The Microbiome: The Protocol II

the microbiome protocolPart one of this post looked at stress management, diet, sleep and physical activity.

In this post we’ll survey the other elements of the microbiome protocol:

  • Drugs;
  • Caffeine;
  • Chemicals;
  • Environment; and
  • Gut health therapies.

Starting with a sneaky one:


Chris Kresser cites research about the benefits of coffee in this podcast and sums up that “it still might be harmful for an individual based on a number of different factors”.

Sarah Ballantyne considers the research in the Pros & Cons of Coffee including the health benefits and it’s effect on cortisol production. She summarizes: “if you are very healthy, have lost most of the weight you need to lose, have regulated your hormones and healed your gut, coffee (in moderation) is likely to provide you a health benefit.”

Coffee 2Dave Asprey, the originator of Bulletproof Coffee, is a advocate of daily low-toxin coffee.

He also suggests coffee naps.

Back in 2008, Mark Sisson cited research on the negative impacts of caffeine and echoes Chris when he asks: “Is it really just a pick-me-up, or is it a band-aid for a larger problem like sleep deprivation, hormonal imbalance, lack of physical activity, lack of adequate sunlight?”

Mickey Trescott writes about Kicking the Coffee Habit.

And while we’re considering the elements of the microbiome protocol for gut health, what about reliance on coffee for gut motility?

Datis Kharrazian considers the need for coffee to provoke a bowel movement as a possible indicator of an issue with the gut-brain axis.

Reduce Chemical Exposure

Everyone agrees. Chemical exposure is a problem. And it’s insidious.

For example, Dave Asprey writes about chemicals in the air at Fitness Centres.

Mark’s Daily Apple considers chemicals in cosmetics and chemicals that harm baby boys (chemicals harm all babies, by the way, including baby girls and babies that don’t subscribe to the gender binary). He also covers 8 ways to reduce your chemical load and environmental toxins and gene expression.

And there’s chlorine in our water,  which indiscriminately kills bacteria, including many of the friendly microbes we’re trying to nurture inside the gut. Chlorine is flagged by David Perlmutter in Brain Maker (he recommends simple water filtration as a solution). It’s also addressed by Josh Harkinson in this Mother Jones article.

Chris Kresser explains how chemicals are making us fat and diabetic.

Datis Kharrazian explains how chemicals can trigger autoimmunity.  If you like a podcast, you can listen to his illuminating conversation with Eileen Laird about autoimmunity and chemicals.

Mindful Drug Use

Drugs aren’t necessarily different from chemicals. Except that they are ingested intentionally.

Over half of Americans are taking prescription drugs daily, according to Chris Kresser.

We all want to minimize pharmaceuticals, but sometimes drugs are appropriate. Eileen Laird considers where medication fits on a healing diet in a guest post on Autoimmune Paleo.

Chris Kresser points out that most drugs simply suppress symptoms and describes the ‘vicious cycle’ of using drugs to counteract the side effects of other drugs, and tells us exactly who makes money from that.

Mark Sisson has an entire ‘Big Pharma‘ category of posts on his blog. In some of these posts, Mark discusses the problems with antibiotics and some possible alternatives and considers harm reduction in We Like Drugs.

Mark also writes about The Pill: What You Need to Know about Oral Contraceptives (and Chris also covers how to recover from long term use of the pill in this podcast).

Attention to Environment

Epigenetics is the study of how the expression of our genes is affected by our environment.

My favorite Healers & Optimizers, from the top, left to right: Angie, Alt, Chris Kresser, Sarah Ballantyne, my husband Matthew~, Eileen Laird, Terry Wahls, Dave Asprey, Mickey Trescott, Mark Sisson

My favorite Healers & Optimizers, from the top, left to right: Angie, Alt, Chris Kresser, Sarah Ballantyne, my husband Matthew~, Eileen Laird, Terry Wahls, Dave Asprey, Mickey Trescott & Mark Sisson

We get issued our genes at conception, but our environment is more within our control.

The environment is exactly what this microbiome protocol is designed to address.

Terry Wahls reminds us that “diet is the most powerful epigenetic factor of all” and goes on to list toxic chemicals, physical activity level, stress, relationships, sleep, and the microbiome itself as other elements of our environment that turn our genes (for health & disease) on and off.

Dr Mercola adds emotions to the list.

Dave Asprey considers how we can optimize diet, behavior and environment to hack body and mind in How Your Environment Hacks Your Genes for You.

Mark Sisson refers to research  that indicates that where we live has significant impact on how our genes are expressed and considers Epigenetics and Depression.

This 2007 documentary on epigenetics is also excellent~.

Gut Health Therapies

All of the elements in this microbiome protocol are gut health therapies.

But additional interventions specifically target the health of the microbiome, including relatively simple approaches like inclusion of resistant starch, fermented foods & probiotics in the diet, and more radical interventions like Fecal Microbiota Transplants.

Let’s consider these therapies:

Resistant Starch

Mark Sisson has posted a definitive guide to resistant starch.

Eileen Laird has details the results of her n=1 resistant starch experiements in The Great Starch Experiment and recently also wrote about white rice as the paleo-non-paleo resistant starch of choice.

Sarah Ballantyne has written the the fiber manifesto, which explores all things fiber, including resistant starch, but she also warns that isolated resistant starch can be problematic.

Dr. Grace Liu has a podcast on Bulletproof titled resistant starch & probiotics.


Almost everyone agrees: fermented foods (and probiotics) are important elements of a gut healing protocol.

Chris Kresser gives an overview of gut heath and recommends both.

Sarah Ballantyne offers a post on the benefits of probiotics.

Mark Sisson covered the health benefits of fermented foods back in 2009.

Eileen Laird offers a podcast with Sarah Ramsden, fermented food expert.

Mickey Trescott, who co-blogs with Angie Alt at Autoimmune Paleo, has a post about how to evaluate supplements, including probiotics, when on a healing protocol.

Other bloggers have some caveats. Dave Asprey has written about Why Yogurt and Probiotics Make You Fat and Foggy. Chris Kresser considers 4 reasons why probiotics or fermented foods may not be tolerated.

Fecal Microbiota Transplants

Jaime Hartman shares a 1st-person account of a successful fecal microbiota transplant on her blog Gutsy By Nature.

Eileen Laird offers a podcast on the subject.

The ever prescient Mark Sisson wrote briefly about Fecal Transplants back in 2010. In 2011 he also referred to research for Do-It-Yourself fecal transplants.

In Conclusion

At the beginning, a protocol like this can seem overwhelming.

Like a whole-life overhaul.

Because that’s what it is~.

But there are ways to make it manageable (and fun). Soon I’ll address how to break it down to by assessing leverage, so it’s easy to create a plan of action.

We got to this point by building a system map. Then we deconstructed that map to determine which elements are actionable.

By understanding the system, we can each develop a strategy to improve our microbial communities~.

Actionable Microbiome 2

4 thoughts on “The Microbiome: The Protocol II

  1. Pingback: The Microbiome: the Protocol | petra8paleo

    • I have a new coffee protocol. I’m trying it out. Coffee for 2 weeks. Green tea for a week. A weekend with no caffeine whatsoever (I make no plans & sleep. A lot). Then back to just green tea until the end of the month. Repeat~. I’m trying it out. So far, it’s working. I have optimum productivity for the 2-weeks after I go caffeine-free, but then it starts to decline if I stay on coffee for too long.

  2. You know why so many people are addicted to coffee?? 🙂 Dehydration thanks to EMFs and WiFi. 🙂 While I haven’t had in 3 years…. my spring water protocol is knocking my socks off! (in a good way!)

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