Meet your Microbiome Workshop March 11th 2018

“Meet your Microbiome”    was a 7 hour workshop I attended on Sunday March 11th, by   Dr Jason Hawrelak.  The event was a sellout, with naturopaths, enlightened GP’s and no doubt many parents resolutely seeking help for their children with issues such as autism. The man really knows his stuff after a few decades of being a researcher and practicing clinician. I have tried to put the info in a nutshell, but it still came out at 7 pages and many of the terms would have to be googled by the average Bear . If you are a busy person you can cut to the chase and see the recommendations (which handily are not that big to write if you use those pesky acronyms) in the  highlighted sections below. I seriously hope this helps the parents who need to help their kids and don’t have time for study.

If you have time for an in depth report, plus my allusions to soil health thrown in,  great! Read on….

Probiotic Advisor is a website  developed by Dr Jason Hawrelak of Illuminate Natural Medicine. Illuminate Natural Medicine is based in Hobart, Tasmania, Australia.

I overheard that Jason’s waiting list for new patients is something like 2 years.

Probiotic is designed for Naturopaths so they can gain guidance in which purported probiotic  products contain the most effective strains of beneficial bacteria for certain conditions, judging by the research to date. Jason is certainly a stickler for research in this area. This is HIS THING!

He has been studying gut microbes for a few decades and in his introduction regaled us with a story from his past in which he tried out a “pre-biotic” diet ( one that fosters the growth of certain beneficial bacteria) on a group of patients, being mainly female office workers. Unfortunately for them and all around, they farted…..and farted….and farted. I immediately liked him. He learnt that what sounds great in the lab doesn’t always work in real life. You can go on the website and listen to his fascinating, myth busting, evidence based presentations on pro-biotic foods and supplements.

There is what is being described now as a new organ in the human body. It weighs between 1 and  2 kgs and  contains a range of cells which all work together for a common goal. It has more than 150 times the genes contained in the rest of our body, and 10 times the number of cells. These cells are engaged in a lot more biochemical reactions per day than the liver, so it is an extremely active organ. This organ’s function can be modified by diet ( it likes a big diversity of whole unprocessed foods) , surgery and medication; it can be negatively impacted by junk food and lack of exercise ; and all aspects of the body can be effected by it’s function. It is called the human microbiome.  It can be called the gastro intestinal tract (GIT)eco-system, or gut biota as well.

There are a number of companies now offering to analyse stool samples, and for a fee ranging from $700 down to $150 for U Biome ( and they sometimes have specials half that), you can get a report on the make up of your own  gut flora based on nothing more than a cottonbud swiped across used toilet paper , posted back to the company . It is really easy to do in the case of UBiome which I used. You then log in and complete a survey , or a series of surveys if you choose to, which adds to the body of research ( so I did) . Some weeks later you receive an email and may log in to see your results. Of the thousand bacteria identified so far that live in the gut of humans , you will probably have about 160. Your gut biome  is as individual to you and is your thumb print, and you have similar communities unique to you living in your navel, ears, eyes and hands…….everywhere!

The first part of the workshop was about examining the pros and cons of the various laboratories /companies  offering this service to Australian practitioners and individuals . Some labs are still using older techniques of culturing bacteria on petri dishes. As Dr Elaine Ingham from the soil microbiology world explained , only 5 % of soil organisms will actually grow on a petri dish in isolation from their habitat and associates there, and it is the same for the human microbiome too. So Elaine prefers direct microscopy in which you make a wet slide with a drop of soil and water mix, and look at it under the microscope. This is good enough for farmers who can learn to identify the various groups of organisms visually. For the gut microbes, most of  which die in oxygen and light, the modern technique of identification is DNA analysis. Each company has a library of bacteria etc and computers can match the DNA of the various bugs to the library. Some companies have better libraries than others. What was disconcerting is the exercise where we looked at results of “samples” from real patients from various companies. They were all very different but later Jason shocked us by revealing that this was one sample sent to 4 different  labs!!  However if you understand the strengths and weaknesses of each lab you can read behind the lines and get a good understanding of what is going on.

