Due to a change in my diet last October I decided to get my gut microbiome sequenced in April of this year to see what was going on. I thought I would share these results with you, and discuss my current thoughts about the microbiome and how my opinions have changed over the past year or so.

I think that the gut microbiome is a fascinating area that has gained a lot of traction in the last couple of years. Having studied this subject through a gut practitioner course I have learnt a fair amount about what lies beneath! However, I’m just not convinced that it is the gateway to optimal health that has recently been promoted as. And, if it turns out that it is, the real question is are we on the right track in terms of the advice we are handing out? There is certainly a lot of research being done at the moment, but we need to remember that it is in its infancy, and there is still so much that we don’t know. Many health practitioners in the spotlight have jumped onto the gut health bandwagon, with books appearing left, right and centre, with advice on how to improve your gut heath – and practically all of them say the same thing. I have written about it myself here, but I am not sure that it should be a “one size fits all” approach.

Certain bacteria in our gut are touted as relating to good health, with respect to lean-ness, general wellness and provision of particular molecules that they produce, such as butyrate, proprionate and acetate. Obesity, disease, and general malaise are associated with other types of bacteria. The problem is that we don’t really know how much of an impact the gut microbiome has on our health. What we do know is that the microbiome is constantly fluctuating and that you can change much of it within a day of changing your diet. According to the research available, the Bacteroides-dominant enterotype is prevalent in individuals whose diets are high in animal fat and protein, whereas the Prevotella-dominant enterotype prevails in individuals with high-carbohydrate diets. So we do know that certain types of bacteria are related to what you are eating, and therefore what you are eating will have an impact on the bacteria present in your gut. But do we need to aim for specific types of bacteria via a particular diet, or is eating “healthily” enough? And what does that actually mean? A healthy diet means different things to different people and is a very contentious subject, which can lead to many heated debates on social media!

As I mentioned in the opening paragraph, I had my own gut bacteria sequenced recently through uBiome, because I was very interested in what was happening in there since I “radically” changed my diet last October. I had previously had a sequencing done, although it was through the British arm of the American Gut Project, so the information is presented differently and not in as much detail, which means it is not really possible to compare the two unfortunately. However, in the graphs presented in the American Gut Project results, I seem to have been pretty average compared to other samples.

So let me give you some background. Prior to last October my diet consisted of whole foods that were rich in low carbohydrate vegetables, with lots of homemade fermented foods such as sauerkraut, kimchi, coconut milk yogurt, various meats, limited amounts of raw dairy (mainly butter, cheese and occasionally cream) and some offal. I ate very low quantities of fruit (primarily berries), no grains, no legumes and no sugar. In October 2017, after having read various books, research papers and testimonials discussing the merits of a purely carnivorous way of eating, I decided to try a “carnivore diet” out of interest. I removed all plant-derived foods and only ate meat, fish, offal, eggs and very limited raw dairy. Within 3 weeks a 20 year issue of loss of smell and taste disappeared! I have remained a strict carnivore since then and my smell and taste is still working well. It’s incredible to be experiencing the wonders of those senses again! I have many thoughts as to why this happened – but I will save those for another post!

With all this going on, I thought a look into my gut microbes would be very interesting. I waited until I had been eating this way for 6 months before submitting my sample.

It is commonly thought that those with “limited”, or “restricted” diets are likely to have a lower diversity, and potentially poorer health because of this, so I have to add at this point that I have never been healthier, am very rarely ill and have an abundance of energy. My weight is stable, with a good body composition – low fat percentage and good muscle ratio. I also do regular strength training with HIIT and cardio throughout the week.

So without further ado, here are my most recent results, which I will do my best to explain. Buckle up and get comfy because this is a bit of a journey!

I have a 95.2% wellness match – what this means is that the overlap between my sample and the average microbiome amongst the selected samples that uBiome Explorer hold is those individuals who report no ailments and have high levels of wellness.

 

 

I have 10/10 of bacteria associated with healthy weight. This score is calculated based on the proportion of bacteria in my sample linked to maintaining a healthy weight, compared with their selected samples. The higher your score, the higher your levels of bacteria linked to weight loss and leaner body types. Note that in relation to what constitutes a “healthy microbiome” (in current thinking) my levels are low. However, my weight is extremely healthy and I maintain a leaner athletic frame.

