“You have to put your poop in a test tube and post it back…” My mum’s face was priceless as I tried to explain to her the logistics of her Christmas present.
I thought I would treat my mum and I to a microbiome test so we could send our poop away in the post and have the genomes of our intestinal bacteria sequenced.
It was quite expensive at €136 per unit but I justified it as I am undergoing a microbiological awakening. As well as that, the opportunity to learn more about our microbiomes in order to optimize our health was very appealing.
What is the microbiome?
The microbiome is a buzzword which is being thrown around a lot in scientific tabloids and self-health subscription email subjects lately. This field of studying mutualistic bacterial relationships inhabiting our gut is a brand new and exciting area of research that has only been explored for about 10 years. Data from Google trends shows the slow gradual incline in interest in this term which didn’t really kick off until 2011.
The microbiome encompasses the thousands of species of harmonious bacteria in your large intestine which benefit from living there and we benefit from their abundance.
These trillions of bacteria live in symbiosis with us. Emerging data from microbiome research is uncovering just how important these microbes are for our health.
Not only do they:
- support immune system functions
- contribute to vitamin and butyrate synthesis
- protect against inflammation
- protect against cardiac disease
- protect against obesity, type 2 diabetes, inflammatory bowel disease, celiac disease and cancer
they also have a huge impact on our mental health.
We can consider our brains as the “captain” of the body or the seat of physiological control. The brain sends and receives electric and chemical messages from the CNS (central nervous system). Your enteric nervous system (ENS) is a series of nerves embedded in your gastrointestinal tract. 90% of your serotonin (5-HT) production and 50% of your dopamine is produced in your gut by your ENS. The ENS or gastrointestinal region is often considered as our “second brain”.
With the gut being our primary source of serotonin production, a neurotransmitter famous for regulating mood, sleep and appetite, it’s not surprising that ENS or gut health is crucial for our general happiness and well being. Extraordinarily, if we peel back another layer of granularity and examine the microflora composition and activity inside our intestines, these nanometer sized beings are also influencing our mood directly and indirectly.
In the landmark paper – Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks – they generated microbiome knock-out mice and observed the neuronal and immune dysbiosis that occurred as a result.
- Mice without a microbiome or “germ-free” (GF) mice had almost no serotonergic neurons in their ENS.
- GF mice which were colonized with microbiota from healthy mice gradually restored their serotonin neuronal network.
- Serotonin released from enteric neurons is known to stimulate and maintain the proliferation of dopamine enteric neurons.
- They showed how microbiota is responsible for the development and maintenance of a healthy enteric neuronal network.
- They showed how microbiota communicate with serotonergic enteric neurons through activation of the 5-HT4 receptor.
- The expression of the 5-HT4 receptor is dependent on the presence of microbiota.
We’ve all heard the sayings “trust your gut” and having a “gut instinct” but how about “happiness stems from your gut”.
Understanding how the metabolites produced by the bacteria in our gut influence our behaviour and health is at the cutting edge of biology. A few points directly listed from the paper titled Microbiome, metabolites and host immunity are:
- The gut encompasses thousands of small metabolites, collectively termed the metabolome.
- The metabolome comprises our diet, our native cells and our microbiome.
- Multiple gut metabolites are bioactive and signal to our immune system.
- Alterations in our gut’s metabolites are associated with defective innate and adaptive immune responses.
A quick glance at this diagram reveals the dense web that is the relationship between microbiome metabolites and our immune system. Butyrate is an important anti-inflammatory SCFA (short chain fatty acid), which generated as a byproduct of bacterial metobolism alongside dietary tryptophan upregulate the class of immunomodulatory molecules interleukins, indirectly inhibit or stimulate NFkB and mobilize other immune cells for action.
The point is our intestine is a complex ecosystem of bacterial and host cell interactions. Bacteria are the oldest phyla on earth meaning they were the first living organisms. These billion year old biochemical beings are highly optimized at safeguarding our internal homeostasis. Our intestines are their home. Our native probiotic bacteria attack and neutralize invasive, malignant bacteria.
It comes in a box like this which contains the test tube, leaflets with instructions and paper you place over your toilet for collecting your poop. The test tube has a serial number which you need to register online. The box you receive is the same box you seal and send back in the post.
