Personalize Your Diet for Weight Loss

Personalize Your Diet for Weight LossWe each respond differently to the same food.

Specifically, our blood sugar responses differ.

And elevated blood sugar leads to all kinds of health issues, including obesity.

A New Scientific Understanding about Obesity

Like most people who have struggled with being overweight for most of their lives, I’ve suspected for decades that our response to food is individualized.

Because I’ve spent those decades watching my effortlessly-slim sister scarf down all the food she wants.

If I ate like she does, I’d be obese.

I know. Because I used to be.


But now, we have scientific proof to back up what most overweight people have always known…

Breaking News: Maybe Overweight People Haven’t Been Secretly Binging & Lying About It All This Time

Continue reading

The Skin Microbiome (& Our Personalized Microbial Cloud~)

The Skin Microbiome Banner

I wish I had microscopic vision.

Because you wouldn’t look like a human, but a mass of microorganisms organized in a human shape, surrounded by cloud of microbes that would swirl every time you moved.

Or scratched yourself.

So pretty~!

We know that the microorganisms that live in our gut are critical for our health.

But we tend to forget about the skin microbiome.

Like the microbes in our gut, the microflora that live on our skin defend their habitat for their own survival, and depending on whether the resident communities of microbes are ‘commensals’ (our allies) or pathogens, these residents either offer us protection or cause us harm. Continue reading

The 5 ‘Rs’ of Gut Healing

Heal your gut, heal your life.Heal your gut, heal your life.

That’s the new mantra.

The new orthodoxy~.

And any orthodoxy deserves skepticism.



The ‘heal your gut, heal your life’ prescription needs to be thoroughly tested, to see if it holds up.

So, I’ve been testing it.


  • What does the science say?;
  • What experiences have my favorite healers & optimizers had?; and
  • How does all that fit with what Matthew and I have been learning through our own n=1 experiments, our attempts at biohacking autoimmune and biohacking peak experience~?

Between these three sources, I’m triangulating my exploration of these ideas. Which has resulted in the creation of a Microbiome Protocol.

Though I’m not suggesting we need yet another healing protocol (there’s already an abundance of those). Just a meta-protocol. That aligns the various healing and optimization protocols & provides a frame through which to contemplate them.

In that spirit, let’s consider the 5 ‘Rs’ of Gut Healing.

But first, a quick diagram of the Microbiome Protocol elements:

The Microbiome Protocol 2

Now let’s consider these elements alongside the 5 ‘Rs’:

The 5 'Rs' of Gut HealingThe 5 ‘Rs’ of Gut Healing

The 5 ‘Rs’ refers to the gut healing principles used in Functional Medicine.

Those principles are: Remove, Replace, Reinoculuate, Repair & Rebalance.


We need to remove everything that negatively affects the gastrointestinal tract.


  • Things we voluntarily consume, like foods that upset the microbiome and cause intestinal permeability;
  • Things we involuntarily introduce, like chemicals that harm friendly microbes; and
  • Any pathogenic microflora lurking in the GI tract, like yeast, parasites or unfriendly (or unbalanced) bacteria.

The removing phase involves a healing diet, like the Autoimmune Protocol, in which all potentially problematic foods are removed.

It also involves removal of chemicals that are harmful to the gut, both external chemicals, like artificial sweeteners, and harmful internal chemicals like excessive cortisol from chronic stress.

It may also involve taking drugs or herbs to eradicate unfriendly bacteria, yeast or parasites. In the event that pathogenic microflora has armored itself inside biofilms, removal also needs to involve eradicating those biofilms, so the microbes inside become vulnerable.

Elements of the Microbiome Protocol covered by the principle of ‘removal’ include an anti-inflammatory diet, stress management, reduced chemical exposure, mindful drug use & mindful caffeine use.


Replacing restores naturally occurring digestive aids, including enzymes, hydrochloric acid, and bile acids that support proper digestion.

These can be taken in supplement form before eating (& aren’t explicitly included in the Microbiome Protocol).


Reinoculation supports and reintroduces beneficial bacteria. Reinoculation includes dietary approaches, like fermented foods, probiotic supplements and resistant starches, as well as medical interventions, like Fecal Microbiota Transplants.

These approaches are covered under ‘gut health therapies’ in the Microbiome Protocol.

In the case of significant gut dysbiosis, attempts at reinoculation through diet may exacerbate symptoms, for a variety of reasons outlined by Chris Kresser.

Chris notes that “the extent to which you react adversely to probiotics and fermented foods and prebiotics… is roughly proportionate to how screwed up your gut is. In other words, the more strongly you react to these things, the more likely it is that you need them over the long term”.


Repair restores of the healthy mucosal lining of the intestinal tract.

This includes supplying nutrients like zinc, antioxidants, and nutritional anti-inflammatories like curcumin and Omega-3 fatty acids, through food or in supplement form.

Bone broth is an excellent restorative for the GI mucosa. As is colostrum.

Repair relates to the ‘nutrient-dense diet’ element of the Microbiome Protocol.


Rebalance refers to the implementation of systemic restorative processes that will support gut health in the long-term.

