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All Disease Begins in the Gut – Hippocrates Had it Right!



TSL Trust Your Gut
(Image from here)

Healing is a matter of time, but it is sometimes also a matter of opportunity. (Hippocrates)

There is just no delicate way to write this post. And, to be honest, I considered not writing it. But, I’ve been on this health caper for some time now. I’m pretty committed. I’m studying integrative nutrition. And, I’m reading all about health in my spare time, too. You could say that I’m my own wee health experiment. So, it’s no surprise that the direction of This Sydney Life is changing with me.

I should also mention that I have this rather crippling aversion to over sharing on the interweb. I am so not selfie-girl. It’s why you don’t see any pics of me posted on my blog. But as I get further along in my studies, I realise that if I’m really serious about this course of action that I’m taking, I’ll have to put myself out there a little more. Something along the lines of more risk, more reward. Maybe.

So, while I’m not quite ready to be posting candid shots of myself all over the place, today’s post is all about gut bacteria and my disastrous results from the Bioscreen Faecal Microbial Analysis I recently undertook. As you can imagine, it may have been easier to have just posted a picture of myself in my undies…

Let’s start with a bit of back story… I started the autoimmune protocol back in February of this year. At the time, I had been suffering from a pretty revolting skin disorder for over twenty years. Skin problems run in my family. I had discovered my skin problems became significantly improved when I removed all gluten from my diet and determined that they were autoimmune in nature. I had been putting on weight, which was proving very resistant to lose, despite having adopted a Primal/Weston A. Price style of diet for over a year. I had just been given the all clear from a particularly nasty parasite infection. And, my very good functional medical doctor, coupled with my equally great Naturopath, had been working with me to identify the root cause(s) of my problems. It turns out I also have Pyrrole Disorder and am positive for MTHFR. Oh yes – and this year I threw in some periodontal surgery for good measure.

So, since February, I have been on a cocktail of supplements for my Pyrrole and MTHFR, stuff for my teeth and gums, not to mention a few other goodies to improve my general well-being. With the exception of the one slip up (which I wrote about here), I have been dedicated to the autoimmune protocol. That means a pretty restrictive elimination diet, working on managing stress, getting enough sleep, and ensuring I get outside in the sunshine as often as possible for Vitamin D (Bella loves that!).

And, on the whole, it has been a really positive experience. I feel better. My skin has never looked so good (people comment on it). I just look healthier.

But, its a chubby healthy. I’m not losing weight. And, given my lifestyle, there should be less of me.

My blood test results don’t send of major alarm bells – just a couple of minor blips – so my GP suggested the fairly pricey Bioscreen Faecal Microbial Analysis.

The purpose of this exercise was to understand the state of my gut health. The Bioscreen test is a specialist assessment that cultures and counts the bacteria that should normally be in a healthy gut.

What if it’s not just our genetic history or our lifestyle, that makes us skinny or fat. Or, healthy or unwell? What if it’s also the makeup of the bacterial ecosystem that inhabits our gut?

It makes sense. Did you know that the human gut contains 10 times more bacteria than all the human cells in the entire body, with over 400 known diverse bacterial species. It has even been said that we’re more bacterial than we are human.

According to the very knowledgable Chris Kresser, “We’ve only recently begun to understand the extent of the gut flora’s role in human health and disease. Among other things, the gut flora promotes normal gastrointestinal function, provides protection from infection, regulates metabolism and comprises more than 75% of our immune system. Dysregulated gut flora has been linked to diseases ranging from autism and depression to autoimmune conditions like Hashimoto’s and inflammatory bowel disease.”

Weightloss Orangatang
Could the state of our gut health impact our weight?
(Image from here)

And, apparently the evidence just keeps mounting that the microbes in our digestive systems are a factor in the global obesity epidemic.

Chris goes on to say that “There is growing evidence that increased intestinal permeability plays a pathogenic role in various autoimmune diseases including celiac disease and type 1 diabetes. Therefore, we hypothesise that besides genetic and environmental factors, loss of intestinal barrier function is necessary to develop autoimmunity”. This is important. Autoimmune diseases are now listed at number 3 in the leading causes of death in the western world. The reason we don’t all read about it more (yet) in mainstream media is that autoimmunity can affect so many different parts of the body. It’s not isolated to one part of the body – like the heart or the brain.

