Olli Sovijärvi

G U T M AST ERY
UNLOCK TH E SE CR ETS O F O P TIM AL GUT H EALTH

1
Gut Mastery: Unlock the Secrets of Optimal Gut Health
1st edition

Publisher:
Biohacker Center Publishing Oü
Jahu 12
10415 Tallinn
Estonia
www.biohackercenter.com
© Olli Sovijärvi 2023

Visual design, layout and illustrations: Paula Karjalainen, Lotta Viitaniemi

Studio critic: Dr. Sam Inkinen
English translation: Olli Sovijärvi
Proofreading: Anne Bellot

ISBN: 643-005-6240-01-5

No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means,
electronic, mechanical, photocopying, recording or otherwise, without written permission of the publisher.

This ebook and its contents cannot be considered as treatment recommendations, nor does it serve as a medical treatment guide. Always discuss your treatment
with your doctor or therapist (e.g. nutritionist, etc.) before starting any supplements or medicines. Some herbal supplements and non-herbal supplements may
affect the effectiveness and pharmacokinetics of medicines. If necessary, mention to your doctor the nutritional supplements and herbal supplements you are
taking, especially in the context of medication. The content of the ebook is primarily intended as self-study material.

2
CONTEN TS

5 DEAR RE AD ER 3. IBS, FODMAP RESTRICTION AND

6 THE AUTHO R DIVERTICULOSIS
7 INTRODU CT I O N 36 I R R I TA B L E B OW E L SYN DROM E (I BS)
39 F O DM A P C A R B O H Y DR AT E S AN D T HE I R
1. TYPICAL GUT-IRRITATING FOODS R E ST R I C T I O N F RO M T H E D I E T
AND THE AUTOIMMUNE PROTOCOL 43 E F F I C I E N T I B S S E L F -T R E AT M E N T
11 REMOVE OR MINIMIZE ANTINUTRIENTS IN YOUR DIET 45 DI V E RT I C U LO S I S A N D H OW TO RE COGN I Z E I T
16 STOP DR I NK I NG MI LK 47 N AT U R A L S E L F -T R E AT M E N T OF D I VE RC ULOSI S
19 W HY DO MO D ER N GR A I NS CAUS E S O M A N Y
INTESTINA L I S S UES ? 4. GUT MICROBIOTA, DIVERSITY
20 AUTOIM MUNE D I ET A ND AUTO I MMU N E PROTO CO L & SMALL INTESTINAL BACTERIAL
(AIP) OVERGROWTH
50 G U T M I C RO B I OTA A N D BAC T E RI AL BAL AN C E
2. CONSTIPATION, DIARRHEA AND 54 SMALL INTESTINAL BACTERIAL OVERGROWTH (SIBO)
INTERMITTENT FASTING 60 F O L LOW T H E S E ST E PS TO E RAD I C AT E Y E AST
26 FIX CONSTI PATI O N WI TH S UI TAB LE N U T R I T I O N OV E RG ROW T H I N T H E I N T E ST I N E S
30 THE MOST CO MMO N R EAS O NS FO R DI A R R H E A A N D
ITS SELF -TR EATMENT
31 FASTING A ND I NTER MI TTENT FA STI N G – T H E K E Y
TO “ RESET” THE GUT?
33 INTERM I TTENT FA STI NG

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5. DIGESTIVE SYSTEM OPTIMIZATION, 7. FOOD INTOLERANCES, ALLERGIES
GERD AND DYSPEPSIA AND HISTAMINE INTOLERANCE
97 F O O D A L L E RG I E S
63 DIGESTION AND OPTIMIZING YOUR DIGESTIVE SYSTEM
98 F O O D I N TO L E R A N C E S & HY PE RSE N SI T I VI T Y
66 PROBIOT I CS
99 H I STA M I N E I N TO L E R A N CE
69 PREBIOT I CS
101 T E ST I N G F O R F O O D A L L E RGI E S AN D
70 OPTIM IZ I NG GAST R I C ACI D S ECR ETIO N I N T H E
H Y PE RS E N S I T I V I T I E S / I N TOL E RAN C E S
STOMAC H
102 DO T H E F O L LOW I N G
73 DYSPEPSI A
75 GASTRO ES O P HAGEA L R EFLUX D I S EA S E ( G E R D)
78 DIGESTIV E ENZ Y MES A ND B I LE ACI DS

6. GUT-BRAIN AXIS, SKIN HEALTH

AND STRESS
82 GUT-BRA I N AXI S
86 INCREAS ED GUT P ER MEAB I LI TY : THE L E A KY G U T
SYNDRO ME
88 SKIN – T HE MI R RO R O F THE I NTESTI N E S
91 STRESS A ND CO ND I T I O N O F T HE GU T G O H A N D-
IN-HAND

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Dear Reader,

Gut Mastery is one of the most comprehensive and prac-

tical science-based gut optimization ebooks. This ebook “All disease begins in the gut.”
also follows the Pareto principle – 20 % of the information
that produces at least 80 % of the results – so you don’t
– Hippocrates (460–370 BCE)
need to do it yourself. This book will teach you the basic
knowledge and tools to identify and self-treat the most
common gut issues. You will also learn about the most
typical anti-nutrients in foods, intestinal microbiota and
microbiome, leaky gut syndrome, the normal functioning
of the digestive system and how stress impacts the gut. In
addition, you will gain a deep understanding of how gut
health affects the brain and shows in your skin.

This ebook is for people who want results quickly and

efficiently and permanently. Whatever your primary goal
or starting point, you will find answers to achieving better
overall balance in your gut and health.

Olli Sovijärvi
MD, head author of Biohacker’s Handbook

5
TH E AU T H O R
W H O IS O L L I SOVI J ÄRVI ?
Dr. Olli Sovijärvi, M.D., is one of the pioneers of holistic medicine in Finland. At the beginning of his
career, Dr. Sovijärvi worked as a medical duty officer at the Finnish Red Cross Blood Service. In 2006,
he graduated from the University of Helsinki with a Licentiate degree in Medicine and became self-
employed in 2008. In 2010–2011 Dr Sovijärvi completed an Integral Theory degree at the John F.
Kennedy University, focusing on psychology and philosophy.

For the first five years of his career as a physician, Dr. Sovijärvi was employed by Finland’s first medical
recruitment agency. The job description involved scheduled patient care as well as emergency care and
being on call. He has worked at nearly 50 different clinics around Finland.

His numerous media appearances, social media articles and Finland’s first health podcast have expanded
the general public’s awareness of what healthcare can be. Dr. Sovijärvi has also acted as a consultant to
various companies and service providers operating in the fields of wellness and health technology.

From 2013–2018, Dr Sovijärvi practiced medicine at a private clinic that specializes in nutrition and
holistic healthcare. The clinic employs physicians and nurses practicing holistic medicine. The clinic
features the only trace element laboratory in Finland. At present, Dr. Sovijärvi focuses primarily on the
production of scientific content for preventive health care and wellbeing. He is the head author of
Biohacker’s Handbook (2019), which is often called “the missing manual of the human body.” He also
runs training sessions and presentations on the topics of biohacking, performance optimization,
nutritional issues and maintaining the intestinal balance. In his free time he enjoys athletics, playing with
his child, music and good humor.

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INT RODU C TI O N
The irritable bowel syndrome has become almost a “national
disease” in Finland: more than half a million Finns (probably
much more) are affected by IBS symptoms daily. Symptoms
associated with IBS are common experiences. It has an
insidious onset and frequently does not result in medical
care. Consequently, there is a discrepancy between the
1
incidence of the first occurrence of symptoms, which occurs
within the community, and the first diagnosis of IBS, which
will occur after visiting a physician. Globally, a 2012 meta-
analysis showed a pooled estimate IBS prevalence of 11.2 %.
There are many different factors behind increasing the
appearance of IBS, from stress to processed food and
environmental pollution. For many, the internal ecosystem
(the microbiota) has been greatly degraded over the last
decades. In other words, the diversity of different bacterial
species in the intestines has decreased significantly. This
phenomenon has clear effects on the overall health and
well-being of the individual. The official term for this
3
phenomenon is “loss of microbial diversity” (LOMD).
However, quite simple changes in your lifestyle can benefit
you a great deal. You can think of your own intestines as an
inner garden: how would you feed it to make the various
microorganisms grow as balanced as possible so that the
actual plants and the different species (metaphorically the
internal organs) would also flourish and feel well?
The Western lifestyle has led to a significant increase
in a number of chronic illnesses, especially in Western
countries. These include inflammatory bowel diseases
2
such as Crohn’s disease, ulcerative colitis, type 1 diabetes,
multiple sclerosis, celiac disease, various allergies, obesity
and type 2 diabetes, colorectal cancer and autism in
children. All of these have in common the loss of microbial
diversity in the gut.
With this book, you will understand the importance of
nutrition and the variety of nutritional factors in the well-
being of your gastrointestinal system and entire body.
When the gut is doing well and the intestinal ecosystem is
in good shape, the rest of the body can generally do well,
maintaining good health and mental alertness.
7
A S S OC I ATI V E LI N K S B E TWE E N WEST ER N L IFEST YL E, H UMAN CONDIT IONS AND LOSS OF MICROBIAL D I VE RSI TY ( LO MD )

Western lifestyle

Hurry and stress

Immunes diseases
Crohn’s disease
Urban environment Ulcerative colitis
without nature Type 1 diabetes
Celiac disease
Allergies
Multiple sclerosis

Drugs
and antibiotics Metabolic diseases
Obesity
Type 2 diabetes

Colorectal cancer
Cesarean section
Loss of microbiol Autism
diversity

Processed foods

Source: Mosca, A. & Leclerc, M. & Hugot, J. (2016). Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key
Predators in Our Ecosystem? Frontiers in Microbiology 7: 455.

8
A NT I B I OT I C S A FFEC T T H E B AC T ER IAL STR AI N OF
T HE I NT E ST IN E
A single course of antibiotics can affect as much as 30 %
of the entire bacterial flora of the intestine and can throw
off the bacterial balance from six months up to two years.
Repeated use of antibiotics can significantly alter and
deteriorate the diversity of the gut microbiota (see above).4
However, antibiotics are necessary when a harmful
pathogenic bacterium, such as Salmonella, Shigella,
9
Campylobacter or Yersinia, has entered the intestine.
Alongside viruses, these bacteria are the most common
causes of traveler’s diarrhea and intestinal infections.
Depending on the individual’s bacterial balance, the liberal
use of antibiotics may cause a predisposition to diarrhea,5
the Clostridium difficile infection,6 and the overgrowth of
other harmful bacteria.7 The increased use of antibiotics
has also increased antibiotic-resistant bacteria worldwide.8
 1.
TYPICAL GUT-
IRRITATING FOODS AND
THE AUTOIMMUNE
PROTOCOL

10
Typical gut-irritating foods
R E MO V E O R M I N I M I Z E A N T I N U TRIENTS
IN YOUR DIET
Antinutrients are natural or synthetic compounds that
prevent nutrients from being absorbed and may cause
health problems, such as gut-related problems, for many.
It is therefore useful to know which foods contain them
and how food can be processed to minimize their harmful
effects. Reducing the antinutrient content in food can dra-
matically improve the function of your gut. Small amounts
of antinutrients are good because this strengthens the
immune system of the gut and the whole body via their
hormetic effects.9
Antinutrients are often found in plant roots and seeds,
nuts, legumes and nightshades. All plants have protective
mechanisms. The purpose of antinutrients is to protect the
plant from external factors such as bacteria, molds, insects
and pests. Indeed, it makes sense for the protective mea-
sures of plants to also cause intestinal problems. Below are
the most important antinutrients that may have an effect
on your gastrointestinal system.
11
L EC T I N S
Lectins are carbohydrate-binding proteins
that appear in plants and animals. Lectins
protect plants from various micro-organisms such as
insects and pests.10 The roots and seeds of plants are par-
ticularly rich in lectins.11 Foods containing lectins include
legumes (beans, peas, lentils, soybeans, peanuts), cereals,
potatoes, nuts and seeds.12 13
Lectins have the ability to bind with the surface cells of the
digestive tract. This may cause increased gut permeability
and disruptions in digestion.14 In addition, lectins in wheat
and other cereals can cause chronic inflammation and
contribute to the development of autoimmune diseases
in genetically susceptible persons.15 Raw kidney beans are
particularly toxic. They contain high levels of hemagglu-
tinin, a substance that has the ability to cause red blood
cells to agglutinate.
It has been suggested that a link exists between lectins
and some autoimmune diseases such as rheumatoid
arthritis.16 17 18 According to one research hypothesis, lectins
may cause leptin resistance (cf. insulin resistance) that may
contribute to the development of obesity and metabolic
disorders.19
• Removing cereals and legumes from the diet, either
temporarily or permanently, can help many people with
intestinal problems.
P HY TAT E S
Phytic acid is present in plants in salt form, i.e.
phytates. Phytic acid can be found in the seeds
of cereals and legumes as well as nuts. Phytic
acid forms chelates with zinc, manganese, copper, iron
and magnesium and may therefore impair the absorption
of these minerals. The same finding has later been made
21
in humans, especially with respect to iron and calcium.
Typically the bacterial strain of the intestines contains few
phytase enzymes that are able to break down phytates.
• You can significantly reduce the amount of phytates in
nuts by soaking them.
• An appropriate amount of nuts and seeds per day is a
handful.
• If your intestines are very sensitive, leave nuts and seeds
out of your diet for a few days and try later again.
OXAL AT ES
Oxalates are compounds consisting of oxalic
acid and anions, salts or esters. Oxalic acid is a poi-
sonous substance that may damage the intestinal wall and
cause kidney stones by forming calcium oxalate crystals.22 23
Plants rich in oxalate include spinach, parsley, wood sor-
rel24 and rhubarb as well as beetroot, black pepper, cocoa
beans, cereals, legumes (particularly soybeans) and nuts.25
• You can significantly reduce the amount of oxalates in
spinach, rhubarb, beetroot and nuts by cooking them.
SAP ON I N S
Saponins are glycosides consisting of steroids
22
and triterpenes. They were named after their
ability to form soap-like foamy structures in
solutions. They are an essential part of the plant’s de-
fense system.26 Saponins are found in vegetables such as
soybeans, beans, peas, as well as quinoa, oats, asparagus,
licorice root, sunflower seeds and ginseng.
Saponins have several beneficial effects (including anti-car-
cinogenic and immune system stimulation).27 On the other
hand, saponins have harmful digestive effects (impaired
absorption of proteins and minerals, particularly in the
12
case of soybeans)28 and hypoglycemic effects (sharp drop
in blood sugar).
• Soy beans and peanuts cause intestinal problems (such
as swelling and flatulence) in many people. Peanuts in
particular are also a highly sensitising and potentially
allergenic food.
• Soybeans are also today, to a large extent, genetically
manipulated (GMO).
GLYCOALKA LO ID S
Glycoalkaloids are organic compounds bound with
various sugar groups. They are naturally-occurring
poisons in certain plants and their purpose is to protect
these plants from animals. Nightshades generally contain
various amounts of glycoalkaloids. A typical example is the
solanine found in potatoes. It is poisonous when ingested
raw in large quantities (breaks down cell membranes29 and
inhibits cholinesterase, i.e. the functioning of substances
that break down acetylcholine, etc.). Potato skins may cause
intestinal damage, particularly when fried and consumed
regularly for long periods of time.30 Raw green tomatoes also
• Eating cold (cooked) potatoes can improve the balance
of the gut microbiota (resistant starch)
• If the intestines are in a particularly poor condition, eating
raw unripe tomatoes can increase intestinal damage.
P ROL AM I N S
Prolamins are nitrogen-storing proteins found in
cereals. Prolamins are rich in glutamine and proline
(amino acids). They include gliadin (a part of the
wheat gluten protein), hordein (barley), secalin (rye),
avenin (oat) and zein (corn). The core parts of oats and
rice grains contain relatively low levels of prolamin.
K E RNE L CO MP O S I TI O N
Bran
The fiber-rich outer layer that
contains B vitamins, trace
minerals and antinutrients.
Endosperm
Carbohydrates (starch)
and proteins.

contain high levels of glycoalkaloids (tomatine).31

Germ
Rich in fats, protein, vitamin E,
• If you eat potatoes, prefer large ones (less B vitamins and antioxidants.
glycoalkaloids) – peel these and cook thoroughly.

13
Prolamins cause intestinal damage particularly in P ROL AM I N CON T EN T I N DIF F ERENT G RAINS
individuals suffering from celiac disease. Celiac disease
involves gliadin attaching itself onto the surface of the GR AI N P ROL AM I N % OF W HOL E PROT E I N

epithelial cells in the intestines and releasing zonulin, which

Wheat Gliadin 69
causes gut permeability by damaging the tight junctions
between the epithelial cells (more about this in chapter Corn Zein 55
6).
32 33
In healthy individuals, the effect of gliadin on gut
permeability is significantly lesser although perceptible.34 Sorghum Kafirin 52

• Avoid cereals (grains) because of their high prolamin Barley Hordein 50

content. White rice contains the least prolamins of all

Rye Secalin 30–50
cereals.
Millet Panicin 40
E NZ Y ME I NH IB ITO RS
Enzyme inhibitors are molecules that occur Oat Avenin 16
naturally in some plants. They interfere with the function of
various digestive enzymes. For example, protease inhibi- Rice Orzenin 5

tors that inhibit the function of trypsin and pepsin can be

found in raw soybeans.35 Amylase inhibitors, high levels
of which are found in kidney beans, are another example
of enzyme inhibitors. Amylase inhibitors interfere with the
breakdown and absorption processes of starch and other
complex carbohydrates in the digestive system.36

• Avoid soybeans and other hard beans.

