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Testing

GI MAP stool testing: DNA and antibiotic resistance genes

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Dr. Ben Lynch interviews Dr. David Brady’s on the Dirty Genes Summit (Jan 22 through Jan 29) and they cover stool testing and antibiotic resistance genes.

The section on antibiotic resistance genes is part of the discussion about the stool testing that Dr. Brady recommends: the GI Map test by Diagnostic Solutions Lab, a PCR/DNA test he helped to develop.

Before they get to the antibiotic resistance genes discussion, Dr. Brady shares more about this 2-year old test and why he has found it superior to other stool testing, sharing that it’s more comprehensive than what the gastroenterologist would do, plus the fact that other functional stool tests rely on culture technologies which has the limitation that you can only test bugs that you can grow. He shares that:

More than 95% of bugs in the gut can’t be grown on a petri dish. They are anaerobes or they are very difficult to culture.

He also discusses the process of testing for sensitivities to herbs (in some of the other stool tests) i.e. what herb will kill what bug, sharing that this is a flawed method:

While dropping specific prescriptive antibiotics on a culture has been methodically worked out to correlate with a certain dose of that antibiotic orally, it’s never been done for herbs and volatile oils.

Dr. Brady does discuss one other major advantage of the GI MAP test:

We look for antibiotic resistance genes, both phenotype and genotype of the microbiotia and looking through the genetic signatures of antibiotic resistance. So if you’re going to use a prescriptive antibiotic, we can tell you if the microbiotia of the patient harbors the genes for resistance to sulfonamide or fluoroquinolones or some others.

I see great value in this beyond finding a solution for addressing the pathogens. This is because we know antibiotics have side-effects and some like the fluroquinolones can actually cause anxiety, depression, insomnia, panic attacks, clouded thinking, depersonalization, suicidal thoughts, psychosis, nightmares, and impaired memory. We cover this in detail in the Anxiety Summit interview with Lisa Bloomquist, fluoroquinolone toxicity patient advocate: Antibiotic Induced Anxiety – How Fluoroquinolone Antibiotics Induce Psychiatric Illness Symptoms

When it comes to genetics work and testing, dr. Brady endorses Dr. Peter D’Adamo, Opus23 and Dr. Ben Lynch, recognizing the importance of science and looking at the clinical presentation of the patient rather than individual SNPs.  I would have loved hearing some examples of what he means by this.  

All in all, this is a fascinating interview and well worth listening to!

Register for the Dirty Genes Summit here – to hear this entire interview and learn from Dr. Ben Lynch and the other experts he interviews.

Hope you can join in!

Please post questions and comments below.

Mitomics – genetics of the mitochondria and food based antioxidants like curcumin

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Dr. David Haase, a functional medicine doctor and a leader in the field of genetics and genomics, covers mitomics in this very interesting interview on the upcoming Interpreting Your Genetics Summit which runs August 21-28, 2017.

Mitomics is the genetics of the mitochondria themselves. The mitochondria have their own set of genes. And that’s often given a lot of importance because we get our mitochondria from our mothers and therefore we inherit this genome from the mother and we get our mother’s energy per se.

But when you step back a little bit, you recognize that the genetics of the mitochondria are not just nuclear. It’s not just thirty-seven genes that hang out in the mitochondria, but rather, there is over a thousand genes that are in the nucleus that control the proteins or make proteins and influence the mitochondria at great levels. I’ve used a company called Courtagen who do whole mitome analysis. And in individuals with chronic fatigue syndrome or bizarre multi-system dysfunction, this is instrumental in giving a new plan of action to address.

He shares the story of a patient who had had chronic pain, fatigue and irritable bowel syndrome (a mitochondrial symptom)

She had tachycardia, palpitations, some dizziness. And so we actually did a whole mitome analysis on her and we found that she had a uniqueness in something called the TRAP1 related disease. I think it’s clever because the acronym is T1RED.

And this TRAP actually codes for a protein, which is a chaperone to the mitochondria and it’s involved in antioxidant defenses. And what’s been shown is that individuals with this TRAP1 related disease will be queasy, they’ll have pain and they’ll be fatigued and highly aggressive.

