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Dr. Daniel Kalish
Breakthroughs in GI Testing and Treatments Using the GI-MAP Test
INTRODUCTION
• 24 years of patient experience,
with over thousands of patients
world wide
• Trained over 1,000 practitioners
in The Kalish Method of
functional medicine
• Conducted a research study with
Mayo Clinic researchers on The
Kalish Method
LEARNING OBJECTIVES
• Building practitioner confidence and understanding in the use of DNA
based stool testing
• Learning effective treatment strategies for complex chronic patients,
GI cases and autoimmunity
• Sequencing treatments to maximize clinical benefits and patient
compliance
KALISH METHOD TREATMENT MODEL
UNDERLYING CAUSE
BODY SYSTEMS
PHYSIOLOGICAL DAMAGE
SYMPTOMS
KALISH METHOD TREATMENT MODEL
Underlying Cause Physiological Damage Body Systems Symptoms
Emotional/spiritual
(trauma/abuse/chronic
stress/addiction)
Dietary (blood sugar, poor diet,
nutrient deficiencies, dairy, food
allergies)
Gluten
GI infections
Toxins (heavy metals, chemicals)
Genetics/Epigenetics
Structural (physical trauma,
chronic injury, pain, posture)
Sleep
Exercise
Medications/surgery
Dental
Lyme, mold, viral or bacterial
(SIBO, environmental exposure)
Inflammation
Catabolic Physiology
Insulin Resistance
Oxidative Stress
Neuroendocrine
GI
Liver
Weight gain
Fatigue
Depression
Anxiety
GI problems (gas, bloating,
constipation, diarrhea, heartburn)
Sex hormone imbalance (low sex
drive, infertility, hot flashes,
nightsweats, PMS, PCOS)
Pain
Allergies
ADHD
Insomnia
Brain fog
Sugar cravings
Skin problems
Autoimmune
DOCTOR- PATIENT EQUILIBRIUM
UNDERLYING CAUSEPHYSIOLOGICAL
DAMAGE
BODY SYSTEMS SYMPTOMS
Emotional stress:
How we perceive an event, rather than the event itself, is most important in generating
a stress response
Dietary stress:
Simple carbohydrate ingestion leads to rapid
elevations in blood sugar which ultimately leads to ‘up & down’
dysregulation via insulin and cortisol responses.
Pain & hidden inflammation:
Pathogens in the gut (e.g. parasites, bacteria, fungus) are often sources of hidden
inflammation
THE THREE MAIN INITIATORS OF ILLNESS
EMOTIONAL
Spiritual & Physical
DIETARY
Blood Sugar Imbalance, Gluten & Allergies
INFLAMMATION
Infection & Toxins
THREE MAIN INITITATORS OF ILLNESS
Body System One:
Stress hormone
increase
Usually precipitated by the three main
Initiators of illness:
• Emotional Stress
• Dietary Stress
• Inflammation
Body System Two:
GI pathogen acquired,
food intolerances,
leaky gut
Decreased immune response
Body System Three:
Detox system
overwhelmedTOXINS
THREE BODY SYSTEM BREAKDOWN
• Healing diet
• Exercise
• Sleep
• Meditation
• Treat H. pylori
• Probiotics
• Enzymes • Support liver cells
• Further improve detox
• Cortisol
• Thyroid
• Brain
CORRECT BODY SYSTEMS IN
ORDER THAT PROBLEMS OCCUR
Neuroendocrine
System
GI System
Detox System
GI
SYSTEM
GI
DETOX
NEUROENDOCRINE
STANDARD TREATMENT SEQUENCE
PROTOCOL ARCHITECTURE
New patient intake
• Pains
• Gains
• Life Goals
Lifestyle tasks
• Food
• Exercise
• Sleep
• Meditation/stress reduction
Supplement programs
• Therapeutic programs
• Long term maintenance
PROTOCOL
FACTORS
GI MICROBIAL ASSAY PLUS (GI-MAP)
METHODOLOGY & DNA ANALYSIS
• The GI-MAP was designed to assess a patient’s microbiome
from a SINGLE stool sample.