Below are the bacteria linked to healthy weight and leaner body types. I have also included the recommendations that the website gives to increase your levels of the particular bacteria. (I have put these in italics to denote the fact that these are not MY recommendations).

Anaerostipes – They produce the molecule butyrate, which may help regulate appetite and weight:

To increase these it is generally recommended to consume inulin, which is a soluble plant fibre available in prebiotic supplements and powders. You can also get inulin from foods such as globe artichokes, asparagus, bananas, bitter gourd, chicory root, endive, jerusalem artichokes, lettuce, onions, peaches, peas, pomegranates, root vegetables, watermelon, shallots, whole grain wheat, whole grain rye, and soft-necked garlic. You can also take prebiotic supplements that contain long-chain arabinoxylans (LC-AX). Arabinoxylans (AX) are also found in foods containing rye, wheat, barley, oats, rice, and sorghum. You might consider eating whole-grain breakfast cereals (recommended intake: 1 ¾ cups per day) for at least 3 weeks.

NOTE: I eat NONE of these – and haven’t done for 10 months, but still have the bacteria present, albeit at a low level.

 Akkermansia Muciniphila – They produce the molecule propionate, which may help regulate your appetite and weight.

To increase your levels of Akkermansia muciniphila, you can:

• Try adopting a diet low in fat and animal products, and rich in fruits and vegetables. (Mine is high is animal fat and products)
• Include fish oil in your diet. (I eat salmon regularly)
• Consume more dietary polyphenols. These can be found in berries, tea, coffee, and wine. They are also available in supplement form.
• Get regular exercise. Doing even low amounts of physical activity on a regular basis can increase the abundance of these microbes. (I do plenty of exercise throughout the week)

Bifidobacterium

To increase your levels ofBifidobacterium, you can:

• Try including apples and kiwifruit in your diet

Research suggests that the pectin in these fruits may help increase levels of Bifidobacterium. The recommended healthy intake of fruit is 2 cups per day.

• Consume more dietary fiber for at least 4 weeks (I consume NO dietary fibre)

Good sources of fiber include beans, brown rice, nuts, vegetables, and whole grains. You might try eating whole-grain breakfast cereals for a few weeks (recommended intake: 1 ¾ cups per day).

• Consume inulin (recommended intake: 12-20 g/day) for at least 4 weeks

You can obtain inulin (a soluble plant fiber) from prebiotic products, such as powders and supplements. You can also get inulin from many foods, including globe artichokes, asparagus, bananas, chicory root, endive, jerusalem artichokes, lettuce, onions, peaches, peas, pomegranates, root vegetables, watermelon, shallots, whole grain wheat, whole grain rye, and soft-necked garlic.

• Consume wheat bran extract (recommended intake: 10 g/day) for at least 3 weeks.
• Take a prebiotic supplement combining equal amounts of inulin and oligofructose for at least 3 weeks (recommended intake: 6-16 g/day).
• Consume arabinoxylan oligosaccharides (AXOS) for at least 3 weeks (recommended intake: 4.8 g/day). AXOS can be found in many foods containing whole grain wheat.
• Consume prebiotic supplements containing xylo-oligosaccharides (XOS) for at least 3 weeks (recommended intake: about 1-3 g/day).
• Consume prebiotic supplements containing galacto-oligosaccharides (GOS) for at least 3 to 5 weeks (recommended intake: up to 15 g/day).
• Consume a prebiotic powder made from agave for at least 3 weeks (recommended intake: 5 g/day).
• Get regular exercise. Doing even low amounts of physical activity on a regular basis can increase the abundance of these microbes. (I get plenty of exercise every week)

 NOTE: I take NO supplements at all

Coprococcus – Some species of Coprococcus also produce the molecules butyrate and propionate, which may help regulate your appetite and weight.

To increase your levels of Coprococcus, you can:

• Take a prebiotic supplement combining equal amounts of inulin and oligofructose for at least 3 weeks (recommended intake: 6-16 g/day).

Eubacterium – Some species of Eubacterium produce the molecules butyrate and propionate, which may help regulate your appetite and weight.

