When Your Genetics and Immune System Work Against You
“Many practitioners would say weight loss would be nearly impossible.”
That’s what I wrote in my notes when Jenny first came to see me. She had two significant factors working against her: an MTHFR gene variation affecting how her body processes nutrients, and Hashimoto’s thyroiditis—an autoimmune condition where her immune system was attacking her thyroid.
She was experiencing constant headaches, hot flushes that disrupted her day, poor sleep, low energy, and stubborn weight that wouldn’t shift despite eating well and staying active.
JB had been told by previous practitioners that her genetic variation and autoimmune condition made weight loss extremely difficult. Some had essentially suggested she learn to accept her current state.
But here’s what most people don’t understand: having MTHFR and Hashimoto’s doesn’t make weight loss impossible. It makes a generic approach impossible.
This is JB’s story of how addressing her unique genetic and autoimmune factors led to releasing 14kg, eliminating her headaches and hot flushes, and finally feeling energised and balanced.
If you have MTHFR, Hashimoto’s, or another autoimmune condition and have been struggling to lose weight, this case study will show you why—and what’s possible when you address the root causes.
The Problem: When Multiple Factors Compound
Jenny’s Initial Presentation
When JB came to my clinic, she was frustrated and exhausted. She’d been doing “all the right things”:
- Eating a healthy diet
- Staying active
- Taking her thyroid medication
- Following general health advice
But her body wasn’t responding. In fact, she felt like it was working against her.
Her main concerns were:
- Persistent headaches that affected her daily life
- Hot flushes (despite not being in menopause)
- Poor sleep quality—waking unrefreshed
- Low energy throughout the day
- Weight that simply wouldn’t budge
- Feeling hormonally imbalanced
What She’d Already Tried
Like many of my clients, JB had tried multiple approaches:
- Various diets (low-calorie, low-carb, paleo)
- Increased exercise
- Different supplements recommended by well-meaning friends
- Followed generic “thyroid diet” advice from the internet
Nothing created lasting change. In fact, some approaches made her feel worse.
Why She Was Frustrated
The most frustrating part? Everyone kept telling her the same thing: “Just eat less and exercise more.”
But JB knew something deeper was wrong. She could feel it. Her body wasn’t just being “difficult”—it was trying to tell her something.
That’s when she found me.
What I Discovered: The Complex Clinical Picture
The Two Major Factors
When I reviewed JB’s case, I immediately recognised the complexity. She wasn’t dealing with simple hypothyroidism or straightforward weight resistance. She had two significant genetic and immunological factors at play:
- MTHFR Gene Variation
MTHFR (methylenetetrahydrofolate reductase—quite a mouthful!) is a gene that controls how your body:
- Processes B vitamins, particularly folate
- Detoxifies harmful substances
- Regulates homocysteine (an inflammatory marker)
- Clears hormones, including oestrogen
When you have an MTHFR variation:
- Standard B vitamins and synthetic folic acid don’t work properly in your body
- Homocysteine builds up, increasing inflammation
- Your detoxification pathways struggle
- Hormone clearance is impaired (explaining her hot flushes)
- Hashimoto’s Thyroiditis
Hashimoto’s is an autoimmune condition where your immune system mistakenly attacks your thyroid gland. This is different from simple hypothyroidism (underactive thyroid).
With Hashimoto’s:
- Thyroid antibodies attack your thyroid tissue
- This creates inflammation
- Thyroid function fluctuates (sometimes too low, occasionally spikes too high)
- You develop food sensitivities
- Your gut health is usually compromised
- Weight loss becomes extremely difficult
What the Blood Work Revealed
JB’s comprehensive blood work showed:
- Thyroid antibodies confirming active Hashimoto’s
- Elevated homocysteine (consistent with MTHFR)
- High inflammation markers (CRP and other inflammatory indicators)
- Signs of oestrogen dominance (explaining her hot flushes)
- Nutrient deficiencies, particularly in B vitamins
The Vicious Cycle
Here’s what was happening in JB’s body:
MTHFR → Poor Detoxification → Oestrogen Dominance → Hot Flushes
Her MTHFR variation meant she couldn’t efficiently clear oestrogen from her body. Excess oestrogen was causing her hot flushes and contributing to weight gain.
MTHFR → Elevated Homocysteine → Inflammation → Hashimoto’s Flares
Her genetic variation was creating inflammatory compounds that triggered her immune system, making her Hashimoto’s worse.
Hashimoto’s → Low Thyroid → Slow Metabolism → Weight Resistance
Her autoimmune condition was damaging her thyroid, slowing her metabolism, and making weight loss nearly impossible with standard approaches.
Inflammation → Hormone Receptor Resistance → Weight Gain
Chronic inflammation was blocking her hormone receptors, so even the hormones she did produce couldn’t work effectively.