• The panel is a comprehensive collection of microbial targets
as well as immune and digestive markers.
• It screens for pathogenic bacteria, commensal bacteria,
opportunistic pathogens, fungi, viruses, and parasites.
• It primarily uses multiplex polymerase chain reaction (PCR),
automated, DNA analysis to give a better view into the
gastrointestinal microbiome.
LIST OF TARGET ANALYTES MEASURED
Bacterial pathogens:CampylobacterC. diff Toxin A & BE. coli o157Enterotoxigenic E. coli LT & ST (ETEC)Shiga-like Toxin producing E. coli stx1 & stx2 (STEC)SalmonellaShigellaVibrio choleraYersinia enterocoliticaViral pathogens:Adenovirus 40 & 41Norovirus GI & GIIRotavirus AParasitic pathogensCryptosporidium
Entamoeba histolyticaGiardia Additional targetsBacteria:Helicobacter pylori and virulence factors, cagA and vacAEnterococcusLactobacillusBifidobacterBacteroides spp.Bacteroides fragilis grpE. coli (total)Citrobacter spp. Citrobacter freundiiProteus spp.Proteus mirabilusProteus vulgaris
Pseudomonas spp.Pseudomonas aeruginosaMorganella spp.Staphylococcus spp. (aureus)Streptococcus spp.Klebsiella spp.Klebsiella pneumoneiaeParasites:Blastocystis hominisDientamoeba fragilisEndolimax nana Entamoeba coliEntamoeba hartmanniChilomastix mesnelliCyclospora cayetanenensisPentatrichomonas hominis
Acid Reflux
Diarrhea
Depression
Bloating
Fatigue
YOUR PATIENTS?
Constipation
Gas
Toxic
Low Libido
Weight Gain
Anxiety/ADHD
2 COMMON FAILURES
Practitioners use wrong sequence with treatments
Everyone wants to treat GI first?
Lab testing issues: most often used tests vs. most accurate tests
Strengthen SIgA levels
through adrenal protocols
Reduce inflammation
through diet and lifestyle
changes
Kill bugs
THE KALISH METHOD APPROACH
Lab testing + diet and lifestyle coaching = health
HOW WE REACT TO STRESS-
GI ALWAYS INVOLVED
What We Eat:
• Too much sugar, processed fats, skipped
meals, not enough pure water, etc.
How We Digest:
• Overeating, poor digestion,
toxin-producing bacteria and yeast
How We Assimilate:
• Decreased absorption, rapid transit
time, inflammation, etc.
How We Eliminate:
• Constipation, faulty detoxification
MUCOSAL BARRIER FUNCTION
• Mucous membranes comprise
the primary interface between
the external environment and
the internal environment of the
body
• Most absorption of nutrients
AND toxins occurs across
mucous membranes
• Most pathogens enter the body
by binding to and penetrating
mucous membranes
Stress hormone
increase
TYPICAL CAUSES OF HEALTH PROBLEMS
Usually precipitated by one of the
following events:
• Emotional Stress
• Dietary Stress
• Inflammatory Stress
GI
pathogen acquired,
food intolerances,
leaky gut
Decreased immune response
Detox system
overwhelmedToxins
ADRENAL DYSFUNCTION
Excessive fatigue
Neck/back pain
Hair loss Irritability
Poor immune response
Insomnia
Cravings Depression
Lightheaded-ness
Lack of concentration
Anxiety
Food allergies
EXCESS CORTISOL
Gets your body to released stored resources:
• Glycogen to become blood sugar
• Bone minerals to release calcium and magnesium
• Glutamine from muscles to be converted to glucose
ALL THIS IS CATABOLIC = BODY BREAKDOWN
• To compensate your body releases
anabolic hormones to help counter the
effect of cortisol and to promote building up
DHEA IS ANABOLIC AND HELPS COUNTER
THE CATABOLIC ACTIONS OF CORTISOL
• However, if this goes on for long enough both
cortisol and DHEA fall into abnormal production
levels and you end up stuck in a breakdown
state and not able to compensate by building up
• High cortisol and high DHEA is actually a normal
stressed out person dealing with things
ABNORMAL LEVELS OF CORTISOL (REMEMBER,
