Dr Nirala Jacobi, BHSc, ND

Author, SIBO Bi-Phasic Treatment Protocol

and the SIBO Bi-Phasic Diet

Medical Director, The SIBO Doctor

and host of TheSIBODoctor Podcast

The Bi-Phasic
SIBO Protocol
Module 2 “Reduce and Repair”
Module 2- “Reduce and Repair”
1. Considering SIBO Causes- a model for targeted treatment
strategies to prevent relapse
2. Phase 1 of the Bi-phasic protocol
• Diet
• Digestive aids
• Healing leaky gut
3. Phase 2 of the Bi-phasic protocol
• Diet
• Antimicrobials covered in Module 3
The SIBO Matrix
SIBO
“The Bucket” Causes
Environmental toxins
Contributing Factors
Detox impairments
Stress
Genomics
Sleep
Microbiome
Treatment Dehydration
Hormonal
Diet Habits/nutrition
Oxidative
Lack of movement
stress/Mitochondrial
Immunological/inflammation
Maintenance
Comprehensive SIBO treatment aims to
address the CAUSE
1. Impaired Motility 2. Impaired Digestion
• Autoimmune/MMC • Hypochlorhydria
• TBI • Poor Bile flow
• Hypothyroidism • Pancreatic enzyme
• Chronic infection • Brush border enzymes
Motility Digestive • Secretory IgA deficiency
• Diabetes Deficits
• Mould toxicity • Chronic Fight or Flight
• EDS • Microbiome dysfunction
• Scleroderma
Outflow/
Obstruction Medication 4. Medication
3. Impaired flow • Opiates/Narcotics
Adhesions
through intestines • Antispasmodics
• Abdominal surgery • Tricyclic antidepressants
• Endometriosis • Proton pump inhibitors
• EDS • cholestyramine
• Ileocecal valve dysfunction
New Patient Questionnaire coming soon
➢To find the cause
➢Up to 2/3 of patients will relapse
if the cause is not treated
Motility Digestive
➢Based on the 4 categories of causes Deficits

• Impaired Motility
• Impaired Digestion
• Impaired Outflow
Outflow/
• Medications Obstruction Medication
Adhesions
1. Impaired Motility
• Autoimmune/MMC- Case of
gastroenteritis/food poisoning/traveler’s
diarrhea lasting for longer than 24h
• Traumatic Brain Injury- Motility Digestive
Deficits
“shaken brain” eg football injury, heading
the ball in soccer, “I fell but didn’t hit my
head” such as horseback riding or bike
accident, or a shock wave such as an
explosion whether or not anything struck Outflow/
the head, falling hard on the coccyx Obstruction Medication
Adhesions
• Hypothyroidism
• Diabetes - vagal autonomic neuropathy
 Impaired Motility cont’d
• Mould toxicity – lack of VIP (vasoactive
intestinal peptide)
• Stealth infection – eg Lyme (affecting
antral accomodation/vagus nerve) Motility Digestive
Deficits
• Scleroderma -thickening of the intestinal
wall alters motility
• Ehler’s Danlos Syndrome – or other
Outflow/
connective tissue condition. (Beighton Obstruction Medication
score as an in office screening test) Adhesions
2. Impaired Digestion

This affects the digestive defense –

bacteria are NOT KILLED in the Small Digestive
intestine Motility
Deficits
• Hypochlorhydria
• Reduced output of
• Pancreatic enzymes Outflow/
• Brush border enzymes Obstruction Medication
Adhesions
• Bile
• Decreased sIgA
Impaired Digestion - symptoms
• Belching or gas within one hour after
eating
• Heartburn or acid reflux
Motility
Digestive
• Bloating within one hour after eating
• Halitosis
Deficits
• Loss of taste for meat
• Sense of excess fullness after meals
Outflow/
• Stomach pains or cramps Obstruction Medication
• Undigested foods in Adhesions

