ARP: Week 46

Focus: Being open to expansion in our journey.
Repetition: I love my body and will keep my mind focused on what it needs. I am open to expansion. Remember that expansion is not a rejection of what you have done up until now. We are incredibly grateful for learning new things that will only help us.

Notes from Mary Ruddick

These are my notes from an interview with Mary Ruddick and Jesse Chappus, along with some of my own supplemental research woven in throughout.

The first thing Mary wanted us to understand is that diversity is not actually what matters in the microbiome — and that conclusion matters, because it came from studying sewage systems, not human bodies. We can’t truly explore the microbiome of a living person the way we’d like to, and since microbes die with us, studying the deceased isn’t a productive option either. What actually matters is which microbes you carry, and that’s shaped by your diet across your entire life, not just what you’re eating right now — different medical and traditional diets can shift your microbiome over time. We are born with about two hundred very important microbes, and they are endangered. Mary has studied people across more than one hundred tribes who are in perfect health, and they don’t necessarily have diversity in their diet at all — what they have is intact microbes from birth, from breastfeeding, and from living with zero modern conveniences.

In her clients, Mary looks specifically at birth microbes — the ones we gain in the birth canal and through breastfeeding. These are incredibly protective for us: they ward off infections, make most of our feel-good chemicals, and help regulate our weight, among other things. If a client still has their birth microbes, she’ll feed them. If she doesn’t see them but the client was born naturally, she’ll try to coax them out of hibernation. And if someone was born via C-section, or has otherwise lost their birth microbes, she’ll help plant the ones we have available to us (we covered this back in Week 26).

Mary is now looking for what she calls pseudopathogens — technically overgrowths of opportunistic microbes, but not the kind you can starve out using the methods we’ve relied on in the past. If you don’t feed them, they will eat your mucosal layer instead, and you can actually end up worse off. You can look for these using a GI Map, though keep in mind a GI Map can only read what’s in the colon, so it isn’t a complete picture of your entire microbiome — it does, however, look at the mucosal layer very well. Mary also loves MicroGenDX (patients.microgendx.com) for this kind of testing. She told us she has never seen this scale of mucosal collapse before in her practice — it’s a genuinely new phenomenon that has emerged in just the past year, and she has identified five distinct stages of it.

The Five Stages of Mucosal Collapse

Here is some supplemental information I researched myself on the five stages of mucosal collapse.

Stage One: Dysbiosis and Loss of Microbial Diversity

This is where the protective flora starts to shift — beneficial microbes decline, pathobionts (bacteria, yeasts, and viruses) begin to overgrow, and microbial toxins increase. The common drivers here are antibiotics, processed foods, stress, a low-fibre diet, infections, pesticides, and emulsifiers.

Stage Two: Mucin and Biofilm Disruption

The mucus layer thins and the biome-mucin ecosystem starts to break down. Goblet cell dysfunction leads to decreased mucin production, mucus-eating bacteria expand (Akkermansia, for example, when the mucin supply is disrupted), and the protective biofilm architecture is lost. The result is that microbes gain closer access to your epithelial cells.

Stage Three: Epithelial Injury

Sometimes called “epithelial exhaustion.” This is where the gut lining begins to suffer real structural damage — tight junctions are disrupted, creating a “leaky” barrier, secretory IgA decreases, Paneth cells and epithelial cells come under stress, and in severe cases the villi themselves start to blunt.

Stage Four: Immune Activation and Inflammation

Both the innate and adaptive immune systems intensify their reactions — cytokines rise, mast cell activation increases, histamine climbs, and T-cell activation and lymphoid tissue response ramp up. This is usually where symptoms start showing up: bloating, GERD, food reactions, fatigue, brain fog, skin symptoms, and systemic inflammation.

Stage Five: Systemic Spillover, or Barrier Failure

At this point the mucosal barrier can no longer protect the organism. Lipopolysaccharides (LPS) enter circulation, immune activation becomes chronic, oral tolerance is lost (meaning food intolerances develop), autoimmune priming or flares can occur, and you may see neuroimmune symptoms like fatigue, mood changes, or sensory sensitivity. This stage often gets labelled “leaky gut” in lay language, but it’s more precisely mucosal immune failure.

Signs and Root Causes

Some key signs associated with mucosal collapse to watch for in yourself: food sensitivities that increase over time, bloating, urgency, or IBS-type symptoms, histamine intolerance or mast-cell symptoms, fatigue after meals, skin flares like eczema, acne, or rashes, heightened immune reactivity, brain fog after eating, and heightened sensory or stress reactivity.