14
 SUM M ARY
ME T HOD S O F R ED U C IN G
ANT I NUT R IEN TS 37 38 39 • Eliminate all cereal products (including gluten-free) and
legumes (soybeans, lentils, beans, peas, peanuts) for two
• Sprouting months from your diet and see how you do after that.
• Soaking (adding lactic acid bacteria, diluted • Soak the nuts and seeds before use; just use a handful a
hydrogen peroxide, iodine, vinegar or baking day maximum.
soda to the soaking water may boost the
soaking process e.g. for removal of phytates)
• Boiling or blanching (reduces oxalate levels, etc.)
• Cooking (significantly reduces lectin and
oxalate levels)
• Lactic acid fermentation (significantly reduces
phytotoxins in cassava and phytic acid in cereal
products)

15
Milk – one of the most common foods
causing gut problems
STOP DRINKING MILK
According to Statista Research Department’s global analysis,
the country with the highest per capita consumption of
fluid milk in 2016 was Ireland. The average person in Ireland
consumed 125 liters of milk in that year. Finland came in
second with 120 liters of fluid milk per person. In the United
States, the average consumption of milk was 69.2 liters per
person (see picture below). 40
Milk sold in the store (homogenized and pasteurized) is
the cause of more and more intestinal problems world-
wide. Many people get stomach swelling, flatulence, diar-
rhea, stomach pains and skin symptoms after drinking milk.
Increased airway mucus production and susceptibility to
sinusitis are also common. For some individuals, giving up
milk entirely may help in the recovery from chronic sinus
infection. The inflammatory cycle is particularly common in
people who unknowingly suffer from milk hypersensitivity.
This is particularly the case in A1 milk via the β-casomor-
phin-7 peptide of which there is plenty in milk and dairy
products.42 Abundant milk intake increases silent inflamma-
tion and oxidative stress in the body. This means that the
body is more easily affected by various diseases.43
The qualities of milk products vary depending on the cattle
breed of origin. Often the terms A1 milk and A2 milk are
used. The distinction is made according to differences in
milk proteins between cattle breeds. A2 milk produced by
indigenous cattle breeds cause significantly fewer health
problems. Conversely, A1 milk proteins are associated with
heart disease and intestinal inflammation.44 45 46 The A1 type
is the most common type found in cow’s milk in Europe
(excluding France), the USA, Australia and New Zealand.
According to a research report and systematic analysis
published in 2017, milk-induced intestinal symptoms are
caused by A1-milk beta-casein. In this situation, choosing
lactose-free milk alone does not help much, even if lactose
intolerance has been established.47 48 A1 milk proteins also
lead to looser stools and delayed stool passage (constipa-
41
tion). In addition, digestive discomfort is correlated with
inflammatory markers in humans for A1 but not A2.49
16
 Ireland 125

Finland 120

Cyprus 107.8

New Zealand 106.6

Australia 106.6

Estonia 99.1

United Kingdom 92.6

Iceland 89.8

Denmark 86.8

Norway 82.5

Sweden 81.8

Spain 78.6

Austria 74.8

Canada 71.6

United States 69.2

Source: Statista (2016).

17
Do the following: AL S O R EM EM B ER T H I S
The milk of grass-fed cows contains significantly more
• If you suffer from stomach upset, remove dairy products omega-3 fatty acids.50 In addition, the proportion of grass
completely from the diet at first. in the cattle diet is directly proportional to the nutritional
• After a month, you can try goat’s and sheep’s milk (A2 value of the butter produced.51 Organic milk products also
milk). Also long-matured Parmesan cheese (over 2 years contain more omega-3 fatty acids and conjugated linoleic
of maturation) may be appropriate for some. acid (CLA) compared to conventional milk products.52
• If these do not cause symptoms, you can try the next
fermented organic milk products.
• If you absolutely want to drink milk, prefer small farm raw
milk (not homogenized or pasteurized).
• Good sources of non-dairy calcium include fish soup and
broth, bone broth, dark green vegetables and herbs,
seafood, seaweed and rosehip.
• If you are concerned about your calcium intake, measuring
your blood calcium levels (both free and ionized) and
make a bone density measurement (DXA scan).
• If necessary, a good calcium supplement is Thorne
Research Dicalcium Malate

People do not need cow’s milk in their diets, but grass-fed

cow’s cheese and raw cheeses can be a good addition
nutrition-wise for those who eat them.

18

WHY DO MODERN GRAINS CAUSE
S O MA N Y IN T E S T I N A L I S S U E S ?
The global consumption of grains is mainly divided into
three different grains: wheat (Europe, Middle East, North
Africa and Australia), corn (North and South America,
Southern Africa) and rice (Asia). The global per capita wheat
consumption is around 67 kg. 70 % of the cereals eaten are
refined. Refining significantly undermines the nutritional
value of cereals (vitamin B complex, zinc, magnesium,
phytoestrogens and selenium are removed with the husk).
GLUT E N, CEL IAC D ISEA SE A N D G LU T EN
HY P E RS E NS I T IV IT Y
Gluten is a large-scale protein molecule that consists of
numerous peptides. At least fifty of these have been found
to destroy epithelial cells in the intestines, disrupt the
immune function and cause leaky gut syndrome. A pioneer
in celiac disease research, Dr. Alessio Fasano, found in his
research that there is increased occurrence of the zonulin
protein in autoimmune diseases such as celiac disease.
19
Zonulin modulates the tight junctions between intestinal
cells. The more zonulin there is, the more permeable the
gut.53
When a celiac individual eats gluten, the production of
zonulin proteins increases immediately.54 This in turn
stimulates the secretion of inflammatory cytokines, causing
the loosening of the tight junctions and, if prolonged, their
destruction. This process can be almost entirely prevented
by avoiding gluten in the diet. Over time, the amount
of zonulin is reduced and the epithelial cells and tight
junctions of the intestines are repaired.
Testing for celiac disease with laboratory tests does
not rule out gluten hypersensitivity, as the latter cannot
currently be reliably tested in a laboratory. However, recent
years have seen the development of laboratory tests (such
as LBP, FABP2 and EndoCAb antibodies) that will make
the diagnosis of gluten hypersensitivity using blood tests
possible in the future.55 Increased gut permeability has not
been found in individuals with gluten hypersensitivity. As a
result, it is not considered an autoimmune disease. Gluten
hypersensitivity and celiac disease are entirely distinct –
gluten hypersensitivity is also many times more common in
humans than celiac disease.56

The term non-celiac gluten sensitivity (NCGS) is now
used as a more suitable term for gluten hypersensitivity.57
However, many who suspect that they are suffering from
gluten hypersensitivity may have stomach problems from
other ingredients in cereals, not necessarily gluten alone.
This should also explain why many gluten-free diets do not
alleviate stomach upset. 58
Many individuals who have experimented with a grain-free
diet report experiencing health benefits. Typically a grain-
free diet is attempted when an individual suffers from
irritable bowel syndrome, celiac disease or other autoimmune
diseases or certain psychiatric illnesses. Many people
59
consider gluten to be the culprit of intestinal symptoms.
In addition to gluten, the cause may be the FODMAP
carbohydrates found in cereals and other cereal proteins
60
and antinutrients (see earlier).
A LS O R E M E M B ER T H IS:
Glyphosate-containing pesticides (such as Roundup) can
predispose one to celiac disease and cause intestinal
problems. 61 62
Glyphosate is used as a pesticide especially
in cereals, genetically modified soybeans and maize.
20
AUTOIM M UNE DIET AN D AUTOIMMUNE
PROTOCOL (AIP)
The autoimmune diet has been developed to support the
treatment of people suffering from autoimmune diseases. If
you do not have an autoimmune disease, you do not need
to follow the diet. Instead, try the guidelines recommended
earlier (grain-free, milk-free, legume-free and
generally minimising your intake of antinutrients in food).
The autoimmune diet and the related autoimmune
protocol (AIP) focus on removing nutrients and foods that
can potentially damage the intestines and generally cause
inflammation. At the same time, the focus is on repairing
the gut surface or lining and reducing inflammation in
the gut. AIP follows the traditional model of Functional
Medicine, known as the 5-R program. It is derived from
the English words remove, replace, reinoculate, repair
and rebalance. The autoimmune diet is based on these
five factors, which, when taken into account, can lead to
significant results in improving one’s health.
Clinical studies of the autoimmune diet in the treatment of
various inflammatory and autoimmune diseases have also
been published in the last couple of years. For example, in
inflammatory bowel diseases like T H E T R IANG L E O F AU TO I MMU NE TRI G G E RS
Crohn’s disease, autoimmune diet
has been found to significantly Genetics
alleviate symptoms and reduce
inflammation.63 Similarly, the so-called
Western diet appears to promote the
development of inflammatory and
autoimmune diseases.64

However, the development of

autoimmune diseases is influenced
by many other factors besides
Autoimmune disorder
diet. These include genetic
susceptibility, the environment
and various toxic environmental
factors, infections and especially
the gut microbiota and its
Environmental Gut dysbiosis
condition. Of these, intestinal factors
microbiota balance is at the core
of autoimmunity – it substantially Source: Campbell, A. W. (2014). Autoimmunity and the Gut. Autoimmune Diseases. 152428.

affects the immune system function

and its possible disturbances.65 The
leaky gut syndrome has also been
found to be the focal point of an
autoimmune reaction.66

21
 1 . R E MO V E
Remove the foods from your diet that can damage
the intestinal surface or irritate the intestines. The
antinutrients, sugars, additives, chemicals, mycotoxins
etc. may aggravate the leaky gut syndrome, which plays a
key role in the onset of autoimmune disease (see more in
detail later in this book). Foods that cause inflammation
and foods that can feed the wrong strain of bacteria or are
severe allergens are also removed from the diet.
Foods to remove include:
• All grain products (note: also gluten-free grains!)
• Dairy products (including sheep’s and goat’s milk)
• All legumes such as beans, lentils, peas, soy products
and peanuts
• All nightshades such as potatoes, eggplant, tomatoes,
peppers etc.
• Seeds (and seed-based spices)
• Nuts
• Processed oils and sugars
• Eggs (especially white; egg yolk may be suitable)
• Alcohol
• Sweeteners
• NSAIDs
22
• Additives
• Foods that cause allergies and hypersensitivity, if already
known
• Caffeine and other stimulants such as cocoa, green tea,
matcha etc.
Foods also come with a lot of harmful substances such
as pesticides, environmental toxins, preservatives and
additives that are not naturally included. For this reason,
it is advisable to favor organic and unprocessed foods as
much as possible.
2. REPLACE
People generally have digestive problems associated
with autoimmune diseases. Digestion can be revitalized
and stimulated with apple vinegar, lemon, herbs, bitters
or other acids (described more in detail later in this
book). You may also want to try digestive enzymes and
hydrochloric acid if they are either deficient or your
digestion is not working as well it could. Special attention
should be paid to the possible use of hydrochloric acid.
Generally, if there is evidence of inflammation in the
stomach or if the gastric mucosa is very sensitive, the use
of hydrochloric acid is not recommended.
 3 . R E I N O C U L AT E
Our body needs a broad spectrum of different bacterial
species that help restore the microbiological balance and
good diversity of your gut. Probiotic bacteria are also
present in the diet. If the wrong kind of bacteria, yeasts or
parasites are likely to present in your body, it is crucial to
eradicate them. At the same time, balancing the bacterial
strain is central to healing. More on pro- and prebiotics
later in this book.
4. REPAIR
Repairing the intestinal mucosa and gut epithelial cells
with the right nutrients and nutrient-dense food plays a
key role. The optimal diet is eliminated from allergens
and antinutrients and is generally anti-inflammatory. Fatty
acids, amino acids, fibers, antioxidants and flavonoids,
as well as certain carbohydrates (such as resistant starch),
vitamins and minerals are needed to repair the intestinal
surface and to reduce the inflammatory state.
23
• Vegetables, root vegetables and vegetables, rich in all
possible colors (except potatoes and raw tomatoes)
• Berries with various colors and tastes (best ones are
bilberries, blueberries, lingonberries and sea buckthorn)
• Fruit maximum 1–2 per day (restriction of excessive
fructose intake when inflammation is on)
• Game and meat from free-grazing and grass-fed animals
• Cold pressed coconut oil, olive oil, avocado oil,
macadamia oil and sea buckthorn oil
• Bone broth and collagen protein
• Anti-inflammatory roots and herbs such as ginger,
turmeric, chard, cinnamon, rosemary, thyme, clove, black
pepper and green tea
• Wild fish and high omega-3 fish species (rainbow trout
and salmon are not the highest quality recommended
choice because of their poor feeding/diet)
• Seafood
Nutritional deficiencies may also be needed to correct
nutrient deficiencies.
 5. BALANCE
In addition to nutrition and a variety of nutritional
factors, restoring the homeostasis of the body requires
an adequate amount of physical activity, enough sound
sleep, adequate hydration, good stress management and
social relationships. Modify your life so that it improves
your well-being and improves your health. No matter how
fine-grained your diet may be, chronic stress can “spoil
everything”; that is, maintain your body’s inflammatory
state.
24
SUM M ARY
The autoimmune diet is intended as a method to reduce
and remove the inflammation of the body and repair
the intestinal lining as quickly as possible. Usually the
autoimmune diet is followed for 3 to 6 months and even
longer, if the general condition and the condition of the
intestines so require.
If the system does not calm down with an autoimmune
diet, consider what other factors could be obstacles to
recovery. These may include, but are not limited to:
• Stress and overload
• Dysbiosis or microbial imbalance
• Food allergies
• Toxins such as molds
• Vitamin and micronutrient deficiencies
• Mitochondrial dysfunction or cellular energy loss
 2.
CONSTIPATION,
DIARRHEA AND
INTERMITTENT
FASTING
The most common reasons for constipation
and its self-treatment
F I X C O N S TI P AT I O N W I T H
S U I TA B L E N U T R I T I O N
Constipation is one of the most common intestinal
problems besides diarrhea and bloating. There are many
reasons for this, but here is a look at the most critical
reasons for constipation and especially on effective
self-care. When functioning optimally, you may go to the
bathroom for a“poop” after each main meal. This is called
the gastrocolic reflex, where stretching of the stomach
lining activates bowel movements. 67
T H E M OST COM M ON C AUSES O F CO NSTIPATIO N: 6 8
• Insufficient fiber intake from food
• Drinking too little (intake of fluids)
• Too little exercise
• Imbalance of the bacterial strain in the gut (dysbiosis)
• Irritable bowel syndrome
• Intestinal parasites
• Many drugs cause constipation (opiate-based painkillers,
numerous antipsychotics, iron medications, diuretics etc.)
• Hormonal imbalance (especially hypothyroidism)
• Chronic stress (can also cause diarrhea)
• Some neurological disorders and spinal cord injuries
may cause constipation

This is a very logical reaction: when food is introduced

into the body, waste comes out at one end. However, for
many, this reflex does not work optimally. Textbooks define
constipation as a condition where the bowel empties fewer
than three times a week. Normally, the intestines should
empty on a daily basis so that removing waste products
from the system is optimal.

26
B RI STOL STOOL C HART

• Separate, small, hard lumps

Type 1 • Feces have remained in the bowel for too long, absorbing the water
• Not enough fiber in the diet

• Solid, firm, visibly lumpy

Type 2 • Often appears when constipated
• Typical of irritable bowel syndrome

• Solid, firm, cracks in the surface

Type 3 • Similar to Type 2 but passed through the bowel more quickly

• Solid, soft and smooth

Type 4 • Good amount of fiber in the diet
(ideal) • Typical of people who defecate regularly once a day

• Separate, soft, clearly defined blobs

Type 5 • Typical of people who defecate 2–3 times per day,
(ideal) after each main meal

• Fluffy pieces, mushy stool

Type 6 • May indicate high blood pressure
• Typical of individuals who react to stress with their stomachs

• Entirely liquid
Type 7 • May be normal diarrhea or appear together with Type 1
• Typical of the elderly and children

27
 STO OL COLOR
Light to medium brown
Normal
Black, tar-like or red
Bleeding in the upper digestive tract or a sign of inflammatory
bowel disease. N.B. Medication or food (for example
blueberry, beetroot, licorice) may cause unusual stool color.
IF YOU CONSTANTLY SUFFER FROM CONSTIPATION,
CHECK THE FOLLOWING FACTORS IN YOUR LIFE:
• Are you drinking enough water / other fluids?
(the recommendation is about 40 ml / kg body weight
including water from food; for example, for a 70 kg person
this means 2.8 liters a day.)
• Try immediately after waking up drinking a glass (3–4 dl)
of water with 1 teaspoon of salt, as well as high-quality
squeezed lemon juice. This significantly increases bowel
movements.
• You can experiment with the so-called “salt flush” to
effectively boost intestinal emptying.
• Put 1 to 2 tablespoons of salt in warm water (approx.
1 liter) and allow it to soak, and then you drink it quite
rapidly. This should within 20–40 minutes accelerate
intestinal emptying quite a bit.
• A light morning exercise can improve bowel emptying
(5–10 minutes after waking up) – also, many rotation
movements present in yoga will improve bowel function.
28
Pale brown, gray or white
Bile deficiency or a sign of cirrhosis, hepatitis or pancreatic disease
Yellow
Gallbladder problem or parasitic infection (Giardia)
• Try to increase fiber intake especially in the morning and
evening (recommended fiber products are discussed
later in this book). N.B. Do not use cereal products!
• Optimize defecation position (squatting is the optimal
posture); a good tool for this is for example Squatty
Potty – also a couple of buckets will do the same thing
(see picture on the next page).
• Soaked prunes and figs may increase bowel emptying.
• Regular stress management practices (such as deep
breathing) relax the sympathetic nervous system and
may help with constipation.69
• Regular meditation helps with chronic constipation.70
• The use of magnesium supplement increases bowel
movements and the amount of water in the stool.71
• Investigate the possibility of hypothyroidism with your
doctor (laboratory tests and clinical assessment).72
 D EFEC ATI ON P OSI TI ON

We are designed Your colon Sitting stops Squatting position

to squat (3–6 feet long) the flow opens the colon

Kinked Open
colon colon

puborectalis
muscle

Humans have squatted for The colon moves waste to The puborectalis muscle The puborectalis muscle
millenia – until the advent the rectum for elimination. partially relaxes, keeping fully relaxes allowing the
of the modern toilet. It has a natural kink that the colon kinked and colon to empty quickly
maintains continence. blocking the flow of waste. and completely.

