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Restoring the Gut: Understanding the 5 Rs to Healing Leaky Gut with Mary Scalf, PA-C

Restoring the Gut: Understanding the 5 Rs to Healing Leaky Gut

Are you ready to take charge of your health? Schedule your free 20-minute discovery call with our New Patient Coordinator to see how you can become a patient at MaxWell Clinic and start your healing journey today.

The health of your gut is the foundation of your overall health. But the opinions on how to restore your gut health are varied, and quite frankly, confusing. It’s time to separate fact from fiction.

After specializing in rheumatology and autoimmune disease for years, I noticed the strong connection between the gut microbiome and autoimmunity. My curiosity about this connection is eventually what led me into functional medicine.

Watch the video on healing leaky gut:

  • Learn our science-based approach to healing leaky gut and restoring gut health.
  • Explore the underlying biological connections that might be at the root of leaky gut.
  • And discover the 5 “R” approach to improve your gut and your overall health.

The 5R Approach to Gut Healing: A Comprehensive Guide

Are you struggling with digestive issues, skin problems, or mood disorders? You might be surprised to learn that the root cause of these health problems could be lurking in your gut. In this comprehensive guide, we’ll delve into the 5R approach to gut healing, a fundamental framework in functional medicine. You’ll discover how understanding and implementing the 5Rs can pave the way to better gut health, potentially alleviating a wide range of health concerns.

Part 1: Remove – Identifying and Eliminating Stressors

The journey to better gut health begins with identifying and eliminating stressors that negatively affect your gastrointestinal environment. These stressors can encompass food sensitivities, allergies, infections, toxins, and more. An elimination diet, which temporarily excludes inflammatory foods, can be a helpful starting point. Common inflammatory foods include gluten, dairy, soy, corn, and processed sugars.

Stressors can also include imbalances in your gut bacteria. Stool tests help to determine the types and quantities of bacteria present in your gut. If an overgrowth of bad bacteria is identified, treatment options may include herbal protocols or antibiotics.

Part 2: Replace – Restoring Digestive Secretions

To restore proper digestion, it’s crucial to replace the digestive secretions your body may be lacking. This includes enzymes, gastric acid, and bile acids. Proper digestion begins in your mouth with mastication (chewing) and the release of salivary amylase.

If you have issues with heartburn and reflux, it’s important to consider the role of stomach acid. Surprisingly, low stomach acid can lead to these symptoms, and replacing hydrochloric acid may be necessary.

Enzymes like amylase, lipase, and protease, released from your pancreas, are crucial for breaking down carbohydrates, fats, and proteins. Those without a gallbladder may need to replace bile acids to aid in fat digestion.

Part 3: Re-Inoculate – Balancing Gut Microbiota

Balancing your gut microbiota is an essential step in gut healing. This phase involves reintroducing beneficial bacteria (probiotics) and providing them with the necessary fuel (prebiotics) to thrive.

Probiotics like Lactobacillus and Bifidobacterium help maintain a balanced gut environment by preventing the overgrowth of harmful bacteria. You can find probiotics in supplements or fermented foods like sauerkraut, kimchi, yogurt, miso, and tempeh.

Prebiotics, found in foods like artichokes, garlic, onions, chicory, and certain grains (such as barley and flax), serve as food for your probiotics, encouraging their growth and activity.

Part 4: Repair – Healing and Sealing the Gut Lining

In this stage, the focus is on healing and sealing the gut lining. Antioxidants, fish oil, and minerals like zinc can play a significant role in this process. Antioxidants such as vitamins C, A, and E, as well as fiber, support the repair of the damaged gut lining.

Glutamine, an amino acid, aids in healing and sealing the gut. It’s important to note that maintaining healthy microvilli, the finger-like projections in the gut, is crucial for proper functioning. These microvilli produce DAO (diamine oxidase), which is essential for breaking down histamines and reducing allergic symptoms.

Part 5: Rebalance – Lifestyle Factors for Gut Health

The final phase of gut healing involves rebalancing lifestyle factors that influence your gut health. Inadequate sleep can negatively impact your gastrointestinal tract, while excessive exercise can act as a stressor on your body, potentially perpetuating inflammation.

Managing stress plays a vital role in this phase. Stress management techniques, such as deep breathing exercises, are essential in signaling to your brain to relax. When your body is constantly in a “fight or flight” mode, it prioritizes survival over healing, impairing digestion.

Regular bowel movements are an important aspect of gut health. If you’re not having daily bowel movements, it’s essential to assess your stool quality. The Bristol Stool Chart is a helpful tool for evaluating stool appearance and identifying potential issues.