• Greasy stools/toilet water after stool

 3. Impaired Outflow – Bacteria are allowed to
remain in SI due to:
• Abdominal surgery: cesarean, hysterectomy, appendectomy,
removal of gallbladder, laparoscopy
• Endometriosis – a major source of relapsing SIBO
• Pelvic inflammatory disease, – pelvic or abdominal surgery or Motility Digestive Deficits
radiation treatment All of these can cause thickening of the bowel
or adhesions which alter motility.
• History of perforated appendix - common cause of adhesions.
• Internal hemorrhage such as ruptured ovarian cyst – another
adhesion cause.
• Blind loops, diverticuli, and other anatomical abnormalities –
Outflow/ Medication
(bacteria “hide out” and are not be flushed out by the migrating Obstruction
motor complex).
Adhesions
• Superior mesenteric artery syndrome – a rare but important cause
of partial duodenal obstruction.
4. Medications and SIBO
• Opiates/narcotics
• Antispasmodics (eg dicyclomine/bentyl,
hyosyamine/levsin, cimetropium) Motility Digestive Deficits
• Tricyclic antidepressants (eg
amitriptyline)
• Alosetron (lotronex)
Outflow/
• Lomotil (diphenoxaylate/atropine) Obstruction Medication
• Imodium (loperamide) Adhesions

• Proton pump inhibitors

• Cholestyramine (cholestipol, questran)

List Credit Dr Steven Sandberg-Lewis

Treating SIBO
Step 1– treat SIBO, which is the RESULT of the underlying CAUSE.
Many practitioners only do this step and many of their patients
will relapse

Step 2– Treat the CAUSE

Step 3 – Microbiome restoration

 The Naturopathic Therapeutic Order

Surgery

Pharmaceuticals
or synthetics
Address pathology- use
specific natural substances
or interventions

Correct structure

Address weakened systems/organs: strengthen immune system,

decrease toxicity, decrease inflammation, optimize metabolic
function, balance regulatory function, enhance regeneration,
harmonize with your life force

Stimulate the Vis Medicatrix Naturae – the healing power of

nature. Stimulate self healing processes

Establish conditions for health. Identify and remove disturbing factors

Credit: Drs Jared Zeff and Pamela Snyder, Bastyr University. Textbook of Natural Medicine
 ongoing
prokinetics

Nutritional support:
eg ALA, Lion’s Mane,
Phoshoplipids, Brain support

Address alignment

Vagal exercises, Neuro-feedback,

Homeopathy, acupuncture

Prevent further food poisoning

Impaired Motility
 PPI, etc

Address alignment

HCL, bitters, enzymes, ox bile

Vagal exercises, Breathing, Mindful eating,

Gut centered Hypnotherapy, homeopathy

Remove stressors, increase Parasympathetic tone

Impaired Digestion
 Adhesion
removal

Address alignment

Connective tissue support: Pancreatic

enzymes, Gotu Kola

Visceral Manipulation, Acupuncture, Cold Laser,

hydrotherapy

Remove stressors, prevent further adhesion formation

Impaired Outflow
 Continue
with Medication

Address alignment,
herbal alternatives

Specific Tissue Support

Hydrotherapy, Sauna, Exercise

Assess reason for medication and treat

- eg stress, social isolation, mental health

Medication
The SIBO Bi-Phasic Diet

• Available for download

• General SIBO diet plans can be
confusing and highly variable
• Patients often need customized
approaches
- Leaky gut, digestive deficits
- Other intolerances: histamine,
salicylates, oxalates etc
- Malnutrition

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 The Bi-Phasic diet allows for
a sequential treatment approach
Phase 1: “Reduce and Repair” (4-6 weeks)
▪ Reduce: fermentable starches and fibers and therefore
bacterial fermentation
▪ Repair: intestinal inflammation, brush border enzymes,
other digestive support
▪ Starts out with very restricted food plan, patients move
into “semi-restricted” as soon as symptoms improve

Phase 2: Remove and Restore (4-6 weeks)

▪ Removing bacteria (and fungi) with antimicrobials
▪ Restore Motility

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Phase 1: “Reduce and Repair”(4-6 weeks)

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Phase 1: “Reduce and Repair”(4-6 weeks)

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Phase 1: “Reduce and Repair”(4-6 weeks)

SIBOTest Professional Education

Phase 1: “Reduce and Repair”(4-6 weeks)

SIBOTest Professional Education

Phase 1: “Reduce and Repair”(4-6 weeks)

SIBOTest Professional Education

Phase 1: “Reduce and Repair”(4-6 weeks)

SIBOTest Professional Education

Phase 2: “Remove and Restore”(4-6 weeks)

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Phase 2: “Remove and Restore”(4-6 weeks)

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Phase 2: “Remove and Restore”(4-6 weeks)

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SIBO Cookbooks
 Phase 1
Patient to follow Phase 1 diet. Start with restrictive, move to semi-
restrictive when patient feels at least 50-60% improved)
RESTRICTED: No grains, dairy, honey, legumes, fruit. Basically protein and
vegetables. Rapid sxs relief with this
For underweight patients – use white rice, more pumpkin, more butter and
macadamia butter if tolerated
SEMI-RESTRICTED: builds on restricted diet, plus white rice and fruit,
always as tolerated