The root causes that commonly drive this whole process include chronic stress and cortisol dysregulation, over-exercising or under-eating, antibiotic or antimicrobial overuse (including herbal antimicrobials), ultra-processed foods, insufficient fermentable fibre, chronic infections (H. pylori, EBV, parasites, mould exposure), low stomach acid or bile impairment, and micronutrient deficits in things like zinc, vitamin A, glutamine, and glycine.

Pathogens and Microbes by Stage

Here’s a more detailed look at the pathogens and microbes that tend to show up at each stage of mucosal collapse.

Stage One: Dysbiosis and Loss of Diversity

You’re seeing a shift away from commensal balance. The bacteria commonly implicated include Escherichia coli (pathogenic strains), Klebsiella spp., Enterococcus faecalis, Clostridioides difficile, Streptococcus spp. (in overgrowth), Morganella morganii, Proteus mirabilis, Pseudomonas aeruginosa, and Citrobacter freundii. On the fungal side, watch for Candida albicans, Candida glabrata, and Saccharomyces cerevisiae when it’s overgrown. And the viruses that disturb the mucosa here include norovirus, rotavirus, adenovirus (enteric), SARS-CoV-2 (through intestinal ACE2 involvement), and enteroviruses.

Stage Two: Mucin Layer Degradation

The mucus is thinning and mucin-eating microbes are expanding. The mucin-interactive bacteria include Akkermansia muciniphila (which is actually beneficial in a normal range, but harmful when it’s excessive relative to your mucin supply), Bacteroides fragilis (specifically the enterotoxigenic strain, ETBF), Ruminococcus gnavus, Prevotella copri, and Desulfovibrio spp. (sulfate-reducers that affect mucus and inflammation). The biofilm-disrupting pathogens at this stage are Helicobacter pylori in the stomach mucosa and Fusobacterium nucleatum.

Stage Three: Epithelial Injury and Permeability

You’re dealing with tight-junction damage and villus stress. The bacteria associated with this stage are pathogenic E. coli, Salmonella, Shigella, Campylobacter, and Yersinia enterocolitica. On the fungal side, watch for Candida in its hyphal transition, when it’s penetrating tissue. And the parasites to know about are Giardia lamblia, Blastocystis hominis (the pathogenic subtypes), and Entamoeba histolytica.

Stage Four: Immune Activation and Inflammation

Your immune system is upregulating its defences. The immune-activating bacterial groups include Klebsiella (which triggers Th17 activation), an overall expansion of Proteobacteria (which are LPS-rich), and Bilophila wadsworthia (a sulfite-reducing, inflammatory microbe). The viruses that can trigger mucosal immune flares here are EBV reactivation (not primarily a gut virus, but it adds to immune burden), enteroviruses, and CMV in an immunocompromised gut. And when helminths turn pathogenic, Strongyloides (rare, but immune-intense) and Trichuris trichiura can show up.

Stage Five: Systemic Spillover and Barrier Failure

You’re looking at endotoxemia and a loss of tolerance. The primary drivers are LPS-producing Proteobacteria — E. coli (via endotoxin), Klebsiella, Enterobacter spp., and Salmonella — along with Fusobacterium, flagellated bacteria (which activate TLR5), and fungal beta-glucans and mannans from Candida. The opportunistic translocation organisms at this stage include Enterococcus faecalis, Staphylococcus spp. (like S. aureus), and the toxic strain of Bacteroides fragilis.

One important note here: many of these organisms can exist in a healthy gut at low or balanced levels. They only become problematic in the context of low mucin production, a chronic stress cortisol pattern, low motility, impaired bile flow, post-infection dysbiosis, or antimicrobial overuse (including herbal). So really, the issue is a loss of ecological balance and barrier function — it isn’t simply a matter of “bad bugs.”

Testing and the Modern Microbiome

Mary likes working with MicroGenDX because they test for 57,000 microbes and have specialised tests for different areas of the body and microbiome — the mouth, the toe for fungus, the vaginal canal, and more.

The modern human microbiome is compromised for several converging reasons: many of us are now second-generation C-section, we’re not eating ancestral foods or living in nature, and we’ve been through multiple generations of antibiotics. We can’t necessarily get all of our birth microbes back, although Mary is working very hard to find a way to stabilise the anaerobic ones. Soil and food microbes are extremely important too, but they’re different from birth microbes and don’t perform the same functions. So what can we do in the meantime, for our best shot at health? Feed the birth microbes we do have.