The Duration of Gut Healing

One of the most common questions about gut healing is, “How long does it take?” The answer varies depending on individual factors, including your history, environment, and medications. Gut healing is not an overnight process; it requires commitment and patience. In many cases, it’s recommended to allow six months to a year to see significant improvements in gut health. The duration may differ from person to person.


Understanding and implementing the 5R approach to gut healing can be transformative for your overall health. By removing stressors, replacing essential elements for digestion, re-inoculating beneficial bacteria, repairing the gut lining, and rebalancing lifestyle factors, you can embark on a journey to better gut health. While it may take time, the potential benefits, such as alleviating digestive issues, skin problems, and mood disorders, make the effort worthwhile.

Remember that personalized systems medicine is key, and tailoring the approach to your specific needs is vital. If you’ve been struggling with chronic health conditions or are looking to optimize your well-being, consider reaching out to a healthcare practitioner well-versed in functional medicine for guidance on your gut healing journey.

Gut health plays a crucial role in your overall well-being, so why not start your journey to better health today?

Are you ready to take charge of your health? Schedule your free 20-minute discovery call with our New Patient Coordinator to see how you can become a patient at MaxWell Clinic and start your healing journey today.

hi everyone hi well
i want to welcome you to this week’s group visit
um we’re going to be continuing the conversation i started
i guess about the last months or so ago
about about intestinal permeability it’s a really important topic in
functional medicine and it’s important that we really lay this as a foundation to everything
we do and i really want you all to kind of understand
why we go about the things we do and or the importance or just kind of how we go about this so
i am mary scout i’m a physician assistant here i may even be your physician assistant
here so just to to bring up a few housekeeping
reminders if the the zoom kind of goes out uh give us maybe about 10 minutes
may take less time but to get back up and running we’ll be going as soon as we can also if you have any questions put
them in the chat box i will address them at the end of
this discussion so so restoring the gut understanding the five r’s to healing
leaky gut
i want to to recap discussed last time and
leaky gut and why that matters so it’s important to know that all
disease begins in the gut um this hippocrates is the kind of founder
of modern medicine and i don’t know why conventional medicine doesn’t follow this
so kind of this is a good depiction of what leaky gut is another more proper term is going to be intestinal
permeability so normally what
we want to see is we want to see these epithelial testosterone cells really
close and tight together these cells are going to be very selective as far as
what they’re going to allow through either nutrients
that kind of cross that prosthetic gut after you kind of break down the food that you consume or liquids they can go
kind of between these cells this is going to be highly selective or if kind of right they can go through
those cells and then they can get to the bloodstream and the bloodstream can help get these
nutrients to the organs and tissues that it needs to to promote and produce health and keep
you going well what happens in leaky gut whether it’s due to
stress alcohol antibiotic use
non-steroidal anti-inflammatory medications proton pump inhibitors like acid
reducers good allergens infections toxins
etc we can get leaky gut and you’ll see where those
junctions between those epithelial cells then widen
or things that are pathogens or food particles are now able
aside from foods they’re now able to get through the cells
between them or through them then we get things into our bloodstream that we don’t want and so on the other side here
starts our immune system reaction and so that can start to create inflammation
that inflammation can get it kind of go systemically i can go to our brains
and then we’ve really got a problem so kind of the problem at hand
and why we want to solve this is that this is going to be linked to so many of our health conditions and
concerns so things like autoimmune diseases being
cautious rheumatoid arthritis psoriasis and many many more some sort of bowel
disease um osteoarthritis hives eczema
other rashes i think martial psoriasis think acne environmental allergies food allergies
of course um acne mood disorders anxiety depression even links to schizophrenia
chronic fatigue issues autism dementia obesity if you’re having trouble losing
weight your gut maybe the issue and then of course
some things that are more obvious things like ibs or irritable bowel syndrome
um this picture kind of cracks me up because i whenever i try to explain leaky gut to
my patients i like to say it’s not that you have these fluids spewing out of your intestines into your body cavity
and so on and so forth but um so this is your not actual leaky gut depiction
so that’s kind of my really brief recap
what i like to think about gut healing and i want to know i want
you to think about what you have heard before maybe coming to maxwell clinic or
from the media or bloggers etc about what you know about guy healing
so before i came to maxwell i think gut healing was like drink kombucha they’ve
got good bacteria in that vinegary fermented substance it’s really good for your health
so i started drinking kombucha little did i know some of those coffee just had a lot more sugar which is actually not
good for your gut health i thought this was kefir or kefir kefir