All disease begins in the gut (Hippocrates)

So, understanding all this, I went off and followed the slightly icky instructions from Bioscreen before submitting my sample for analysis. And, given my autoimmune-driven skin issues, I expected to learn that I had some form of gut dysbiosis. I just didn’t expect it to be quite so extreme. It turns out that I have an over abundance of the bad types of bacteria and not nearly enough of the good ones. When I asked my GP to rate how serious my gut issues were on a scale of 1 to 10, she felt my gut problems sit at about an 8 or 9. Pretty bad, really. In her opinion, if I hadn’t been religiously following the autoimmune protocol over the past few months, it is quite likely that I would be a very sick girl.

Not Happy Jan!
(Image by TSL)

But why is my gut so unhealthy?

Well, it turns out that antibiotics are particularly harmful to the gut flora. Recent studies have shown that antibiotic use can cause a massive and very rapid loss of diversity and a shift in the composition of your gut flora. This diversity is not recovered after antibiotic use without some form of intervention. And, if you were given courses of antibiotics in your early childhood and teenage years, as you were developing, your gut is likely to be more compromised. It just so happens that I had a particularly serious case of scarlet fever when I was quite young, and then I was prescribed the fateful Roaccutane for my very bad teenage cystic acne.

So that means it’s back to the drawing board for me. Super strict autoimmune protocol. For three months. And better than that – no sugar. And, in case you don’t know – that means no fruit, dates, maple syrup, or honey, too. None. Zip. The fun police are camping out at my place.

TSL Bone Broth
Gut Healing Bone Broth
(Image by TSL)

And, in addition to that, I’ve got a special four week protocol to follow. It involves consuming large quantities of bone broth and taking all sorts of goodies to kill off the bad bacteria, before I can start rebuilding my gut with good bacteria. Oh goody!

If we could give every individual the right amount of nourishment and exercise, not too little and not too much, we would have found the safest way to health. (Hippocrates)

I’ve been doing my research. Apparently, if you have gut dysbiosis, things you should be doing are:

  • Removing all food toxins from your diet. Check – that’s the autoimmune protocol.
  • Eating plenty of fermentable fibers (starches like sweet potato, yam, yucca, etc.) I can do that.
  • Eating fermented foods like kefir, yogurt, sauerkraut, kim chi, etc., and/or take a high-quality, multi-species probiotic. I already make my own fermented vegetables and I have a high-quality, multi-species probiotic prescribed as part of the protocol.
  • Treating any intestinal pathogens (such as parasites) that may be present. Done!
  • Taking steps to manage your stress. This is an ongoing part of the autoimmune protocol. A big part. I need to refocus on this one.

What all of this means is that my reintroduction phase of the autoimmune protocol has come to an abrupt stop. Hopefully, it’s temporary. I’m going to be back to AIP recipes – only with less of the treats. And, I’ll share what I’m learning about the gut micro biome while I’m at it. I’ve got a sneaky wee feeling I’m not the only one experiencing those problems… Stick with me?

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Comments (33)

Thank you so much for sharing your journey – I have also started taking more bone broth (including fish bone and tofu broth) – very delicious.

You’re brave making fish broth! I haven’t quite got the courage yet (smelly!)! 🙂

It’s great to have on hand for chowders, bouillabaise type soups and thai type soups. I was really feeling deprived after my supply ran out and am delighted now that I’ve got some again. (It’s halibut season here).

Thanks for sharing TSL and good luck with fixing your flora. I also have a pretty bad case of gut dysbiosis, trying to fix it through diet and herbal antiobiotics. It’s an uphill battle but one that’s totally worth it! Keep us posted

Awww – Cheers PI.

To be honest, I was a little shell-shocked at the result. I can’t remember the last time I’ve been out for meal. It feels like I’ve been on this AIP caper for so long – and STILL my gut is in such dire straits. It’s a bit of a mission, this seeking health gig. So good to have peeps like you out there with whom to compare notes.