But when we found that she had this heterozygote for this particular abnormality – and it was associated with her having a lot of oxidative stress and elevation of hydroxyguanidine, which is a marker of genetic damage and oxidative damage, and elevations in her CK [creatine kinase], which was a marker of muscle injury. We went into this very intense antioxidant program with a lot of food-based antioxidants: sulforaphane, curcumin, resveratrol, CoQ10 and alpha-lipoic acid.

We went after this as aggressively as I think I’ve ever gone after this in a single patient with doses that are in excess of what I would typically use. And she had a remarkable recovery.

I share this snippet because with the tachycardia (an abnormally fast resting heart rate of at least 100 beats per minute) and palpitations, you may think it’s anxiety with a root cause such as low GABA or low serotonin or high cortisol or even Hashimoto’s thyroiditis, when in fact these symptoms are caused by mitochondrial TRAP-1 related disease.

I hope you can join us on Interpreting Your Genetics Summit, August 21-28, 2017. You can register here.

Here are some other reasons to attend:

  • once you register you’ll have immediate access to these interviews: Epigenetic Mastery for Everyone from Andrea Nakayama, CNC, CNE; The Current State of Genetics from Jeffrey Bland, PhD; and Your Genetics and Autoimmune Diseases with Dr. Tom O’Bryan, DC, CCN.
  • my digital ebook is available to you if you choose to purchase the series: Anxiety, Benzodiazepines and Your Genetics
  • as part of the lead up to the event, summit host, James Maskell will even be doing three of his own genetic tests and getting them interpreted by speakers from the summit

James Maskell has gathered world-renowned leaders from genetics, genomics and functional medicine and this promises to be a cutting-edge online event. These pioneering experts are on the front lines interpreting genetic data!

Hope to “see you” on the summit.

UPDATE August 11: I just went to the site and see this message today “Courtagen has closed its diagnostic laboratory and will no longer be accepting samples.”

They have a link to this press release of July 18 so it’s a brand new change: “Courtagen Life Sciences Inc. announced today that the company will be shifting the core focus of its business to medicinal cannabis genetics and testing. As the company reorients its business to respond to the growing opportunities in the medicinal cannabis industry, the company has made the decision to wind down its diagnostic neurology testing division.”

A RCT of a dietary intervention for adults with major depression (the “SMILES” trial): study protocol

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shish-kebab

Even though this study protocol is dated 2013, it’s worth a mention now because the International Society for Nutritional Psychiatry Research just posted this on the ISNPR facebook page.

Recruitment for this important ‘world first’ trial is finally complete (it is hoped that results will be published in late 2015/early 2016)

It’s very exciting! And don’t you just love the name: the “SMILES” trial!

A randomised, controlled trial of a dietary intervention for adults with major depression (the “SMILES” trial): study protocol

Adrienne O’Neil, Michael Berk, Catherine Itsiopoulos, David Castle, Rachelle Opie, Josephine Pizzinga, Laima Brazionis, Allison Hodge, Cathrine Mihalopoulos, Mary Lou Chatterton, Olivia M Dean and Felice N Jacka.

BMC Psychiatry 2013, 13:114  doi:10.1186/1471-244X-13-114

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-244X/13/114

© 2013 O’Neil et al.; licensee BioMed Central Ltd.

Abstract

Background

Despite increased investment in its recognition and treatment, depression remains a substantial health and economic burden worldwide. Current treatment strategies generally focus on biological and psychological pathways, largely neglecting the role of lifestyle. There is emerging evidence to suggest that diet and nutrition play an important role in the risk, and the genesis, of depression. However, there are limited data regarding the therapeutic impact of dietary changes on existing mental illness. Using a randomised controlled trial design, we aim to investigate the efficacy and cost-efficacy of a dietary program for the treatment of Major Depressive Episodes (MDE).