Scooping a minuscule serving of my own poop with a spatula, scraping it into a test tube and shaking the tube so my shit forms a uniform brown liquid with the stabilizing solution is not my proudest moment. I’m still in fact trying to convince my mum do do the test as she says “it’s not very dignified to send your shit away in the post”. She’s not wrong.
Beyond my hobbyist, hypochondriac biohacking interests, there is definitely real value in taking these measures as the insights generated could lead you on a path to improving your diet, restoring your microbiome’s health and drastically improving your well-being.
Something that concerned me was the sheer amount of time it took for the sample to arrive back in the lab. So much so that I emailed Atlas Biomed asking if they had received my sample as I was worried it had been lost in the post. It took over 1 month from the sample being posted for it to arrive in their lab.
They replied with a reassuring email that the testing kit is designed to retain your sample’s stability for up to 8 weeks. What concerned me was that first my sample had to go to the Netherlands for registration and then be forwarded on to UK for testing. To me this is a bottleneck in their process and I would appreciate my sample being tested ASAP to preserve the snapshot of my microbiota composition at the time of testing. Why is it so slow?
I did some research into the stabilizing fluid used in tests like this and found a paper by Nature titled Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study.
Here they outline a few points regarding the nature of stabilizing solutions in production:
- Microbiome testing labs can either remove the sequences of bacteria which are known to proliferate at room temperature or
- fecal samples can be collected in stabilizing solutions, such as:
- 95% ethanol
- RNAlater or
- They found that the microbiome profiles were stably maintained in OMNIgene-GUT solution for 21 days
- The abundance relationships among metabolites were well preserved, although their absolute abundances slightly varied over time.
So essentially the ratio of metabolites produced by the microbiome are preserved by the solution for 21 days even if their relative quantities are different from when the sample was first taken.
I’m not sure which solution Atlas Biomed use but if I had to put a bet on it I would say they are using the OMNIgene-GUT solution as in this paper it states the “kit includes stabilizing solution and a mixing ball in a tube, which allows immediate homogenization of a standard volume of fecal material and stabilizing solution at the point of collection.” This exactly describes what is provided in the test kit box.
This is great that the metabolites are conserved for 21 days but what about in the case of 28 – 40 days? The turn-around time for the test is simply too long and needs to be optimised to have my full confidence in the accuracy of the results.
I have to say the results were interesting, regardless of my questioning their accuracy. The UI of the dashboard displaying the results and the general design of the website is beautiful which definitely boosts morale.
The measures they report on are:
- Your propensity for diseases – Diabetes type II, Obesity, Crohn’s disease, Ulcerative colitis and Coronary heart disease
- The diversity of your microbiome
- Your microbiome potential to produce butyrate, B and K vitamins as well as essential fatty acids
- Your level of probiotics (beneficial bacteria)
- Your enterotype
- Your dietary fibre intake
- The nationality of your microbiome
I had no idea what an enterotype was before doing this test. The bibliography on the site is brilliant and provides a spring board to deepen your knowledge on the microbiome and dive into understanding the significance of certain species of bacteria. An excellent paper they reference is Arumugam et al’s 2011 Enterotypes of the human gut microbiome.
This research reveals that the composition of the human gut microbiome can be largely grouped into 3 clusters or enterotypes of bacterial populations which are characterized by one dominant species of bacteria that positively or negatively affect the occurrence of other existing microbiome bacteria in their inter-species dynamic. Each species is uniquely adapted for generating energy via their own routes. Interestingly, geographic distribution does not correlate to enterotype.
- Enterotype 1 – dominated by Bacteroides is commonly found in Western, protein-rich diets.
- Enterotype 2 – dominated by Prevotella are largely found in tribes people from the Amazon and Africa or a western vegetarian diet rich in plant fibre with hardly any simple sugars, meat or fat.
- Enterotype 3 – dominated by Ruminococcus, is the most common enterotype (in the Danish experimental sample anyway).
A key takeaway I found extremely interesting was that although each enterotype performs all the vitamin metabolism pathways, they differ in their focus of vitamin pathway production.
Enterotype 1 maximises the synthesis of biotin, riboflavin, pantothenate and ascorbate while enterotype 2 produces thiamine and folate in higher quantities. The paper unfortunately doesn’t mention enterotype 3 in relation to vitamin synthesis.