Pharmaceutical laxatives do not treat the cause of
constipation but mainly relieve the symptoms. Therefore,
it is of utmost importance to find out the cause of
constipation. A functional medicine doctor or an open-
minded gastroenterologist with specific knowledge
can help. In any case, if constipation is chronic, I
recommend a doctor’s consultation. There are also a
variety of medications for treating constipation, which vary
significantly in effectiveness depending on the individual.73

29
T H E MO S T C O M M O N R E A S O N S F OR
D I A R R H E A A N D I T S S E L F - T R E ATM ENT
Diarrhea, or a loose stomach, is quite a typical
phenomenon before an exciting event such as an exam,
lecture or performance. Acute and occasional diarrhea is
usually treated with awareness of the cause and relaxation
exercises. However, if it gets chronic, diarrhea may indicate
intestinal and body imbalances, which are discussed in
more detail below.
The textbook definition for prolonged diarrhea is more
than three stools per day for more than three weeks when
the stool is watery or loose. 74
P OS S I BLE CAU SES O F D IA R R H EA FROM TH E D I ET :
• Lactose intolerance (or intolerance to milk proteins)
• Gluten intolerance or reactivity to the various constituents
of cereal products
• Sweeteners that increase fluids in the colon (such as
xylitol, sorbitol, erythritol, maltitol etc.)
• FODMAP carbohydrates (see later in the book)
• Food hypersensitivity and/or allergies (see last chapter
of the book)
• Excessive use of magnesium
30
• Excessive use of vitamin C
• Coffee and alcohol
OTH ER C AUS ES OF C H RONIC DIARRHEA:
• Antibiotics and many prescription drugs (antibiotics also kill
useful strains of bacteria and can cause diarrhea as a result)
• Chronic stress and nervousness
• Over-training (sports) and continuous overload
• Intestinal infections (especially traveller’s diarrhea);
bacteria, viruses and parasites
• Celiac disease and inflammatory bowel disease (Crohn’s
disease and ulcerative colitis)
• Small intestine bacterial overgrowth (SIBO)
• Bile dysfunction
• Various toxins (such as arsenic and insecticides)
IF YOU HAVE CHRONIC DIARRHEA, CHECK THE
FOLLOWING FACTORS IN YOUR LIFESTYLE: 75
• Try a grain-free, dairy-free and legume-free diet
• Consider FODMAP restriction if the diet change
described above does not help within two weeks
• Check your diet for insoluble and soluble fiber
• Increase use of fermented foods (sauerkraut, kefir,
kombucha; fermented dairy products, if you tolerate
them) – these are not for everyone, especially for people
suffering from SIBO
• Remove all sweeteners and excess sugars from your diet
• Reduce coffee and alcohol use (replace with tea)
• Excessive sports can also cause diarrhea (chronic
intestinal stress); reduce physical activity
• Try Saccharomyces boulardii probiotic – Boulardii is also
particularly effective in acute diarrhea 76
• Traditional probiotics (containing Lactobacillus and
Bifidobacterium strains) are also often effective (more
about probiotics in a specific chapter of this book)
• Begin daily relaxation and breathing exercises
• Bentonite clay and activated charcoal can improve
the excretion of toxins from the intestines and ease
symptoms (old but useful methods) 77
• If these are not helpful, I recommend that you do a
broad stool analysis (GI360 x3 Stool Test) and Food
Sensitivity Test (Nordic Food Panel 184 IgG – Food
Intolerance Test)
• You should also consider doing the small intestinal
bacterial overgrowth (SIBO) test (Small Intestinal
Bacterial Overgrowth Test)
Drugs for diarrhea in pharmacies usually alleviate symptoms
but can cause constipation (e.g. Loperamide). Treating the
cause of diarrhea is also a key factor here. If you have blood
in your stool, are constantly losing weight, have variable fever
or are generally very ill, consult your doctor.
31
FASTING AND INTERM ITTENT FASTING
– THE KEY TO “RESET” THE GUT?
Fasting and intermittent fasting (IF) have been heavily
featured in the headlines of various magazines and media
in recent years. Fasting has been used, among other
things, as a therapy for a variety of ailments and to cleanse
the body. Juice fasting has become more common and
fasting has taken various forms from 5:2 fast to three-day
fasts. Simply put, people are clearly more interested in the
health effects of fasting than before.
Already the ancient Greek philosopher Plato (427–347
BCE) is known to have said, “I fast to be more effective
both physically and mentally.” The Roman philosopher
Plutharkos (45–125), at the beginning of our time, said:
“Instead of taking medicine, fast the day.” The well-known
Swiss alchemist and physician Paracelsus (1493–1541) has
similarly stated that, “Fasting is the most important cure,
your own internal doctor.”
Indeed, fasting has played a very important role in the
well-being of many different cultures and in the treatment
of many diseases. However, many seem to have forgotten
the medical effects of fasting, even though much research
has been done about the role of fasting in physiological
changes in the body. About a hundred years ago, fasting
was used to treat obesity, convulsions and various
neurological disorders. Fasting has also been used as a
treatment method for metabolic disorders.78
Rauli Mäkelä, a retired physician and functional medicine
doctor in Finland, treated his rheumatic and intestinal
patients for decades by starting the treatment with “soft
fasting” (including gut supporting supplements and juices)
for 5–7 days, followed by an anti-inflammatory diet similar
to the autoimmune protocol. Mäkelä’s treatment results
in these patients were significant. In 2017, a Mäkelä-led
clinical survey was finally published where patients with
inflammatory arthritis were treated with the so-called
DDP therapy consisting of diet, nutritional supplements
and probiotics. Treatment results were very positive with
regard to symptom relief and reduction of inflammation.
In a study published in 2005, 8-day fasting was found
to significantly relieve symptoms in rheumatoid arthritis
patients. Previously, a study published in The Lancet,
80
patients with rheumatoid arthritis benefited significantly
from a 7–10 day fast in the beginning of their treatment. It
was reported to alleviate symptoms and overall improved
quality of life.81
According to a human pilot study published in 2015,
fasting significantly changes the gut microbiota, or
bacterial strain, in a health-promoting direction. The
study found, among other things, that the number
bacterial strains increased in the fasting group and in
general, bacterial diversity increased (more different
bacterial species, i.e. better variety). Fasting increased
the number of beneficial Bifidobacteria, Akkermansia,
Faecalibacterium prausnitzii and Lactobacilli.82
In another study in controlled hospital premises in Japan, ten
days of fasting therapy significantly improved the symptoms
79
of people suffering from irritable bowel syndrome (IBS). In
particular, abdominal tension, abdominal pain and many
psychiatric symptoms, such as anxiety and depression, were
alleviated after fasting therapy.83
32
I N T E R MI T TE N T FA S T I N G
Intermittent fasting means fasting for a significant portion
of the day (for example 16 hours) and consuming the
daily food intake during the remaining eating window (for
example 8 hours). The simplest way to implement this is
to extend the overnight fast by skipping breakfast and
enjoying the first meal of the day in the afternoon. 84
The concept of intermittent fasting came about to counter
the trend of “six small meals a day” promoted by the
food industry and fitness culture of today. Grazing is often
rationalized using claims of activating the metabolism and
making weight management easier. However, no scientific
basis has been found for such claims. 85 86
In fact, the basal metabolic rate (BMR) increases slightly
after a 36-hour fast – it is only after 72 hours that the BMR
begins to slightly decrease. Intermittent fasting is helpful
87
in achieving the desired calorie restriction if the goal
88
is removing waste products from the body (autophagy)
or weight loss. Improvements in the regulation of sugar
metabolism have also been detected in conjunction with
intermittent fasting.
89
33
Intermittent fasting has been found to be an effective
means of weight management.90 In addition, it has been
found to modify metabolic markers such as fasting blood
sugar, fasting insulin, leptin hormone levels, liver and
cholesterol values.91 Weight loss due to fasting also alters
the bacterial strain in the gut: studies have shown that the
gut microbiota correlates with the loss of body fat caused by
weight loss. According to one study, an increase in strains
of archaebacteria and akkermansia muciniphila has been
observed with the reduction of adipose tissue. Likewise,
the number of Lactobacilli, a beneficial strain of lactic acid
bacteria, increased significantly with weight loss.92
Intermittent fasting works well in practice because it allows
you to eat until you are very satisfied during the eating
window without getting too high in your daily energy intake.
The effects of fasting on intestinal function have been
extensively studied in animals – far more than long-term
fasting. Studies in animals and fruit flies have shown
that practicing intermittent fasting produces long-
lasting positive effects on the gut microbiota, reducing
inflammation and improving condition of the gut lining.
In addition, studies have shown that intermittent fasting
increases the life cycle of these test animals.93 94 95
Research into the effects of intermittent fasting (IF) on
human intestinal balance is increasing at an accelerating
rate. Over the next couple of years, we are likely to get
more accurate results on the effects of IF (and fasting) on ​​
gut balance in humans. Many people who have tried and
practiced IF have reported that it has provided the necessary
“rest” for the intestines when there is no food to digest
continuously. It is also very likely that the gut’s own repair
mechanisms will work more effectively (gut autophagy).
Especially in inflammatory bowel diseases, this natural
repair process (autophagocytosis) has been
observed to be impaired. By supporting autophagy for
96
example via fasting and IF, it is possible to
help the gut to recover from the inflammatory condition
faster.97 The process of autophagy has also been found to
eliminate harmful microbes through so-called xenophagy.
There are various methods of intermittent fasting:
• Fasting for 24 hours 1–2 times per week (“Eat. Stop. Eat.”)
• Fasting for 20 hours followed by a 4-hour eating window
(“The Warrior Diet”)
• Fasting for 36 hours followed by a 12-hour eating
window (“The Alternate Day Fast”)
• Fasting for 16 hours followed by an 8-hour eating
window (“Leangains”)
• Fasting for 18 hours (fatty coffee allowed) followed by a
6-hour eating window (“Bulletproof Intermittent Fasting”)
You can try these out in a format that suits you. It is also worth
noting that getting used to fasting may take days or weeks
depending on your previous eating patterns and habits.
Take into account the following factors when fasting:
• If you want to try longer-term fasting, I recommend that
98
you do it together under the guidance and supervision
of a nutritionist or nutrition coach
• You can independently try short 2–3 day water/juice fasts,
but you should use expert help to support longer fasts
• Many use a variety of ready-made intestinal cleansing
juices to support fasting, which may help in getting used
to fasting
• Water fasting, in addition to providing enough salt and
minerals, is the most effective method of activating
autophagy
34
 3.
IBS, FODMAP
RESTRICTION AND
DIVERTICULOSIS
I R R I TA B L E B O W E L S Y N D R O M E (IBS)
Irritable bowel syndrome is a syndrome as the name
implies, which may have a number of different
reasons. The syndrome is commonly referred to as IBS,
which is also used in this guide afterwards. 99
The incidence of IBS is very common, probably more
common than studies show. Globally, irritable bowel
syndrome affects about 11 % of the total world population.
Only about 30 % of people who suffer from IBS are in
contact with their doctors.100 It has been estimated that
well over 500,000 Finnish people (total population of 5.5
million) suffer from IBS “in quiet” because they consider the
symptoms (bloating, abdominal pain, flatulence, diarrhea or
constipation etc.) normal. Globally, the trend is very similar.
Irritable bowel syndrome may be classified into three
major types (ROME III criteria): 101
• Constipation-predominant IBS (IBS-C)
• Diarrhea-predominant IBS (IBS-D)
• Mixed IBS (IBS-M)
36
In IBS, the gas production in the gut is markedly increased.
Typical of IBS is the fluctuation of symptoms and possible
other symptoms associated with intestinal symptoms
(arthralgia, mood swings, fluctuations in energy levels etc;
more on this later in this book). The most common intestinal
symptoms in IBS are abdominal pain, straining stomach,
muscle aches, rushing to the toilet, bloating and general
feelings of illness.102 In the development of IBS there has also
been identified a genetic component, but its significance
and importance has not yet been established. Indeed,
environmental factors play a greater role in this syndrome.103
T YP I C AL N UT R I TI ON -B AS ED CAU SES O F IBS: 1 0 4
• Increased food processing (e.g. modified starches,
additives, sweeteners, polydextrose etc.)
• Abundant use of cereals and legumes and heavy
drinking of milk
• Changes in intestinal bacterial balance and dysbiosis
(including unnecessary antibiotic courses, poor soil
nutrition and micronutrient deficiencies)
• Silent (low-level) inflammation of the body
OT HE R CAU SES O F IB S: 105
• Chronic stress and rush 106
• Intestinal infection (IBS occurring after infection) 107
• Small intestinal bacterial overgrowth (particularly in
IBS-D, in which diarrhea is a major symptom) 108
• Malfunctions of the gut-brain-microbiota axis 109
– Serotonin metabolism disorders (especially 5-HT3 and
5-HT4 receptors)
– In IBS-D, serum levels of serotonin (5-HT) are usually
too high in most cases
• Correspondingly, serum levels of serotonin (5-HT) in
constipation-predominant IBS are often too low 110
• Sitting and lack of exercise 111
• Depression and other mood disorders 112
• Certain drugs and their long-term use (e.g.
benzodiazepines and opiate-based medicines and
analgesics)113
Risk factors for the development of IBS after intestinal
infection are genetic deficiencies in natural immunity
and balance of the intestinal surface (epithelial) cells.
IBS-like symptoms can also be caused by inflammatory
bile acid absorption disorders, intestinal disorders, celiac
disease, intestinal infections, parasites and Helicobacter
pylori infection. For this reason, it is usually good to see
your doctor to rule out other more serious causes of the
symptoms.114
The treatment of IBS requires familiarity and understanding
of the syndrome on a comprehensive basis. This is not just
an intestinal disease, but rather a systemic syndrome created
by environmental, physiological and psychosocial factors
(see picture on next page). Often, diet alone is not enough,
and treatment requires a systematic self-assessment of
lifestyle and, in particular, high-quality stress management
measures.115

37
FUN C TI ON AL GASTROI N TE STI N AL DISOR DERS – CONCEPT UAL MODEL

Early life Psychosocial factors

• Genetics • Life stress
• Environment • Psychological state
• Coping
• Social support

Functional Outcome
Brain Gut
Central nervous Enteric nervous
Gastrointestinal • Medications
system system Disorders • Medical visits
• Symptoms • Daily function
• Behavior • Quality of life
Physiology
• Motility
• Sensation
• Inflammation
• Altered bacterial flora

Source: Drossman, D. (2006). The functional gastrointestinal disorders and the Rome III process. Gastroenterology 130 (5):
1377–1390. Review.

38
F O D MA P C A R B O H Y D R AT E S A N D THEIR
R E S T R I C T IO N F R O M T H E D I E T
According to recent studies and reviews, the most
effective treatment for IBS is the restriction of FODMAP
carbohydrates. About 70 % of IBS patients experience
significant symptom relief through FODMAP restriction.
The word FODMAP comes from Fermentable Oligo-, Di-,
Mono-saccharides and Polyols. In practice this means that
these particular carbohydrates are fermented by bacteria
living in the colon. The end products of fermentation are
short-chain fatty acids (SCFA), which have remarkable
health-promoting effects. 117
The caveat here is that the
fermentation process also produces lots of gas and water,
which can cause straining and bloating, eventually leading
to pain in the gut. Flatulence is also a typical side effect of
fermentation.118
FODMAP restriction fits very well to people suffering
from IBS. The recommendation is to reduce daily
intake of FODMAPs from the diet to less than 10
grams. FODMAP restriction comes quite easily with very
low carbohydrate diets (< 20 net grams / day), where
automatically many of the FODMAP carbohydrates are
excluded from the diet. 119
There are three phases in FODMAP restriction:
1. FODMAP restriction
2. FODMAP reintroduction
3. FODMAP personalisation
116
The key points in this latest FODMAP recommendation over
previous recommendations is that after a specific restriction
period window (4–8 weeks), FODMAP carbohydrates are
reintroduced individually and followed up for 6 to 10 weeks,
preferably with a nutritionist (or physician) for possible
symptoms. By identifying clearly the most symptomatic
FODMAP carbohydrates, one can individually tailor a
suitable FODMAP diet that is not overly restrictive, but on
the other hand is sufficient to keep symptoms in check.120
Long-term follow-up studies have shown that following
and personalizing FODMAP restriction to help treat
irritable bowel syndrome in the long term (over one year
follow-up period) is a very effective method.121 Based on a
study published in 2018, a low FODMAP diet is the most
effective way to treat IBS in the long run.122 FODMAP
restriction is also effective in children’s IBS, particularly
stomachaches.123
39
THRE E P HASE S OF FODMAP RESTRICT ION

FODMAP restriction FODMAP reintroduction FODMAP

4–8 weeks 6–10 weeks personalization

FODMAP
tolerance
threshold
Gut symptons
FODMAP
intake

Counselling from Counselling from

dieterian dieterian

Source: Whelan, K. & Martin, L. & Staudacher, H. & Lomer, M. (2018). The low FODMAP diet in the management of
irritable bowel syndrome: an evidence‐based review of FODMAP restriction, reintroduction and personalisation in
clinical practice. Journal of Human Nutrition and Dietetics 31 (2): 239–255.

40
W HAT ARE F O D M A P C A R B O H YD R AT ES ?
FODMAP carbohydrates are shown in more detail in the
picture below. There are many foods belonging to the
FODMAP group, but already restricting a few groups
in particular can produce significant results (relief of
IBS symptoms). In the first chapter of this book, it was
recommended trying to limit/eliminate cereals (fructans,
raffinose), legumes (galactans, raffinose) and dairy
products (lactose). This can relieve up to 80 % (sometimes
even completely) of symptoms. If this does not help,
remove all fructan-containing foods from your diet (such
as kales and onions) and reduce polyol foods (sweeteners,
apples, avocados, mushrooms etc.).124
Some probiotic preparations may also contain added FOS
(fructo-oligosaccharides) as a growth substrate for good
bacteria; however, many people with IBS may develop
symptoms because of this. Inulin has also been added to
many probiotics, which can cause bloating and flatulence.
NOTE! The so-called “gut health” yogurts and many
health/fiber drinks are high in fructans (at most 15 g /
2 dl), being problematic for many.