ARP Expansion Instructions, as per Mary Ruddick’s Wisdom

If you’ve experienced quite a bit of healing at this point, this is your next step (please see the chart below). You can begin introducing tiny amounts of plantain, HMOs in supplement form or human breast milk from a healthy source, acacia fibre (or PHGG), and lactose. We want to begin feeding the birth microbes at this stage, even if these foods are technically “off the menu” for you — I’d just do a tiny bit of each until you hit the two-year mark, or until you’ve been in remission for more than three months. For example: a quarter of a green plantain chip (just make sure it isn’t cooked in seed oils) or a cooked slice, a teaspoon of raw milk, a pinch of HMOs. You can also add chitosan or ground-up shrimp or crawfish shells, larch arabinogalactans (you can use birch tree bark tea or buy this in supplement form), hibiscus tea, and colostrum. We’re already including some of these food sources elsewhere — if you’re not doing chicory tea, add in a pinch of inulin or a pinch of Jerusalem artichoke instead. Once you’ve been in remission for three months, or you hit the two-year mark, you can increase these amounts to whatever your body is asking for. And if you’re maintaining ketosis, keep in mind that some of these can knock you out of it, so be mindful of your amounts if that matters to you.

If you’re not feeling amazing at this point — or if you’re actually feeling worse — please begin here first, and we’ll feed the birth microbes once you’re prompted to, a little later on. Your mucosal lining needs the pathogens removed, plus zinc and a good number of minerals. Make sure you’re incorporating zinc if you aren’t already, along with electrolytes and sodium. I’d focus on building up the mucosa before feeding the birth microbes. Begin with Fermentum CEC and HMOs (or well-sourced human breast milk) as the food for the CEC, and also take HU58. You’ll stay on this combination for a few weeks before we move to the next step, and we won’t stop the CEC at that point either — all three of these supplements (links below) will continue as we work on the mucosa. Make sure to take all three daily; you can start with just a speck of the microbes if you need to, and a pinch of the HMOs is enough. The one thing to really watch is not running out of your HU58 — going without it during this process can genuinely make you feel terrible. You can start with a quarter capsule of each microbe. You’ll be prompted for your next step from here.

Vaginal-Birth Microbes

This isn’t an exhaustive list — Mary notes there are around 200 of these — but here are some of the vaginal-birth microbes and what feeds them:

Lactobacillus crispatus — Human milk oligosaccharides (HMOs), lactose
Lactobacillus jensenii — HMOs, lactose
Lactobacillus gasseri — HMOs, lactose, inulin
Lactobacillus iners — HMOs, lactose
Bifidobacterium longum subsp. infantis — HMOs (primary), lactose
Bifidobacterium breve — HMOs, lactose
Bifidobacterium bifidum — HMOs, lactose, mucin
Bifidobacterium adolescentis — Resistant starches, inulin
Bifidobacterium dentium — HMOs, lactose
Prevotella bivia — Resistant starches, fibres
Prevotella timonensis — Fibres, resistant starches
Gardnerella vaginalis — Glycogen (maternal), mucin
Streptococcus salivarius — Lactose, HMOs
Streptococcus thermophilus — Lactose, dairy sugars
Streptococcus mitis — Lactose, HMOs
Staphylococcus epidermidis — Skin lipids, breast milk fats
Staphylococcus aureus (low load) — Amino acids, breast milk proteins
Corynebacterium spp. — Skin lipids, amino acids
Enterococcus faecalis — HMOs, lactose
Enterococcus faecium — HMOs, lactose
Veillonella parvula — Lactate (from lactobacillus/bifido metabolism)
Megasphaera spp. — Lactate, short-chain fatty acid intermediates
Atopobium vaginae — Glycogen, mucin
Peptoniphilus spp. — Amino acids (maternal peptides)
Finegoldia magna — Amino acids
Actinomyces spp. — Mucin, oligosaccharides
Mobiluncus spp. — Glycogen breakdown products