Methods/Design

One hundred and seventy six eligible participants suffering from current MDE are being randomised into a dietary intervention group or a social support group. Depression status is assessed using the Montgomery–Asberg Depression Rating Scale (MADRS) and Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders (Non Patient Edition) (SCID-I/NP). The intervention consists of 7 individual nutrition consulting sessions (of approximately 60 minutes), delivered by an Accredited Practising Dietitian (APD). Sessions commence within one week of baseline assessment. The intervention focuses on advocating a healthy diet based on the Australian Dietary Guidelines and the Dietary Guidelines for Adults in Greece. The control condition comprises a befriending protocol using the same visit schedule and length as the diet intervention. The study is being conducted at two locations in Victoria, Australia (a metropolitan and regional centre). Data collection occurs at baseline (pre-intervention), 3-months (post-intervention) and 6– months. The primary endpoint is MADRS scores at 3 months. A cost consequences analysis will determine the economic value of the intervention.

Discussion

If efficacious, this program could provide an alternative or adjunct treatment strategy for the management of this highly prevalent mental disorder; the benefits of which could extend to the management of common co-morbidities including cardiovascular disease (CVD), obesity, and type 2 diabetes.

Although the abstract doesn’t mention anxiety, when you read the full study protocol you’ll see these secondary outcomes and aims too:

Secondary outcomes include; depressive and anxiety symptoms, functioning, quality of life, and changes in targeted dietary behaviours, cardiovascular and metabolic risk. A secondary aim is to evaluate the cost efficacy of the intervention from a societal perspective at 3 months.

When I posted this on Facebook, here is a very positive comment I received:

Quote from the article: “A dietary intervention for depression as an adjunct to standard care, has the potential to be cost-effective, highly acceptable and widely applicable. This approach may lead to improved outcomes for individuals with MDE and reduce the public health burden of psychiatric illness.” This is very encouraging, from someone who has suffered from depression my entire life. I’ve had to be my own advocate, especially with the diet connection and finding a way to stay off medications with difficult side effects. Thanks for sharing!

Someone else made a comment about the amount of protein in the study:

17% protein in the study?

This was my response:

Yes it is rather low and the study includes low fat dairy and whole grains too – but it’s a start – it’s a wonderful start!

We can hope that the next step after this one has been published is to do more like this and hopefully have them include more protein (and discuss the quality of the protein), include more full fat dairy and exclude gluten and even one that excludes all grains.

The long term goal will be to dietary interventions as part of the standard of treatment for anxiety, depression and other mental health disorders.

Dr. Felice Jacka talked about this study and the long term goals during our interview on season 1 of the Anxiety Summit: The Research – Food to prevent and treat anxiety and depression?

This is beyond exciting and we so appreciate the researchers and study participants!

How excited are you to see this research being done?

 

Nutritional testing for figuring out the root cause/s of your anxiety

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test

This blog covers the nutritional or functional testing I use with my clients, and what tests I’d run (and/or have my client’s doctor run) if everyone had unlimited funds.

Often it can be challenging to figure out the root cause/s of your anxiety, but that’s where questionnaires, nutritional/ functional/ testing, and a good practitioner (or team of practitioners like nutritionist, functional medicine doctor, nurse practitioner, therapist etc.) comes in – so you can put all the puzzle pieces together.

The following are what I have most of my clients do:

  • The basic blood work that I like to see is a lipid panel, a CBC (complete blood count), a metabolic panel, an iron panel that includes ferritin, and a thyroid panel that includes TSH, free T3, free T4, reverse T3, thyroid antibodies (antithyroglobulin and antithyroperoxidase), vitamin D, and CRP (C-Reactive Protein). There is much we can determine by looking at functional values: digestive status, possible gut dysbiosis, adrenal function, malabsorption, inflammation, as well as low iron, low vitamin D etc. I’ll share more about the markers on this panel of tests in a later blog post.  
  • I also like to see an adrenal saliva test, which measures four times cortisol. So it’d be a saliva collection first thing in the morning, noontime, 5:00 PM, and 10:00 PM. It also shows DHEA; Secretory IgA; and an anti-gliadin antibody (a marker of gluten sensitivity)
  • I rely on the Pyroluria Questionnaire and response to the supplements. The pyroluria urine test is a possibility. But I seldom have clients do it, because we can often see a false negative.
  • For neurotransmitter imbalances – low serotonin, low GABA, low catecholamines and low endorphins – I rely on the Amino Acid Questionnaire and response to amino acids. Vitamin Diagnostics offer a platelet serotonin/dopamine/norepinephrine and epinephrine panel, which is the most accurate way to measure neurotransmitters, if you really wanted to measure them. I don’t ever recommend urinary neurotransmitter testing. It just doesn’t seem to correlate with symptoms.
  • B12 levels. To determine a B12 deficiency, you would want to measure B12, methylmalonic acid (or MMA), and homocysteine.
  • The 23andme genetic testing. This will measure MTHFR, COMT, MAOA, CBS, GAD and many more polymorphisms.