is a fermented kind of dairy beverage again probiotics are the theme here
probiotics in general so there are so many probiotics on the market
but i’d like to i would encourage you to use these judiciously meaning
there’s a probiotic may not be right for everyone and higher doses of probiotics especially may not be right for a
particular individual you’re probably going to be safe with a lower dose probiotic think something about 30
billion cfus but otherwise you may run into some problems especially if you have
something called small intestinal bowel overgrowth and actually make your symptoms of like abdominal pain bloating
worse so just because they say probiotics are good doesn’t mean they’re right for you
being gluten-free i think in the last maybe five ten years we have seen this explosion of
gluten-free products and items it’s become almost more like a marketing term and then people have begun to assess or
to identify gluten-free as healthy well everything gluten-free is not necessarily healthy a lot of gluten-free
items are still heavily processed foods and could still cause inflammation in the bodies
and then bone broth bone broth is actually really beneficial to our gut health but that was something
i remember and trying to get on board with as well
so what actually is gut healing
it’s the 5r framework so i want to start to dig into that
now so the 5r framework is is very
foundational for functional medicine practitioners and it’s something that we
are all taught as we become certified in this type of medicine
so because a functioning digestive system is so essential to
good health and you’re you’re gonna these these issues
can cause more than just kind of your gastrointestinal complaints you might not just have floating gas
diarrhea like i said earlier it’s going to underlie your chronic health conditions um
that i mentioned earlier so there’s so much that can go wrong in our
gut and so if you think about our gut um our gut is a tube running from our
mouth to our anus and it is where our out the outside environment intersects
with our body so we want to keep that that health intact or else that
leakiness like i kind of showed in that picture earlier was going to wreak havoc in our bodies so
what are the five r’s in functional medicine
here is the 5r approach so we want to
remove what do we want to remove we want to remove
stressors what are those stressors it’s not necessarily going to be things like mental emotional
physical stressors that will kind of play into this as well we want to think about stressors that negatively affect
the environment of our gastrointestinal tract and these could be
food sensitivities or allergies and this is why like why we recommend
quite a few of our patients to go through an elimination diet that will get rid of the most
inflammatory foods that are likely for keeping that cycle of leaky gut going and by removing those foods the gut has
time to heal by decreasing that overall inflammatory load while the foods themselves may not
be the reason a leaky gut it’s definitely not doing us any favors the immune system is always reacting to
these foods now the immune system can see because of that gut leakiness
also part of those food sensitivities are going to be part of those the pretty ubiquitous in the standard american diet
so that’s where gluten-free actually may help a lot of people it’s going to decrease inflammation in the body but
also corn dairy soy peanuts processed sugars egg
this all may cause an issue so well something about bacteria think about parasites think about yeast
so at some point or other in your journey at maxwell clinic you have done or you’re likely to do a
stool test it’s probably one of the favorite things that our patients do
not really i have some that ask me not to do it again so it gives us so much important
information though about how to best help you how i mentioned probiotics earlier
these stool tests will tell us kind of what your gut needs and by the amount of bacteria we see this beneficial
probiotics were able actually to recommend the right probiotic for you to
aid in building your health if you have bad bacteria in your gut
that’s going to continue that inflammatory issue and that gut leakiness so we’ll
have to use some kind of protocol using herbals or maybe even depending on your symptoms and antibiotic
aeroscience parasites they do happen um not everybody has them but the
stool test that we recommend gets three stool samples those parasites are sneaky and they like
to hide and by doing three samples we can usually catch that and they are really difficult to get rid
of but they do help to get rid of them for your health
yeast yeast overgrowth we have yeast that inhabit our guts um not normally
but if we have that imbalance of bacteria in our gut that can lead to a yeast overgrowth and
that’s why many people after you take an antibiotic you might women especially might get a yeast
infection yes also can kind of show up on your skin
and show up kind of in your mouth and on your tongue and show up kind of uh
and under skin folds and in kind of your your private areas so that could also signal a yeast
overgrowth in your intestines so again we might use uh some antifungals nectar antifungals or
anti-yeast medications and dietary interventions to help
balance that yeast our hope though with removing foods is
not to have you have to remove them forever though you may notice that you feel best if you have
if you continue to remove gluten or dairy from your diet or whatever you find that you react to after an elimination
diet we want to replace um what do we want to replace well we want
to replace those digestive secretions and what are those digestive secretions
well just like in the name you think of them as your digestive enzymes