Perineal / Gut-Origin Birth Microbes

Bacteroides fragilis — HMOs, mucin, resistant starch
Bacteroides vulgatus — HMOs, mucin, fibres
Bacteroides dorei — HMOs, mucin, fibres
Bacteroides thetaiotaomicron — Human mucin, plant polysaccharides
Escherichia coli (commensal strains) — Lactose, small sugars
Clostridium butyricum — Resistant starches, prebiotic fibres
Clostridium leptum group — Resistant starch, arabinoxylan
Clostridium coccoides group — Fibres, starches
Ruminococcus bromii — Resistant starch (green plantain)
Ruminococcus gnavus — Mucin, HMOs
Ruminococcus obeum — Resistant starches
Akkermansia muciniphila — Human mucin (and increases with polyphenols)
Faecalibacterium prausnitzii — Ferments plant fibres, resistant starch
Roseburia spp. — Resistant starch, fibres
Blautia spp. — HMOs, resistant starch

Skin/Contact and Milk-Associated Microbes

Cutibacterium acnes — Skin lipids
Malassezia spp. (yeast) — Skin lipids
Candida albicans (low load, normal) — Lactose, glycogen
Rothia mucilaginosa — Lactose, HMOs
Micrococcus luteus — Skin lipids

Breast-Milk Delivery Microbes

In addition to the above:

Lactobacillus reuteri — HMOs, lactose
Lactobacillus fermentum — HMOs, lactose, polyphenols
Lactobacillus salivarius — HMOs, lactose
Bifidobacterium kashiwanohense — HMOs
Bifidobacterium longum — HMOs, lactose
Bifidobacterium pseudocatenulatum — HMOs + fibres
Streptococcus lactarius — Lactose

Key Food Categories for Birth-Seeding Microbes

HMOs — Breast milk only
Lactose — Breast milk, raw dairy
Mucin — Endogenously produced gut mucus
Resistant starch — Green plantain, green banana flour
Inulin — Chicory, onion, garlic (plant sources later in infancy)
Polyphenols (support some species) — Berries, rosehip tea, herbal teas (maternal diet impacts milk)
Amino acids/peptides — Maternal tissues, milk proteins
Skin lipids — Skin-contact organisms

Simplified “Birth Core Microbe Diet”

If you want the short version, here’s the simplified birth core microbe diet: HMOs (exclusive to human milk, and the number one substrate), lactose, mucin, resistant starch, inulin and other prebiotic fibres, maternal skin and glycogen exposure, and occasional amino acids from milk proteins. And if you’re a ketogenic parent, don’t worry — you still supply HMOs through breast milk, since HMOs aren’t reduced by maternal carb restriction.

Practical Guidance

Mary also shared some general practical guidance: don’t use harsh soaps, and she personally wouldn’t take antibiotics unless it was a life-threatening situation. Eat traditional foods, and share touch and food and drinks with healthy people. Someone born via C-section is populated at birth by the medical staff, the hospital, and the people who touch and hold them — which leads to more pathogens and overgrowths. We want to try to add in a lot of “Staph E” (the kind we’d normally get from our parents) if possible — it would come from the skin of a healthy person — and keep an eye out for products that may emerge to help with this.

Mary also teaches that we’re missing oxytocin — our bonding hormone — in autism and other mental health disorders. Keep an eye out for her ongoing research and future information releases; you can join her email list at maryruddick.com.

For Those Conceiving or Expecting

For those who are ready to conceive, or who have a C-section baby on the way, Mary recommends using the microbe L. Fermentum CEC — sprinkle it on the nipple and areola before feedings, in case you do need a C-section. This builds up the mucosa that will allow the other birth microbes to take hold later on, when it’s time to plant them (we covered this in Week 26). The mother should also lean into activities that keep her in a parasympathetic state — increasing joy and oxytocin, and paying attention to light and circadian hygiene and timing. Our microbiome is affected by light just as much as it is by food, and it’s deeply affected by the state of our nervous system. After about a month of this, you can plant the other microbes.

Here’s how to identify or search for a microbe, since the exact name matters enormously. Take the example Bifidobacterium longum BB536: Bifidobacterium is the genus, longum is the species, and BB536 is the strain. Strain designations can be numbers, letters, or a combination — think DSM 17938, NCFM, or 299v. So the code after the species name is the strain identifier, and you should never use a microbe without its full name — that strain identifier is incredibly important when you’re choosing between products. Also worth knowing: IV antibiotics are more destructive than oral ones. Mary is working on a chart of microbes and how we can plant and feed each one.