To increase your levels of Eubacterium, you can:

• Take prebiotic supplements that contain long-chain arabinoxylans (LC-AX). Arabinoxylans (AX) are also found in foods containing rye, wheat, barley, oats, rice, and sorghum. You might consider eating whole-grain breakfast cereals (recommended intake: 1 ¾ cups per day) for at least 3 weeks.

Roseburia – They also produce the molecules butyrate and propionate, which may help regulate your appetite and weight.

To increase your levels of Roseburia you can::

• Consume more foods containing chitin-glucan fiber, such as mushrooms and fungi-derived foods. Chitin-glucan fiber is also available as a supplement (recommended intake: 2-5 g/day, for at least 4 weeks).
• Take prebiotic supplements that contain long-chain arabinoxylans (LC-AX). Arabinoxylans (AX) are also found in foods containing rye, wheat, barley, oats, rice, and sorghum. You might consider eating whole-grain breakfast cereals (recommended intake: 1 ¾ cups per day) for at least 3 weeks.
• Get regular exercise. Performing even low amounts of physical activity on a regular basis can increase the abundance of these microbes. (I get plenty of exercise every week)

 Ruminococcus – Some species of Ruminococcus produce the molecule propionate, which may help regulate your appetite and weight.

To increase your levels of Ruminococcus, you can:

• Consume more dietary fiber. Good sources of fiber include beans, whole grains, brown rice, nuts, and vegetables. You can also eat more foods made with rice bran.

As you will note – these bacteria associated with health and wellness all produced the short chain fatty acids, butyrate, proprionate (and presumably acetate, although they do not specify this one) – ie; healthy fats that our body needs to thrive.

I appear to have all of these, albeit it in low quantities, without consuming the products that are recommended. However, if you are eating animal products then you are automatically eating these same short chain fatty acids (SFAs) that are required for health, you are just cutting out the “middle man” ie; the gut bacteria, because your own body is able to digest it. With a plant and fibre heavy diet these particular gut bacteria are present because your body cannot digest it and the bacteria do the work for you in order to produce the necessary fatty acids. So my diet is providing all the necessary SFAs via the food that I consume. I am also presumably maintaining a low level of the “necessary” bacteria through regular exercise.

 

My Diversity:

8.53/10

87^th percentile

 

“Diets high in fibre have been shown to correlate to increased diversity”. This may be true if you are eating a “standard diet” which is low in saturated fats, SFAs etc. Your body NEEDS the fibre to produce the acids essential for health – therefore you will have more diverse microbiome because of the AMOUNT and VARIETY of plants you are eating. There will be a wider range of bacteria necessary to ferment the different foods. But does this type of diversity actually mean better health? It appears that it is possible to still have diversity without eating these foods and having a narrower range of foods in the diet, but the foods that I eat are very nutrient dense and require different bacteria to help process it.

In my opinion, it highlights the fact that certain diets require certain bacteria. Therefore if the well-studied Hadza tribe, in Tanzania, have the type of bacteria that is currently being promoted as the “healthiest”, it is because their diet is full of fibre and plant foods. However, I would suggest that a more holistic viewpoint of their lives MUST be taken into consideration: they are in contact with the soil which would also provide a more diverse selection of microbes, they move around a lot during their day, which means that exercise is contributing to their gut bacteria diversity, they are living in their natural circadian rhythms. Their whole environment is very different to that of Westerners. So just attempting to apply the same type of diet to achieve “perfect gut health” is very short sighted, and probably way off track, because the TYPE of plant and fibre the Hadza eat is very different to what we in the developed world eat. They have very starchy, almost unpalatable tubers, of which it is necessary to eat a lot to obtain enough nutrients from. They are not eating a whole load of flax and chia seeds on their muesli every morning. They have to eat MORE fibre because it takes more from the foods available to produce the same amount of SFA’s because of the high indigestibility. I have written more about fibre here.

Unique Bacteria

This is very elusive bacteria are those found in fewer than 5% of all samples.

I have 10 of these rare bacteria: Note: These are all the Genus, not the individual species (of which there can be many in a genus). I have done my best to research these bacteria and have identified what are probably the most likely species within the genus for some of the more elusive, but that is purely guesswork at this point.