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Supportive Treatment for Phase 1
• Digestive Support
• Healing Leaky Gut
• Nutritional repletion - especially
- B12
- Magnesium
- Trace minerals
- Careful with B complexes
- Iron
Digestive Support
• Hydrochloric acid- start with 1 capsule with meals, increase by 1 capsule daily
until at 2 caps 3x daily with meals
- Betaine HCL, pepsin- not with gastritis
- No need to feel the “burn”
• Herbal Bitters
• Pancreatic Enzymes 1-2 caps with meals
• Brush border enzymes
- Eg Maltase, isomaltase, alpha galactosidase, Dipeptidyl Dipeptide 4
(DPP4)
• Bile – oxbile, cholagogues
Layers of Lumen to Basement membrane

Lumen

Outer, less dense Mucus

Inner protected mucous

Glycocalyx

Mucin strands on epithelial cells

Epithelial cell

Basement membrane

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 Mucous, Glycocalyx, and Tight Junctions
[Link]: loosely adherent mucus layer provides lubrication and protection. Provides
antimicrobial and immune proteins. Mucous provides habitat for local microbiome
[Link] dense inner layer protects epithelial cells. Major component of mucous is mucin,
secreted by goblet cells, composed of glycoproteins. These are peptide back bone
linked to oligosaccharide chain
[Link] – mucin strands integrated with the epithelial cell membrane. Prevention
of microbial adherence
[Link] cells – dependent on luminal nutrients, require a large amount of energy.
Dietary amino acids are their major fuel
[Link] junctions: seal adjacent cells.
[Link] membrane – layer of ECM. Provides structural support, acts as additional
barrier, regulates epithelial proliferation
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Support for Phase 1 and 2: Mucosal repair
N-acetyl glucosamine – glycocalyx support
Amino acids
• Threonine, proline, serine - Mucin support
• Glycine- important in basement membrane, GSH production
• L-Glutamine – next slide
Probiotics
• [Link] – increases sIgA, anti-inflammatory, villous repair
• Nissle strain [Link]- motility, anti-inflammatory, abdominal
hypersensitivity
• L. rhamnosus GG: motility, abdominal hypersensitivity, anti-
inflammatory
Lactoferrin/Colostrum - immune support, antiinflammatory
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Support for Phase 1 and 2: Mucosal repair
• Tight junction repair
• Vit D – facilitates mucosal barrier homeostasis, decreases
inflammatory cytokines
• Vitamin A – 20,000-50,000 IU for a few weeks, then reduce
• Quercetin 500mg TID or more
• Epithelial cell repair
• zinc carnosine 75mg BID
• L-Glutamine 5g-10g/d
• increases production of GSH
• Major fuel source for enterocytes/epithelial cells
• Supports tight junctions
• Reduces IL-6 and IL-8, increases IL-10
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Herbal mucosal support
• DGL – deglycerrhinated licorice
• Curcumin (careful with salicylates)
• though high in polysaccharides and/or fiber, these seem to be well
tolerated by most
- Aloe gel/juice ½ cup 2-3 x daily
- Slippery Elm powder
- Arabinogalactans
- PHGG
Problematic ingredients in Gut Healing Formulas
• Prebiotics
- Inulin
- FOS
• Xylitol and other sugar alcohol sweeteners
• Cane juice and other sugars
• Resistant starch
• Psyllium fiber
Other support
GOAL: increase circulation (blood and lymph), reduce sympathetic tone and
increase parasympathetic tone in ENS

• Relaxation! Especially before eating

• Meditation, apps, inner balance
• Breathing exercises (Buteyko)
• Constitutional Hydrotherapy
• Acupuncture
• Gut Centered Hypnotherapy
Phase 2
• Patient to move to Phase 2 diet, paying attention
with introduction of dairy, honey)
- More generous than phase 1
• Antimicrobials and Prokinetics (Module 3)
• May need to continue with Phase 1 digestive or
mucosal support
• Die- off support

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Die-off
• “Hercksheimer reaction” – massive increase in LPS and other
bacterial and fungal toxins as these organisms die

• Patients often react to this, especially when their “bucket is full”,

and especially if constipated

• Noticed after a few days of initiating antimicrobial treatment

• Pt often thinks they are “reacting to the product” and discontinue it

Die-off Support
General:
• Stop the antimicrobial for a few days until sxs subside, then start again at a
much lower dose
• Increase water intake to 3 Litres/quarts daily
• Vitamin C 1000mg 3x daily if tolerated
Increasing systemic circulation:
• Sauna
• Exercise
• Hydrotherapy
Die-off support
Binders:
• Activated Charcoal 2 caps 3 x daily
• Bentonite clay (can be constipating)
• Zeolite/clinolyptite
Treatment Flow
Step 1:
Start with Phase 1 restricted diet. As soon as patient’s sxs improve, move to Phase 1
semi-restricted diet.
This phase typically lasts 1 month

Don’t start antimicrobials until phase 2.