For pregnant women, dads, and the rest of the family of a baby on the way, Mary recommends doing the ARP or a similar gut-healing protocol, replacing synthetic fibres, and using Blis Probiotics for the whole family, along with probiotic skin creams. A vaginal swab is a good idea for a C-section baby — even though it may not be enough on its own, it’s still worth doing, alongside implementing the full protocol and planting. And if the swab does happen but the microbes aren’t then fed, they’ll simply die, so it’s important to still implement the feeding protocol regardless. Breastfeed for at least two years if you can — some microbes will go dormant for six months to a year, waiting on the foods they need, but they still need the breast milk in the meantime. We don’t have to know all the science if we’re willing to just do things the old-fashioned way; we can’t replicate what nature creates. For young children, the best way to support the microbiome is simply this: if you’re healthy, touch your kids a lot, and try to keep them at home when you can. Traditionally, if we lost a microbe, we gained it back because we ate together as families, ate with our hands, and slept in a pile with our people. We’re designed to pass microbes back and forth, and we want to make sure we’re passing along the best microbes possible — our modern society tends to pass along more pathogens than good microbes, so we want to keep our families and our communities as healthy as we can.

What We Can Do Now

In the meantime, while we wait for more of Mary’s research to become available, here’s what we can do: reduce your stress load, a lot. Wake and eat at the same time each day, dance, cuddle, cultivate deep relationships, walk, get sunshine, make eye contact, and keep your blood sugar steady by avoiding whatever spikes it for you personally — we don’t want our immune system suppressed for 48 hours at a stretch. Use natural soaps, and stop using antimicrobials. We want to keep ourselves joyful and in a parasympathetic state as often as we possibly can, for the sake of our immune system.

A quick supplement note here: Plantarum 299V, L. Fermentum CEC, and HU58 are useful after antibiotics, and for feeding the birth microbes.

Not a Diet Change

I want to be clear that Mary is not telling anyone to change their diet. She herself had to follow a restrictive diet while healing, and you may need to as well — she isn’t suggesting you abandon whatever is currently working for you. What she is saying is that you may want to add in the foods that feed the birth microbes, if you can tolerate them, even if that just means bringing them in by the tiniest of pinches. She isn’t teaching someone else’s system either; she has created her own, and the foods that feed the birth microbes weren’t allowed on the diet she originally came from. She’s still working with ancestral foods, bringing in birth microbes in tiny amounts, bringing histamines down, and bringing in the food for the birth microbes in tiny amounts as well, until more is tolerated. The carnivore tribes are born with a perfect microbiome and live in perfect community with nature, so they can be carnivore long term — but we can’t. Carnivore is still useful for us when we don’t tolerate plant foods, while we’re healing, and with the intention of bringing the necessary plants back in down the road. A good diet for the birth microbes includes hibiscus tea, shrimp shells, dairy, the off-cuts of animal foods, a quarter teaspoon of plantain, and acacia fibre (which is traditionally used in Africa).

When Mary was first in practice, carnivore was magic for histamine issues, MCAS, and schizophrenia, among other things — but it isn’t something we should be stuck on forever. If you can’t return to plant foods, that’s actually a sign of a lack of birth microbes and the presence of mucin eaters, like chronic strep. Classic histamine issues and hormonal issues are often an indicator that you’re in mucosal collapse — for example, klebsiella is often at play in sex hormone imbalances. Your feel-good chemicals and your melatonin are also getting blocked by mucin eaters. Melatonin is extremely antimicrobial, and the mucin eaters have actually evolved to eat the precursor to melatonin, just so they can stay alive.

Here’s how the good microbes work against pathogens: they take out competing pathogens, take over the territory, or neutralise their toxins — they go to war for you.

Biofilms and Pathogens

Sometimes you also need a biofilm buster, or a toxin neutraliser. For example, Saccharomyces boulardii will neutralise the toxin from shiga toxin. Mary told us she doesn’t often reach for antimicrobials herself — in her clinical experience they’re rarely the right first move — but she does reserve them for specific, more severe situations, like a pseudomonas overgrowth.

Biofilms are created by microbes to hide from the immune system and to proliferate. For example, someone could have a chronic kidney infection with enterococcus — noted by very smelly urine — and it won’t show up on standard medical testing, because most testing only looks for four microbes. The biofilm is what’s actually causing the enterococcus to stick around; it’s extremely sticky. Hibiscus tea can actually get at this kind of biofilm. Some biofilms will react to your environment too — certain microbes don’t like mould, for instance, and will get fiercer around it, building even bigger and stronger biofilms in response. Different biofilms require different strategies. NAC (N-acetylcysteine) is one that Mary likes, and it’s worth trying if you want a biofilm and pathogen strategy — she doesn’t see a lot of die-off from it, and you can take it an hour away from your other supplements, then add good microbes back in once the biofilm has been weakened. NAC won’t work for everything, but it can be a great place to start.