digestive really begins in your mouth you have this mechanical digestion with this fun word called mastication this is
where you’ll start to get some of that chemical breakdown with cyber salivary kind of amylase to
start breaking that food down as you kind of go into the stomach you’re going to have
gastric acid that we want to replace hydro hydrochloric acid some issues with um
heartburn and reflux actually are because of low stomach acid and not too much stomach acid so
when you have those symptoms and you get prescribed something like nexium or or
pepcid or actually reducing acid more may actually continue to cause issues
we may need to replace hydrochloric acid we may need to replace
things like amylase lipase protease i come from your pancreas and help to break down proteins
fats and carbs
you also want to think about replacing bile acids if you don’t have a gallbladder you might have trouble digesting fats
you have insufficient action from your gallbladder you may have trouble digesting fats if you
notice that your stool is really greasy and you have to wipe a lot well you might have trouble digesting fats
so using uh enzymes like ox file can help kind of replace that
and help improve that if we’re not digesting uh our foods well
um then you won’t be able to again get the all the goodness from our foods when you go
through all that trouble to change your diet and eat better so medications aging
are also going to change kind of how much of those enzymes we secrete our ability to do so
the third are re-inoculate
what do we re-inoculate well we want to re-inoculate prebiotics and
we want to re-inoculate with probiotics probiotics are a good bacteria
when we have enough of those good bacteria the beneficial ones mostly
being our favorites are lactobacillus and bifidobacterium
they help to keep the ph and the gut low they help to ward off or kill off any bad bacteria from overgrowing so if
you’ve insufficient amounts of that that can cause that dysbiosis to imbalance bacteria in your gut
so you are going to find probiotics and supplements as well as foods so
we want to help i always want to encourage nutrition overtaking things if we can
but sometimes to make a big intervention we need those consecrated concentrated doses of probiotics or of certain
minerals and nutrients in order to help get you better faster so
but fermented foods think about sour corn sauerkraut kimchi
yogurt miso tempe can be very beneficial for probiotic
health so prebiotics prebiotics i want you think about prebiotics to be like the food for
your probiotics they help to stimulate the growth of those beneficial bacteria
they if you’re taking a probiotic those prebiotics condense those probiotics that you’re taking to stay and move into
your gut so prebiotics are going to be coming
from fiber that fiber is going to be called inulin you’re going to get that from artichokes
from garlic beaks onion chicory tofu
and other soy products don’t recommend soy products if you have a sensitivity with soy though
also going to be in grains again are you sensitive to any type of grains and make sure they’re gluten free
but barley flax and oats um wheat not gluten free
but it’s a good prebiotic inulin source
when we what happens when we have that right balance again it
helps to keep the ph and the gut low um keeps bacteria from overgrowing protects you from any if you have to get
antibiotic antibiotic side effects
want to repair your gut as well how do we do that
so we’re going to repair we’re going to repair that gi lining we want to help tighten
those epithelial cells from being so leaky
how we do that we’re going to use antioxidants we’re going to use fish oil
we’re going to use zinc those antioxidants we’re going to use
are like vitamin c vitamin a vitamin e fiber so fiber
fiber is going to be food for those probiotics probiotics love fiber
they chomp down on that fiber and when they do they start to make these short chain fatty acids which help
to repair that gut lining as well
glutamine l-glutamine is an amino acid that helps to heal and seal the gut so again we’re trying to bring those cells
back to their healthy status something i want to mention too is
using 5-htp so
5-htp i wish i had that picture of the those
that cells again but if you notice on the in those gut cells on the tips of them they have these microvilli these little
finger-like projections that help to increase the surface area so what happens when that we have that
leaky gut depending on balance about it is and those microvilli can get worn down
and what we lose most microglia get worn down is something called dao diamine oxidase and that helps us to to deal
with histamines in the body and break them down um and so if you lack that dao you may have a lot of allergic type symptoms
so if those are denuded you have to try to grow those again to
help get your gut health back together and one thing that helps with that besides just supplementing with that dao
enzyme or cme is going to be 5 htp so 5 htp
aside from being a precursor to the neurotransmitters um
serotonin and melatonin in the body that help to support your mood and sleep they’re also
going to help grow those intestinal microphili i think that’s really uh fascinating
also because your gut actually is responsible for about 70 of those neurotransmitters
so if you’re having problems with like depression anxiety um i hope you are starting to see that
link of why that gut health matters
and then the last star is rebalance i know
i hope you don’t think you’re going to get away without some lifestyle recommendations so
we bounce what if we want to rebalance we want to make sure we have enough sleep and inadequate sleep can affect
our gi tract we want to exercise
kind of no we don’t want to exercise too little we don’t want to exercise too much too much exercise can be a stressor