Everything was connected. And this is why a generic approach wouldn’t work.
The Solution: Precision Personalisation
Why This Required Clinical Expertise
JB’s case required understanding the interaction between:
- Her genetic methylation issues
- Her autoimmune thyroid condition
- Her hormonal symptoms
- Her inflammatory state
A standard Metabolic Balance coach would have given her a food plan based on her blood work. As a naturopath with additional training in thyroid recovery and nutrient biochemistry, I could interpret the deeper mechanisms and personalise her approach accordingly.
The Nutritional Strategy
- MTHFR-Aware Food Selection
Standard B vitamins and synthetic folic acid don’t work for people with MTHFR variations. Her body needs the methylated forms.
Her personalised plan emphasised:
- Foods naturally high in methylated folate (leafy greens, legumes, asparagus)
- Complete avoidance of foods with synthetic folic acid (many fortified products)
- Foods supporting her body’s detoxification pathways
- Strategic meal timing to support hormone clearance
- Autoimmune Protocol
With Hashimoto’s, certain foods can trigger immune responses and create thyroid antibodies.
We needed to:
- Identify foods creating immune reactions in HER body (this varies person to person)
- Remove inflammatory triggers
- Support gut healing (70% of immune system is in the gut)
- Provide nutrients shown to reduce thyroid antibodies
- Oestrogen Metabolism Support
Her hot flushes weren’t random—they indicated oestrogen dominance due to poor clearance.
Her plan included:
- Cruciferous vegetables (support oestrogen metabolism)
- High-fibre foods (help eliminate excess oestrogen)
- Foods supporting liver function (primary site of hormone clearance)
- Strategic timing to support natural hormone rhythms
- Anti-Inflammatory Focus
Reducing inflammation was critical for:
- Calming her autoimmune response
- Allowing her thyroid hormones to work
- Reducing homocysteine
- Improving insulin sensitivity
The Supplement Strategy
Unlike generic recommendations, these were targeted to her genetic and immune needs:
Methylated B Vitamins: Her MTHFR variation means she needs the methylated forms her body can actually use (methylfolate, methylcobalamin).
Selenium: Research shows selenium supplementation can reduce thyroid antibodies in Hashimoto’s by up to 40% in some studies.
Vitamin D: Critical for immune regulation and shown to help modulate autoimmune responses.
Gut Healing Support: To address the gut-immune-thyroid connection.
Liver Support: To help her body clear excess oestrogen.
The Mindset Component
Autoimmune conditions often have an emotional component. Stress flares autoimmune responses.
I used:
- NLP techniques to address the stress and frustration around her health struggles
- Guided meditations to support nervous system regulation
- Coaching around self-compassion (many people with autoimmune conditions are very hard on themselves)
The Results: True Healing, Not Just Weight Loss
After 12 Weeks
Physical Transformation:
- Released 14kg
- Down 13cm waist, 9cm hips, 10cm thighs
- Body composition dramatically improved
Symptom Resolution:
- Headaches completely gone
- Hot flushes eliminated
- Dramatically improved sleep quality
- Waking refreshed with energy
- Felt hormonally balanced for the first time in years
In Jenny’s Words
“Jeannette is amazing! So giving, caring and supportive & I am so grateful to have her as my practitioner. The experience has literally been life changing!”
What This Meant for Her Life
Beyond the numbers, JB’s transformation was about reclaiming her life:
- She could plan her day without worrying about hot flushes
- She woke up with energy to tackle her responsibilities
- She finally felt “like herself” again
- She had hope for her long-term health
- She understood her body instead of fighting it
Practitioner Insight: Why This Worked When Nothing Else Did
The Critical Difference
JB’s case demonstrates why the same program doesn’t work for everyone—and why naturopathic training matters.
What Most Practitioners Miss:
Most weight loss programs, even personalised ones, don’t account for:
- Genetic variations affecting nutrient processing
- Autoimmune mechanisms
- The gut-immune-thyroid connection
- Detoxification capacity
- Hormone clearance issues
They provide “healthy eating advice,” which is generic and often includes foods that worsen these conditions.
Understanding MTHFR and Weight Loss
The MTHFR Connection Most People Don’t Know:
MTHFR variations affect approximately 40% of the population to varying degrees. But most people have no idea they have it, and even fewer understand how it impacts weight loss.
Here’s what happens:
Poor B Vitamin Processing → Standard supplements don’t work → Nutrient deficiencies → Slow metabolism
Impaired Detoxification → Toxins and hormones build up → Oestrogen dominance → Weight gain (especially hips/thighs) + hot flushes
Elevated Homocysteine → Increased inflammation → Insulin resistance → Difficulty losing weight + cardiovascular risk
Without addressing MTHFR specifically, these mechanisms continue sabotaging weight loss efforts.