Mary is working on a book for us, and her suggestion is not to start with biofilms — start with the birth microbes, daylight, laughter, dancing, real food, and real fats. That said, go with less ketosis if you have streptococcus, and lower fat in general if you have mucin eaters (a sign of this would be doing ARP well and still feeling worse at the one-year, eighteen-month, or two-year mark — that’s your cue to lower ketosis and start working on the birth microbes instead). Add in touch, feed the birth microbes, plant L. Fermentum CEC with HMOs as its food, and then after a month, begin NAC and whatever microbial defence strategy you may need. You can look up the benefits of any microbe by its full name and see what you might be lacking, based on what that microbe offers.

You can also feed the birth microbes through the single-microbe yogurt you’re cultivating — you feed the culture the substrate it needs, so you don’t have to eat that food source directly yourself.

Environment, Light, and Breath

Get out of the house as much as you can, and away from plastic clothing — get outside, it’s so important! Indoor living is something we can change at no cost — at minimum, open your doors when you can. Microplastics are being inhaled, and our houses are largely made of plastic. Your breathing rate matters enormously for your microbiome too — slower breathing, and fully exhaling toxins, are both crucial. Sound and frequency affect our microbiomes immensely, and laughter really is the most important medicine.

Mary also lets us know that we should have microbes that protect us from metals and poisons, like glyphosate.

Plant the keystone species when you can — they’ll help each other out.

For Those Stuck in Healing

If you have a lot of histamine issues and feel stuck at some point on your healing journey, try bringing in tiny sprinkles of the birth microbe foods and see if that helps — just a pinprick amount is all you need to tolerate. You can absolutely keep the carnivore diet or other medical diet you’re on. Mary used one herself and said, “I would not have healed without those diets, they are amazing” — but try bringing in the microbial food first, even the tiniest speck. If you’re already healing, bringing in these foods for your “little guys” is most likely all you’ll need to pop into remission, alongside the rest of the protocol. This advice is specifically for people who have done the medical diets perfectly and are still stuck or getting worse — you most likely have a mucin eater and need an additional strategy, not a reason to stop what you’re doing. Birth microbes can survive a stretch of time without their foods, so even if you feel great on a medical diet with no plants, try sprinkling in the food for the microbes anyway, just to keep them alive. The starvation method we’ve used in the past is still useful alongside feeding the birth microbes, because mucosal collapse is a new thing — the mucin eaters are a relatively new addition to our microbiome that we haven’t always had to deal with. They’ve shown up because of a combination of things: incoming toxins, our compromised terrain and immune suppression, pathogens moving into our nervous systems and becoming chronic rather than staying acute, and exposure to travel food and fresh water while travelling.

Detective Work with Past Infections

What infections have you had over your lifetime? You can use this strategically to figure out which microbes you might be missing. For example, if you’ve had tuberculosis, you’re likely missing Rhamnosus GG from your microbiome — otherwise you probably wouldn’t have gotten TB in the first place. You can apply the same logic to viruses. Cytokine screening can also be very helpful here. Basically, you can use the illnesses you’ve had, past or present, to do some detective work and figure out what microbes you might be missing.

From the 1940s through the 1990s, we killed off microbes arbitrarily, assuming they were all bad, and that has led directly to a lot of the problems we’re facing today. That said, we also need to recognise that some microbes really can be harmful — not all microbes are friendly — so we do want to stay mindful and treat pathogens and harmful microbes in our environment with real respect.

On Fibre

“Eat the rainbow” was never actually helpful advice for the general public, because it feeds indiscriminately. In general, fibre isn’t healthy for the modern person right now, because a compromised microbiome will use it to feed overgrowths instead. Long-chain polysaccharides can be helpful, but you don’t need to eat a salad — you can always take the tiniest amount of a plant and use it medicinally and strategically instead. For someone with a modern, compromised microbiome, fibre will most likely need to be avoided altogether. If you’re healthy and fibre makes you feel great, then by all means, eat it. If it makes you feel worse, take a break from it and spend time on soft foods to rebuild your villi instead, the way you would during the intensive gut-healing phase.

Glyconutrients

Glyconutrients are amazing — they’re sugars that heal (not sweet ones), and they help regulate the immune system, block certain pathogens, and block lectins. You can bring them in through food or as a supplement, and there are eight medical glyconutrients worth knowing about.