IT’S CATABOLIC)
• Promotes fat storage
• Undermines mood and
emotional stability
• Reduces Secretory IgA
• Interferes with ovarian
hormones
• Triggers inflammation &
allergies
• Reduces resistance to stress
Cortisol
Pregnenolone
B5Acetyl CoA
Cholesterol
Androstenedione
19 - Hydroxy -androstenedione
Estrone
Estradiol - 17β
17α - Hydroxylation
Testosterone
5α - Dihydro -testosterone
19 - Hydroxy -testosterone
Estradiol - 17α
Progesterone
17 - Hydroxyprogesterone
11 - Deoxycortisol
Cortisone
CORTISOL STEAL
Androstenediol
17- Hydropregnenolone
DHEA – De-hydro -epi-androsterone
Pregnenolone
Aldosterone
(kidneys)
Progesterone DHEA
Androstenedione
Testosterone
(testes)
Cortisone
(liver)
Cortisol
Estrone↕
Estradiol↓
Estriol
(ovaries)
Aldosterone
(adrenals)
(general circulation)
Low Density Lipoprotein
Modified after Brook, C.G.D. & Marshall, N.J.; Essential Endocrinology, 3rd ed., Blackwell
Science, 1996.
CORTISOL STEAL
Cholesterol (← Acetyl CoA ←
CORTISOL AND BODY FAT
• Consistently high blood glucose levels along with insulin
suppression lead to cells that are starved of glucose –as
a result of these actions, the body experiences an
increase in appetite
• Unused glucose is eventually stored as fat
• Cortisol can mobilize triglycerides from storage and
relocate them to visceral fat cells in locations like the
abdomen
• Cortisol aids adipocyte development into mature fat cells
THE STRESS RESPONSE
2 major systems – the brain and the adrenal hormones
Catecholamines (dopamine, epinephrine and norepinephrine) and
cortisol:
Catecholamines – Prepare the body to act, the Brits call epinephrine
adrenalin - you may want to use that term with patients (they also call a
car trunk a boot and spell organize organise?)
Cortisol – mobilizes energy (glucose) and other substances to fuel the
action
Elevations in cortisol lower serotonin
Catecholamines:
Overall effect is to conserve energy for the central nervous system and
skeletal system for proper body function in relation to a stressful
situation
STRESS RESPONSE GONE TOO FAR
Chronic illnesses/conditions influenced by stress response:
•Diabetes mellitus
•Cardiovascular disease, high blood pressure, elevated blood fats
•Infectious diseases
•Gastrointestinal illness
•Autoimmune/inflammatory illnesses
•Infertility, menstrual irregularities
•Osteoporosis
•Detoxification problems, e.g. multiple chemical sensitivities
•Brain damage & psychiatric illnesses, e.g. Alzheimer’s, depression
•Chronic fatigue syndrome
Glucocorticoid (cortisol) receptors are found
in almost every cell in the body
ADRENAL EXHAUSTION STAGE 1: THE GOOD
GI condition detected early stage:
• No severe symptoms present
• Protocol is uncomplicated and
likely to work quickly with resolution
in a 3-6 month period
Improved by botanical protocols, dietary
changes, nutritional support:
• Rarely need antibiotics
• Rarely need leaky gut protocols
ADRENAL EXHAUSTION STAGE 2: THE BAD
• GI problems present for many years will
require more significant intervention, longer
healing time
• Longer-lasting botanical programs or
multiple rounds of antibiotics sometimes
necessary
• Complete recovery can be accomplished,
but will take up to full year
• Leaky gut programs often useful
either prior to, during or after pathogen
protocols
ADRENAL EXHAUSTION STAGE 3: THE UGLY
GI problems extensive:
• Organ and tissue damage may be present (ulcer, colitis)
• Will take one year or more to fully resolve case
• Adrenal depletion reduces ability to fight GI infections (remember D-
Day?) so every step made more challenging
• Leaky gut programs required either prior to, during or after pathogen
protocols