Vagococcus Genus 0.5%

Vagococcus is a genus of gram-positive bacteria. They are motile or non-motile cocci which do not form spores. Vagococcus species can be motile, which is an unusual property for a lactic acid bacteria.

Vagococcus carniphilus species. nov. – this is isolated from ground beef. Perhaps this is related to the amount of beef that I eat?

Carnobacterium Genus 0.7%

Carnobacterium are gram-positive rod-shaped lactic acid bacteria. Although they are lactic acid producing bacteria, they grow in a PH range of 7-9. Most of the species produce lactic acid through the fermentation of carbohydrates such as glucose. However the presence of Carnobacterium can be found in seawater as well as dairy, fish, & meat products.

Allobaculum Genus 0.7%

Allobaculum is a Gram-positive, non-spore-forming bacterial, strictly anaerobic and non-motile genus from the family of Erysipelotrichidae, with one known species -Allobaculum stercoricanis. Interestingly I found a study that showed that Allobaculum was the dominant genus in helping to create an impenetrable gut mucus lining, keeping the bacteria separate from the epithelium. This is very important as it reduces the possibility of the immune system being compromised.

I wonder whether this has been helpful in the healing of my intestinal permeability, and therefore in the restoration of my smell and taste. Certainly the foods I am now eating have had a major impact on the restoration of my smell and taste, and perhaps this is actually more to to with the fact that my leaky gut has now resolved.

Quotes below from the study.

“The dominant genus within this class contributing to this difference was the genus Allobaculum, which was also found in higher relative abundances at all locations and significantly so in the lumen samples”

 “The Erysipelotrichi class and the genus Allobaculum was found in higher relative abundances in ileum and distal colon, as well as in caecum when the mice were fed Food B in Room 1”

 “Mice from Room 1 secreted mucus that was impenetrable to the beads, whereas the mucus on explants from mice housed in Room 2 was more penetrable”

 “A good separation of bacteria and epithelium by a stratified inner mucus layer was only present in mice from Room 1”

Aerosphaera Genus 1.0%

Of the Firmicutes phylum – very rare – can be a pathogen, but this is context dependent upon the health of the individual, the overall health of microbiome and environment.

Rahnella Genus 1.3%

Rahnella sp. (strain Y9602) is a Proteobacteria – a facultatively anaerobic, nitrogen-fixing, Gram-negative bacterium usually found in fresh water and human intestinal microflora. It is non-pathogenic. It has a multitude of roles including:

Gluconeogenesis (making of new glucose from protein)

Metabolism of fatty acids & amino acids (from protein)

B vitamins metabolism

Folate metabolism

Nitrogen metabolism

It has many more roles but the above are very relevant to my diet.

Hafnia Genus 1.5%

Hafnia is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria in the family Enterobacteriaceae.

Hafnia alvei (species) is a psychrotrophic bacterium, it originates in raw milk & is present as a dominant species during the ripening of raw milk cheese. [Hafnia produces a protein called Caseinolytic Protease B (ClpB) which has been shown to be a mimetic of the hormone α-MSH which is implicated in satiety.

Some Enterobacteriacae bacteria, such as Hafnia alvei have been shown to naturally regulate the appetite.

TargEDys, a French based company, has developed a technology, ProbioSatys™ which uses Hafnia alvei to stimulate satiety via the ClpB protein and help to naturally control appetite and lose weight. ProbioSatys™ showed promising results in in-vivo models including: reduced food intake, reduced body weight, improved body composition, increased lipolysis and activation of central satiety pathways.

TargEDys has developed a probiotic dietary supplement based on this technology, EnteroSatys™ that contains Hafnia alvei.

Caldicoprobacter Genus 3.1%

Caldicoprobacter is a genus of bacteria from the family of Caldicoprobacteraceae.

It is from the Firmicutes phylum and is from the order Clostridia. These are a very important group of gut bacteria; some performing very beneficial functions. They are major butyrate producers but also produce secondary bile acids from bile acids – which are essential in the breakdown of fats. This is particularly interesting as someone who eats a high fat diet.