I’m sticking with you! Thank you for this update & for resisting your “crippling aversion to over sharing on the interweb”. I’ll be thinking of you as you go deeper with the AIP & your healing process. Matthew just took the same test (I believe) & I suspect he might be joining you on a super-strict regime from this side of the planet…

Petra – at least I spared you a pic of me in my undies. You may well have fled for the hills…

The biggest issue for me will be the sugar – and I wasn’t eating that much of it. At the beginning of the consult, I actually mentioned to the GP that I thought I had an issue with sugar (resulting in flares). Her response was that, given my test results, she was not at all surprised. She reckons every time I eat something sweet, there’s a party in my gut…

Oh no! So sorry to hear that. I hope that is the very root of your problem and by going through all this, you’ll be able to finally heal. It is no fun to go without sugar, though, but you can do it! At least it’s not December. 🙂

Thanks SoA. Its a bit of a bugger, isn’t it? – NO sugar! Ah well – hopefully there’s a new me at the other end…

what have you done to treat intestinal pathogens?
thanks so much!

I had a very resistant batch of Blasto’ parasites diagnosed in August/September 2013. Tried treating them with herbs, which takes
a g e s – didn’t work. Finally had an antibiotic infusion via colonoscopy in early February. Its a very successful procedure that was pioneered here in Australia.

Hi TSL, My sympathies about the periodontal surgery…I’m a periodontist :). I have said for years that I truly believe some perio diseases are autoimmune in nature and that there is a connection between gut health and oral health!!! In my experience, when your gut health is improved, you will likely see a direct correlation in improvement in your ability to fight periodontal disease. I am walking the dysbiosis walk with you! Have been on strict AIP for 2 months, symptoms improving and was hoping to reintroduce some things soon. After reading your post I think I’m going to wait another 2 months for good measure. I will be looking forward to hearing about your healing! Blessings to you!

Hi Erin – it was so lovely to receive your message. Cheers!

When I had my periodontal surgery, I said to Luke (my periodontist) that I was sure he was a perfectly nice man, but we were never going to be best friends. He said he got that a lot!

I am convinced that my poor gut health is directly contributing to my gum issues. How can it not be if I have bad bacteria populating my system? Here’s hoping all this ‘introspection’ and work will help…

The funny thing with AIP – well, at least for me – is that you improve so much that you get scared to try reintroduction. And, you definitely learn patience. This healing caper won’t be hurried.

Best of luck to you. I’ll keep you posted from this end! 🙂

The body is fascinating, love being part of your journey, Kxx

Bless your cotton socks, K


Really interesting post-As a crohns sufferer, I knew gut bacteria played a role in our health but no idea how big: would love (perhaps the wrong word) to try this test myself

Hey J – It’s a very interesting field. The more I learn, the more fascinated I become (and my brain is not wired towards science). I have long suspected that my health issues were centred on my gut – here’s hoping that there is some improvement. Will keep you posted.

Hey, I just found this blog and am at a similar place. Been on AIP for awhile. About to go sugar-free AIP and deal with this dysbiosis once and for all. Are there particular products that worked for you? Have you updated us after the 3-months? I had 3 months of anti-biotics to treat Lyme disease last year. The treatment created a whole ‘nother set of problems for me. Thanks for any help.

Hi Sarah – Happy to talk further. I feel my ‘gut healing regime’ has made a big difference.

I’m in NZ and not online as often as usual this week. Back on home turf next Tuesday. Let’s touch base then – perhaps we can organise a Skype/Facetime session? Cheers

I would LOVE that! Thanks for your generosity. Feel free to email me to set up at time: Take care!

Hi THS, it was great to find this article and people as open as you have been make it easier for us following in your footsteps some months later.

Hi Alison

Thanks for your thoughtful message. I love receiving comments like yours!

I’m guessing you are referring to HS when you talk about your horrible, embarrassing and painful disease. And if so, I know exactly how it feels. HS is my autoimmune issue, too. Stage II for over 20 years. It’s interesting that you left your lovely message this morning – I’ve just posted a wee update today on the blog. I’d love to hear your thoughts.


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