health, have good type 2-4 bowel movements, and you are prescribed prophylactic antibiotics for something. You could then freeze your stool, take the med, and do aFMT afterward.
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For more, see https://humanmicrobiome.info/fmt/#autologous
How to maintain or develop a healthy gut microbiome?
What can I do generally to try and maintain or develop a healthy gut microbiome?
Is dirt good for your microbiome?
Will eating dirt improve gut health? According to the Hygiene Hypothesis, ingesting dirt will strengthen our immune system right?
This notion is widespread, both on social media and in books written by microbiologists and doctors. But it has largely been debunked. This article goes into depth on the topic.
Some of the key takeaways are:
- Dirt is contaminated by harmful heavy metals and other toxic pollutants.
- Dirt has pathogens that are only harmful.
- The known beneficial microbes are the host-native ones that are passed down generationally via vaginal birth and breastfeeding. Microbes that you pick up from the environment are not the same and are more likely to be harmful.
- Antibiotics are one of the primary things you want to avoid if you're worried about your microbiome. Eating dirt and practicing poor sanitation increases your odds of contracting an infection and needing antibiotics.
Here are a number of other scientific papers refuting the hygiene hypothesis: [1][2][3][4][5].
The more accurate alternative hypothesis is Missing Microbes.
Prebiotics vs probiotics?
I heard probiotics don't generally colonize and thus prebiotics are better. Is this true?
Both probiotics and prebiotics modulate the gut microbiome. In fact, virtually everything you do or ingest changes the gut microbiome. Probiotics modulate the gut microbiome by adding microbes. Prebiotics modulate the gut microbiome by changing the percentages of what's already there, based on which microbes most readily feed on the substrate you ingest. Both prebiotics and probiotics have the potential to be beneficial or harmful, depending on person-to-person variation based on each person's unique gut microbiome.
Most current probiotics do not colonize, but they have a variety of other mechanisms through which they can cause short-term or long-term shifts and impacts.
Prebiotics with probiotics?
Do you need to take prebiotics with probiotics?
No. Probiotics have been shown to be beneficial on their own [1]. Synbiotics are specific pairs of pre and pro-biotics that are synergistic, and can boost the impacts of the specific probiotic. But not every pre and pro-biotic mix is a synbiotic.
A healthy, whole foods diet is important, but it is its own thing.
Is it die-off? A Herx reaction? Keto flu?
If I get bad side effects after eating something good it must be die-off, right?
This may be one of the most harmful notions that still gets widely spread. It often causes people to continue taking something that is only harming them. It is often used by providers of advice or products to avoid blame for the harm from the advice or product they sold you.
The notion originates from the Jarisch-Herxheimer Reaction, and has been misapplied to numerous other interventions. The Jarisch Herxheimer reaction is a specific set of temporary symptoms that occur within 24 hours of antibiotic treatment of spirochete infections.
Similarly, there are "keto flu" symptoms that some people experience when starting a ketogenic diet. These are typically short-lived (a few days to a week) symptoms. Be very wary of people encouraging you to continue the diet for months or years despite you feeling worse.
You can see throughout this wiki that diet, probiotics, prebiotics, and even FMT, are all individualized. Each person will need to figure out what works best for them.