Anaerovorax Genus 3.2%

The strictly anaerobic, Gram-positive, non-spore-forming bacterium strain NorPut1T ferments putrescine to acetate, butyrate, molecular hydrogen and ammonia. Putrescine is defined as a volatile diamine that results from the breakdown of fatty acids in the putrefying tissue of dead bodies. This relates to the ingestion of animal flesh that is then broken down into its amino acids. Primary aliphatic amines are formed during oxygen-limited decomposition of organic matter rich in protein. These are strictly anaerobic, non-spore-forming bacteria of fermentative metabolism, often metabolizing amino acids. This bacteria is a relatively new discovery “A new genus, Anaerovorax, is proposed comprising a new species, Anaerovorax odorimutans, as the type species” (study year 2000). These bacteria would seemingly then be related to making sure that protein, and specifically the by-product putrescine, is fermented and therefore non toxic.

Acinetobacter Genus 3.5%

These are important soil organisms, where they contribute to the mineralization of, for example, aromatic compounds. In healthy individuals, Acinetobacter colonies on the skin correlate with low incidence of allergies; Acinetobacter is thought to be allergy-protective. The genus Acinetobacter comprises 38 validly named species, some of which are pathogenic. Acinetobacter species are widely distributed in nature, and commonly occur in soil and water. They appear to be involved in the fermentation of lactose. Perhaps this relates to my limited intake of raw dairy?

Olsenella Genus 4.2%

“From the family Actinobacteria. Actinobacteria are chemoorganotrophic and play an important role in the biodegradation and recycling of organic matter. Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium).”

Not much could be found about olsenella – there are many different species but nothing in the literature specifically. Considering I don’t have any Bifidobacterium in my sample, it is strange that I should have olsenella as it relates in the gut, as opposed to oral. It is possible that it is through soil inhabitants and therefore in Streptomyces. Interestingly, Streptomyces is the largest antibiotic-producing genus, producing antibacterial, antifungal, and antiparasitic drugs, and also a wide range of other bioactive compounds, such as immunosuppressants. Some are also involved in the inhibition of protein kinases. Because protein kinases have profound effects on a cell, their activity is highly regulated. Kinases are turned on or off by phosphorylation (sometimes by the kinase itself – cis-phosphorylation/autophosphorylation), by binding of activator proteins or inhibitor proteins, or small molecules, or by controlling their location in the cell relative to their substrates.

 With regards to these unique bacteria – sometimes these bacteria exist in such small numbers that they are difficult to detect. Others may be more common in some parts of the world, but rare in other environments. Seldom seen bacteria are less likely to have been studied in depth, but the rarity of these specimens does not indicate they are beneficial or harmful.

 

HOW I COMPARE:

Probiotics:

Bifidobacterium compared to Selected Samples:

I have 0 – This is not surprising as Bifidobacteria are necessary for carbohydrate metabolism, and I eat zero carbohydrates.

Lactobacillus compared to Selected Samples:

I have 0.38

 

MY BUTYRATE MICROBES

Percentage: 23%

The abundance of your butyrate-producing bacteria is 23% of the abundance in 100 selected samples.

Your sample has a lower abundance of butyrate-producing microbes than our group of selected samples. Butyrate-producing microbes include Anaerostipes, Faecalibacterium prausnitzii, Eubacterium, and Roseburia.

“Butyrate is a type of helpful fat called a short chain fatty acid (SCFA). SCFAs are important to your gut health and immune system. Butyrate, in particular, plays a key role in reducing inflammation. It may also help protect against colon cancer.

Bacteria in your gut produce butyrate by breaking down certain types of non-digestible carbohydrates, primarily fibers. If your abundance of butyrate-producing microbes is low, eating certain fiber-rich foods, or taking supplements, can help increase levels of these gut microbes.”

 NOTE: Butyrate is found in abundance in butter, cheese and ghee.

MY PROPIONATE MICROBES

Percentage: 54%

The abundance of your propionate-producing bacteria is 54% of the abundance in 100 selected samples. Your sample has a lower abundance of propionate-producing microbes than our group of selected samples. Propionate-producing microbes include Akkermansia muciniphila, Eubacterium, Roseburia, and Ruminococcus.

 Propionate is another type of short chain fatty acid (SCFA). Like butyrate, propionate plays an important role in reducing inflammation. Bacteria in your gut produce propionate by breaking down certain types of non-digestible carbohydrates, primarily fibers. If your abundance of propionate-producing microbes is low, eating certain fiber-rich foods, or taking supplements, can help increase levels of these gut microbes.