41
F O DMAP C ATEGORI ES

F O D M A P

Oligosaccharides Disaccharides Monosaccharides Polyols

Apple, apricot,
avocado, blackberry,
cherry, nectarine,
Fructans Galactans Raffinose Lactose Fructose
persimmon, peach,
• Humans lack the enzyme capable • Humans lack the enzyme • Insufficiently absorbed plum, watermelon,
of breaking down these linkages capable of breaking in the intestine mushroom,cauliflower
• They are not absorbed in the down these linkages and certain sweeteners
Milk, yoghurt, Agave nectar,
small intestine and therefore (isomalt, maltitol,
cream cheese, mango, raisin,
often cause bloating and mannitol, sorbitol
Cabbage, soy, mascarpone honey, apple,
laxative effects and xylitol)
Legumes such as beans, whole and ricotta watermelon,
pinto bean, kidney grains and pear and cherry
bean, navy bean asparagus
Wheat, rye, barley, leek, and lentils
onion, garlic, artichoke,
asparagus, beetroot,
chicory, dandelion,
radicchio, broccoli,
brussels sprouts, fennel,
cabbage and cacao

42
 E F F I C I E N T I B S S E L F - T R E AT M E N T
LIMIT YOUR DAILY INTAKE OF FODMAP CARBO-
1 HYDRATES TO LESS THAN 10 GRAMS PER DAY
• Remove cereals and legumes completely from the diet.
• Avoid lactose (preferably avoid all cow’s milk products at
least in the beginning).
• Avoid kale and onions.
• Avoid sweeteners (xylitol, sorbitol, maltitol and
mannitol).
• Avoid products with added fiber (inulin, FOS and other
oligosaccharides) –> especially the so-called gut yogurts
and fiber health drinks!
• If you still have symptoms, reduce the following foods
further: apples, pears, cherries, asparagus, plums,
mushrooms, watermelon, artichokes.
2 R ED UC E T H E B ODY ´S GENERAL STRESS LOAD
• Do daily breathing exercises (for example, for 5 minutes:
4 seconds in, 7-second breath hold, 8 seconds out or 5
seconds in and 5 seconds out).
• Practice meditation or mindfulness-based techniques
(proven to reduce stress when practiced regularly).125
• Exercise daily (walking and light gym workout).
• Acupuncture, based on scientific research, helps in
treating IBS.126
• Cognitive psychotherapy and hypnosis can also help.127
3 D R I N K EN OUGH WATER DAILY (ABO U T 4 0 ML/KG )
UR INARY COLOR CH ART FOR H YD RATI O N ASS E S SME NT
1 2 3 4 5 6 7 8 9 10

Many times building a FODMAP-restrictive diet will require

the help of a good nutritionist or a functional medicine
practitioner, so don’t be afraid to try this to get your diet off
to a good start.

43
4 US E HI GH- Q UA L IT Y P RO B IOT IC S
• In particular, Bifidobacterium strains (Bifidobacterium
infantis, in particular) have been shown to • The FODMAP restriction and overall anti-inflammatory
alleviate IBS symptoms. 128
• Certain Lactobacillus strains, together with
Bifidobacterium strains, are also effective (for example,
Vivomixx Probiotic). 129
• Probiotics are especially helpful for stomach pain,
bloating and flatulence.
5 PSYLLIUM FIBER (SOLUBLE FIBER) CAN HELP
PARTICULARLY IN CONSTIPATION-DOMINANT IBS
• Start with a small dose (1 teaspoon); add gradually.
• Take breaks (e.g. using psyllium one week per month).
• Use only pure (psyllium-only) preparations (not Vi-Siblin,
for example, because it contains sorbitol –> may worsen
symptoms).
6 P E P P E RM I NT O IL IS EFFEC T IV E FO R R EL I EVI N G
I BS SY M P TO M S 131
• Get peppermint oil capsules that are enteric-coated.
• Particularly relieves pain and spasms (also in children).
• Slows down gastrointestinal transit time.
7 R ED UC E S I L EN T I N FL AM MATIO N IN THE BO DY
( AN D GUT)
diet plays a key role in this.
• Adequate intake of omega-3 fatty acids
• Turmeric and ginger reduce silent inflammation of the
intestines and body.
• Further advice on reducing silent inflammation is coming
further in the book.
8 AVOI D EXC ES S I VE S I T T I N G
130
• Do not sit for more than 40 minutes at a time.
• Try to sit for less than 6 hours a day.
9 M EAS UR E TH E B AL AN C E O F THE INTESTINAL
M I C ROB I AL FLOR A AN D I NV ESTIG ATE
T H E P OS S I B I L I TY OF S M ALL INTESTINAL
B AC TER I AL OVERGROW T H (SIBO ) 1 3 2
• More information coming in later in this book; SIBO can
cause up to 50 % of IBS cases!
NOTE! If you have weight loss, fatigue, blood in your
stools, constipation for several weeks, history of
intestinal cancer or severe discomfort and you have
difficult symptoms of IBS, seek medical attention.
44
DIVERTICULOSIS AND
H O W T O RE C O G N I Z E I T
Diverticulosis refers to the condition wherein the wall of the
colon (sigmoid colon in particular) has several bulges. These
bulges are also called diverticula. The onset mechanism is
thought to be mostly mechanical, wherein the inside pressure
of the bowel over the years would cause the intestinal
thinner face to bulge outward. Contributing factors include
constipation and a low-fiber diet. The genetic inheritance of
diverticulosis is about 40 %.
133
Studies have shown that diverticula occur with aging.
According to statistics, 10 % of the 45 years old have
diverticula (single changes); about half of those occur in
people in their 60s and most of them in their 80s. Many
have diverticula in their intestines, but these often do not
cause any symptoms of diverticulosis. It is estimated that
about one-fifth of people with diverticula get symptoms.
In addition, it is estimated that 5–15 % of those with
diverticulosis experience bleeding.134
45
Patients with symptomatic diverticulosis have been found to
have a slightly elevated fecal calprotectin value (64.3 %
of patients), whereas in irritable bowel syndrome, the
calprotectin value is not increased at all. The calprotectin
value indicates the severity of the intestinal inflammation.135
Connective tissue disorders such as Marfan syndrome,
Ehlers-Danlos syndrome or other similar conditions may
predispose one to diverticulosis. Loose connective tissue
is predominant in the gut, thereby causing the intestines
to stretch.
Inflammation of the diverticula can lead to diverticulitis, the
most critical complication of diverticulosis. Diverticulitis can
develop with a silent inflammatory state of the intestine if, at
the same time, stools become “stuck” in the diverticulum or
if a micro-perforation occurs at the base of the diverticulum,
i.e., a small hole develops. For people with diverticulosis, a
typical high-fiber anti-inflammatory diet and other healthy
lifestyle choices can prevent diverticulitis.136 Diverticulitis is
usually treated with antibiotics.
Symptoms associated with diverticulosis include:
• Abdominal bloating and cramps
• Abdominal pain (often colic-like but may also be
persistent)
• Flatulence
• Irregular defecation rhythm
• Rectal bleeding (diverticular bleeding)
Symptoms of diverticulosis are easily mixed with IBS
symptoms. Diverticula are usually found by chance in
colonoscopy. In some cases, a colonic contrast agent MRI
may also be performed.
NOTE! If you have already been diagnosed with
diverticula in the gut and you are suffering from severe
stomach pain, it is always a good idea to seek medical
attention.
46
Risk factors for the development of diverticulosis
include:
• Aging
• Obesity and large waist circumference
• Low-fiber diet
• Meat-rich diet (while not getting enough fiber)
• Smoking
• Lack of exercise
• High use of NSAIDs
There is a considerable contradiction in treating
symptomatic and uncomplicated diverticulosis (SUDD).
While some studies appear to lessen high fiber intake,
some studies have found that very high fiber intake can
even worsen the symptoms of diverticulosis. Antibiotics
such as rifaximin and mesalazine are also used to treat
symptomatic diverticulosis. These appear to be quite
effective in relieving symptoms – the side effects have also
been minor. Medical studies have also found that certain
probiotic bacterial strains are helpful in the treatment of
SUDD (Lactobacillus casei subgroups).137
 N AT U R A L S E L F - T R E AT M E N T O F 3 M OVI N G DAI LY – WAL KI N G IS THE BEST
D I V E R C U LO S I S 138 T R EAT M EN T FOR D I VERC U LO SIS

If you suffer from constipation, the treatment of

4 R ED UC E OR D I S CON T I N UE ALCO HO L
constipation should also be at the center of the treatment CON S UM P TI ON
of the symptoms of diverticulosis. With regular bowel
movements and normal bowel movement, the symptoms
5 QUI T OR D EC R EAS E EAT I NG PRO CESSED MEAT
of diverticulosis are usually alleviated at the same time. AN D GR AI N -FED R ED M EAT
• Grass-fed and wildflower-fed meats do not have the

1 I NCRE AS E YO U R DA ILY CO N T EN T O F QUAL I TY same inflammatory potential as the above.

F I B E RS – TARG ET 20– 30 G / DAY • Poultry and fish are more gut-friendly alternatives for
• Vegetables, berries, low-sugar fruits, vegetables protein intake.
• Cucumber, lettuce and spinach have been found to be
associated with a reduced risk of diverticulosis.
6 I N C R EAS E TH E DAI LY AD MINISTRATIO N O F
• High-quality optional added fiber includes psyllium, P ROB I OT I C FOOD S AN D PRO BIOTICS
acacia fiber and sensitive oat fiber • Read more about probiotics in Chapter 5.

2 A D D A NT I - I N FL A M M ATO RY FO O D S TO YOUR D I ET
7 E.COL I P ROB I OT I C ( M UTAF LO R) MAY REDU CE THE
• Bone broth, turmeric, ginger, berries (especially SYM P TOM S OF D I VERC ULO SIS 1 3 9
blueberries/bilberries), dark green vegetables, olive oil, • Requires a prescription from the doctor
coconut oil etc. • May cause some side effects and in the long-term use
• Omega-3 fatty acids and herbs such as chamomile, even predispose to cancer (based on animal studies)
marshmallow and slippery elm

47
 8 RE D UCE OR STO P SM O K IN G TO B ACCO

9 AVOI D US I N G N SA ID S
• For example, ibuprofen

10 US E D I GE ST IV E EN ZYM ES IF N EED ED TO H EL P
D I GE ST I ON

11 T RY ACUP UN C T U R E TO R EL A X
T HE I NT E ST IN ES A N D IM P ROV E G U T M OT I L I TY

12 I F YOU A R E H AV IN G A B D O M IN A L O B ES I TY, YOU

S HOULD CO N C EN T R AT E O N LO SIN G T H E EXT R A
W E I GHT

48
 4.
GUT MICROBIOTA,
DIVERSITY & SMALL
INTESTINAL BACTERIAL
OVERGROWTH
Microbiological balance of the intestines,
yeast and SIBO
G U T MI C RO B I O TA A N D
BACTERIAL BALANCE
Microbiota refers to the colonies of symbiotic (both parties
benefit from each other), commensal (one party unilaterally
benefits from the other) and pathogenic (illness-causing)
micro-organisms. These colonies exist, for example, on the
skin’s surface, on the mucous membrane of the mouth, the
conjunctiva and the intestines.
It is estimated that there are 500–1,000 distinct bacterial
species living in the intestines. The most common bacterial
species in the intestines are Bacteroides, Clostridium,
Fusobacterium and Bifidobacterium. Other known
strains include Escherichia and Lactobacillus. 140
The
Bifidobacterium and Lactobacillus strains are typically
present in probiotic products due to the fact that these are
most widely studied. 141
The functions of the bacteria in the intestines include
breaking down carbohydrates (fermentation) that the
body cannot otherwise digest. The bacterial strains of the
50
intestines also play a role in the absorption of K vitamins, B
vitamins and some minerals (magnesium, calcium and iron)
in the production of bile acids and in the immune system.
In addition, they act as protective walls against various
pathogens.142
AN T I B I OTI C S D EST ROY N OT O NLY THE
PAT H OGEN I C B AC T ER I A BU T ALSO BENEF ICIAL
B AC TER I AL STR AI N S OF THE INTESTINES
A single course of antibiotics can affect as much as 30 %
of the entire bacterial flora of the intestines and can
throw off the bacterial balance from six months up to
two years.143 However, antibiotics are necessary when
a harmful pathogenic bacterium, such as Salmonella,
Shigella, Campylobacter or Yersinia, has entered the
intestine. Alongside viruses, these bacteria are also the
most common causes of traveler’s diarrhea and intestinal
infections.
Depending on the individual’s bacterial balance, the
liberal use of antibiotics may cause predisposition to
diarrhea144 and Clostridium difficile infection,145 146 as well as
overgrowth of other harmful bacteria.147 The increased use
of antibiotics has also resulted in an increase in antibiotic-
resistant bacteria around the world.148
DIET CAN ALTER INTESTINAL MICROBIOTA AND THE
CONDITION OF THE INTESTINAL LINING
The bacterial strain of the intestines changes quickly
whenever dietary adjustments are made. Studies on mice
have found that upon changing the diet, the microbiota
may change overnight. Similar changes also take place in
humans but the exact time span is currently not known. 149
Switching to a more intestine-friendly diet has brought
positive results in the treatment of chronic inflammation,
obesity and gut permeability.150
The general saying is, “You are what you eat.” It would be
more correct to say, “You are what you are absorbing,” as
digestive health and nutrient absorption are the key. Diet
and choices of foods that improve gut health and reduce
inflammation can affect the health of the entire body very
quickly. The effects have been assessed to be largely
mediated by changes in the bacterial strains in the gut and
in the overall microbiota.
151
51
N UTR I T I ON AL FAC TORS
S UP P ORTI N G T H E M I C ROBIOTA:
• Fermentable fibers, i.e. prebioticts152 153
– For example inulin, pectin and oligofructose (Note: do
not use if you suffer from IBS)
• Other soluble fibers such as psyllium, acasia fiber, apple
pectin and sensitive oat fiber as well as nutritional fiber
in fruit, berries, vegetables, nuts and seeds etc.)154 155
• Fermented foods156 157
• Resistant starch (see below)158 159
– Found, for example, in green bananas, cooked and
subsequently refrigerated rice and potatoes
• Polyphenols (such as berries and colorful vegetables)160 161
• Dark chocolate (contains polyphenols and fermentable
fibers)162 163
• Pistachios (increase the production of butyrate in the gut)164
• Long-chain omega-3 fatty aids (EPA and DHA)165
• Probiotics (certain bacterial strains, particularly soil-
based ones – see later in the book for more details)
• Eating a wide variety of vegetables and wild plants
RE S I STA NT STA RC H
Resistant starch (RS) differs from conventional starch in that
it is not absorbed by the digestive tract. Thus, the term
resistant refers to this fact. Resistant starch is a good food
for intestinal bacteria, meaning its role in nutrition is similar
to that of oligosaccharides and soluble fibers.
For example, in the Finnish nutrition database (Fineli),
resistant starch is now counted as fiber. The dietary intake of
resistant starch has not been estimated in Finland, but it is
probably at the same level as in Sweden (approx. 3 g/day).166
According to a study done in 2008, Americans consume 3–8
grams (on average 5 grams) of RS per person per day – less
than the minimum of 6 grams of resistant starch per meal
recommended for health benefits. 167
The energy produced
by resistant starch is 2.5 kcal/g (cf. starch 4 kcal/g).
Resistant starch is found in raw bananas, cooked and cooled
white rice and potatoes, broad beans and some other
legumes, and to some extent, whole grains. Potato starch
also has high levels of resistant starch that can be used to
feed intestinal bacterial strains. 168
In addition to general
prebiotic health benefits, resistant starch has been shown
to have beneficial effects on insulin sensitivity and obesity
as well as hunger regulation both in rodents,169 170 171 and
humans.172 173 174 175
52
Resistant starch is classified into five different categories:176
RS1 (physically inaccessible starch)
• Starch that is resistant to digestion due to its physical
density or physical protective structure.
• Starch from seeds, whole grains and pulses.
• Grinding and careful chewing releases at least some of
the resistant starch to the digestive tract.
RS2 (granular starch with the B- or C-polymorph)
• Resistant to digestion due to physical density and the
dry nature of starch.
• From the outside these may not look dry (e.g. raw
potatoes and bananas).
• Cooking releases starch resistant to digestion.
RS3 (retrograded starch)
• The most resistant starch.
• Amylose becomes resistant when heated and then
cooled.
• For example, boiled and refrigerated potatoes or
cooked and cooled rice.
RS4 (chemically-modified starches)
• Industrially-modified starch used as an additive in the
food industry.
RS5 (amylose-lipid complex)
• Stearic acid-complex high-amylose starch.
• Amylose-lipid complex formation is an instant reaction
and the complex can reform after cooking; type V
resistant starch (RSV) is considered thermally stable.
Resistant starch may not be suitable in IBS, as it is
fermented in the same way as FODMAP carbohydrates.
53
N UTR I T I ON AL AN D L I FESTYLE FACTO RS
D I S RUP TI N G T H E M I C ROB IOTA:
• Antibiotics (unless absolutely necessary for
the treatment of illness)177
• Pesticides containing glyphosate (including Roundup)178 179 180
– Used as a pesticide particularly on cereals, genetically-
modified soybeans and corn
– Meat from animals that have fed on the plants
mentioned above
– May be one of the main factors contributing to the
development of celiac disease181
• Smoking182 183
• Alcohol184
• Processed, high-sugar and nutritionally poor food
(typical Western Diet)185
• Low-grade inflammatory fatty acids (sunflower oil,
rapeseed oil, soybean oil, corn oil and other artificial,
highly oxygenated, hydrogenated and high omega-6
fatty acids)186 187 188
• Chronic stress189 190
• Continuous negative thoughts and feelings192 193
S MA L L I N TE S T I N A L B A C T E R I A L
O V E R G R O WT H ( S I B O )
Small intestinal bacterial growth (SIBO) literally means just
that: an excess of bacteria growing in the small intestine.
Although many doctors do not yet recognize SIBO as a
medical diagnosis, it has accumulated quite a bit of medical
research over the last 10 years, which will lead to increased
knowledge on the existence of SIBO. 193
Normally, only
small amounts of bacteria grow in the small intestine. Most
bacteria live in the colon (large intestine). However, there are
situations where the level of bacteria in the small intestine
may increase to harmful levels and lead to many serious
health problems.
HEALTH FACTORS PREDISPOSING ONE TO SIBO:
• Reduced gastric acid production or hypochlorhydria, an
acid-free stomach or achlorhydria, caused, for example,
by continuous use of proton pump inhibitors (PPIs).
• Small intestinal motility disorders
• Disorders of pancreatic digestive enzyme production
• Small intestinal diverticula
• Systemic diseases (celiac disease, Crohn’s disease, fatty liver)
• Intestinal surgery
• Intestinal blocks (strictures, tumors, ulcers)
Other factors associated with SIBO in IBS patients include
aging and female gender and predominance of bloating,
flatulence and diarrhea.196
The symptoms caused by SIBO are often similar to those
caused by other causes of gut problems. Therefore, IBS
and SIBO are often mixed together. In fact, according to
a scientific meta-analysis published in 2009, 54 % of IBS
patients have SIBO.197 According to a survey published
in 2017, 4–78 % of IBS patients and 1–40 % of “healthy”
controls suffer from SIBO.198
T YP I C AL SYM P TOM S OF S IBO
• Diarrhea (hydrogen is dominant in gas formation)
• Constipation (methane is dominant in gas formation)
194 195
• Flatulence
• Intestinal cramps and pains
• Systemic general symptoms such as fatigue, joint pain,
anxiety, depression
– Often caused by the release of bacterial neurotoxins
(mainly constipation-prone SIBO)
54
THE SIBO PATH: Bacterial overgrowth –> Hydrogen gas
–> Arcanobacterial overgrowth –> Methane gas
When bacteria ferment fibers, they produce hydrogen gas.
Similarly, so-called arcanobacteria live on hydrogen and
produce methane gas. Methane is usually associated with
constipation-prone bacterial overgrowth, while diarrhea-
prone bacterial overgrowth is caused by hydrogen.
Hydrogen-dominant SIBO is usually easier to treat than
methane-dominant SIBO.
E F F I CI E NT TR EAT M EN T O F SIB O :
• If possible, do a lab test to find out the possibility
of SIBO (breath test for hydrogen [H2] and methane
[CH4]).199
– Options are either 2-hour or 3-hour assessments.
– The 3-hour SIBO profile provides insight into gas levels
over a longer period of time and is recommended
for patients with slower gastrointestinal transit or
constipation.
• Evaluate the level of gastric hydrochloric acid production
(e.g. Gastropanel lab test and self-produced gastric
hydrochloric acid test).
55
• FODMAP restriction is an effective solution here too;
a ketogenic (very low carbohydrate) diet can also be a
temporary or even permanent solution.
• Antibiotic treatment is effective in SIBO (especially Rifaximin
– an antibiotic that is not absorbed from the gut into the
bloodstream, and thus causes very few side effects);200 201
other antibiotics have also been used to treat SIBO.
• During the antibiotic regimen and slightly (1–2 weeks)
before it makes sense to eat FODMAP carbohydrates
to better detect the harmful bacteria for antibiotic
treatment.
• The herbal treatment protocol is estimated to be
as effective or even more effective than antibiotic
treatment; herbal combinations used in the study
(protocols: John Hopkins University, Baltimore, US).202
– FC Cidal and Dysbiocide (Biotics Research
Laboratories): 2 capsules 2 times daily for 4 weeks
OR
– Candibactin-AR and Candibactin-BR (Metagenics): 2
capsules twice daily for 4 weeks.
• An herbal product Atrantil has also been found to be an
effective treatment method for SIBO;203 204
(this is also the favourite product for the author):
2 capsules 1–3 times per day as long as needed.
• After any antibiotic treatment, an effective non-fibrous
probiotic is started (the fibers may aggravate bacteria, but also no yeast growth. Medical publications
the symptoms).
• Too long or too short meal spacing can exacerbate
symptoms; optimum would be 3–4 hours between
meals (except night time). On the other hand, in some
situations fasting and intermittent fasting may also help.
• After 4 weeks, test your bacterial overgrowth with
a new breath test; if the treatment is successful, you can
gradually and incrementally restore fiber and FODMAP
carbohydrates to your diet.
• Limit your intake of caffeine (e.g. up to 1–2 cups of
coffee per day).
• Stress management methods.
• Lower intestinal inflammation and optimize the functions
of the gut’s surface epithelial cells (more details later in the
book).
56
The small intestine should have very little growth of
have also disclosed observations of the “small intestinal
overgrowth of yeast” or SIFO (Small Intestinal Fungal
Overgrowth). Many people with SIBO may also have SIFO,
which means that there is too much yeast (usually Candida
varieties) in the small intestine.205
N.B. Be careful with probiotics, especially if you have
or have had SIBO and brain fog due to the condition.
Particularly so-called D-lactic acid-producing probiotic
strains (such as Lactobacilli) may be harmful,206 since
D-lactic acidosis is common in patients with brain fog.207
I N T E S T I N A L Y E A S T O V E R G R O W TH
– “Y E A S T S Y N D R O M E ”
Traditional schools of medicine do not recognize yeast
syndrome as a disease. Candida albicans, the cause for yeast
syndrome in most cases, is found on the skin and mucous
membranes of the body. For example, up to 75 % of people
have yeasts of the Candida species on the oral mucosa;
however, in healthy individuals the amount of yeast is low.
a difference in results between laboratories; therefore, it
would be advisable to take a sample from several different
laboratories if there is a suspicion of intestinal yeast
infection.
Generalized yeast fungal overgrowth is about impaired
functioning of the body’s immune system. Therefore, the
treatment is to holistically balance the immune system.
208