• This helps to reduce die-off and addresses the issue of “feeding whilst killing”

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Treatment Flow
Step 2

After 1 month, and test results indicate SIBO+, start with Phase 2 diet and
antimicrobials

Customise this as per your patient’s needs

• Food allergies (dairy, eggs, almonds)
• Food intolerances (histamine, salicylates, etc)
• Raw vs cooked foods

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Treatment flow

How long on phase 2?

Once you’ve started Antimicrobials, typically methane gas will reduce by

20-30ppm with each 4-6 week course. Hydrogen gas is less predictable

So if someone has high levels of methane and/or hydrogen you can

expect them to be on antimicrobials for a good 2-3 months.

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Treatment flow
Step 3
If symptoms are not 80%-90% resolved: Retest!
(to ensure all the bacteria are gone)
If levels are still high, keep going with antimicrobials or change herbs.

Step 4
once the test is clear, start with Prokinetics another 3-6 months and begin
reintroducing some fermentable carbohydrates (increasing amounts of
vegetables etc).

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Typical Treatment Flow
• You suspect SIBO – patient orders breath test
• Start with Phase 1 of Diet, gut healing nutrients if
1st patient
visit indicated, bitters

• SIBO breath test positive

• Initiate appropriate antimicrobials
2nd patient
visit 3-4 weeks • Move to phase 2 of diet

Consider another round of antimicrobials

Consider prokinetics
3rd patient visit
4-6 weeks Consider re-testing

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Re-testing
SIBO suspected

Lactulose and/or
Glucose Breath test

Antibiotics,
Herbal Antimicrobials,
Elemental Diet Bi-Phasic
Bi-Phasic Diet
Diet

90% Partial
improvement improvement

Retest
Prokinetic, Biphasic
Diet, Prevention
Change herbal Consider other Dx
antimicrobials, repeat
rifaximin, consider
elemental diet

Credit to Drs Allison Siebecker and Steven Sandberg-Lewis

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Special Bi-phasic Diet Adjustments
Vegetarians/Vegans
Replace existing protein category with
• Plain firm tofu 2/3 cup (160g)
• Plain tempeh 100g
• Increase eggs if vegetarian
• Pea protein (less than 1g fiber) - 1 serve
twice daily in unsweetened almond or
rice milk
• Sprouted Mung beans 2/3 cup
• Canned lentils ½ cup (drain and rinse)
Special Bi-phasic Diet Adjustments
IBS-C positive Methane
• High baseline methane on test, stays high throughout the test (LI methane
contribution)
• A diet high in protein and low in fiber can worsen constipation
• Replace some animal proteins with the vegetarian protein choices (especially
tofu and tempeh)
• Increase fibers if tolerated: flax seeds or PHGG (usually fairly well tolerated-
start with ¼ scoop and work up to 1 scoop)
 Elemental Diet
• Complete meal replacement for 2-3 weeks
• Specifically formulated free form amino acid powder (NOT whey,
pea or other types of protein powder), mixed with rapidly
absorbing glucose, MCT or other oil.
• Used instead of herbal or conventional antimicrobials – absorbed
within the first 60cm of the SI. Starves bacteria but feeds the
patient
• We see the most dramatic gas reduction with elemental diet
(150ppm in some cases)

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 Elemental Diet
• Vivonex is commercial brand–
expensive
• PED - Expensive but tasty. (May need
to use an antifungal)
• Patient can order ingredients and
make at home.
• Get the handout from
[Link]
• Dr Siebecker also has made 3
videos – available for free
• Tips: listen to podcast with Dr Lela
Altman
SIBOTst Professional Education 2017
©
Considerations on the SIBO Diet
• There is no “one size fits all” to dietary
SIBO treatment
• Consider working with a nutritionist or
holistic dietician
• Do not use the low FODMAP diet or
Bi-Phasic diet indefinitely

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 Thank You
Module 3 – Antimicrobials,
Prokinetic and Biofilm treatments

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