 MY POLYAMINE MICROBES

Percentage: 49%

The abundance of your polyamine-producing bacteria is 49% of the abundance in selected samples.

Your sample has a lower abundance of polyamine-producing microbes than our group of selected samples. Polyamine-producing microbes include Bifidobacterium.

 Polyamines play many roles in the growth, survival, and renewal of your cells. They can also help reduce inflammation. Bacteria in your gut are an important source for these anti-inflammatory molecules.

Akkermansia muciniphila

LOW

WHAT METABOLIC FUNCTIONS DOES THIS BACTERIA PERFORM?

Propionate Metabolism

RECOMMENDATIONS TO INCREASE THIS BACTERIA IN YOUR GUT:

Food – Consume more dietary polyphenols. These can be found in berries, tea, coffee, and wine. They are also available in supplement form.

Other – Get regular exercise. Performing even low amounts of physical activity on a regular basis can increase the abundance of these microbes.

Anaerostipes

LOW

WHAT METABOLIC FUNCTIONS DOES THIS BACTERIA PERFORM?

Butyrate Metabolism

RECOMMENDATIONS TO INCREASE THIS BACTERIA IN YOUR GUT

Supplement – Consume inulin (recommended intake: 12 g/day) for at least 4 weeks. You can obtain inulin (a soluble plant fiber) from prebiotic products, such as powders and supplements. You can also get inulin from many foods, including globe artichokes, asparagus, bananas, bitter gourd, chicory root, endive, jerusalem artichokes, lettuce, onions, peaches, peas, pomegranates, root vegetables, watermelon, shallots, whole grain wheat, whole grain rye, and soft-necked garlic.

Take prebiotic supplements that contain long-chain arabinoxylans (LC-AX). Arabinoxylans (AX) are also found in foods containing rye, wheat, barley, oats, rice, and sorghum. You might consider eating whole-grain breakfast cereals (recommended intake: 1 ¾ cups per day) for at least 3 weeks.

 Faecalibacterium prausnitzii

LOW

WHAT METABOLIC FUNCTIONS DOES THIS BACTERIA PERFORM?

Polyamine Metabolism

RECOMMENDATIONS TO INCREASE THIS BACTERIA IN YOUR GUT

Other – Get regular exercise. Performing even low amounts of physical activity on a regular basis can increase the abundance of these microbes.

Roseburia

LOW

WHAT METABOLIC FUNCTIONS DOES THIS BACTERIA PERFORM?

Butyrate Metabolism

Propionate Metabolism

RECOMMENDATIONS TO INCREASE THIS BACTERIA IN YOUR GUT

Food – Consume more foods containing chitin-glucan fiber, such as mushrooms and other fungi-derived foods. Chitin-glucan fiber is also available as a supplement (recommended intake: 2-5 g/day, for at least 4 weeks).

Supplement – Take prebiotic supplements that contain long-chain arabinoxylans (LC-AX). Arabinoxylans (AX) are also found in foods containing rye, wheat, barley, oats, rice, and sorghum. You might consider eating whole-grain breakfast cereals (recommended intake: 1 ¾ cups per day) for at least 3 weeks.

Other – Get regular exercise. Performing even low amounts of physical activity on a regular basis can increase the abundance of these microbes.

Eubacterium rectale

LOW

WHAT METABOLIC FUNCTIONS DOES THIS BACTERIA PERFORM?

Butyrate Metabolism

Propionate Metabolism

RECOMMENDATIONS TO INCREASE THIS BACTERIA IN YOUR GUT

Supplement – Take prebiotic supplements that contain long-chain arabinoxylans (LC-AX). Arabinoxylans (AX) are also found in foods containing rye, wheat, barley, oats, rice, and sorghum. You might consider eating whole-grain breakfast cereals (recommended intake: 1 ¾ cups per day) for at least 3 weeks.

 GLUTEN-DIGESTING GUT MICROBES

Percentage: 0%

Your sample has a lower abundance of gluten-digesting gut microbes than our group of selected samples.

Our guts are home to a variety of bacteria that can help break down gluten, including Enterococcus faecalis, Lactobacillus rhamnosus, Bacillus licheniformis, Bacillus subtilis, and Paenibacillus jamilae.