The Hashimoto’s Challenge
Why Hashimoto’s Makes Weight Loss So Difficult:
Hashimoto’s isn’t just about low thyroid hormone. It’s about:
- Fluctuating Thyroid Function
- Your thyroid swings between too low and occasional spikes
- This makes your metabolism unpredictable
- Weight can fluctuate dramatically
- Food Sensitivities
- Autoimmune conditions create “leaky gut”
- This leads to food sensitivities
- These sensitivities create inflammation
- Inflammation blocks weight loss
- Immune System Hyperactivity
- Your immune system is in overdrive
- This creates systemic inflammation
- Inflammation blocks thyroid hormone receptors
- Even if your thyroid produces hormone, your cells can’t use it
- The Gut Connection
- 70% of your immune system is in your gut
- Hashimoto’s almost always involves compromised gut health
- You can’t heal your thyroid without healing your gut
The Interconnection
What made JB’s case so complex—and her results so remarkable—was understanding how everything connected:
MTHFR → Poor Detoxification → Oestrogen Dominance → Hot Flushes
MTHFR → Elevated Homocysteine → Inflammation → Hashimoto’s Flares
Hashimoto’s → Low Thyroid → Slow Metabolism → Weight Resistance
Inflammation → Hormone Receptor Resistance → Weight Gain
By addressing the root causes (genetic variations, autoimmune dysfunction, poor detoxification), everything else resolved naturally.
Why Generic Approaches Failed
The Problems with Standard Advice:
“Just eat healthy” → But which foods are inflammatory for HER body? With Hashimoto’s, even “healthy” foods can trigger immune responses.
“Take B vitamins” → But standard B vitamins don’t work with MTHFR. They can even make things worse.
“Cut calories” → But her metabolism was blocked by inflammation and thyroid dysfunction. Cutting calories just slowed it further.
“Exercise more” → But her body was already stressed from autoimmune activity. More exercise just raised cortisol and worsened inflammation.
Generic advice doesn’t account for genetic variations or autoimmune mechanisms.
Could This Be You?
Signs You Might Have MTHFR
MTHFR variations are common but often undiagnosed. You might have MTHFR if you:
- Have a family history of cardiovascular disease, blood clots, or stroke
- Experience anxiety or depression
- Have chronic fatigue
- Struggle with detoxification (sensitive to chemicals, medications)
- Have elevated homocysteine (if tested)
- Experience hormonal imbalances (oestrogen dominance, difficult menopause)
- Have other family members with autoimmune conditions
- Don’t feel better on standard B vitamins or multivitamins
Signs You Might Have Hashimoto’s
Hashimoto’s often goes undiagnosed because doctors only test TSH. You might have Hashimoto’s if you:
- Have hypothyroid symptoms (fatigue, weight gain, hair loss, cold intolerance)
- Your thyroid medication doesn’t fully resolve symptoms
- You experience symptoms that fluctuate (sometimes better, sometimes worse)
- You have other autoimmune conditions
- You have digestive issues or food sensitivities
- You struggle with weight loss despite healthy eating
- You have a family history of thyroid problems
- You’ve never had your thyroid antibodies tested (TPO, TgAb)
The Critical Tests
For MTHFR:
- MTHFR genetic testing (simple blood or saliva test)
- Homocysteine levels
- Methylmalonic acid (MMA)
- Active B vitamin status
For Hashimoto’s:
- TPO antibodies (thyroid peroxidase)
- TgAb antibodies (thyroglobulin)
- Complete thyroid panel (not just TSH)
- Inflammatory markers
Most GPs don’t test for these. This is where working with a naturopath makes a difference.
What Makes This Approach Different
Why Qualification Matters
JB’s case required knowledge that extends beyond standard nutrition coaching:
Genetic Biochemistry: Understanding how gene variations affect nutrient processing and recommending appropriate forms of supplements.
Immunology: Understanding autoimmune mechanisms and how to modulate immune responses through nutrition.
Thyroid Physiology: Understanding the difference between hypothyroidism and Hashimoto’s, and how to address each.
Detoxification Pathways: Understanding phase 1 and phase 2 liver detoxification and how to support hormone clearance.
Blood Work Interpretation: Reading blood work beyond “normal ranges” to identify optimal levels and subtle patterns.
This is why I invested in becoming a qualified naturopath with additional thyroid recovery training. Generic approaches don’t work for complex cases.
The Metabolic Balance Difference
Why Metabolic Balance worked for JB when other programs didn’t:
Blood-Based Personalisation: Her plan was created from 36+ blood markers, identifying her specific imbalances and nutrient needs.
Individual Food Selection: Not based on “good” and “bad” foods, but on which foods support HER unique biochemistry.
Scientific Foundation: Metabolic Balance was developed in Germany by doctors and nutritionists with decades of research.
Structured Phases: The four-phase approach allows the body to heal progressively rather than shocking it with sudden changes.