It is also recommended that you get familiar with the

For many, yeast grows at much higher levels than usual, Biohacker’s Handbook’s Immunity E-Book.
especially in the intestines.209
This in turn can cause a
variety of intestinal and general symptoms. Candida-
colonized guts also seem to be related to other intestinal
diseases such as inflammatory bowel disease, gastric
ulcer and small intestine ulcers. Studies have shown that
intestines colonized by Candida albicans do not heal as
rapidly as intestines without candidiasis.210

Officially, instead of calling it “yeast syndrome,” it is more

specifically referred to as an overgrowth of intestinal
yeast.211 Yeast can be detected in stool by a cultivation/
culture method. However, it is good to note that there is

57
FACTORS P R ED ISP O SIN G O N E TO YEAST Candida albicans is found in small amounts in the
OV E RGROW T H O R C A N D ID IA SIS: 212
intestines and is part of a habitat where hundreds of
• Poor nutrition (high levels of processed foods, sugar, different bacteria and other yeast species grow. When
additives, flour and mold) overgrown, Candida can form a fungal mycelium in the
• Long-term use of antibiotics, cortisone and birth control intestines, which among other things penetrates the
pills mucous membranes and other parts of the body. This
• Intestinal bacterial strain imbalance (dysbiosis; probiotic condition is called candidiasis.213 In a person with a very
beneficial bacterial deficiency) weak immune system (e.g. HIV or untreated diabetes),
• Constipation and slowed bowel function yeasts can become wild throughout the body. This is
• Intestinal inflammation and intestinal parasites why taking care of your body’s immunity is also key to
• Trace element deficiency preventing yeast infections.
• Some systemic diseases (diabetes, cancer, inflammatory
bowel disease) SYM P TOM S C AUS ED BY FU NG AL/YEAST
• Surgery and radiation OVERGROW T H : 214
• Pregnancy and childbirth As yeast growth increases to above normal levels, and
• Chronic stress especially for prolonged periods, it can affect many
• Smoking and heavy drinking different target organs and cause different general
symptoms due to the toxins (mycotoxins) secreted by
M AJ OR I NT EST IN A L FU N G A L / YEA ST STR AI N S : yeast. For example, biofilm produced by Candida during
• Candida species (e.g. albicans, which is the most its outbreak has been shown to cause symptoms; biofilm
harmful) must also be destroyed when treating the yeast.215
• Cryptococcus species
• Trichosporon species • Diarrhea or constipation (may also occur alternately)
• Geotrichum species • Excessive gas formation, bloating and possibly gut
spasms

58
• Anal itching and recurrent urinary tract infections (in
women)
• If the yeast has spread, there may be many common
symptoms:
– Skin: foot/fingernail, skin rash, itching
– Mind: fatigue, depression, mood swings, brain fog
– Head: headache, dizziness, balance problems
– Ear, nose, throat, respiratory tract: recurrent upper
respiratory tract infections, obstruction, allergic
symptoms
• In addition, a person may have a very high craving for
sweets and sugars (yeast/fungi live on sugar)
The symptoms are also suitable for a number of other
diseases, so it is important to investigate the possibility
of the yeast either in the gut and/or in any other target
organs.
59
I F YOU S US P EC T TH AT YOU MIG HT HAV E YEAST,
TAKE T H E FOL LOW I N G TESTS (IN O RDER O F
I M P ORTAN C E) :
• Microbiological analysis of the gut (including yeast
cultivation and extensive species identification and
sensitivity to various drugs and natural products); for
example, GI 360 test216
• Stool cultivation for yeast; identifies Candida as a
species but no other species
• Intestinal permeability measurement (such as Genova
Diagnostics)217
• Blood antibody testing (IgG and IgA antibodies) may be
performed if a yeast infection is suspected.
• Mucosal specimens (mouth, throat, skin, vagina, anus)
• Differential diagnosis test: the possibility of small
intestinal bacterial overgrowth (SIBO)
 F O L L O W TH E S E S T E P S T O E R A DICATE
Y E A S T O V E R G R O W T H I N T H E I NTESTINES
1 STOP Y E A ST G ROW T H W IT H T H E R IGH T D I ET:
• In general, limiting FODMAP carbohydrates (< 10 g/day)
works very well
• Minimize the use of white sugar and cereal products
(especially wheat) in your diet
• Limiting the amount of carbohydrates usually inhibits
yeast growth
• Avoid dairy products, especially lactose
• Avoid foods/products containing yeast
• Temporary restriction of very sweet fruits and berries
often inhibits yeast growth
2 KI LLI NG Y E A ST / FU N G I 218
The most effective approach on killing yeast/fungi is to first
destroy the biofilm because it forms a physical barrier that
keeps most immune cells from detecting the pathogenic
fungi (or bacteria). After removing the biofilm, it is easier
to kill the pathogenic microbe, such as Candida. 219 220
• Nystatin (a non-absorbable antifungal – the first choice if
the problem is mainly in the gut; requires prescription)221
60
• Fluconazole and other antifungals (as evaluated by a
doctor; requires a prescription but single doses are also
sold as over-the-counter medicine)
• Lactoferrin (prevents growth of Candida and promotes
degradation of drug-resistant biofilms in particular)222
– 250–500 mg once per day (sometimes higher doses
required)
• Natural medicines:
– Caprylic acid (as a nutritional supplement or in MCT oil
and coconut oil)223
– Garlic (standardized extract in capsule form or garlic oil
capsules): recommended dosage is 1,200–4,800 mg/
day or 0.03 to 0.12 ml/day of oil224 225
– Grapeseed oil: the recommended dose is 10 drops
three times a day or 100–200 mg capsules three times
a day226 227
– Berberine (250–500 mg/day)228 229
– Oregano oil (45–450 mg/day)230 231
– Tea tree oil (dosage may vary)232 233
• Biofilm-disrupting enzyme Preparations:
– Kirkman Labs Biofilm Defense
– Enzymedica Candidase
 NOTE! Not all medicines or natural medicines are to be
taken at the same time. Talk to a knowledgeable doctor
or functional medicine nutritionist about the treatment.
If you are pregnant or lactating, do not use these
products without your doctor’s advice.
3 EFFECTIVE PROBIOTIC TREATMENT PROGRAM: 234 235
• Boosts the immune system
• Restores intestinal pH to the right level
• Removes living space from yeasts and fungi
• Lactobacillus rhamnosus GG strain in particular is very
effective in candidiasis treatment236
• Recommended strains and products:
– Saccharomyces boulardii (yeast probiotic) 237 238
– Saccharomyces cerevisiae (yeast probiotic; especially
in non-albicans Candida species) 239
– Seed Synbiotic (scientifically tested and crafted combi-
nation of probiotics, prebiotics and polyphenols
– Primal Probiotics
– Garden of Life Primal Defense ULTRA
61
4 US I N G FI B ER S UP P L EM EN TS
• Effectively eliminates yeast toxins from the intestines
with feces
• Maintaining sufficient defecation density and composition
• See more specifically high-quality fiber supplements in
later in the book.
5 OT H ER S UP P ORT I N G C AR E
• Improve the condition of the intestinal surface (epithelial
cells) – fix possible leaky gut (read more in detail in the
next chapter of the book)
• Regular stress management and minimize extra stress
• Sufficient amount of exercise (self-recovery as a good
measure; excessive exercise impairs intestinal recovery)
• Avoid alcohol, tobacco and mold toxins (e.g. in the
environment or in food)
• Successful removal of yeast/fungi often requires patience
and several months of time
 5.
DIGESTIVE SYSTEM
OPTIMIZATION,
GERD AND
DYSPEPSIA
Gastrointestinal optimization, probiotics, The importance of chewing for nutrient absorption is
prebiotics and digestive aids often insufficiently considered. Eating slowly and chewing
the food thoroughly may create a greater feeling of
D I G E S T I O N A N D O P T I M I Z I N G Y OUR fullness and increase the absorption of nutrients.240 Eating
DIGESTIVE SYSTEM slowly can also help with weight management – slower eaters
gain less weight and eat less at once than fast eaters.241
The digestive system consists of organs whose functions
involve digestion, nutrient absorption, waste product removal See more specifically, the structure of the digestive tract in
and the formation of feces. The digestive tract reaches from the illustration on the next page.
the mouth all the way to the anus. The most important parts
of the digestive tract in terms of functions are the esophagus,
stomach and duodenum in the upper gastrointestinal tract FAVOR TH E FOL LOWI N G PREPARATIO N METHO DS:
and the jejunum, ileum, colon and rectum in the lower • Slow cooking
gastrointestinal tract. The digestive system also includes the • Boiling
salivary glands, pancreas, liver, spleen and gallbladder, each • Stewing
with their own role in digestion. • Steaming
• Oven-baking slowly
The main function of the digestive system is to break down • Sous-vide
food and absorb nutrients from the small intestine into • Raw food
the circulatory system. Digestion can be divided roughly • Fermentation
into two functional phases: mechanical digestion (the food • Frying with water
is broken into smaller pieces by chewing) and chemical
digestion (enzymes break down food into molecules).

63
F O O D ’ S JO U R N E Y THROUGH THE B ODY
R EVI EW EATI N G HABITS:
• Chew carefully (for example, 20–30 times per
mouthful; put the fork on the plate when not
using it)
• Avoid stress at mealtimes (if stressed out,
take 1–2 minutes to breathe deeply and calm
yourself down)
• Spend at least 20 minutes eating
• Avoid drinking liquids during meals (dilutes
stomach acids)
• Don’t eat alone – social eating improves food
digestion and overall well-being242

R EVI EW D I ETARY SU PPLEMENTS THAT

S UP P ORT D I GESTIO N: 2 4 3
• Hydrochloric acid and pepsin
• L-glutamine (5–10 grams 2–3 times per day;
start with 5 grams per day):244 245 246
– Maintains the condition of the intestinal
mucous membrane
– Repairs gut permeability
• Lactoferrin:247
– Lowers the inflammation on gut surface
– Reduces/fixes gut permeability