We then went through the good, the bad and the ugly bacteria that resides in most people’s gut, and what they are up to in there. You may have heard of the recent operation which can be done at Fiona Stanley hospital and others around the country which is the faecal transplant, or which doctors call “fecal microbiota transplantations,” or FMTs, colloquially “transpoosion” or poop transplant. This is used to treat stubborn cases of things like obesity, inflammatory bowel disease and chronic diarrhea caused by Clostridium  Difficile . This method of treatment came about because of articles like this:

“ When the feces of one mouse was transplanted to another mouse, the recipient mouse either gained or lost weight. But can these transplants —…— have the same effects in humans?”  Live Science

We don’t yet have the data to answer that question but early results have been encouraging. But what is interesting is the difficulty of finding good donors. The ideal poo donor is a home birthed ( definitely not C section delivered ), breast fed, unvaccinated  person whose mother and father were not in the habit of using medicine , even the contraceptive pill. This person will eat at least 40 whole plant foods from an organic farm or garden a week,  drink pure rainwater untreated with chlorine and have never used cosmetics, factory made soap, body care or  cleaning products, deodorants, air fresheners etc. Neither would they have used the really bad- for- biomes antibiotics, Panadol, Non Steroidal Anti Inflammatory Drugs, ( NAIDs, ) or Proton Pump Inhibitors (PPIs) . Obviously they have steered clear of recreational drugs and never drunk alcohol to excess.  Plastics and heavy metals would not be in their environment, and just for good measure, they are not exposed to EMR so have no mobile phone and use the internet by ethernet cable.  A few years ago I would think this person would be boring, smelly and have oily hair, but now I know just water, vinegar and baking soda satisfactorily take the place of the normal arsenal of  personal and home “care” products, and such a person would be beaming with happiness.

Dr Jason has met just the candidate who could poo for the world. He is  from Europe and is an extremely happy, lovely  guy of 51 years of age in great health. What a pity the unscathed are so rare. In most of us from the minute of birth where we inherit our parent’ s microbiome, which can be faulty often, modern life simplifies our populations of microbes even further.

I certainly was compromised and had arrived at the workshop dejected as I had received my sample results from UBiome a few days before, and they said I was heavily tilted to firmacutes which is associated with obesity in mice. Worse, I was on the 17th percentile for diversity of microbes.  There was only one person at the workshop with less diversity than that, she got a score of 7 percent, meaning 6 % of the total world population who have sent in samples to U Biome have less diversity than her, and 93% have more. Jason asked whether this person had taken antibiotics…. and yes, she had taken a cocktail of 3 recently.

The Ubiome report said I had only 0.01% of lactobacilii, and added that I should eat grapes and berries.  In response I stuffed myself with iced vo vo biscuits. For goodness sake, Ive struggled against surgar addiction and been on a 99% sugar free for a couple of long years. We  had just been through berry season where I live on all kinds of raspberries and blackberries,  prior to the sample taken in February. I eat out of a garden year round! I should have been awesome! Still mortified by my result I publicly blurted out to Jason  “What about me? I’m on the 17th percentile, live on an organic farm growing in excess of 100 species of fruit, nut and vegetable, haven’t had an antibiotic in 30 years nor any other medication….and I went on ….I eat kimchee and sour dough spelt all the time! I demand a re-count!”

Dr Jason immediately asked about my early life – diet and antibiotic use…Yes, well that was all very S.A.D. ( stands for Standard American/Australian Diet ) and 3 times antibiotics saved my life as a young adult, plus the vaccinations, fluoride , chlorine, mercury fillings, and all the rest we are all exposed to (unless we or our parents take steps to avoid or reverse). Well I had worked to improve it  all over a long time, and had even had my mercury out via a biological dentist specializing in this procedure ( Dental on George, East Fremantle) about a year ago. At morning tea a few people kindly expressed their sympathy for my poor diversity.  I said “Thanks, but I feel good…..?

As the day moved along we went through the various bacteria phylums. After the beneficial functions of each group was explained, we divided into 9 groups and found the member of our group with the lowest percentage of that bug, and the person with the highest reading. It was then that I started to feel better. First, Dr Jason said another study had found just the opposite about firmacutes in obese mice. YAY!!  Also, we learnt that lactobacilii are only found in very low concentrations in the best of us, and do a powerful lot of good even so. Then it became apparent that some of the very beneficial bacteria we had been discussing were in enormous numbers in ME! I was the highest in the room for microbes that make butyrate. I was often the lowest in the bad bugs we covered. As the highest and the lowest in the room were all written up on the board, despair gave way to pleased curiosity….  I stacked up against a room full of Naturopaths pretty well!

For Faecalibacterium,  Dr Jason’s power point slide said these were of major importance as butyrate producers and the highest percentage he had seen was a 25. He will have to re- write that slide as mine was 37.7 !  My Rhuminococcus score did not appear so I took that as a zero but later just now found under the advanced tab an Excell spreadsheet with Rhuminococcus family on the list in a concentration of 39.6 percent.