Glucose we make on our own. Mannose comes from egg yolk, shrimp shells, chicken cartilage, aloe vera, and cranberry, and it’s neuroprotective — helpful for UTIs, allergies, nerve repair, and mitochondrial support. Galactose comes from cheese, yogurt, dairy, colostrum, and some organ meats. Xylose comes from birch tree bark, connective tissue, and chicken skin, and it’s useful for dental issues and ear infections, as a preventative. Fucose comes from shiitake and maitake mushrooms, wakame seaweed, oysters, nutritional yeast, and human breast milk. N-Acetyl-Glucosamine (GlcNAc) comes from shellfish shells, meat stock, fungi, seaweed, and microbial fermentation foods — it supports joint and cartilage health, enhances glycoprotein and mucin production, and aids intestinal lining repair. N-Acetyl-Galactosamine (GalNAc) comes from red algae (dulse), cartilage, meat stock, and shellfish connective tissue, and it’s essential for forming glycoproteins, supporting cellular communication, and maintaining gut lining integrity. And N-Acetyl-Neuraminic Acid, or sialic acid, comes from colostrum, whey protein, egg yolk, brain, and dairy — it’s crucial for brain development and cognitive function, supports immune system signalling, and promotes the growth of beneficial gut microbes (it tends to run low in people with autoimmune conditions, Parkinson’s, and other nervous system disorders).

If you’ve tried a medicinal mushroom and it made you sick, you most likely have mucosal collapse. As with everything else here, tiny amounts are plenty — though you can use more if you’re actively sick. There’s also a glyconutrient tea that tastes pretty yucky but will save you a ton of money: fenugreek, shiitake, kelp, whey protein, bovine cartilage, and psyllium husk. You’ll likely notice lower autoimmunity, fewer illnesses, and more energy from this, assuming you don’t have other issues going on.

SIBO

Mary explained that SIBO shows up in multiple forms — methane, sulfur, or hydrogen-producing bacteria — and in her experience, you want to treat other underlying health issues first before attempting a SIBO protocol, or it will just come back. It used to be that SIBO was basically traveller’s diarrhoea, and treatment was a slam dunk. Now, either histamine is being overproduced, or the mucosal layer has collapsed and is affecting the ileocecal valve (located about an inch and a half to the right of your belly button), which then can’t open or close properly. If it stays open, you’ll usually get diarrhoea, which tends to be, though not always, the hydrogen form. If it stays shut, you’ll get constipation, which is more often the methane-producing variant. Address the histamines first — the lacking microbes, the lacking mucosa, the lacking DAO, and so on. The biggest issue Mary works with is nervous system disorders: people are missing their myelin sheath, and the migratory motor complex — which lives in the gut and makes up about 70% of our nervous system — isn’t moving at the correct speed, so you have to address the nervous system itself (this is something we do address in the ARP). Take an eagle-eye view: work on your overall illness first, build your foundation, and then address SIBO last, if you still need to.

Mary’s Approach in Hindsight

Mary shared how she’d approach her own recovery differently if she were doing it again now. She followed her routines and nervous system work with military precision, and for two years ate almost nothing but chicken soup with ghee — which did get her into remission, and did it well. But a lot of people ended up developing SIBO on that restrictive a diet, or gained a lot of weight, so what she’d do differently now is sprinkle in the foods for the birth microbes every day from early on, and work on lowering histamines through food as well. She explained that the gut-healing diet she used was itself a graduation from the Specific Carbohydrate Diet (SCD) — very similar, with only minor changes, but those changes made a big difference. This is actually traditional in the world of dietary healing: given all the microbial damage we’ve sustained, graduations and upgrades are needed over time. As she put it, “And now we are needing an upgrade — I am working on that now.” So she’d eat less soup at the start, feed the birth microbes like it was her job, and — while she personally gets a GI Map every three months — she suggests the average person can opt to get one just at the beginning. She’d graduate off the restrictive diet as soon as possible, bringing in other foods for specific purposes (not potatoes or rice, but foods for the birth microbes). She used glyconutrients then and would use them again, and she’d immediately be feeding Faecalibacterium prausnitzii and Roseburia. In the early days of her practice, she used almost no testing, but she does use the testing that’s necessary now. And if you don’t have your birth microbes, you are more vulnerable — but that isn’t necessarily a life sentence.