Here is other testing that may be helpful for certain individuals:

  • A sex hormone saliva test. This will measures progesterone, estriol, estrone, estradiol, and testosterone.   I have a wonderful nurse practitioner that I work with, and, if need be, will refer people out to the nurse practitioner if we need support when it comes to bioidentical hormones.
  • A food intolerance test that measures IgG antibodies to 60+ foods. This shows a delayed reaction to the foods.
  • A fatty acid test. This will measure omega-3s (EPA and DHA), omega-6s and omega-9s. And it’ll also measure trans fats. Doing this test is really helpful if you have pyroluria or think that you may have pyroluria.
  • A RBC (red blood cell) magnesium test. Dr. Carolyn Dean talked about the usefulness of this test season 2 of The Anxiety Summit: Take magnesium and melt your anxiety away
  • A stool test. Metametrix/Genova and Diagnostechs offers functional stool testing. It’ll show good bacteria, yeast, parasites, bad bacteria, and digestive markers.
  • A hydrogen breath test or SIBO test. Genova offers this or you can ask your conventional doctor to order this.
  • The H/pylori antigen test. Genova offers this or a conventional doctor can do this.
  • Intestinal permeability profile. Genova offers this.
  • A celiac panel. Genova offers this, or a conventional doctor can do this.
  • The Cyrex panels, which will show gluten and food cross-reactions, and various autoimmune markers.
  • The histamine whole blood is a useful test to see if you have high histamine/histadelia or low histamine/histapenia. This is offered by Vitamin Diagnostics and must be WHOLE blood.
  • Spectracell shows vitamin and mineral deficiencies.
  • A VAP test. If you have concerns about high cholesterol and heart disease, this is going to measure particle size, fibrinogen, Lp(a) and other cardio markers (since looking at only high total cholesterol is not particularly useful).
  • The OAT/Organic Acid Test. Great Plains offers this and it has markers of digestion, yeast overgrowth, infections, B vitamin status and neurotransmitter function.
  • A hair mineral analysis. This is a great way to look for toxic metals and mineral status. You want to look at ratios, not just levels. This is a good marker for copper toxicity as well. Analytical Research Lab offers this test.
  • If you think your copper is too high, or you’ve got low zinc, you can measure copper or ceruloplasmin. This is in serum.
  • Porphyrin testing. This is a measure of the effect of heavy metals such as lead and mecury. Kris Homme talked about this in Season 2 of the Anxiety Summit: Your hidden mercury burden – A likely root cause of the other root causes of anxiety – part 2
  • An amino acid profile, which is a plasma or blood spot test. It’s not something that I use very often, but I have seen people with this test.
  • You can also test candida antibodies in blood, which is not terribly accurate, but sometimes will show up.

I want to look into the following testing:

What functional/nutritional testing have you had done and have found to be helpful? Which of the above tests would you like more detailed information about?

The Anxiety Summit – The Parasite/Anxiety Connection

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Ann Louise Gittleman PhD, CNS, author of The Fat Flush Plan and Guess What Came to Dinner, was interviewed on the Anxiety Summit by host of the Anxiety Summit, Trudy Scott, Food Mood Expert and Nutritionist, author of The Antianxiety Food Solution.