on our bodies and can perpetuate inflammation so we have to kind of figure out what is right for you
also need to manage stress well dr woods did a really good um group visit
a couple weeks ago on breathing and it’s one of
the more difficult recommendations that we prescribe for people to follow i don’t it’s it
takes a lot of discipline but it can have the biggest impact because what we are trying to do is send a signal to
your brain to to relax if you have that fight or flight mechanism always on
the the body is not prioritizing healing it’s protect this prioritizing survival so you’re not going to be in thriving
mode you’re going to be in survival mode so it’s going to further impair digestion
so even if you’re like man i’m eating really well but i still feel like crap but if you’re over exercising you’re not
prioritizing sleep you’re not taking moments to relax then
that’s your problem so
those are our five r’s so i’d like to know
if you have any questions i’m gonna try to go ahead and
answer one for you so a lot of questions a question i get all the time is you know how long does
gut healing take and that depends we practice personalized
systems medicine and how long this takes kind of depends on where you’re at because
a lot of times you’re not going to get into the state of unhealth overnight
so that can almost take about as much time as a chit key to get unwell but i would have set an expectation for
somewhere i would say i mean try to look at least six months to a year
uh and that again is going to vary from person to person depending on your history and your needs
beyond what your environment’s like and what medications you’re already on
so i will see people that are relatively young and healthy and not a lot of issues i see them get
better they do an elimination diet we replenish omega-3 fatty acids iron vitamin d
and after like a couple months amazing they’re they’re feeling great others
there’s a lot more time so but um some patients may see benefit in
three months some six i’m a year but again depends on all the issues that are kind of found
well i do hope this has been really helpful um
about our approach to gut healing and
hopefully why i hope you understand why we’ve recommended some of the things we do in order to get you well so even though i
listed those five r’s in a particular order those some of those mechanisms are going to happen all
at once um or maybe they’ll be gradually layered on we always want to tailor what we do to
you i never want anyone to feel overwhelmed with what we’re doing
but also how much we’re able to do at a time may give us more robust results and
healing so the expectation needs to be depending on what we’re doing it might
just take more time
i appreciate that expression of thankfulness
any other questions i would love to help you understand
anything about this topic more so
i’ll leave this just for maybe another minute i really appreciate you spending
friday afternoon with me
you would like to explore any of these options i encourage you to reach out to your
maxwell clinician we are very passionate about this topic
so i would say if you find yourself not getting better and it’s been a while since we’ve looked at your gut
i i would ex i would have recommended reassessments
i think after the first of the year is a great time to reset an elimination diet
this is what you notice that you might have forgotten
i also want to you to pay attention to this is a really awkward question that i
ask patients that that matters so
what’s your school like you ask everybody if you have a bowel movement daily and
growing up i never paid attention to it and i realized as i get older it’s how important it is
and and kind of the traditional teaching is that you just go as much as you need to
go so regular for some was believed to be if you go every three days and you go every three days
but honestly if you’re eating food you should be eliminating daily
so ideally if you look at a bristol school chart it has a
a gradient of what school should look like so the basics though as you know is your
stool is it looking like pebbles is it looking like logs is it looking like a snake is it looking like pudding
or is it looking like tea the ideal stool is going to look like a snake
if you’re looking kind of more like logs you might need more hydration or more fiber
you have pebbles that’s more constipation may need some magnesium citrate uh fiber water maybe probiotic if you’re
having loose stool pudding tea again we think about
maybe you need digestive enzymes or vital acids your gut has your entire nervous system
and so if you are kind of an anxious and nervous person then
kind of again not taking that time to de-stress that’s going to regulate that sympathetic that fight or flight you’re
going to have quicker evacuation of your stool so your body does not prioritize
breaking down foods into their nutrients and micronutrients and
and it’s just fast and accumulation so that could be an infection as well so
there’s so much we can learn about our poop so
even if you don’t have any digestive symptoms issues could still be coming from your
and there’s much we can do and look into to help improve that so
well once again i appreciate your time and i hope this has been very informative
and hopefully interesting have a great weekend

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Mary Scalf, PA-C

Mary is passionate about addressing the whole person and not just an isolated set of symptoms. Witnessing what traditional medicine has offered her mother’s chronic disease battle as well as her father’s dementia diagnosis, Mary is driven to use a science-based approach which strongly emphasizes root cause analysis and harnessing the body’s natural healing powers.