PROGRESSION OF STAGES IN
ADRENAL EXHAUSTION
ANTI-INFLAMMATORY FOODS
Anti-inflammatory diet:
• Focus on plant foods and moderate
portions of animal products
ANTI-INFLAMMATORY FOODS
Grass-fed beef and other
animal foods:
• Contains anti-inflammatory
omega-3s, but in lower
concentrations than cold
water fish
• Free-range livestock that
graze in pastures build up
higher levels of omega-3s
• Meat from grain-fed animals
has virtually no omega-3s
and more saturated fat
Salmon:
• Contains anti-inflammatory fats called omega-3s
• Wild salmon has more omega-3s than farmed
salmon
ANTI-INFLAMMATORY FOODS
Olive oil:
• Great source of oleic acid, another
anti-inflammatory oil
• Oleic acid promotes better insulin
function and lower blood sugar
Salads:
• Dark-green lettuce, spinach, tomatoes,
and other salad veggies are rich in
vitamin C and other antioxidants
• Antioxidants dampen inflammation
ANTI-INFLAMMATORY FOODS
Cruciferous vegetables:
• Broccoli, cauliflower, Brussels sprouts
and
kale, are also loaded with antioxidants
• Provide sulfur, which the body needs to
make its own high-powered
antioxidants
Cherries:
• Reduce inflammation
• Packed with antioxidants
• Relatively low on the glycemic index
ANTI-INFLAMMATORY FOODS
Blueberries:
• Reduce inflammation
• May also protect the brain
from many of the effects of aging
Turmeric:
• Contains a powerful, natural
anti-inflammatory compound
Garlic:
• May have some anti-inflammatory
and glucose-regulating benefits
• May also help your body fight infections
ANTI-INFLAMMATORY FOODS
Ginger:
• Known for its
anti-inflammatory benefits
• Research suggests
that it might also help
control blood sugar
Green tea:
• Contains natural anti-
inflammatory compounds
• May reduce risk of heart
disease and cancer
Gluten free, anti-inflammatory
diet for at least 60 daysConsultation
First Round Adrenals Second Round Adrenals
Treatment of Bugs
Months
Adrenal Test
(Saliva)
Stool Test
Organix Test
(Urine) Liver Detox
Nutrient Replacement, Esp. AA
- Labs In -
Report of
Findings
PATIENT TIMELINE
1 2 3 4 5 6 7 8 9 10 11 12
WHY DO GI TESTING
Patient non-responsive to diet changes and supplements after 2-3 months
For patients who have a long history of non-GI related health problems, unexplained symptoms of fatigue or weight gain, depression or female hormone imbalances
For those with obvious long standing GI problems
USING UP THE GUT
• As gut becomes damaged, people experience damage to many
physiological mechanisms from serotonin production to
immunoglobulin production -> creates symptoms ranging from
depression to immunosuppression
• Gut cells are used up by the following:
Food allergies, yeast overgrowth, bacterial infections,
parasites, prescription meds, NSAIDs, heavy metal toxicity,
emotional stress
GI INFLAMMATION / STRESS CONNECTION
• Glutamine drops due to gluconeogenesis, easily lost under stress
• Gluconeogenesis finds gut lining easy to draw from, which leads to
leaky gut from abnormal diet, bacterial endotoxins and mucosal
atrophy
• Dysfunction of gut can lead to systemic inflammation BUT inflammation
in other parts of body can impact the gut too
PATIENTS WITHOUT GI COMPLAINTS CAN STILL HAVE GI ISSUES
Yeast (Candida albicans)
Bacteria (H. pylori, C. difficile)
Parasites (Cryptosporidium, Giardia, E. histolytica)
TYPES OF PATHOGENS
We become susceptible to these infections when adrenal glands
burn out and SIgA levels drop
COMMONLY DETECTED PARASITES
Amoeba:
• Cryptosporidium
• Giardia
• Entamoeba histolytica
(dysentery)
• Blastocystis hominis
BACTERIAL INFECTIONS OF THE GI TRACT
Clostridium difficileHelicobacter pylori
HELICOBACTER PYLORI
H. Pylori