The Parasite/Anxiety Connection

  • How common are parasites and how do we become infected (even if we live in a first world country)
  • How do parasites contribute to anxiety and depression and even schizophrenia
  • Other symptoms of a parasitic infection
  • How to avoid being exposed to parasites
  • How to test for parasites and how do we get rid of the parasite/s

Here are some gems from our interview:

Parasitic infections in the USA are far more common than you would expect – in fact the estimates are that 1 in every 3 people have a parasite or more than one

Parasites can contribute to or cause anxiety and fear by altering “hormonal and neurotransmitter communication and/or direct interference with the neurons and brain regions that mediate behavioural expression”

According to folklore, parasites are more active around the full moon, so testing and treating around this time may yield better results

Toxoplasma gondii is one parasite that has been researched a great deal and is one that has big implications for anxiety and other mood conditions, especially schizophrenia.

Ann Louise shared this interesting article from Scientific American called Toxoplasma’s Dark Side: The Link Between Parasite and Suicide

In 2003, E. Fuller Torrey of the Stanley Medical Research Institute in Bethesda, Maryland his colleagues noted a link between Toxoplasma and schizophrenia – specifically, that women with high levels of the parasite were more likely to give birth to schizophrenics-to-be

scientists have discovered a link between suicide and parasite infection

In 2006, researchers linked Toxoplasma infection to neuroticism in both men and women.

When we are infected with a parasite like Toxoplasma gondii, our immune system goes on the offensive, producing a group of molecules called cytokines that activate various immune cell types. The exact mechanism by which cytokines cause depression and other mental illnesses is poorly understood, but we do know they are able to pass the blood-brain barrier and alter neurotransmitters like serotonin and dopamine in the brain.

Here is the parasite testing and products we discussed:  

The Expanded GI panel (for testing)

Colon Cleaning kit with Verma-Plus and Para- Key (together with a probiotic)

Verma-Plus contains the Native American herb called Centaury (aerial portion) (Centaurium erythraea)

It seems to have antimicrobial properties too: Volatile organic compounds from Centaurium erythraea Rafn (Croatia) and the antimicrobial potential of its essential oil.

And gastroprotective effects: Gastroprotective effect of small centaury (Centaurium erythraea L) on aspirin-induced gastric damage in rats.

We also talked about using filtered water for washing fruits and vegetables and this is the water filter Ann Louise recommends: Countertop Ultra-Ceramic Water Filter. “It purifies your tap water for the removal of incoming contaminants including parasites, chlorine, chloramines, heavy metals, cloudiness and sediment. The ceramic filter also inhibits the growth of bacteria”

Ann Louise has written many wonderful books.  Here are three of them that were mentioned in this interview:

Guess What Came to Dinner? Parasites and Your Health (this is the book about parasites)

Ann Louise Gittleman_guess what came to dinner

 

 

 

 

 

 

 

 

Before the Change: Taking Charge of Your Perimenopause (this is the one that helped me so much when I was in my late thirties and having perimenopausal symptoms – with the zinc, vitamin B6 and evening primrose oil )

Ann Louise Gittleman_before the change

 

 

 

 

 

 

 

 

The Fat Flush Plan (this is one of many her classic weight loss books)

AnnLouiseGittleman_fat flush plan

 

 

 

 

 

 

 

 

Here is her gift: a 50-Page Report on Parasites – Still the Greatest Masqueraders of All Time

If you are not already registered for the Anxiety Summit you can get live access to the speakers of the day here: www.theAnxietySummit.com

Missed this interview or can’t listen live? Or want this and the other great interviews for your learning library? Purchase the MP3s or MP3s + transcripts and listen when it suits you.

You can find your purchasing options here: Anxiety Summit Season 1, Anxiety Summit Season 2, and Anxiety Summit Season 3.

Organic Acids Testing by Great Plains Lab

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greatplainslabThis is a 1-day professional training being held in Berkeley, CA on January 24, 2015: An Overview of Organic Acids Testing and Why it is so Important

Hundreds of organic acid metabolites are found in the urine of all mammals including humans. These metabolites can be used for both diagnostic and therapeutic measurements for: detecting abnormal gastrointestinal overgrowth or dysbiosis, assessing mitochondrial energy production, detecting genetic diseases, assessing malnutrition and suboptimum nutrition, revealing toxic exposure, finding alterations of neurotransmitter metabolites in neurological and psychiatric disorders, and assessing metabolites that cause severe inflammation in a variety of chronic illnesses.

