Recent studies link the microbiome to mood and behaviour via the gut-brain axis. Earlier this year I (or rather my poo) participated in a unique pilot study aiming to better understand the gut and its relationship with the brain. The study was designed to help those living with Autism and / or Irritable Bowel Syndrome (IBS) or other chronic gut concerns.
The test was a collaboration between smartGUT and The Australian Centre for Genomic Analysis (TACGA). Half of the study (300 participants) were on the Autism spectrum with IBS. The second half were a control population (300 participants) with gut issues without Autism. My gut-health history qualified me to participate.
I admit to being possibly a little obsessed with delving into the unknown inside my gut. It wasn’t that long ago that I participated in another gut analysis – I wrote about that test here. This test grew and counted gut bacteria in a petri dish. Transit and environmental factors mean that method cannot be 100% accurate.
The sequencing method of smartGUT is very different however. It sequences the DNA of the thousands of bacterial species present in the stool sample. The results are like a fingerprint of your gut bacteria at that moment in time. The analysis tells you the percentages of the various types of bacteria in your gut.
One third of our gut microbes are common to most people, while two thirds are uniquely specific to each of us. The number and amount of microbes will vary greatly from person to person.
Two tests – different results
Given the different methods of analysis employed by each test, I’m not surprised the results didn’t align. For example, the first test indicated I had low bacteroides while the smartGUT test showed I have high numbers. Did I change my diet enough to improve this count over 2 years? I’ll never be sure.
The follow up consultation
A comprehensive report charting your results, in comparison with the general population will be emailed to you. A follow up consultation (phone, Skype or in person) with an authorised practitioner is then necessary to discuss:
- How to read the graphs in the report
- Which pathogenic bacteria are present or out of balance
- How low or high levels of bacteria may be affecting your overall heath
- Dietary and life style changes that may need to be implemented
- Tailored supplementation advice (prebiotics, probiotics, anti-bacterial herbs or nutrients).
A brief overview of my smartGUT results
It was apparent to my practitioner that I have been eating fermented foods because my results showed levels of bacteria that were not representative of someone with a history of inflammatory bowel disease. Generally speaking, the latest test showed that my gut bacteria are in a surprisingly good state. Not optimal by any stretch, but not bad either. The results did however come with a few surprises – I’ll share those further in the post.
Dietary results and recommendations
The following results and dietary recommendations are specific to me, but they raise interesting questions about what percentage of species determines ‘good’ health in all of us.
The bacteria identified are recorded according to ‘phylum’ (Large groups of organisms) and then sub-categorised into families ‘spp.’(species)
A ‘healthy’ ratio
Bacteroidetes & Firmicutes are the two most common groups of organisms, representing more than 90% of the bacteria in the human colon. They assist in breaking down food and producing valuable nutrients and energy that the body needs. Together, they are good indicators of fitness and the relative proportion of these is critical for determining health and your risk for illness.
My results showed 48.2% Bacteroidetes and 42.5% Firmicutes which is a good ratio to have and is in line with my body weight. The reversed ratio is an alarm bell, as “higher levels of Firmicutes can actually turn on genes that increase the risk for obesity, diabetes and cardiovascular disease”. Dr David Perlmutter. ‘Brain maker’.
Bacteroides spp. 40.71% – (too high – should be only 5-18%)
Bacteroides assist with the immune system, help resist pathogens (disease causing organisms) and assist fermentation and digestion of food. An over population may indicate reduced microbial diversity, inflammation, weight gain or insulin resistance.
Foods that are known to assist to reduce these are: green tea, high fibre whole foods, and prebiotics.
One particular strain, Bacteroides Vulgatus, is pathogenic and inflammatory in the bowel and also common in autistic children. Antibiotic botanical herbs were recommended for this strain.
Provotella spp. 4.15% – (to high – should be 1-4%)
This family of bacteria are commonly found in cattle and other ruminant animals but are also found in people with fibre-rich plant, based diets (vegetarians and non-westerners). Provotella can co-exist harmlessly but their presence can also be linked to bowel disease, type 2 diabetes and poor bacterial diversity in the gut.
One strain, ‘Provotella Ruminicola’ is pathogenic in humans and is known for creating periodontal disease. I will never know how long I have had ruminicola but it wouldn’t surprise me if I have carried it all my life. When I was 10 years old I had eight decayed molars removed. From then on, despite good oral hygiene, I’ve had a lifelong battle with cavities and gum infections. A course of antibiotics was recommended.
Clostridium spp. 0.52% – (low levels indicated – should be 2 – 5%)
Some of this family of bacteria are pathogenic. Both high and low levels can contribute to bowel disease. High levels of some species are also reported in children with Autism.
Faecalibacterium Prausnitzii 15% – ( ideal amount)
This should be the most abundant bacteria (5-15%) in healthy adults. It’s reported to have anti-inflammatory effects on the gastrointestinal tract but, if too low, can be associated with obesity and diabetes. It requires a diet rich in prebiotic fibre.
Roseburia spp. 2.14% – (medium levels – advised to increase above 3%)
Abundance is associated with good bacterial diversity. Lower levels are found in people with IBS, particularly with constipation, IBD and early onset rheumatoid arthritis.