64
• Hydrolyzed collagen protein/peptides:248
– Based on animal studies it can reduce inflammation in
the gut and fix tight junctions.
– Includes lots of glycine amino acid, which is important
for the gut surface (epithelial cells)
• Silica and silicic acid-carmellose gel:249
– Protects the mucous membrane of the stomach
• Magnesium
– May facilitate defecation and improve the movements
of the digestive tract
– An important mineral for the intestinal epithelium
• Vitamin B12 and folate
• Vitamins A, D and E:
– Improve the regeneration of mucous membranes
• Phospholipids and lecithin:
– Promote the absorption of fats
• Digestive enzymes (see more specifically at the end of
this chapter)
65
R EVI EW FOOD S T H AT S UPPO RT DIG ESTIO N:
• Fresh carrot juice (supports intestinal mucous
membranes)
• Celery juice (promotes intestinal movements and
alleviates constipation)
• Carminatives reduce gas in the intestines:
– Orange, fennel, ginger, cinnamon, cardamom, cilantro,
caraway, licorice, oregano, parsley, peppermint oil,
rosemary, sage, lemon balm, dill, thyme, garlic
• Bitters stimulate the production of stomach acid and
digestive enzymes:
– Jerusalem artichoke (do not use if you have SIBO
and/or IBS), Angelica sylvestris root, yellow gentian,
Angelica archangelica root
• Other foods that support digestion:
– Aloe vera, pineapple, chia seeds, chlorella, sauerkraut,
currants, Iceland moss, chamomile, cranberries,
oats, meadowsweet, blueberries, oregano, chaga
mushrooms, papaya, linseeds, horse radishes,
lingonberries, psyllium, rhubarb, plantago, rosehip,
spirulina, sea buckthorn, raspberry leaf, wheatgrass,
valeriana
Probiotics and prebiotics
P R O B I O T I CS
Probiotics refer to living microbes that have positive
effects on health. The official definition for a probiotic is:
“Live microorganisms that, when administered in adequate
amounts, confer a health benefit on the host.” 250
As indicated in the original FAO/WHO (2002) report,
there are certain expectations required to call an
organism “probiotic.” These clearly must include:252
1. Microbes must be alive in an adequate number when
administered.
2. Strains must be identified genetically, classified using
the latest terminology, and designated by numbers,
letters or names.
3. Appropriately sized and designed studies must be
performed to designate a strain as probiotic and using
the strain(s) on the host to which the probiotics are
intended (human, livestock, companion animal etc.)
4. Strains shown to confer a benefit for one condition may
not be probiotic for another application.
5. Strains that are probiotic for humans but are being used
in animal studies should be clearly designated as human
probiotics under experimental testing.
Fermented foods, prebiotics, fecal microbiota transplants
and microbial strains of the same genus or species as
documented probiotic strains but have not undergone
appropriate testing on the target host should not be
considered as probiotics based on adherence to the
251
scientific definition.
The benefits of probiotics become apparent through the
balancing of the microbiota (microbiological ecosystem) and
microbiome (microbiological genome) in the digestive tract.
P ROB I OT I C S H AVE N UM ERO U S HEALTH BENEF ITS
T H AT H AVE B EEN WI D ELY STU DIED IN META-
AN ALYS I S STUD I ES :
• Alleviating constipation253
• May help in the treatment of acute diarrhea254
• Preventing traveler’s diarrhea (particularly
Saccharomyces boulardii)255
• Facilitating the treatment of irritable bowel syndrome256
66
• Stopping the progress of inflammatory bowel diseases,
may facilitate recovery (particularly Lactobacillus
acidophilus and Bifidobacterium lactis) 257 258
• Facilitating recovery from non-alcoholic fatty liver
disease259
• May prevent a common cold 260
• Preventing and treating diarrhea caused by antibiotics
Dietary probiotics are available from, for example,
sauerkraut and other fermented vegetables, as well as
fermented vegetable juices, kefir and kombucha drinks.
In addition, traditional Japanese fermented natto and
tempeh are high in probiotics. If you are able to use
dairy products, fermented natural yogurt also has a fair
amount of probiotic bacteria. Coconut yogurts, which can
be a great addition for dairy intolerant people, have also
entered the market.
Different bacterial strains affect the secretion and
production of histamine. Therefore, it is advisable to
choose the correct bacterial strains, especially if you
suffer from histamine intolerance (more in detail in the
last chapter of this book).
1 B AC TER I AL STR AI N S P RODU CING HISTAMINE
( US E L ES S , OR I F YOU H AV E HISTAMINE
I N TOL ER AN C E, D O N OT U SE):
• Lactobacillus casei (many probiotic preparations contain
this but usually in very small amounts)
• Lactobacillus bulgaricus (most yogurts)
261
• Lactobacillus helveticus
• Lactobacillus delbrueckii
• Streptococcus thermophilus262
• Bacillus coagulans SL5 & Bacillus licheniformis A7263
2 N EUTR AL B AC T ER I AL ST RAINS F O R HISTAMINE:
• Lactobacillus acidophilus
• Lactobacillus lactis
• Lactococcus lactis
• Saccharomyces boulardii
• Lactobacillus reuteri (this causes the conversion of
histidine to histamine, but the overall effect is anti-
inflammatory via its effect on cAMP)264
3 H I STAM I N E-D EGR AD I N G BACTERIAL STRAINS:
• Lactobacillus rhamnosus (especially GG; reduces
histamine receptors and anti-inflammatory effect)265 266
• Bifidobacterium infantis (also, for example, in breast milk)
• Bifidobacterium longum
67
• Bifidobacterium bifidum
• Bifidobacterium lactis
• Lactobacillus plantarum
• Lactobacillus gasseri
• SBO (soil-based organism) probiotics

RECOMMENDED PROBIOTIC SUPPLEMENT OPTIONS

These are high-quality, clinically researched products that
have received extremely positive feedback from their users.
• Seed Synbiotic
• Vivomixx (contains up to 450 billion living bacteria
–> particularly effective in balancing the gut from
major dysbiotic states; scientifically well studied and
documented)
• Saccharomyces boulardii (for example:
Thorne Research Sacro-B Probiotic)
• Living Nutrition Your Flora-probiotics
(Symbiotic probiotics)
• Advanced Orthomolecular Research Probiotic 3
• Life Extension Florassist Balance
• Primal Probiotics
• Garden of Life Primal Defense ULTRA
• Dr. Ohhira’s probiotics (such as Professional Formula)
• Enzymedica Pro-Bio Potency Probiotic

68
PREBIOTICS
Prebiotics refer to non-digestible fiber compounds, such
as oligo- or polysaccharides, used by the bacterial strain
of the intestines as growth media. The use of prebiotics
increases the growth of good quality probiotic bacteria such
as bifidobacteria and lactic acid bacteria in the intestines.
Prebiotic intake can have positive effects, among other
things, in the absorption of trace elements, 267
immunity,
268
blood pressure 269
and lowering colon cancer risk. 270
Prebiotics (inulin and oligofructose) are the most abundant
in weight in chicory root, artichoke, dandelion leaves,
garlic, leek and asparagus. If you have a problem with IBS
or SIBO, do not use these foods or any fiber-containing
fructo-oligosaccharides or inulin, as they will make
symptoms worse due to excess fermentation.
Prebiotics are also abundant in potato starch, which in
recent years has been used as a dietary supplement to
support the intestinal bacterial balance. Potato starch is
rich in so-called resistant starch, which can be used by the
69
bacterial strain of the gut. In addition to the general health
benefits of prebiotics, resistant starch has been shown to
have beneficial effects on insulin sensitivity and obesity
and on hunger control.
R ECOM M EN D ED P R EB I OT I CS THAT DO NOT
CON TAI N I N UL I N OR FOS
These are high-quality, clinically researched products that
have received extremely positive feedback from their
users.
• Now Foods Psyllium Husk Powder
• Jarrow Formulas Prebiotics XOS+GOS
• Life Extension Florassist Prebiotic Chewable
• Prebiotin Prebiotics
• Garden of Life DetoxiFiber
• Now Foods Apple Pectin
• Heather’s Tummy Care Organic Acacia Fiber
• Bob’s Red Mill Potato Starch
O P T I MI Z I NG G A S T R I C A C I D S E CRETION
I N T H E S TO M A C H
The stomach is located between the esophagus and the
duodenum in the top left corner of the abdominal cavity,
immediately below the diaphragm. The stomach contains
two sphincters that control the volume and movement of
the stomach contents: the lower esophageal sphincter and
the pyloric sphincter allow the mass of food to enter the
duodenum.
The stomach secretes gastric juice, which contains hormones
and enzymes necessary for digestion, hydrochloric acid for
breaking down food and intrinsic factor (IF) required for
the absorption of vitamin B12. 271
The acidity of gastric juice
destroys harmful micro-organisms present in food. However,
many people suffer from a deficiency in the production
of hydrochloric acid due to stress, poor diet or harmful
chemicals.272
70
Hypochlorhydria (the low level of hydrochloric acid)
contributes to nutritional deficiencies, osteoporosis,273
various infections274 and stomach cancer.275 Long-term
use of acid blockers may cause anemia,276 vitamin B12
deficiency277 and overgrowth of stomach and small
intestinal bacteria (SIBO).278 In addition, acid blockers
(proton pump inhibitors [PPIs]) have been found to
predispose to the development of food hypersensitivity
with gastroesophageal reflux disease.279
According to one study, as many as 30 % of those over 60
have already developed atrophic gastritis (very little or no
acid production in the stomach).280 Another study found
that 40 % of postmenopausal women had no gastric acid
production at all.281
Untreated Helicobacter pylori infection can predispose
one to atrophic gastritis (acid-free stomach and damaged
gastric mucosa). Therefore, it is important to investigate the
possibility of Helicobacter pylori infection in the presence
of various upper abdominal symptoms (heartburn, belching,
abdominal pain, upper abdominal bloating etc.).282 283
SY MP TOM S O F D ISRU P T ED H YD RO C H LOR I C H YD ROC H LOR I C AC I D T ESTING AT HO ME:
ACI D B ALAN C E IN T H E STO M AC H O R Get hydrochloric acid tablets or capsules (called Betaine-
HY P OCHLOR H YD R IA : 284
HCL) from the health food store. The strength of the
• Abdominal bloating after food capsule may vary from 300 to 600 mg.
• Belching
• Heartburn 1. Eat a meal that contains about 200 g of protein-rich food
• Flatulence after food such as meat, fish or chicken and is high in vegetables.
• Stomach pains 2. Take one Betaine-HCL (hydrochloric acid) tablet at the
• Diarrhea or constipation beginning of the meal.
• Non-digestible food in stool 3. Eat another meal.
• Bad breath 4. Feel if you notice any sensations in the stomach or
• Other possible symptoms: esophagus.
– Splitting nails
– Acne OP T I ON S :
– Anemia 1. If the level of hydrochloric acid in your stomach is
– Depression/fatigue (due to optimal, you will feel a slight feeling of warmth, heartburn
low levels of vitamin B12 absorption) or lightheadedness and/or nausea after taking one tablet.
2. If no symptoms appear, your stomach’s hydrochloric
Symptoms may overlap with other GI-tract/intestinal acid level is likely to be insufficient. If you did not feel
problems. However, it is a good idea to take a so-called any symptoms, take two tablets with your next meal.
hydrochloric acid test at home, which gives an indication Continue doing this until you have a situation where you
of how well your stomach’s hydrochloric acid level is.285
feel the symptoms mentioned in Step 1.

71
NOTE: Take hydrochloric acid up to a maximum of
1,800 mg per meal! Do not do the test if you have a
history of stomach ulcers, Helicobacter pylori infection,
inflamed esophagus or other inflammatory conditions
of the stomach. The test result may also be incorrect if
the gastric mucosa is already well damaged. In this case,
symptoms may appear after only one tablet because the
mucous membrane in poor condition reacts with acidity.
In such situations, it is useful to perform a GastroPanel
laboratory test (more on this below).
LAB OR ATORY T EST IN G FO R H YD RO CH LOR I C AC I D
B ALANCE :
Many laboratories today offer GastroPanel test, the largest
complete laboratory test to determine the functional and
inflammatory state of the stomach. This examination will
also be able to identify situations in which the subject
needs further gastroscopy.
72
The study investigates the following markers in the
blood:
• Pepsinogen I (gastric body function – moderately
correlated with hydrochloric acid production)
• Pepsinogen II (structure and function of the entire gastric
mucosa – correlates with gastric inflammatory
status)
• Gastrin-17 (Function of gastric fundus – correlates with
gastric acid production)
• Helicobacter antibodies
N.B. After stopping long-term PPI (acid blocker)
treatment, there is a very strong rebound in gastric
hydrochloric acid production (“acid rush”), which results
in the patient’s recovery of severe heartburn symptoms
(gastrin-17 levels are usually very low). Long-term use of
acid blockers should therefore always be phased out.
The GastroPanel test requires medical interpretation
and follow-up.
D Y S P E P S IA Symptoms of functional dyspepsia include abdominal
bloating, an early feeling of fullness, nausea, vomiting,
Dyspepsia refers to unspecified upper abdominal loss of appetite and retching. Similarly, epigastric pain
discomfort. The underlying problem may be more of a syndrome includes upper abdominal pain and abdominal
functional reason, the most important of which are motility cramps.287
problems (the problem of gastric motilityand in electric
activity), abnormal touch sensation of internal organs and P R ED I S P OS I N G L I FEST YL E FACTO RS TO DYSPEPSIA
visceral hypersensitivity, Prevotella and H. pylori infection, I N C LUD E:
the permeability of the small intestine (duodenum in • Smoking
particular) and psychological factors. Symptoms of • High caffeine use
dyspepsia include, but are not limited to, pain or discomfort • High alcohol consumption
in the upper abdomen, feelings of “full stomach,” rapid • Use of NSAIDs
feeling of satiety, belching, abdominal bloating and nausea. • High-fat processed food
The prevalence of upper abdominal disorder (dyspepsia) • Large-portioned meals
due to functional reasons (excluding reflux disease, • Abdominal obesity
stomach ulcer, gallstone disease, cancer etc.) is in the
range of 10–20 % of the population. Dyspepsia has been D I AGN OSTI C C R I T ER I A FO R DYSPEPSIA (RO ME III)
found to be more prevalent in women than in men. 286
AR E AS FOL LOWS : 288
All three criteria listed below must be met.
Functional dyspepsia can be subdivided into two
subtypes based on the Rome IV classification: 1. At least one of the following:
• Postprandial Dyspeptic Syndrome (PDS) • A difficult feeling of fullness and over-fullness after eating
• Epigastric Pain Syndrome (EPS) • Rapid onset of satiety
• Abdominal pain
• Burning sensation in the upper abdomen

73
2. Other medical conditions have been ruled out (with N OTE! S EE A M ED I C AL D OCTO R IF :
gastroscopy or other diagnostic method) • Symptoms occur daily or several times a week and are
3. Symptoms have continued for several months detrimental to life
• Symptoms are new and have started quite suddenly
T RE AT M E NT G U ID EL IN ES FO R FU N C T I ON AL • You are over 55 at the onset of symptoms – older people
DYS P E P S I A : 289
are more likely to have a medical condition
• Invest in the optimization of the digestive system as a requiring medical treatment
whole • You have other alarming symptoms such as weight loss,
• In some cases, pharmaceutical treatment may be helpful a feeling that food sticks to the esophagus,
(PPIs, H2 blockers, etc.) vomiting, irradiation of pain in the back or dark stools
• Prokinetic drugs may be of mild benefit
• Significant benefits of hypnosis have been observed
• Acupuncture may be helpful290
• Herbal treatments (rikkunshito in Japan)
• Meditation and mindfulness291
• Ginger292 and artichoke extract293
• Metoclopramide may provide temporary relief of nausea
and rapid filling of the stomach

74
GASTROESOPHAGEAL REFLUX
D I S E A S E (G E R D )
Gastroesophageal reflux disease (GERD) literally refers to
the reflux of food or gastric fluids back into the esophagus.
Reflux itself is caused by an increase in intra-abdominal
pressure.294
Symptoms include, in particular, heartburn, but
also some other symptoms such as burning behind the
sternum, stomach bloating, feeling of a lump in the throat
and pain when swallowing. Some also have constipation.
According to various estimates, 10–20 % of the adult
population in the West suffer from reflux disease. 295
Two types of reflux disease can be distinguished: non-
erosive reflux disease (NERD) and erosive reflux disease
(ERD). Of these, NERD is far more common. Non-erosive
means that there is no erosion of the stomach mucosa
such as Barrett’s esophagus or erosive esophagitis
(inflammation of the esophagus).
75
Reflux itself is a normal physiological phenomenon during
relaxation of the esophageal sphincter (LES). However,
in reflux disease these relaxations last longer than usual,
leading to symptoms. Coffee, alcohol, chocolate, fatty
meals and many drugs such as beta-blockers, nitrates,
calcium channel blockers and anticholinergics all enhance
and prolong LES relaxation. Also, progesterone (a
glandular hormone) and nicotine increase the relaxation of
the esophageal sphincter.296
Intra-abdominal or intraperitoneal pressure will increase
further (perhaps unexpectedly) by low gastric acid level
(hypochlorhydria), which in turn may lead to small intestinal
bacteria overgrowth (SIBO) and carbohydrate absorption
problems.297
Treating GERD with acid blockers does not focus on the
actual causes of the problem, since reflux disease is rarely
caused by excess acid production in the stomach. The
use of acid blockers masks and removes the symptoms
momentarily but has no effect on intra-abdominal pressure
or the function of the lower esophageal sphincter.
LOW STO M AC H AC I D LEV E L (HY P OC HLORHY DR IA) CAUSES
B AC TE R IA L OV ERGROWTH P R ED I S P OS I N G FAC TORS FO R G ERD INCLU DE: 2 9 8 2 9 9
• Genetic factors
• Abdominal obesity
Low stomach acid
(hypochlorhydria) • Male sex
• Diaphragmatic hernia
• Aging
• Certain pharmaceuticals (see above)
• Helicobacter infection
Bacterial
overgrowth + Cabrohydrate
malabsorption • Smoking
• Alcohol
• Gastrointestinal inflammation and silent inflammation in
the body300

Increased intra-abdominal
• Connective tissue disorders (especially scleroderma)
pressure (IAP) • Food allergies and hypersensitivity301
• Untreated celiac disease and gluten hypersensitivity/
allergy302 303
• Carbohydrate malabsorption and small intestinal
bacterial overgrowth
Heartburn
& GERD • Pregnancy
• Excessive endurance training/sports
• Magnesium deficiency
Source: Robillard, N. (2005). Heartburn Cured: The Low Carb Miracle.
Self Health Publishing. • Artificial sweeteners
• Processed foods and highly spicy foods
• Soft drinks

76
GE RD S E LF -T R EAT M EN T G U ID EL IN ES: 304 N OTE! I F YOU H AVE R EFLU X AND HEARTBU RN,
• Identify potential food sensitivities and allergies S EE A D OC TOR I N T H E FOLLOWING SITUATIO NS
• Contribute to improving the overall condition of the • Despite self-medication (see above), annoying heartburn
digestive tract (see above) occurs several times a week for several weeks
– Hydrochloric acid supplementation and digestive en- • In addition to heartburn and sternal burning, there are
zymes (such as BiOptimizers HCL breakthrough) other pains in the abdomen or chest
– Zinc carnosine 305
and zinc
306
• Other symptoms such as vomiting, difficulties in
– Probiotics swallowing or weight loss occur
– Chamomile tea and ginger
– Magnesium
– Apple cider vinegar (ACV)
• If you have moderate obesity, lose weight
• Reduce the use of esophageal sphincter-relaxing
nutrients and other substances (see above)
• Stop smoking
• Increase regular daily physical activity
• Avoid heavy alcohol drinking
• Try an anti-inflammatory and very low carbohydrate diet
(VLCD)307
• Avoid big meals just before bedtime
• In some cases, a short course of treatment with PPIs may
help; avoid long courses of acid blockers though
• Raising the end of the bed relieves the symptoms of
reflux at night