But here’s what’s critical: Metabolic Balance provides the foundation, but my naturopathic training allowed me to interpret her blood work through the lens of her MTHFR and Hashimoto’s, and adjust her plan accordingly.
The Key Takeaways
If you have MTHFR, Hashimoto’s, or another autoimmune condition:
- Your Genetics and Immune System Matter: Weight loss isn’t just about calories in vs. calories out. Your genetic variations and immune responses affect metabolism fundamentally.
- Standard Advice Won’t Work: Generic “healthy eating” advice doesn’t account for your specific needs. In fact, it can make things worse.
- The Right Supplements Matter: Standard B vitamins and folic acid don’t work with MTHFR. You need methylated forms.
- You Can’t Out-Exercise a Compromised Metabolism: More exercise often makes autoimmune conditions worse. You need to heal first, then build.
- Food Sensitivities Are Real: With Hashimoto’s, even “healthy” foods can trigger immune responses. Personalisation based on YOUR body is critical.
- Healing Takes Time, But It’s Possible: JB’s transformation took 12 weeks. Healing doesn’t happen overnight, but it does happen with the right approach.
- You Need Someone Who Understands: Working with a practitioner who understands genetic variations, autoimmune mechanisms, and thyroid function makes all the difference.
Your Next Step: Is This Approach Right for You?
You Might Benefit from This Approach If:
✓ You have MTHFR, Hashimoto’s, or another autoimmune condition
✓ You’ve tried multiple diets without lasting success
✓ You’re on thyroid medication but still struggle with symptoms
✓ You have unexplained hot flushes or hormonal imbalances
✓ You experience headaches, fatigue, or brain fog
✓ You feel like your body is working against you
✓ You want to understand the root causes, not just chase symptoms
✓ You’re ready to invest in a personalised, clinical approach
What’s Involved
Initial Naturopathic Consultation (90 minutes, $140):
- Comprehensive health history
- Symptom review and assessment
- Review of any existing blood work
- Discussion of Metabolic Balance program
- Determination if this approach is right for you
Comprehensive Blood Testing ($159):
- 36+ markers including full thyroid panel
- Inflammation markers
- Metabolic indicators
- Nutrient status
Metabolic Balance Program ($1,396):
- Personalised nutrition plan based on your blood biochemistry
- 7 coaching consultations (weekly, then fortnightly, then three-weekly)
- Ongoing email support between sessions
- App access with your personalised plan
- Private Facebook group support
- Mindset coaching and hypnosis support if needed
Payment plans available
Book Your Free 15-Minute Discovery Call
Not sure if this approach is right for you? Let’s talk.
On this free call, we’ll discuss:
- Your specific health concerns and history
- Whether you’ve been tested for MTHFR or Hashimoto’s
- What you’ve already tried and why it didn’t work
- Whether Metabolic Balance with naturopathic support is appropriate for your situation
- What the program involves and timeline
There’s no pressure, no sales pitch—just an honest conversation about whether this approach can help you.
About Jeannette Scapens
Advanced Diploma of Naturopathy
Certified Metabolic Balance® Coach (March 2018)
Certified Thyroid Recovery Practitioner (Level 1)
Certified NLP Practitioner and Hypnotherapist
ATMS Member #27097
Over 240 clients coached through Metabolic Balance since 2018, with specialisation in thyroid conditions, autoimmune disorders, and complex metabolic cases.
Clinic Location: Brighton, South Australia
Services Available: Australia-wide via Zoom and phone consultations
Frequently Asked Questions
Do I need to get tested for MTHFR before starting?
No, but it’s helpful. The Metabolic Balance blood work doesn’t include MTHFR testing, but I can arrange this separately if needed. Even without specific MTHFR testing, your comprehensive blood work will show indicators (like elevated homocysteine) that tell me we need to adjust your approach.
Will this interfere with my thyroid medication?
No. This approach works alongside your existing medical care. Many clients are able to reduce or eliminate thyroid medication over time (under their doctor’s supervision) as their thyroid heals, but this is a gradual process monitored by both me and your GP.
How long until I see results?
Most clients notice improvements in energy, sleep, and symptoms within 2-4 weeks. Weight loss typically begins within the first month. JB released 14kg over 12 weeks, but timeline varies based on individual circumstances.
Can I do this if I’m vegetarian or have other dietary restrictions?
Yes. The Metabolic Balance plan is created around your food preferences and restrictions while still providing the nutrients your body needs.
What if I don’t have MTHFR or Hashimoto’s but still struggle to lose weight?
This approach works for many metabolic and hormonal conditions, not just MTHFR and Hashimoto’s. The free discovery call will help determine if it’s right for your situation.
This case study represents a real client experience. Results vary based on starting health, adherence to the program, and individual biochemistry. All health changes should be made under professional guidance.