These are the powerful lifestyle factors that can get neglected when we focus exclusively food and supplements, like sleep, physical activity and stress management practices (yoga, meditation & mindfulness) which are core elements of the Microbiome Protocol.

Putting the 5 ‘Rs’ into Action

Matthew started a new 3-month treatment this week to address the debilitating nausea that is not responding to dietary treatment.

The current hypothesis is that he has biofilm-protected yeast colonies in his gut.

Yeast can grow roots, called hypha, which puncture the intestinal wall and perpetuate intestinal permeability. Therefore, until these armoured yeast colonies are banished, all of his other efforts at removal, replacement, reinoculation, repair and rebalancing can’t fully heal his gut.


Here’s how his current treatment lines up with the 5 ‘Rs’:

Remove: This treatment targets removal of the biofilms with a plant chemical called Biocidin (in 3 forms: drops/advanced formula, capsules & throat spray) and removal of the yeast with Fluconazole, a pharmaceutical treatment available by prescription. Fluconazole needs to monitored with regular bloodwork due to its toxicity.

These removal strategies are in addition to the removal of every possible food, chemical and environmental influence that we know of (& have control over) for the past 20 months, including attempts to eradicate the yeast through diet~.

Replace: The treatment plan includes proteolytic enzymes with every meal. Which, for Matthew, has been all of one meal day for many months, due to severe nausea.

Repair: The final element of this new treatment includes a bovine colostrum product called GI Restore from NuMedica for gut healing.

Reinonculate: Matthew is unable to tolerate any fermented foods, probiotic supplements or resistant starches, but if the current treatment is effective and his gut heals, he should begin to tolerate dietary reinoculation. If not, his functional medicine doctor has suggested a trip to the Taymount Clinic in England for a Fecal Microbiota Transplant.

Rebalance: Matthew will continue with all his rebalancing practices, which are now his entire life~.

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

Biohacking Tip #6: What’s Actionable?

Biohacking Tip 6Last week I considered the Origin of Illness.

I made a system map, to portray the role of the microbiome in our health.

That map ended up being a crazy bunch of interacting elements, linked by a tangle of arrows and feedback loops, leading to a sort of doomsday scenario of increasingly crappier outcomes.

It was a spaghetti diagram~.

Just contemplating it is stress-provoking.

And stress leads to elevated cortisol levels, which leads to gut dysbiosis, intestinal permeability & inflammation.

And we want none of those things.

Which is why this post is going to deconstruct that spaghetti diagram and get us on a more positive footing with this whole situation.

But before we start the deconstruction, here it is:

Microbiome 4

(For a break-down & explanation see The Origin of Illness).


Before the deconstruction begins, let’s acknowledge that this map is incomplete.

It omits unknown system elements. We don’t know what they are, so we can’t map them.

It also ignores known system elements, like mitochondria and blood sugar.

Like any model, it’s a simplification.

One day I’ll create a more comprehensive one. More elements. More arrows.

But the working hypothesis here is that what’s good for the microbiome is good for the body.

And in any case, there’s plenty to take action on here.

Constructing & Deconstructing a System Map

Anytime we encounter a complex system, we can attempt to understand it through mapping.

Once it’s mapped, we can identify which elements are actionable. To help us change it.

Last week I created a system map. This week, I’ll identify the actionable elements. They’re yellow:

Actionable Microbiome 1

Clarification: ‘Actionable’ doesn’t mean you can control these elements. It just means that you can try.

Necessary Caesarean births happen.

Some of us need to take life-saving or pain-reducing drugs.

As adults, we can’t change the method of our birth or the type of food we ate as children.

So, the yellow elements are potentially actionable. Starting from the beginning of life.

But let’s simply things further and just focus on what adults can do to hack their own biology in the present.

Here are those present-tense action-items for adults, in green:

Actionable Microbiome 2

But this spaghetti diagram just got worse, right? More boxes, more arrows.

Here’s the fun part~.

Even though we’ve established that we’re adults, this is where we get to be preschoolers. After building this elaborate tower, we get to knock the whole thing down.

Even better, we get to keep the all good stuff (the green bits) & toss out the nasty parts (everything else).

After the creative deconstruction, here’s what remains:

Actionable Microbiome 3

There it is. The protocol. Yours & mine.

Next post, I’ll explore these elements, including a quick tour of the blogosphere to find out what our favorite Health & Optimization experts have to say about each of them~.

But first a quick overview. Of how to change.

Create Change

Some steps for creating intentional change in complex systems:

  1. Understand the system;
  2. Identify what is actionable;
  3. Assess leverage;
  4. Take action;
  5. Observe impacts & measure outcomes; and
  6. Repeat.

The Origin of Illness helped with the first step: understanding the system.

This post tackled the second: Determining what is actionable. We’ll begin to explore those actionable elements in The Microbiome: The Protocol.

And soon we’ll consider #3: Assessing leverage~.

I’ve already covered #5: Observing Impacts & Measuring Outcomes in previous Biohacking Posts, including in Biohacking Tip #1: Gather Data.

The Origin of Illness (the Microbiome~)

My understanding of the microbiome is evolving.