As my score went up on the board on a few occasions Dr Jason asked our group “Who got that?” “Me again !” said I proudly. I was off the Richter scale for some really good bugs, which is why I guess I was not very diverse. But I have ZERO, NADA, Bifidobacterium, and Eubacterium and as any yogurt pot reader knows, Bifdiobacter are really important. At least there is room for improvement and I am excited by the possibility that I will get these up soon and may feel FANTASTIC. Meanwhile I am so glad to have done something right by my microbes who make butyrate because that is important to mood and the integrity and Ph of the colon, keeping it acidic.This keeps many pathogens in check as they need an alkaline habitat to breed.

Interestingly, one should stop eating fermented food of great benefit such as kimchee and yogurt for 2 weeks before doing the UBiome test, because we want to know the indigenous populations which have colonized your gut. Myth buster Jason emphasized that “you can not re- seed, re- populate or populate your gut with probiotic foods”. There is no argument there with my heroine Dr Natasha Cambell McBride, originator of the GAPS diet . She also says people with severe gut imbalance (such as the kids with autism she has been able to completely cure on many occasions) need to eat these fermented foods regularly and take a good probiotic supplement daily for life, as sometimes a person’s vital microbes have been permanently extinguished by heavy metals ( in vaccines) medication or pesticide.

In the soil we know that good bugs don’t come back magically after local extinction by fertilizers, ploughing, fire and pesticides, you need to re-populate the good critters with a spray of compost tea.   I am reminded of the saying “To err is human, to really stuff things up requires a computer”  It seems to really stuff up your health requires intervention with pharmaceuticals. Today many doctors are just following the advice of the pharmaceutical company reps. that visit regularly and drop off glossy brochures on the wonders of their company’s drugs. I gained the impression from Sunday that Naturopath’s caseload comes mainly from people who have been terribly harmed by modern medicine. Similarly, to really bugger up your soil requires Agri chemicals, the other arm of Big Pharma., and they have agronomists and Ag departments and other salespersons dispensing misinformation worldwide. This is seriously screwing with our climate, make no mistake, and we should all be buying nothing but organic produce if we want to survive the next decade as a species.

Imbalances of the bacterial communities either in or on the body is called  Dysbiosis.

It is where communities of pathogens, usually kept in check by beneficial bacteria, proliferate

and   is associated with many diseases of the GI tract :

Alcoholic fatty liver disease, antibiotic associated diarrhoea, chemo related diarrhea, Clostridium Difficile ( C Diff) associated disease , Coeliac disease, Crohn’s disease, Diverticular disease, Irritable bowel syndrome, liver cirrhosis, Non alcoholic fatty liver disease, radio-therapy associated disease, SIBO, Ulcerative Colitis.

Non GI conditions include Alzheimer’s disease, Anxiety, Asthma, Atopic eczema, Autism, Chronic fatigue syndrome, Depression, kidney stones, Metabolic Syndrome, Multiple Sclerosis, Obesity, Parkinsons, Rheumatoid arthritis, Type 1 and type 2 diabetes.

Dysbiosis is diagnosed primarily using the patient’s medical and dietary history. Anti biotics, chemotherapy, radiotherapy, proton pump inhibitor use, non steroidal anti inflammatory drugs ( NSAIDs) can all bring on dysbiosis. So can very high stress levels.  So can restrictive diets, which are low in whole, raw, plant food diversity: so the S.A.D. or Western -style diet of breakfast cereals and white bread ,biscuits,  foods fried in oil etc, or some renditions of the ketogenic, high fat/ low carb , high protein /low carb, high processed carb, low fiber, low FODMAP diets could also be the cause. Specialised stool testing as mentioned above can also diagnose dysbiosis.

By boosting populations of the good guys, life is made uncomfortable for the bad bugs. This concept is familiar to those who have done our soil courses as this is just what happens in the garden.

Antibiotics in people corresponds to Round Up and a myriad of other “icides” in farming, users of which wipe out the good with the bad, and the bad come back quicker and cause mayhem with PH, bad gases, alcohols, formaldehydes, phenols and the like. In soil these kill plant roots. In people they can form brain poisons, carcinogens, and other agents of dis- ease. One example of a toxin made by bad GI T microbes is Lippopolysaccharides (LPS), aka endotoxin. This toxin makes for leaky gut and is found in the blood of alcohol binge drinkers in high concentrations, but also in people who don’t care what they eat and fall prey to the foods of commerce. It leads to low grade systemic inflammation, altered Kynureine /tryptophan pathway, brain inflammation via CNS cytokine production, compromised blood brain barrier ….all of which can lead to depressed mood, heart failure, Alzheimer’s and more. There are concepts here some of us may need to google for sure.