77
D I G E S T I V E E N Z Y M E S A N D B I L E ACIDS the structure of the small intestine villi and microvilli, the
surface area available for nutrient absorption is enormous
T HE I M P ORTA N C E O F D IG EST IV E EN Z YM ES FOR – roughly one half of a badminton court.308
T HE W E LL- B EIN G O F T H E B O DY
The small intestine receives pre-digested food from the SYMPTOMS AND PROBLEMS OF INADEQUATE
stomach and continues to break down ingredients. The PRODUCTION OF DIGESTIVE ENZYMES:
digestive process is assisted by bile (formed in the liver • Various food sensitivities
but secreted through the gallbladder) as well as pancreatic • Abdominal bloating
juice, which contains plenty of digestive enzymes. • Stomach pain
• Flatulence
The small intestine breaks • Heartburn
down three main groups • Non-digestible foods in stool
of nutrients: proteins, fats • Fatigue
and carbohydrates. Proteins
are broken down into D ETER M I N I N G T H E D I GESTIV E ENZYME LEV ELS:
peptides and amino acids. • Fecal elastase-1 test
Fats are broken down into • Fecal chymotrypsin test (as part of CDSA study; see last
fatty acids and glycerol. chapter of the book for details)
Carbohydrates are broken • Putrefactive short-chain fatty acids (measures protein
down into monosaccharides absorption; as part of CDSA and CDSA 2.0 studies)
(e.g., glucose) and starch • Various fatty acids in stool (measures fat absorption; as
into oligosaccharides. Once part of CDSA and CDSA 2.0 studies)
broken down, the nutrients • Fecal pH (low level indicates carbohydrate
are absorbed through the malabsorption)
intestinal wall. Thanks to

78
E F F E CT I V E D IG EST IV E EN ZYM E P RO DUC TS : T H E I M P ORTAN C E OF B I L E ACIDS F O R THE
• BiOptimizers MassZymes W EL L -B EI N G OF T H E B ODY
• BiOptimizers KApex Bile is secreted from the gallbladder into the small
• All Enzymedica products: intestine during the digestive process. The gallbladder is
– Digest Gold ATPro located below the right lobe of the liver. It is a small organ,
– Digest Basic approximately 8 centimeters in length, and its main function
– Digest Spectrum (great for food intolerances) is to store the bile produced by the liver. The gallbladder
– In addition, a variety of more specific enzyme prepa- and the hepatic duct merge to form the bile duct, which
rations such as Lypo Gold (for fat absorption), Candi- leads bile into the small intestine from the ampulla of Vater
dase (for yeast treatment), Repair Gold (for support of (a merging point with the pancreatic duct).309
muscle and joint pain) and more.
• Now Foods Super Enzymes Bile facilitates the formation of
• Thorne Research Bio-Gest (Contains hydrochloric acid, micelles, which are essential
pepsin, pancreatin and bile) for the absorption of fats. Bile
• Life Extension Enhanced Super Digestive Enzymes also has an important role in
the absorption of fat-soluble
If you need a digestive enzyme supplement, take it at the vitamins (A, D, E and K) and
beginning of your meal. Begin with one capsule, adding the recycling of bilirubin in the
to 2–3 capsules per meal if necessary. Roughly speaking, body.310 Bile acids function in
if you feel lighter with a digestive enzyme supplement a manner similar to hormones,
and feel better in your gut, these have been helpful. If the participating in metabolism
enzyme supplement mainly causes a feeling of accelerated (energy balance, regulation of
hunger, there are probably already too many enzymes fat metabolism and glycemic
doing their thing. control).311 Deficiency in the
production of bile and bile acids

79
may cause significant health problems such as excess
weight gain and insulin resistance. 312
The gallbladder may also form gallstones due to indigestion
or imbalanced diet. For instance, a deficiency in the
production of bile salts in the liver, in combination with a
diet rich in cholesterol, may be a predisposing factor for the
formation of gallstones. 313
Risk factors contributing to the formation of gallstones
include excess weight, rapid weight loss, constipation and
the decreased intake of fiber and nutrients (folate,
magnesium, calcium and vitamin C). A dietary supplement
of vitamin C may prevent the formation of gallstones. 314
Melatonin may also be used to prevent the formation of
gallstones and possibly even treat cholelithiasis. 315
SY MP TOM S O F D EFIC IEN T B IL E AC ID FOR M ATI ON
A ND S E CR E TIO N :
• Heartburn / epigastric burn
• Upper abdomen bloating
• Fat digestion problem / fatty diarrhea
• Fat-soluble vitamin absorption problems and
deficiencies
• Hepatic impairment
80
In some cases, there may be genetic defects in the
production of bile acids – this should be investigated by a
specialist if necessary.
T ESTI N G AN D M EAS UR I N G BILE ACID SECRETIO N:
• Secondary bile acids in stool (as part of CDSA 2.0 test)
• Determination of fat in stool (triglycerides, long chain fatty
acids and phospholipids; also stool total fat) –> as part of
the CDSA and GI360 tests
I N GR ED I EN TS AN D COM P OU NDS THAT PRO MOTE
T H E P ROD UC T I ON OF B I LE AND BILE ACIDS
AS W EL L AS TH E FLOW OF THE BILE ARE AS
FOL LOWS :
• Soluble fiber (for example, from oats; do not use if you
are on a grain-free diet)
• Phenolic compounds (for example, from artichoke)
• Turmeric
• Flavonoids
• Orange
• Dandelion
• Bitters
• Apple cider vinegar (ACV)
 6.
GUT-BRAIN AXIS,
SKIN HEALTH
AND STRESS
Gut-brain axis, gut-skin axis, microbiota and
microbiome – and the systemic effects of stress
on gut function
W HAT E XAC T LY IS G U T M IC RO B IOTA?
Gut microbiota is the collection of microbes inside the
gut (in the intestines). These include bacteria, fungi and
viruses, some linked to better health and others to disease
(beneficial or harmful microbes, respectively). A human
hosts about 10 trillion microbes in the gut, and microbiota
composition is unique for every individual – thus, it is like a
fingerprint in the gut.316 The microbial community, including
the beneficial bacteria, supports health by living in mutual
synergy with the host organism. Microbiota helps strengthen
the intestines’ surface, metabolize energy from food,
protect the body from harmful bacteria and process bile
acids. Notably, the gut microbiota has strong links to brain
functioning. A balanced microbiota is linked to improved
cognition and better overall health. For example, 95 % of the
neurotransmitter serotonin (important for memory, mood and
cooperative behavior) is produced in the gut. For that reason,
gut problems such as celiac disease, IBS, leaky gut and
upset stomach can lead to brain fog, anxiety, lowered mood,
slowed thinking and decreased stress tolerance. 317 318
82
GUT- BRAIN AXIS
The gut-brain axis refers to the neurological and biochemical
connection between the enteric nervous system (meaning
the nervous system of intestines) and the central nervous
system. There is indeed a direct link between gut health and
the function of the brain; sometimes the gut is even called
“the second brain.“ The intestinal microbiota (bacterial strain)
is known to affect the function of the immune system, the
nervous system,319 behavior,320 stress tolerance,321 mood322
and mental health such as anxiety and depression.323 In the
past two decades, in particular, there has been a growing
understanding of the significance of the intestines for the well
being of the brain.
H OW T H E GUT AN D TH E BRAIN ARE CO NNECTED
To better understand how your brain health is affected by
gut health, it is important to understand the nature of the
communication between the brain and intestines. Recent
studies strongly suggest that there is a bi-directional
brain-gut-microbiota (BGM) interaction. A good example
of brain-to-gut connection is a strong emotional reaction,
such as an experience of fear or love. During such a reac-
tion, the changes in the brain’s emotional processing alter
the function of the nervous system (including the vagus
GUT AN D B R AI N AR E L I N K ED IN SEV ERAL WAYS :326
nerve) and modulate the activity of the intestines, causing
the sensation of “butterflies in the stomach.”324
1. The vagus nerve. Vagus nerve connects the brain to
several internal organs (for example gut, lungs, heart,
Another good example of gut-to-brain connection is after
liver and kidneys). Gut modulates the functions of the
eating, when the intestines send the brain information about
brain and central nervous system mainly via hormonal
the food eaten. The first signs of impaired brain function
and neuroimmune mechanisms, which often involve
may also be detectable in the digestion: the impaired
the vagus nerve. Molecules in the gut also play a part.
secretion of pancreatic enzymes, weak gallbladder activity
These include short-chain fatty acids (SCFAs), secondary
and the general impairment of intestinal balance and
bile acids and tryptophan metabolites.
function.325

2. Sympathetic and parasympathetic nervous system.

Microbiome and microbiota are sometimes used
Both branches of the autonomic nervous system (ANS)
interchangeably, but these two terms have clear differences.
contribute to the signaling between the gut and the
The microbiome refers to the collection of genomes from
brain. They regulate gut functions linked to bowel
all the microorganisms in the environment. For example, the
movement, gastric acids, gut fluids, gut cell structure,
human microbiome refers to a collection of microorganisms
gut permeability and gut immune response. These
all around the body (including skin microbiome, eye
important changes in gut physiology affect the gut
microbiome, gut microbiome and so on). Microbiota usually
microbiome and its composition.
refers to specific microorganisms that are found within
a specific environment. In this case, microbiota (i.e., gut
3. Neurotransmitters and hormones that are produced
microbiota) refers to all micro-organisms, such as bacteria,
in the gut. Hormones that are linked to motivation
viruses and fungi found in the gut.
and mood, such as serotonin and dopamine, are also
produced in the gut and modulate gut activity. Their
precursors (i.e., tryptophan and tyrosine, respectively)

83
 SYST EM’ S BIOLOGICAL MODEL OF BR AIN-GUT-MICROBIOME I NTE RACTI O NS
can also travel to the brain via the blood,
cross the blood-brain barrier (BBB) and
Brain connectome
are used in hormone production in the • Stress reactivity
• Mood
brain. The specific mechanism of gut • Sleep
• Visceral sensitivity
hormones in neuromodulation is still
unclear, but it is believed that the ability to
Central nervous system
produce hormones such as serotonin and
Gut-derived molecules
dopamine in the gut affects mood and Microbe-derived • Neuronal

brain function. neuroactive molecules • Immune

ANS modulation • Neuroendocrine
• Motility
• Secretion
• Permeability
4. Chemicals and molecules that alter • Microbiome

the function of the blood-brain barrier

(BBB). BBB regulates traffic between the
Microbe-derived molecules
blood and the cerebrospinal fluid of the
brain and the central nervous system. Gut
Gut-derived molecules
microbiota and several microbially-driven Gut microbiota
molecules can up-regulate the expression
of tight junction proteins, therefore Gut connectome
decreasing BBB permeability. • Immune
• Neuronal
• Neuroendocrine

5. Blood-brain barrier. BBB protects

the brain from harmful pathogens and Source: Martin, C. & Osadchiy, V. & Kalani, A. & Mayer, E. (2018). The Brain-Gut-Microbiome Axis.
improves overall immunity of the brain. Cellular and Molecular Gastroenterology and Hepatology 6 (2): 133–148.

84
B LOOD - BR A IN B A R R IER & IN T EST IN A L B AR R I ER
There are two natural barriers to signaling within the BGM-
axis: the intestinal barrier (IB) and the blood-brain barrier
(BBB). The intestinal barrier is characterized by two layers:
a basal monolayer of epithelial cells interconnected by
tight junctions and a mucus layer whose thickness and
composition changes over time and that contains secretory
IgA and antimicrobial peptides.327 The blood-brain barrier
is a diffusion barrier that impedes the influx of most
compounds from blood to the brain. Three cellular elements
of the brain microvasculature compose the BBB-endothelial
cells, astrocyte end-feet and pericytes. Tight junctions,
present between the cerebral endothelial cells, form a
diffusion barrier, which selectively excludes most blood-
borne substances from entering the brain.328

Because gut microbes, stress and inflammation can

modulate the permeability of both structures, the amount
of information reaching the brain from the gut is highly
variable, depending on the overall health of the individual.

85
I N C R E A S E D G U T P E R M E A B I L I T Y:
THE LEAKY GUT SYNDROME
Gut permeability refers to the changed state of the
epithelial cells on the surface of the intestines. Normally
nutrients are absorbed through the epithelial cells.
However, sometimes, the cells and the tight junctions
between them start to “leak” and allow harmful substances
into the circulation. Celiac disease is a typical example
of an autoimmune disease involving gut permeability.
Increased gut permeability (leaky
gut syndrome) is one of the key
factors in the development of
autoimmune diseases. However,
whether it is a cause or an effect
is currently not known.329 330 Intestinal
mucosal cells
The continuous inflammatory condition or imbalance of
the intestines may cause deterioration of the links between
the enterocytes on the surface of the intestine, causing gut
permeability. Similarly, impaired brain function or stress-
related hyperactivity of the sympathetic nervous system
undermines the function of the vagus nerve.332 This impairs
the function of the immune system and reduces blood
circulation in the intestines, which in turn increases the
DIFFER ENCE BET WEEN INTACT AND L EAKY G U T E P I TH E L I AL CE L L L I NI NG
Leaky and
inflamed
Normal tight junction

A study published in 2018 found

that many neurodegenerative
diseases such as Parkinson’s
disease are associated with Blood stream Circulating immune complex
increased intestinal permeability
and inflammatory status of the
gut surface.331 Blood brain barrier Inflammation Autoimmunity Malabsorption and
breach nutrient deficiency

86
growth of harmful fungi and bacteria in the intestines.333 • Fatigue
They can damage the surface tissue of the intestines and • Depression and anxiety
aggravate gut permeability (leaky gut syndrome). 334 335
• Joint pain
• Headaches
A continuous low-grade inflammation of the system • Various skin problems
may also aggravate gut permeability. 336 337
This results in • Digestive problems
the production of cytokines (inflammatory messenger • Weight gain
substances) in the intestines.338
Due to gut permeability, • Metabolic syndrome
the messenger substances are able to enter the circulation • Malabsorption and nutrient deficiency states
and the brain via the blood-brain barrier. The inflammation
causes the blood-brain barrier to also become permeable, CON T R I B UT I N G FAC TORS TO LEAKY G U T
which in turn activates the connective tissue cells of the SYN D ROM E:
brain, also known as microglia cells. 339
The result is a • Low quality processed diet / high in toxins and anti-
chronic inflammatory condition of the brain that impairs nutrients (see Chapter 1 for more details) as well as
brain function and may cause anxiety and depression. 340
sugars and rancid fatty acids
Thus completing the vicious circle, which will get worse • Chronic stress
unless corrective measures such as those outlined in this • Heavy metals and other environmental chemicals and
book are implemented. toxins
• Imbalance of the gut microbiota
P OS S I BLE SY M P TO M S C AU SED BY L EA KY GUT: • Severe intestinal infections and parasites
• Bloating • Alcohol and tobacco
• Food hypersensitivity • Use of antibiotics
(numerous; often also with high IgE elevations) • Oral contraceptives
• Hypothyroidism • Mycotoxins

87
T E ST I NG F O R L EA KY G U T SYN D RO M E: 8. Lactoferrin 250–500 mg/day
• Intestinal Permeability Measurement 9. Mt. Capra Goat Colostrum
– Measure the permeability of the intestinal epithelial 10. High-quality fish or liver oil packaged in a dark glass
cells and those between. bottle (omega-3 fatty acids)
• Intestinal Permeability and Absorption Test 11. If necessary, select one of the following:
– Measure nutrient absorption and malabsorption, – Biotics IPS (Intestinal Nutrition Supplement)
intestinal permeability and intestinal damage in – Thorne Research Perma-Clear
various parts of the intestine. 12. Use of digestive enzymes with food (improves nutrient
• Extensive digestive analysis (e.g. GI360, which also tests absorption; see recommended products in the
for potentially harmful bacteria, fungi and parasites) previous chapter)
• Measurement of zonulin protein in stool and 13. Intestinal toxin removal and absorption:
circulation341
– Activated charcoal (1–2 capsules 1–2 times a
day; taken separately from pharmaceuticals and
T RE AT M E NT M ET H O D S FO R FIX IN G L EAKY GUT supplements just before bedtime)
SY ND ROME : 342
– Bentonite clay (for toxin removal)
1. Diet (grain-free, dairy-free, legume-free; no processed – Chlorella (purifies heavy metals from the intestines
foods, oils and sugars) and reduces inflammation)
2. Adequate intake of vitamins A and D and fixing – Calcium-D-Glucarate 500 mg (1 capsule 3 times
deficiencies daily; removes excess toxins)
3. Adequate intake of long-chain omega-3 fatty acids
and fixing deficiencies NOTE! Not all preparations should be used at the
4. Regular stress management same time. I recommend a good functional medicine
5. Meditation and breathing exercises practitioner or a physician to help you choose the right
6. Probiotics products. However, the basic principles work well for
7. L-Glutamine (5–20 g/day) everyone.

88
 T H E R EL AT IONSH IP BET WEEN INT EST INA L B ACTE RI A AND SK I N H E ALTH

S K I N – T HE M I R R O R O F T H E I N TESTINES Dysbiosis
Normal microflora Gut microbiota

The link between skin problems and mental health Short-chain

fatty acids (SCFAs)
problems has been recognised for a long time. However,
Neurotransmitter
only in recent years has the connection between the release

intestines, the brain and skin been more fully understood.

In fact, instead of just speaking about the gut-brain axis we
Intestinal lumen
should rather speak about the gut-brain-skin axis.

Gut epithelium
Many inflammatory bowel diseases are also associated
with skin diseases. These include pyoderma gangrenosum,
erythema nodosum and many oral skin disorders.343 344
Similarly, celiac disease is, for example, associated
with alopecia, vitiligo and dermatitis herpetiformis.
Immune
Correspondingly, psoriasis is strongly linked to Crohn’s cells

disease.345 Indeed, in recent years tremendous amount

of studies have been published on how skin diseases Healthy normal skin Inflammatory skin disease

are often linked to intestinal dysbiosis. Other intestinal

dermatological conditions include rosacea and atopic Marked Fatty acids
inflammation Triglycerides
dermatitis.346
Atopic dermatitis is also known to be Proprionibacterium
acnes
associated with food allergies. It is therefore advisable to
consider these in the context of the disease in question.347

Source: Vaughn, A. & Notay, M. & Clark, A. & Sivamani, R. (2017). Skin-
gut axis: The relationship between intestinal bacteria and skin health.
World Journal of Dermatology 6 (4): 52–58.