If your abundance of these bacteria is low, eating certain foods or taking supplements can help increase their levels.

This is not surprising at all since I have not consumed gluten for approximately 5 years.

 

Phew! I hope you managed to stay with me through that! Let’s finish by taking an overview of the gut microbiome and where I would like to see future studies headed…

The definition of an enterotype is “a classification of living organisms based on its bacteriological ecosystem in the gut microbiome. The discovery of three human enterotypes was announced in the April 2011 issue of Nature by Peer Bork and his associates. They found that enterotypes are not dictated by age, gender, body weight, or national divisions. There are indications that long-term diet influences enterotype. Type 1 is characterized by high levels of Bacteroides, type 2 has few Bacteroides but Prevotella are common, and type 3 has high levels of Ruminococcus.” – Wikipedia (my highlighted text)

“A recent study compared European children, who eat a typical Western diet high in animal protein and fat, to children in Burkina Faso, who eat high-carbohydrate diets low in animal protein. The European microbiome was dominated by taxa typical of the Bacteroides enterotype, whereas the African microbiome was dominated by the Prevotella enterotype. There are, of course, many differences between Europe and Burkina Faso that might influence the gut microbiome, but dietary differences provide an attractive potential explanation. Having confirmed enterotype partitioning and established the association with dietary patterns, it will be important to determine whether individuals with the Bacteroides enterotype have a higher incidence of diseases associated with a Western diet, and whether long-term dietary interventions can stably switch individuals to the Prevotella enterotype. If an enterotype is ultimately shown to be causally related to disease, then long-term dietary interventions may allow modulation of an individual’s enterotype to improve health”.

What does the above really mean? African children in Burkina Faso were unlikely to be eating or drinking any of the highly processed foods that the European children were eating. It is not necessarily the protein and fat per se, but the TYPE of fat particularly and the other incidentals eaten WITH the protein and fat eg; is it a roast meat dinner with vegetables or is it a burger with fries and a coke? Likewise, the carbohydrates eaten by the African children were likely very different from those eaten by European children – eg more tuberous and less processed. Also, the environment is completely different. The African children would have been exposed to soil microbes, would not be continuously “washing hands” after touching dirt, animals etc, thus their microbiomes would be exposed to many more bacteria, and their immune systems possibly better because of it. Just because the prevalence of a certain enterotype is indicated within this community, I do not believe that it is the ULTIMATE one to strive for. Prevotella is a necessary bacteria for fermenting carbohydrates, but does that make it a particularly desirable bacteria overall, and one we should be advocating for everybody? There is very little in the literature as yet, and studies on other cultures, such as the Masaai and Inuit, and others eating a primarily carnivorous, zero carbohydrate diet have not yet been done, and yet these are extremely healthy, lean, and disease free populations, who are likely to have a completely different enterotype (eg Bacteroides) from both the Africans in Burkina Faso and the Hadza, whose diets are predominantly carbohydrate based.

In a recent presentation at Low Carb Down Under, Dr Paul Mason discussed low carb diets, the myth of fibre and the microbiome. Interestingly, he stated that, despite the fact that we are constantly told that we need fibre in order to enable our gut bacteria to produce Short Chain Fatty Acids (SFAs) we actually get MORE SFAs via gut bacteria fermentation in animal-based products. Dr Mason is an excellent speaker, and makes the subject very accessible for everyone to understand. I highly recommend watching it.

To sum up I would be very interested to see more samples from people with different types of diets, including carnivorous. I think it would be very helpful to explore the gut microbiome of traditional cultures such as the Masaai and Inuit Eskimos (those still eating their traditional zero carb diet) and others. My elusive bacteria, for example, may not be that elusive compared with people in cultures where animal products are the main foods consumed. It would be interesting to find out. By investing in these studies we could then start to make real comparisons, and develop more of an idea of what is going on in the gut microbiomes from really different types of diet, and examine the health of those consuming them.

Only then can we start to make more informed decisions about what really influences optimal health – and whether, in fact, the gut microbiome has as much of an effect as is purported.

Have YOU had your gut microbiome explored? Please feel free to share your results and let’s get the conversation going!