Conversely those who have strong gut walls with tight junctions between cells ( and these healthy cells are created by butyrate) , who have a balanced GI ecosystem and who consume a fibre rich diet, have only miniscule amounts of LPS in their blood.

Many a case of severe depression lasting 7 years has been triggered by antibiotics. Garlic is an example of a  wonderful food and antibiotic because it targets and kills baddies but leaves alone the good guys, even promoting populations of some beneficial microbes. No wonder garlic is almost a cure all plant in ancient and modern Herbals. Another point highlighted on Sunday was that medicinal herbs are very effective, containing polyphenols which make their way to the colon to do their work. Eg.,herbs to increase bile production were prescribed to patients by Jason and he knew they were working because  a stool sample showed populations of bile- eating bacteria had gone way up.

So it seems microbiota diversity is as important in us as it is in the soil. Diversity is the spice of life, and diverse colonic microbes = a healthy ecosystem. Lack of diversity is associated with body wide inflammation and the list of diseases mentioned above. At last we come to the HOW TO FIX section:

Jason says, to improve your diversity take prebiotic supplements daily and eat at least 40 whole , raw and unprocessed plant foods a week, with emphasis on the polyphenol rich, black or dark coloured ones. Each different variety of apple or eggplant counts towards the tally. Proteins such as meat, eggs and fish although excellent do not count towards your 40 plus per week, however the curry powder you cook them in , or dandelion coffee or coffee beans you wash it down with, does. We found it very easy to reach 60 plant foods available, either fresh , or fermented or in storage on Merri Bee Organic Farmacy in any given week. We also found without changing a thing we were consuming 50 such foods a week.

I would caution that it would be good to read and follow the GAPS diet initially. Dr Natasha Cambell McBride says fibre can equally well breed bad bugs if you or your loved ones are host to large populations already and are suffering autism, schizophrenia, ODD, OCD and other results of this condition. In serious cases like these we heal and seal the gut first. You must start with a bone broth fast of 3 days duration, very soon adding small but increasing amounts of home made yogurt and sauerkraut juice to the broth. Big note here courtesy of Jason: VAALIA brand, ( by Parmalatt company) yogurt is the only yogurt available in Australia which has 3 types of fantastic bacteria in it. Use as your starter, or buy yogurt from us.

Breaking the fast you can add meat to the broth next. Then slowly introduce vegetables, watching for return of symptoms. For full details of the protocol I highly recommend Dr Natasha’a book . After 25 years in a busy clinic treating kids with autism she knows how hard it is to have your child eat anything let alone purple carrots, however she has a chapter devoted to getting around this, eating disorders and more.

Gut and Psychology Syndrome ( GAPS) . I get my latest copies from the Wordery for $28 delivered.

You Tube abounds with free talks by Natasha .

However if you have healed and sealed your leaky gut already with a bone broth fast , these are the prebiotic supplements and the daily amount recommended:

Acacia tummy fiber ….10 gms a day

Lactulose (obtainable from chemists as a syrup)   ….5 mls a day

Partially hydrolysed Guar gum  ( made from a bean grown in India) PHGG  …….5 gms a day

Galactooligosaccahride (GOS) ……………… at least 3 gm a day

Fructooligosaccharides ( FOS) ………………….at least 3 gm a day

The last 3 would be available from health food stores or I Herb or my fave  Dr  Josh Axe online

Here are some biome friendly foods

Fermented dairy such as yogurt and the even more powerful Keiffer. Fermented vegetables like sauerkraut and kimchee, well fermented kombucha. Build up from a teaspoon daily as the die off reaction, in which bad bugs are killed off by the good army and release poison, can be severe.

Foods rich in pre biotic FOS include : **Jerusalem artichoke, *Yacon, *Chicory, **Asparagus, *Burdock, dandelion, *Onions, **garlic ( * all available fresh, organically grown, from us, in limited amounts. ** means in abundance usually , but climate change is not helping)

Foods rich in GOS include lentils, legumes of all kinds, fresh beans, *beetroot, **brassicas ( that’s your kale, cabbage, radish, rocket, bok choy etc), pepita or pumpkin seed, sunflower seed, *Linseed, LSA mix, buckwheat.

Pre-Biotic like foods include green tea, dark cocoa, almonds and brown rice

Resistant starch rich foods include raw potatoe ( grate some, squeeze out  and drink the juice), and raw green bananas.

Retrograde resistant starch  cooled down cooked potatoe, baked or steamed being good as the starch hasn’t been thrown out with the cooking water.

Now to the benefits rendered to us by some ‘key player ” bacteria, how to boost them with food and thereby correct dysbiosis. And thanks to Jason, the following is all backed up by plenty of research.