The dark blue splodge in the shape of the United States represents my enterotype. I’m definitely proud to fall into the enterotype 2 category as I do love my veggies and consciously try to limit my meat intake for animal welfare and environmental reasons. I did take this test directly after Christmas where meat was definitely consumed.
Additional interesting reading: Stereotypes About Enterotype: the Old and New Ideas
Probiotic species diversity
Another aspect of the results I found fruitful was the quantity of bacteria species that I have. They gave a breakdown of the quantity of bacteria I had for around 13 species of bacteria and were grouped according to their functions
- Lactic acid bacteria and bifidobacteria
- Bacteria with unique characteristics
- Prevent obesity and weight gain
- Butyrate producers
Interestingly I have a lot of the rare species Barnesiella compared to the average microbiome. According to Atlas Biomed Barnesiella is a…
Recently discovered bacteria found in healthy microbiomes. Bacteria of the Barnesiella genus are rare. Research has shown that they prevent pathogenic vancomycin-resistant enterococci from colonising the gut, which is a very important function for a person’s health. Barnesiella is a promising oncomicrobiotic because it can increase the effectiveness of immunomodulatory therapy for certain types of cancer.
I also saw that I had 0% Akkermansia species.
Most distant relative of other bacteria in the microbiome. These microbes live in the mucous membrane that lines the gut. The presence of Akkermansia is an indicator of a healthy metabolism and body weight. Elevated levels of these bacteria are observed in lean people and associated with healthy glucose metabolism. Akkermansia are typically less represented in patients with inflammation and type II diabetes. On the other hand, they are significantly more abundant in those who have suffered from prolonged starvation, because they can consume mucin produced by the gut lining in the absence of nutrients.
Commonly observed in “lean people” and those who undergo “prolonged starvation” it is not surprising this species is scant in my chonk body. From reading online it seems a sure bet to increase the health of your microbiome is to eat less and less often. Intermittent fasting and ketosis are cited to reduce inflammation. Try telling that to my carbohydrate craving brain.
A number of other interesting insights I benefited from knowing was my microbiomes ability to produce essential fatty acids. From the ones I am lacking, I can research foods which will help stimulate the production of these SCFA’s.
Atlas Biomed use 16rRNA sequencing to identify the bacteria in your stool sample and calculate each species quantity as a percentage of the total ecosystem. Using the Chao index formula, they quantify the number of bacteria in your colon according to the index value. The higher the index value the better the diversity and health of your gut.
From reading the graph, my Chao indicator is 250. Smack bang in the middle of this Gaussian distribution. I will really have to make an effort to diversify my microbiota as I am quite conservative about trying new foods and tend to stick to a few dishes that I love so I just eat and repeat.
Luckily, Atlas Biomed updates your dashboard with weekly recommendations of food types that are recommended for promoting your probiotic bacteria. I presume they are personalized recommendations as I had never tried any of the foods listed before so I am excited to try incorporate some of these recommended foods into my diet.
From an educational perspective it is an excellent product considering the nascency of the field and our limited knowledge of how our microbiome affects us. I enjoyed learning about my microbiome and dissolving my paranoia that I am an unhealthy sack of shit. I would really love for an expert to provide confirmation on the accuracy of these tests and the stability of bacterial populations jostling in a test tube for over a month. If you had a major health concern I would recommend trying to get this test through your doctor or hospital as the turn-around-time is very long if you are urgently awaiting results. The composition of your microbiome might have changed from when you took the test. This is definitely another question I would pose to an expert – how much does our microbiome composition fluctuate over time? Or how long would it take to convert your gut population into a different enterotype?
Enhancing our endogenous bacteria to overcome antibiotic resistance
In case you weren’t aware, we are losing the arms race against bacteria. Pathogenic bacteria are becoming resistant to antibiotics. Taking antibiotics in the first place kills all the bacteria in our bodies, including our microbiome environment our probiotic bacteria work so hard to create and maintain. Mass feeding animals antibiotics just to keep them alive in unnatural conditions long enough for us to eat them was never going to turn out well.
Encouraging our endogenous bacteria to flourish is the only hope we have in remaining healthy and protecting ourselves against infections. So go eat some fiber, drink some kefir and express gratitude for your bacterial partnership!