Causes damage to stomach lining and reduces stomach acid production
Common in patients with heartburn, GERD, bloating shortly after eating
YEAST: CANDIDA ALBICANS
Candida albicans
• Form of yeast that exists among the
normal human gut flora
• Causal agent of opportunistic oral
and vaginal infection in humans
• Overgrowth results in candidiasis
• Healing diet
• Exercise
• Sleep
• Meditation
• Treat h. pylori
• Probiotics
• Enzymes • Support liver cells
• Further improve detox
• Cortisol
• Thyroid
• Brain
CORRECT BODY SYSTEMS IN
ORDER THAT PROBLEMS OCCUR
Neuroendocrine
System
GI System
Detox System
GI
DETOX
NEUROENDOCRINE
STANDARD TREATMENT SEQUENCE
PATHOGEN SEQUENCE/TIMING
• Step 1: Healing diet along with adrenal program to restore SIgA –
Month 1 and 2
• Step 2: Clear GI bugs, while supporting liver detoxification, if
needed, month 3 and 4
• Step 3: Repair damage from infection, including anti-yeast
program, probiotic replacement, and leaky gut repair, month 5
and 6. Month 4-6: Re-test to ensure pathogen is gone
The Road to Immunity:
Kenneth Bock, M.D.
Deregulating factors• Medications• Alcohol• Food allergies• Infectious agents• Pollutants• Stress• Low stomach acid• Low secretory IgA
GI tract is
overburdened;
imbalances result
Poorer absorption
of nutrients
Higher levels of toxins &
allergens are absorbed
through gut mucosa.Creates food
allergies
Liver is
overburdened
Fewer nutrients are
available for defense
and repair
Bioaccumulation of
toxins that are not
excreted
More detoxifying
creates increased
oxidant stress
• Metabolic poison• Chronic illness• Alterations in organ function
• Immune suppression• Cellular damage
• Free radical damage• Mitochondrial problems
Additional burdensToxic chemicalsHormonesAntigen/antibody complexes
DETOXIFICATION
GI DAMAGE LEADS TO OXIDATIVE STRESS
• Poor GI function leads to malabsorption,
so nutrients are not being properly
absorbed
• Also leads to inflammation and oxidative
stress and mitochondrial damage
ISSUES ASSOCIATED WITH LEAKY GUT
• Food allergies
• SIgA
• Gluten intolerance
CATABOLIC PHYSIOLOGY LEADS TO
LEAKY GUT
Graphic from: www.leakygutcure.com
• Leaky gut refers to the breakdown
of intestinal lining and subsequent
“leaking” of particles and
substances into the bloodstream
• Caused by stress physiology
and intestinal infections such as
bacteria, yeast or parasites
• Body takes up glutamine for fuel
source when catabolic
KEY TO SUCCESS STRENGTHENING SIgA
THROUGH NEUROENDOCRINE
PROTOCOLS
Test
neuroendocrine
Determine stage of
adrenal exhaustion,
NT system, thyroid Treat and clean up
lifestyle stressors
GUT ECOLOGY: INTESTINAL FLORA
Symbiosis - dysbiosis
Intestinal permeability
100,000,000,000,000
bacteria in large intestine
Powerful chemical
factories
BENEFICIAL BACTERIA
The harmless strains of Escherichia coli
are part of the normal flora of the gut, and
can benefit their hosts by providing vitamin
K2, and by preventing the establishment of
pathogenic bacteria within the intestine
Image from http://en.wikipedia.org/wiki/Escherichia_coli
DYSBIOSIS
Overgrowth of harmful bacteria in GI tract caused by antibiotic use, poor eating habits, poor digestive function, birth control pills
Bacteria both capable of making vitamins and destroying toxins (symbiosis), and also capable of destroying vitamins and making toxins (dysbiosis)
Bi-products of dysbiosis (i.e., ammonia) hinder normal brain function and cause cognitive symptoms
IMPORTANCE OF FOLLOW UP TESTING
Redo symptom questionnaires and compare to initial screening
Retest for bacteria, yeast and parasites; sometimes new bugs arise
Retesting confirms protocols worked, which aids in patient compliance!