89
In particular, patients suffering from leaky gut syndrome
are usually also suffering from skin problems. Increased
intestinal permeability causes both systemic and local
inflammation, which is frequently seen on the skin. A
weakened bacterial strain of the skin causes an increase
in the neurotransmitter substance P, which for example
increases the inflammation of the skin. This compound can
also increase anxiety, restlessness and nausea. 348
According to a study published in 2017, the current
hypothesis for changes in the gut microbiota and the skin is
as follows (see image before): the gut microbiota produces
neurotransmitters in response to stress, which accordingly
modifies skin function. These neurotransmitters have
access through the gut epithelium into the bloodstream
and cause effects on the systemic level. In addition to the
neurotransmitters, the intestinal microbiota produces short-
chain fatty acids (SCFAs) that also enter the bloodstream and
act directly on the skin. The researchers also mentioned that
diet can cause inflammation of the skin by releasing long-
chain fatty acids and via nutrient signaling. Correspondingly,
this results in stimulation of a specific protein (SREBP-1) on
the skin and synthesis of certain fatty acids and triglycerides,
thereby increasing the growth of Propionibacterium acnes
90
associated with acne.349 In summary, diet has a direct effect
on the health and well-being of the skin.350
As many as 40 % of people with acne develop problems
with acid production in the stomach (hypochlorhydria, see
previously). One study found that up to 66 % of patients
with acne had leaky gut syndrome. About half of acne
sufferers also have significant changes in the intestinal
bacterial strain compared to healthy people.351 In addition,
patients with rosacea are ten times more likely to have
small intestinal bacterial overgrowth (SIBO) compared to
healthy people.352
In general, when treating skin problems it is important to
make corrective movements to improve the balance of the
gut. Adding colorful and pigment-rich plant-based foods
such as berries, vegetables and fruits can have a positive
effect on both skin color and condition within a few weeks.
In practice, this means brighter and more intense skin,
both on the face and elsewhere on the body.353
TIP: Removing milk and sugar from your diet can improve
skin conditions and acne.
STRESS AND CONDITION OF
THE GUT GO HAND-IN-HAND
In practice, stress means either an acute or prolonged
threat to the balance of the body (homeostasis). Exposure
to stress causes changes in the gut-brain axis and, if
prolonged, can lead to the development of various
intestinal problems. These include inflammatory bowel
diseases (IBD), irritable bowel syndrome (IBS) and other
functional gut disorders, food allergies, ulcers and
gastroesophageal reflux disease (GERD). 354
CHA NGE S I N T H E G U T C AU SED BY STR ES S :
• Intestinal motility disorders (diarrhea and/or
constipation)
• Intestinal wall ”irritation” (increased visceral sensation)
• Disorders of the secretion of hydrochloric acid, digestive
enzymes and other fluids
• Increased intestinal permeability (leaky gut)
• Reduction in capacity to regenerate the intestinal cell
wall and deterioration of blood flow to the gut
• Negative effects on the gut microbiota and microbiome
91
The intestines and immune system are particularly
susceptible to various stressors (physical, psychological
and spiritual). In recent years, psychosocial and
environmental stressors (such as noise and mold,
overstimulation in the workplace etc.) have been
recognized as some of the causes of intestinal problems.
H PA AXI S , GUT AN D I M M U NE SYSTEM
The HPA axis (hypothalamus-pituitary-adrenal) is
the body’s most important physiological feedback
system regulating stress response. This is a so-called
neuroendocrine system, which means that hormones are
secreted from the nerve endings of certain system parts
(such as the hypothalamus and pituitary gland). When a
stressor triggers the stress response, the hypothalamus
produces and secretes corticotropin-releasing hormone
(CRH) and vasopressin, the antidiuretic hormone (ADH). In
particular, CRH (but also ADH) regulates pituitary function
by stimulating adrenocorticotropic hormone (ACTH)
secretion. Correspondingly, ACTH activates the adrenal
cortex to secrete glucocorticoid hormones such as cortisol,
slightly androgenic dehydroepiandrosterone (DHEA) and
mineralocorticoids such as aldosterone.355
 H PA AX I S RE G U L ATI O N

Cortisol secretion from the adrenal glands is intermittent

Hippocampus Amygdala
(pulsed) – it follows both circadian (daily) and ultradian _
(hourly) rhythms. For example, in the morning, cortisol
excretion is at its highest, helping to wake up and
significantly increase alertness. Cortisol secretion declines
_ +
gradually towards the evening and is normally at its lowest
Hypothalamus Paraventricular nucleus
at midnight.356 Studies have shown that this is one of the _
most stable circadian rhythms in the body.357

The HPA axis and the gut microbiota have significant CRF

_
interactions with each other since birth (and apparently
already during pregnancy). A normally developing stress
control system has a beneficial effect on the bacterial strain
Pituitary
in the intestines; balanced and rich intestinal bacterial strain
on the other hand, normalizes the function of the HPA axis.
_ Regulation of brain
Animal studies have shown that early maternal separation Glucocorticoids and peripheral
function (stress
can cause long-term adverse changes in the functioning of ACTH
response)

the HPA axis and the development of the gut microbiota. 358

Adrenal cortex

Glucocorticoids

Source: Hyman, S. (2009). How adversity gets under the skin.

Nature Neuroscience 12: 241–243.

92
 H PA AXIS´ EFFECT ON INT EST INAL L INI NG AND TH E I MMU NE SYSTE M
During the stress response, the cortisol-re-
leasing hormone (CRH) secreted from the
hypothalamus acts not only on the pituitary
Hypothalamus
gland but also in the intestines. There, it
increases the inflammatory status of the sur- CRH
AVP
face cells, the permeability of the intestinal
Pituitary
lining and the sensitivity to bowel move-
ments (stomach pains). As the inflammatory Afferent
ACTH
Efferent
sensory sympathetic
condition worsens, lipopolysaccharides nerves nerves

(LPS) secreted by harmful bacteria enters

the bloodstream. These further increase Adrenal gland

the inflammatory response through the

TLR4 (Toll-like Receptor 4) receptors of the Corticosteroids
Catecholamines
innate immune system (see The Biohacker’s
Handbook’s Special Edition, “Invincible LPS Cytokines PGE2 Circulation

Immunity”), which are cellular proteins that Immune

Lamina propria cells
recognize different microbial structures. This
leads to over activation of the HPA axis and
increased cortisol secretion by the adrenal Epithelial cells

glands (see detailed in the image). 359

Gut lumen

Source: Bailey, M. et al. (2011). Exposure to a social stressor alters the

structure of the intestinal microbiota: implications for stressor-induced
immunomodulation. Brain Behavior and Immunity 25 (3): 397–407.

93
 B LO O D - B RAI N B ARRI E R
With bacterial or viral infections,
the body’s immune system secretes
various inflammatory cytokines, such Astrocyte Nucleus

as interleukins and tumor necrosis

Endothelial cell
factor-alpha (TNF-α). In particular,
Pericyte
interleukin-1 (IL-1) is also very effective
at activating the HPA axis.360 IL-1 and
Neuron
lipopolysaccharides (LPS) activate Lumen of the
capillary
receptors in various parts of the brain,
causing prolonged inflammatory Mitochrondrium

Basal membrane
conditions, which can lead to, among
other things, a variety of neurological
disorders,361 362 363 autonomic nervous
system disorders364 and depression.365
Blood

When the condition of the gut is

poor, so-called “leaky brain” can
also be detected. This means that Tight junction

the permeability of the blood-brain Endothelial cell

barrier (BBB) between the brain and Basal membrane

the circulation is increased. BBB is Astrocyte Neuron

known to mediate the communication Microglia

between the intestines and the brain.366

Brain
The permeability of the blood-brain
barrier exposes the brain to various

94
toxins and increases entry of lipopolysaccharides and EFFEC TI VE STR ES S M AN AG EMENT METHO DS:
inflammatory cytokines into the brain. • Meditation (different approaches possible; e.g.
mindfulness)
Animal studies have shown that a completely absent or • Relaxation therapy (breathing exercises are at the core)
antibiotic-destroyed intestinal bacterial strain predisposes • Acupuncture
the HPA axis to overactivity. This means that the poor • Cognitive behavioral therapy
condition of the gut increases susceptibility to stress • Dynamic psychotherapy
reactions.367
Similarly, research in mice shows that prolonged • General stress management means
social stress diminishes the expression of beneficial • Connection with nature and moving around in nature
Bacteroides strains in the intestines and increases the
number of harmful Clostridium strains in the caecum.368

A well-balanced and well-functioning bacterial strain in the

gut can alleviate the stress response by directly affecting
the mucosal cells (enteric nervous system) and thereby
the central nervous system (brain and hypothalamus). A
well-functioning microbiota also reduces inflammation and
soothes the activity of intestinal nerve terminals, reducing
pain reactions.369

95
 7.
FOOD INTOLERANCES,
ALLERGIES AND
HISTAMINE
INTOLERANCE
Food intolerances & hypersensitivities, food
allergies, histamine intolerance and laboratory
markers for quantifying these
Many foods and ingredients affect the digestive system both
positively or negatively. Allergenic foods, toxins occurring
naturally or artificially in food and intestinal bacteria reacting
to food all represent unique challenges. On the other
hand, many ingredients reduce the inflammatory reaction
of the intestines, facilitate the digestive process or provide
materials necessary for tissue regeneration.
FOOD ALLERGIES
A food allergy is an adverse immune response to a
particular protein in the food. The immune system treats
the foreign protein as harmful, causing a quick antibody
response (immunoglobulin E). Food allergies unrelated
to the immunoglobulin E reaction, such as celiac disease
and enterocolitis, are rarer. Factors that may increase
the likelihood of allergies include the liberal intake of
antibiotics in early childhood, 370
the allergenic diet of
97
the mother,371 certain vaccines,372 373 and particularly the
adjuvants thereof,374 as well as various chemicals (such as
dichlorophenol-containing pesticides).375
The foods that most commonly cause allergic reactions are
nuts (tree nuts), milk products, cereal products,
egg, fish and shellfish, as well as peanuts, soy and
other legumes. Together they represent 90 % of all
food allergens. Food allergies are often found during
childhood, and they may disappear with age. Allergic
reactions to food are usually quick and intense compared
to hypersensitivity reactions, which involve symptoms that
are milder and more varied.376
T YP I C AL FOOD AL L ERGY REACTIO NS:
• Nettle rash/hives
• Itchy skin
• Difficulty swallowing
• Runny or blocked nose
• Sneezing
• Nausea and vomiting
• Abdominal pain
FOOD INTOLERANCES & FOOD H YP ERS EN S I T I VI TY SYMPTO MS INCLU DE
H Y P E R S E NS I T I V I T Y T H E FOL LOW I N G:
• Abdominal pain
Food intolerances are far more common than food allergies. • Various aches and pains
The symptoms of hypersensitivity/intolerances are also • Reflux/heartburn
significantly more diverse. Food hypersensitivity is usually • Asthma
transient, especially if the condition of the gastrointestinal • Arthritis
system can be improved with various methods (diet, • Abdominal swelling
probiotics, fibers etc. – methods presented in this guide). • Constipation
• Diarrhea
THE CAUSES OF FOOD-RELATED HYPERSENSITIVITY • Continuous fatigue
REACTIONS OF THE BILE ARE THESE: 377
• Eczema on the skin
• Digestive malabsorption • Fibromyalgia
• General digestive disorders • Headache/migraine
• Increased gut permeability • Nausea
• Immunological reactions (immunoglobulins) • Rashes
• Toxins (additives and natural compounds) 378
• Runny or blocked nose
• Psychological reactions • Sinusitis
• Urticaria
The symptoms of food hypersensitivity are quite varied • Sneezing
and can cross with many different diseases. However, if you
have many of the following symptoms (see list), you should
always look into the possibility of food hypersensitivity.

98
A L L E RG IC R E ACTI ON
HISTAM INE INTO LERANCE
Initial contact
Histamine and
with allergen
other chemicals
Allergic reaction Food hypersensitivity may also be caused by
Allergen
histamine, tyramine or other biogenic amine
present in the food (chocolate, red wine, tuna or
fermented ingredients such as cheese). In some

B cell
cases, food (for example tomato or pineapple) may
Allergen release histamine in the body. This is referred to as
Released
lgE antibodies histamine intolerance syndrome (HIS).379 Individuals
Granule
with HIS typically have a low level of diamine
oxidase, an enzyme that metabolizes histamine in
lgE -receptor
the system.380 This is due, among other things, to

Plasma cell
genetic factors and mutations in the DAO gene.381
The DAO polymorphism rs10156191, which causes
Subsequent contact
with allergen impaired metabolism of circulating histamine,
Mast cell
is also associated with the clinical response in
crossed-hypersensitivity to NSAIDs.382
Source: Biohacker’s Handbook (2019)

This is something to consider if tests do not show a

clear root cause but the individual still suffers from
symptoms. Typically histamine increases the heart
rate and causes nasal congestion and flushing.

Histamine may also cause intestinal symptoms

such as diarrhea and abdominal pain as well as

99
 N

neurological symptoms such as dizziness and headaches. • Cow’s milk

Tyramine may trigger a migraine attack.383
Intense • Papaya
NH2
histamine reactions may be prevented with antihistamines • Pineapple
or enzyme preparations containing diamine oxidase (DAO). • Citrus fruits HN
• Strawberry
F OOD S R I CH IN H ISTA M IN E O R OT H ER • Nuts
VA S OACT I V E A M IN ES: 384
• Tomato
• Wine, alcoholic cider, beer and other fermented • Spinach
alcoholic drinks • Pork
• Fermented foods (sauerkraut, wine vinegar, soy sauce, • Egg white (raw)
kefir, yogurt, kombucha) • Food additives
• Aged cheeses
• Processed meat products (sausage, ham, salami, bacon) D I AM I N E OXI DAS E B LOC KERS:
• Smoked animal products • Alcohol
• Dried fruit • Black tea
• Nuts (walnut, cashew, peanut) • Energy drinks
• Yeast (promotes histamine production in food) • Green tea
• Products made from wheat • Yerba maté
• Eggplant, spinach and tomato
• Certain types of fish such as mackerel, tuna, anchovies A person sensitive to histamine may get very severe
and sardines symptoms, for example, at a dinner containing alcoholic
beverages, aged cheeses and pizza (tomato, cheese,
FOODS THAT RELEASE HISTAMINE IN THE SYSTEM: 385
processed meat, yeast). If you suspect that you are sensitive
• Banana to histamine, try reducing the amount of histamine-
• Chocolate and cocoa containing and releasing foods described above in your diet.

100
Identifying harmful and stressful foods is particularly
important, as eliminating them will significantly improve
your physical and mental performance and, above all,
improve your overall health. Adequate intake of dietary
cofactors that affect the action of diamine oxidase can also
help with symptoms. These nutrients include vitamin B6,
copper and vitamin C. 386 387
Also, some drugs may increase histamine release or inhibit
the action of the DAO enzyme. These potential drug-
induced histamine symptoms should also be considered.
Commonly used drugs that increase histamine exposure
include cimetidine, amitriptyline, verapamil, amiloride,
metoclopramide, NSAIDs, aspirin, methimazole and
dobutamine. 388
T E S T I N G F O R F O O D A L L E R G I E S AND
H Y P E R S E NS I T I V I T I E S / I N T O L E R ANCES
Identifying the foods that are harmful or detrimental
to the function of the body is particularly important.
Eliminating these makes for significantly better physical
and psychological performance and, above all, improved
overall health.
101
T ESTI N G FOR FOOD AL L ERG IES:
• Trial elimination diet
• Skin prick test
• IgE antibody tests (for example Genova Diagnostics IgE
Food Antibodies)
• Open food challenge (milk and cereals)
T ESTI N G FOR FOOD I N TO LERANCES:
• Nordic Food Panel 184 IgG – Food Intolerance Test
With food allergies, it is important to completely remove
the allergenic food from your diet. Even a small amount
can cause symptoms. Fortunately for food hypersensitivity,
the situation is easier: remove a food from the diet for three
months and then reintroduce it at low doses.
T ESTI N G FOR H I STAM I N E INTO LERANCE:
• Daily urine methylhistamine (NMHIN)
• Histamine DAO test (e.g., Nordic Laboratories)
 DO THE FOLLOWING:

1 TAKE T HE F O O D SEN SIT IV IT Y T EST A N D /OR

5 C H EC K TH E FOOD S EN S I TIV ITY TEST AND
HI STA MI NE IN TO L ER A N C E T EST A N D CON S ULT AN EXP ERT I F NECESSARY
CONS ULT AN EX P ERT W H EN N EED ED

6 TAKE T H E M EAS UR ES N EC ESSARY F O R THE

2 R E M OV E F OO D ( S) C AU SIN G H YP ERSE N S I TI VI T Y R ES ULTS OF T H E TEST

F OR 3 MONT H S
• Ascertained by IgG test NOTE! Unfortunately, food hypersensitivity tests are not
100 % reliable and can sometimes give false positive results

3 F OCUS ON CO R R EC T IN G T H E G U T B AL AN C E WI T H and in some cases may not show food hypersensitivity-

A D I V E RS E D IET causing foods. If you suffer from a variety of hypersensitivity
• Probiotics, prebiotics and other methods outlined in this symptoms, it is a good idea to begin by removing the most
training common foods that cause hypersensitivity and allergies (see
first chapter of the book).

4 R E T URN 3 M O N T H S A FT ER IN D IV ID UAL
HY P E RS E NS IT IV IT Y FO O D S D IET
• Start with small doses and wait a few days before your
next dose

102
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W H AT N E X T ?

You have probably already tried the methods mentioned in this book and found out what your
symptoms might be. If you need more detailed analysis and follow-up on your symptoms,
I recommend consulting a physician, a nutritionist or a functional medicine practitioner for your
convenience.

I hope your quality of life and your health have improved with this book.
Thank you for reading!

Warm regards,
Olli Sovijärvi, M.D.

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