Polyphenol rich foodsinclude: *Black elderberries, black currants,  *blueberries , *Cherries, *strawberries, **blackberries ( U pick) **purple plums, **apples, *black grapes, flaxseed meal, *chestnuts, hazelnuts, *pecans, black sesame/tahini, *purple carrots, red cabbage, spinach, broccoli, *red onions , *orange and red carrots, red rice, black rice, *red and black quinoa, *sourdough rye bread, *black olives and olive oil

The good guys

Probiotics or “pro  life microbes” do the following for us:

*modulate the immune system : protect against allergy development and up-regulate non specific immunity

*promote normal gut motility

*improve nutritional status: B vitamins, Vitamin K, mineral absorption ( eg calcium, magnesium, zinc)

* energy salvaging

* ”Xenobiotic metabolism: polyphenols, phytoestrogens, glycosides” … maybe half a day on google?

*Colonization ( by bad bugs) resistance”. Ie  they increase your immunity to invasion by pathogens

*Blood glucose control and insulin sensitivity

*Produce short chain fatty acids ( SCFAs)

* Weight management

*Mood management

* Good impacts on our inflammatory milieu


Examples of the star  Good Bacteria include

Bifidiobacterium spp.   Takes away stress response, do polyphenols transformation ( important for activity of many medicinal herbs and absorption of dietary polyphenols)

Ideal population    > 2.5 to 5%       To RESTORE, daily consume pre biotic supplements as above, polyphenol rich foods, pre-biotic -rich foods, pre-biotic like foods, and resistant starch foods. Cover your needs until indigenous populations return by having kimchee and Vaalia yogurt daily.



Lactobacilus Spp.

Short chain fatty acid ( scfa) production and  lactate production for inhibition of pathogens. Ideal population is 0.01 to 1% . To increase , take lactulose at higher dose such as 15 ml daily, phgg. Get into those green tea and dark organic cocoa pre-biotic and polyphenol rich food and drinks too.

Also consider “Konjac glucomannan”, and here again I call on the inimitable Dr Axe to explain about this purported weight loss herb:

Akkermansia    Good populations associated with healthier metabolic status and better outcomes from weight loss interventions. This is my kind of microbe! High fat diet decreases this bacteria BUT, HUGE BUT!!, they are INCREASED by the GOOD fats from *avocados and **grass fed organic animal products  rich in n-3 fats, the omega-3 family derived from the essential fatty acid, alpha-linolenic acid. These two fatty acids are ‘essential’ because they cannot be made in the body. Also to increase Akkermansia levels : FOS, lactulose, red fruits such as *pomegranate, *red grape seeds and skins, red apple skin, Lignonberries and red dragon fruit . Seems red things  breed up Akkermansia. Hypothetically also…slippery elm.

Faecalium Bacteria

Considered an important indicator of GIT health. The most abundant bacterium in the GIT of healthy adults, comprises 10 to 15% ( but remember I was 37.27 before the iced vo vo  episode) . The major butyrate producer. Amazing benefits of butyrate in the gut include: intestinal wall integrity as opposed to permeability , decreases visceral sensitivity and systemic inflammation. Populations negatively affected by gluten free diet ( sorry) low FODMAP diet, chemo.

To increase: GOS, FOS, lactulose, PHGG, apple pectin (stewed apple with skin on) high fiber diet with regular lentil based meals ( hippy slops), Psyllium husks, buckwheat, soaked oats as opposed to cooked oats for their resistant starch, Polyphenols, and probiotic supplementation with Bacillus coagulans and bifdobacterium longum.

Other Butyrate producers are Roseburria, Blautia, Eubacterium, Rumninococcus, intestibacter, Pseudobutyrivibrio, coprociccus, Anerostipes, Subdoligranulum spp.


Now in closing a little look at a bad guy….

E Coli is interesting because even within the same species and strain, with a few genes turned off it can go from a pathogen that causes death  to a beneficial bacteria which induces gut cells to produce more serotonin ( which fixes constipation) and also to manufacture vitamin K. It makes one shudder to think how glibly the genetic engineers are cutting and pasting genes with happy abandon as if they have a clue what they are doing !

To DECREASE pathogenic E Coli, it is thanks to God, the same ol’ high fibre whole foods diet is your answer. Plus daily consumption of pre biotic supplements, polyphenol rich foods, pre-biotic -rich foods, pre-biotic like foods, and resistant starch foods. Make sure to get kimchee and Vaalia yogurt daily.

Here’s to our collective impending super health, strength, energy  and longevity my friends. Best wishes, from Bee at Merri Bee Organic Farmacy Nannup 0897561408



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