Gluten free, anti-inflammatory
diet for at least 60 daysConsultation
First Round Adrenals Second Round Adrenals
Treatment of Bugs
Months
Adrenal Test
(Saliva)
Stool Test
Organix Test
(Urine) Liver Detox
Nutrient Replacement, Esp. AA
- Labs In -
Report of
Findings
PATIENT TIMELINE
1 2 3 4 5 6 7 8 9 10 11 12
GI PROGRAM
Step 1 • Address adrenals and lifestyle changes
Step 2• Kill bugs while
supporting liver detoxification
Step 3• Put in healthy
bacteria and repair leaky gut
INTEGRATIVE
TREATMENT PROGRAM
Step 1: Neuroendocrine support, stress reduction and anti-
inflammatory/digestive system healing:
• Adrenal protocols, GI repair products, addressing food
allergies
Step 2: Treatment Phase:
• Antibiotics or herbal products to eliminate bugs
Step 3: Re-colonization:
• Introduction of probiotic, repair of GI tissues damaged
STEP 1: NEUROENDOCRINE, STRESS AND DIET
THAT ADDRESSES INFLAMMATION
Begin patient on neuroendocrine
protocols, coaching to reduce
emotional stress and proper diet for
two months first. For diet using one of
two methods:
• General diet: plant based nutrition
• Use lab tests to determine specific
food allergies
Start anti-inflammatory repair
supplement program for some
Step 1 is first AND most important
step: Remember D-Day? ever take
children on a ski trip?
DIGESTIVE ENZYMES
• Pepsin
• Papain
• Ox Bile
• Beet Root Powder
• Betain
• Pancreatin
STEP 2: CLEANSING - KILLING BUGS
• Introduction of GI bug cleansing protocol
to kill bugs found on labs – may also
need to support liver detoxification
pathways
• Some cases also will require anti-
inflammatory/leaky gut repair program
during this initial 60 days, hopefully most
won’t
GI ANTIMICROBIAL INGREDIENTS
• Berberine
• Olive Extract
• Grapefruit Seed Extract
• Sweet Wormwood
• Uva Ursi
• Clove
• Mastica
STEP 3: RE-COLONIZATION, REPAIR, RE-
EVALUATION
• Re-colonization of intestines with
healthy bacteria to continue GI repair
process
• May also use leaky gut repair
programs at this stage now that
pathogens gone
• Continued adherence to diet changes
• Retest two months after completion of
pathogen protocols, stop probiotics
two weeks prior to retesting
GI ANTI-INFLAMMATORY INGREDIENTS
• L-Glutamine
• N-Acetyl-D-Glucosamine
• Citrus Pectin
• Licorice Root
• Aloe Vera Extract
• Slippery Elm
• Mucin
• Marshmallow Root
• Chamomile
• Okra Extract
• Cat’s Claw
• Methylsulfonylmethane
• Quercetin
• Prune Powder
• Zinc Carnosine
PROBIOTICS
• Bifidobacterium Bifidum
• B. lactis
• Lactobacillus Acidophilus
• FOS
• S. Boulardii
GI-MAP CASE STUDY REVIEW
