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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). But the only thing that will restore the host-native microbes that were killed off is FMT (fecal microbiota transplant).

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. But results will vary significantly from person to person.

FMT (fecal microbiota transplant) is the most complete option, but may not be readily available for everyone. And current evidence suggests that not even FMT may 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?

  1. 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.
  2. The vast majority of the population is in poor health and have 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.
  3. 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 afterwards.

For more, see

How to maintain or develop a healthy gut microbiome?

What can I do generally to try and maintain or develop a healthy gut microbiome?

  1. Avoid unnecessary antibiotic use [1], and C-sections [1].
  2. Breastfeed for as long as possible [1].
  3. Eat a healthy, whole foods diet [1].
  4. Exercise [1].
  5. Sleep well [1].
  6. Avoid various environmental pollutants as much as possible [1].

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, and 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.