New research is surfacing almost every day. Some of it I don’t fully comprehend.

Most recently, I’ve been reading David Perlmutter’s Brain Maker, which simplifies things enormously.

Here’s a step-by-step (with diagrams~) of my current understanding of the origin of illness. As ever, I welcome your thoughts.

The Origin of Illness

Both health and illness begin in the microbiome.

Here’s the basic idea:

Microbiome 1

My initial understanding involved a 3-step process:

  1. Inflammatory food upsets the balance of the bacteria in the gut, resulting in intestinal permeability.
  2. This allows foreign particles to leak into the body, causing systemic inflammation.
  3. Inflammation causes disease.

The connection between diet and gut health is the foundation of the nutritional elements of the Autoimmune Protocol as outlined in The Paleo Approach by Sarah Ballantyne, (as well as all other evidence-based healing protocols like the The Wahls Protocol and The Bulletproof Diet).

But not only autoimmune conditions are caused by an unhealthy imbalance in the microbiome: it seems that most illnesses are.

The notion that most chronic health conditions are at least partly caused by inflammation is, in itself, a radical departure from the previous, mechanistic understanding of health. But this story gets way more interesting:

Microbiome 2

Inflammation isn’t the only cause of health problems.

We also need to consider genes & environment. Which leads us to…


Epigenetics is the study of the interaction between genes & environment. It’s partly this interplay that determines whether or not a genetic predisposition to a particular disease gets activated in response to systemic inflammation.

And helps explain why one person might get Psoriasis while another one gets Multiple Sclerosis.

Here’s a cute overview on Epigenetics:

The Origin of Gut Dysbiosis

Gut dysbiosis is an unhealthy imbalance in the microbiome and as mentioned, it is this imbalance that is a primary culprit in illness.

What causes an imbalance?

In addition to an unhealthy diet, chemicals (like chlorine); environmental factors (like excessive hygiene); side effects from drugs (including antibiotics); Caesarean birth and formula or bottle feeding all contribute to dysbiosis.

Before we are born, we have a minimal microbiome. We begin to acquire a robust one at birth. A vaginal birth followed by breastfeeding is the best possible way to get a healthy and protective microbiome started.

Interestingly, Dr Natasha Campbell-McBride suggests that a newborn receives microbiota from both the mother and the father (or the mother’s other sexual partners) during vaginal delivery. Which gives a whole new meaning to the term ‘dirty sex’~!


Stress is a really big deal.

Not only does ongoing stress contribute to gut dysbiosis through elevated cortisol levels, but gut dysbiosis causes stress.

And because chronically elevated cortisol levels contribute directly to intestinal permeability and inflammation, stress creates a nasty reinforcing loop of disease-provoking conditions in the body.

What causes stress?

Modern life.

We just weren’t designed for living this way.

Microbiome 3

 Toxins in the Brain

We used to think that the blood-brain barrier protected the brain from toxins. According to David Perlmutter in Brain Maker, that isn’t so.

Intestinal permeability allows toxins into the body and some of these travel up to the brain.

This is one explanation for the mental health epidemic we are now experiencing, including widespread depression and anxiety.

Remarkably, toxins can stress the brain into perceiving threat, which automatically triggers a neurological takeover by the limbic system.

The limbic system does a great job of protecting us from old-school hazards like predators, but is incapable of higher reasoning or anything approaching enlightenment, and simply can’t navigate the complexity of modern life.

So these toxins not only provoke depression and anxiety, but can render us incapable of making good decisions.

The Collateral Damage of Chronic Health Conditions

Compounding the problem, people who end up with chronic health conditions end up dealing with a host of other factors that contribute to stress, including pain, financial impacts and negative effects on relationships, which add add to the stress fest that help create their illness in the first place.

Microbiome 4

Mental Health

Obviously, the presence of toxins in the brain isn’t the only cause of mental health issues. The whole point of creating a convoluted spaghetti diagram like this one is that the origin of illness is complex.

In addition to epigenetics (genes & environment), trauma & brain architecture are significant factors to consider when thinking about our mental health.

I haven’t seen any reference to the connection between microbiome research and neurological development research in the literature, but it’s highly relevant.

(Still with me? We’re almost done~!)

Toxic Stress & Brain Architecture

Neurological research over the past 20 years has demonstrated that toxic stress in childhood changes the architecture of the brain.

The Harvard Centre on the Developing Child is a wonderful repository for this research.

The basic idea is that all children experience stress, but prolonged stress without the support of a caring adult is toxic to early brain development and permanently impairs executive functioning.

The ability to handle stress, fascinatingly, is wired into the same part of the brain as executive function skills, so that reduced executive function capacity also results in reduced ability to handle stress throughout the lifespan.

Executive function skills are also exactly what become impaired in an adult who experiences brain fog as a symptom of systemic inflammation.

Trauma & Nervous System Dysregulation

Finally, trauma, whether it occurs during childhood or adulthood, can result in nervous system dysregulation, which also impairs the body’s ability to manage stress.

So there it is.

My current (& no doubt flawed & incomplete) understanding of the origin of illness.

Next up: what we can do about it~!