Mushrooms, fungi, oats, green banana flour, chicory root, Jerusalem artichokes, onion, garlic and asparagus are all known to increase Roseburia.
Ruminococcus spp. 0.39% – (low levels – should be 1.3-3%)
These bacteria help digest resistant starches; the complex carbohydrates found in high fibre foods such as lentils, beans, and unprocessed whole grains. Eating more of these foods will increase the numbers. It is more likely to be problematic if you have too much of this family of bacteria than having too little.
Veillonella spp. 0.03% – (too low – should be between 0 – 0.2%)
Both too little and too many cause IBS. Good to increase this because it has anti-inflammatory effects. Eating more fermented foods can help increase Veillonella.
Lactobacillus spp. 0.79% – (medium level but good to increase to above 0.1%)
Higher levels are associated with a healthy gastrointestinal tract and biodiversity. Lactobacillus produces Gaba – a natural antidepressant, which has a calming effect that reduces excitability in the nervous system (a perfect antidote for my anxiety).
After Bacteroides and Firmicutes, Proteobacteria are the most common gut microbes in Westerners. This family of bacteria include a lot of pathogens and an imbalanced gut often arises from an increase in these communities. I have nearly 6% which is considered high. A healthy range is considered 2.0 – 4.6%. Higher proteobacteria is common in people with Irritable Bowel Disease (IBD), IBS and Autism.
This family of bacteria are so important to a healthy microbiome that they are fortunately available as probiotic supplements. A healthy microbiome should have up to 3%. Mine are 1%.
Bifidobacterium spp. 0.88% – (high but should be even higher up to 5%)
This family of bacteria can turn on anti-inflammatory genes, enhance digestion and absorption, help vitamin production and prevent harmful bacteria from overpopulating. Lower levels are reported in IBS and IBD, while supressed levels are found in people with Autism and Type 2 diabetes.
Daily consumption of plant-based, high fibre foods, plus resistant starch and prebiotics can help populate Bifidobacterium species.
Bifidobacterium Longum 0% – (absent but should be up to .005%)
These bacteria are associated with improved biodiversity and can inhibit the growth of harmful bacteria. They are known to treat constipation, reduce inflammation associated with IBD, prevent high cholesterol and reduce certain allergies” A multi-strain probiotic was recommended.
Verrucmicrobia Mucinphila Phylum
Akkermansia Mucinphila 0.454% – (medium levels – should be 1 – 5%)
These bacteria live in the lining of the gut wall and help to make sure the gut doesn’t become permeable (leaky). Increased levels also help to control weight and obesity and have an anti-inflammatory role preventing inflammatory bowel disease.
To increase Akkermansia it is important to consume omega-3 fats, gelatin rich foods, such as bone broth and gummies. Levels can also be improved by eating certain prebiotic foods such as mushrooms, chicory, garlic, jicama, leeks, onions, bananas, asparagus, plus increased polyphenol-rich foods such as: pomegranate, grape seed extract and cranberries. Source.
Many of the low-level bacteria reported need high fibre, prebiotic foods to ensure they expand. These foods are mostly high FODMAPS which I had, until only very recently stopped eating completely. Fortunately, I am steadily repairing my gut and gaining increased tolerance. These results prove to me that removing FODMAPS is not a long-term solution for a healthy microbiome.
General dietary recommendations
- Lots of gut healing gelatin and broths.
- Consume resistant starch foods such as banana flour, yakon and baked (then cooled) potatoes
- More fucose rich foods – medicinal mushrooms such as reishi and shitake and seaweeds
- More inulin rich foods – asparagus, chicory and Jerusalem artichokes
- Eat foods high in galactose – dried figs, watermelon juice, persimmon, papaya
- More calcium rich foods – such as bone broth, soft nibbled bones, tinned fish including bones
- Increase consumption of fermented foods, sauerkraut, kimchi, yoghurt
- Eat foods high in oligosaccharides – onion, leek, parsnips, broccoli
- Moderate consumption of apples and pears
- Reduce high oxalate foods slowly, such as beets, dark leafy greens, rhubarb, strawberries, nuts, chocolate, tea and beans
- Cut out all dairy products
- Include broccoli sprout supplements
- Diet rich in Omega 3 fatty acids or fish oil
- Take a multi-strain probiotic
- Use a multi-strain probiotic as a starter culture for homemade coconut yoghurt
The test and the advice is not a quick fix
The follow-up consultation recommendations are around lifelong healthy diet changes and supplementation to help improve your quality of life.
Most of the information in this post is based on notes I took during my follow-up consultation. I augmented this information with some internet research but found little health information on many of the bacteria discussed. Microbiome sequencing is shaping the future of health-care so this will soon change.
Microbiome sequencing is currently still expensive. Let’s hope that changes too! Despite being a pilot study, participation in the study was only slightly subsidised. The test is $395 plus the follow-up consultation fee. See the smartDNA website for more details.
The smartGUT report was the exact guidance I needed. I have a lot of new foods to experiment with and reintroduce. I’m looking forward to a lot of fun food experiments happening in my kitchen!