The Interrelationship between Chronic Yeast and Various Issues

The OAT evaluates for various fungal toxins, including specific markers for Candida. Many people rely on stool testing for Candida diagnosis and miss the presence of Candida toxins through the Organic Acid Test. Candida can lead to neurochemical imbalances in the brain, as well as sensory problems and self-stimulatory behavior (often seen in autism).

The Interrelationship between Clostridia and Various Health Issues

The OAT evaluates for two specific toxins related to Clostridia bacteria – HPHPA and 4-cresol. Both of these toxins can inhibit a dopamine converting enzyme, leading to excess dopamine and toxic reactions in the brain and nervous system. Problems such as moodiness, irritability, aggression, self-injurious behavior, sleep difficulties and more can be associated with Clostridia bacteria overgrowth.

Correlating Oxalate Problems

The OAT includes glycolic and glyceric acids in the oxalate section, which can differentiate between genetic and nutritional components in disturbed oxalate metabolism. Oxalates are compounds found in many foods, and can be worsened from Candida overgrowth. High oxalates are associated with pain in the joints, muscles, and connective tissues. They can also trap heavy metals (such as mercury, lead, and arsenic) in the body and lead to mineral imbalances. Certain behavioral issues and self-injurious tendencies have been associated with high oxalates.

Organic Acids Testing and Neurochemical Imbalances

The OAT evaluates for imbalances in serotonin (an important brain chemical for mood, fine and gross motor skills, and calmness), as well additional markers that can indicate toxic stress in the brain and nervous system, such as Quinolinic Acid. High Quinolinic Acid suggests toxic stress in the brain and is important to evaluate before prescribing certain supplements, particularly L-Tryptophan which is commonly used to help with sleep.

Case Studies

This presentation will highlight various patient cases from clinical practice that show the role of biomedical intervention for various patient scenarios such as dietary therapy, yeast and Clostridia treatment, and methylation support.

All of the above, together with start and end times, and breaks can be found here on the presentation schedule page

Presenter: Kurt N. Woeller, D.O., has been an integrative medicine physician and biomedical autism specialist for 15+ years. He is an author of several health books including “Autism – The Road To Recovery,” “Methyl-B12 Therapy For Autism,” “Methyl-B12 for Alzheimer’s Disease and Dementia,” and “5 Things You MUST Do Right Now To Help With Your Rheumatoid Arthritis.” He is a lecturer (United States and International), educator and experienced clinician offering specialized treatment and testing for individuals with complex medical conditions such as Autism-Spectrum Disorders, Chronic Fatigue Syndrome, Mental Health Disorders, Multiple Sclerosis and other chronic health conditions.

I’m sharing this training on behalf of Dr. Kat Toups, M.D., Distinguished Fellow APA, Functional Medicine Psychiatry, BayAreaWellness.net

Dr. Toups shared this with me and I would suggest you call Great Plains Lab if you are unsure whether you are eligible to order testing:

This includes a free test kit. My understanding about the free test kits at the Organic Acid Testing conference is that they are available for anyone licensed to order testing. You do not have to be a Physician. Their website says the following: “Please note that to receive the FREE Organic Acids Test practitioners must be qualified as MD, DO, NP, NMD, DC, PsyD, PA, LAc or otherwise have the authority to order laboratory testing. Other healthcare practitioners will receive a voucher for 50% off one Organic Acids Test.

The pricing will increase by $40 on 12/22/14, so please register as early as possible to allow time to receive your OAT kit, complete it, mail back and get results before the conference. Things may get a little backed up around the holidays.

For those of you new to Organic Acid Testing, you can also request a complimentary consult at Great Plains once you receive your results. They will go over them with you.

Register here  Early bird expires 12/22/14

Location details are here