Books, Supplements, and Ketosis

Mary is releasing three books and has published over 200 articles, including material on birth microbes for your self-healing journey and on relevant medical studies. She also shared a caution: if your mitochondria are really struggling, consider not using methylene blue, NAD, or MOTS-C, because they can actually make you feel worse in that state — either work with someone highly skilled, or hold off on those supplements. If you’re already quite healthy, though, they can be wonderful. Creatine can also be helpful, especially if you have a cellular deficiency. Ketosis bypasses the Krebs cycle and uses fat for energy — the transition phase isn’t fun, but what you get afterward is real, stable energy that’s great for the brain. Mary said she’d personally choose ketosis for a loved one with dementia, Alzheimer’s, or cancer: it stabilises mood, gives energy, and is even anti-viral, making you less likely to get sick.

Ferments

Traditional ferments often carry a beneficial microbe that acts as an antagonist to the pathogens common in that region, which is part of why we want our own traditional ferments. We use them as condiments, not as side dishes. If you’re not ready for ferments yet, that’s fine — you can leave them out until you are. They’re important, but not a cure-all; they’re wonderful helpers when you’re ready to bring them in, but they won’t replace specific microbes that are missing from the human microbiome. Fermented food has its own job and its own pathway to health, and the microbes we should already possess have their own separate jobs too.

Some microbes are regional, and we can use imported ferments when we need a specific microbe medicinally — L. Sakei in Korean kimchi, for example. That said, having a huge rotation of store-bought ferments isn’t especially ancestral or traditional. It’s great to keep a few homemade ferments going, and to purchase specific ones medicinally when you need to, so you can cultivate them into your own ferments over time.

Oral and Skin Microbiome

You shouldn’t have stinky breath, or be stinky in general! Our oral microbiome has been damaged by modern oral care — mouthwashes, toothpaste, plastic floss, and the like — and this affects our ability to make nitric oxide. You can suck on cloves if needed, or reach for birch-sourced xylitol gums or mints made with real ingredients (be wary of anything listing “natural flavours” as an ingredient). It’s worth addressing the underlying issue behind your dental symptoms too — a dry mouth points to sympathetic dominance, exhaling more than you inhale, left-nostril breathing, and general nervous system work. Stinky breath is a microbiome issue from the stomach on up, so use oral probiotics like Salivarius M18 and K12 (and there are many others), and for the nasal passages, L. Sakei and others work well. Oil pulling is great too, and ozone oil specifically for gum issues. In general, move away from antimicrobials and toward nourishment and probiotics.

For skin, the issue is that we’re overwashing and over-fragrancing, and we should be using products made from genuinely edible ingredients — oils, fats, and salt bars (which can help with tinea versicolor). Think traditional lye-and-fat soap, fermented dairy, skin probiotics, and sunlight. Getting outside half an hour before sunrise and staying out for an additional hour after is imperative for your circadian hormones, which plays a huge role in mental health recovery. To get good sleep and feel-good hormones, we need sunlight in our eyes and on our skin. In the morning, we should be producing cortisol, serotonin, and dopamine to help us pop out of bed, and that morning light exposure is what triggers melatonin properly at night, regardless of the weather. This also shifts your skin microbiome — when Mary visits tribes that have been colonised and are wearing donated synthetic clothing, they develop skin fungus that the uncolonized tribes simply don’t have. Fabric and light matter enormously. Vitamin D is actually made from microbes, and we really want to be making our own hormonal vitamin D — tinkering with nature here has gotten us into a lot of trouble. We want plenty of sun, and plenty of cholesterol in our diet. Long-term vitamin D supplementation will deplete the animal form of vitamin A, which most of us are already deficient in thanks to high-plant diets. Vitamin A needs to come in its animal form, in the correct ratio with K2, the way it’s found in whole foods — low vitamin A caused by vitamin D supplementation sets the stage for cancer.

Sound and Frequency

There’s a natural order to the way the world wakes up — the birds wake the animals and the plants, including us — and we need the sounds of nature in our lives. The green light filtering softly through the trees triggers gamma waves, which are responsible for gratitude, bliss, and awe, and the sounds of nature help regulate our entire circadian rhythm. The low-grade buzzing inside our homes, by contrast, isn’t good for our microbiome. We want to genuinely get outside as often as we can — be in nature, listen to the sounds, look up into the sky and the treetops to stimulate feel-good chemicals and open your lymph (looking down actually closes it), and just pretend the modern world doesn’t exist for a few hours a day.

Keep opening to expansion — your “little guys” are counting on you, and so is every version of you still to come.