Researchers studied the several remaining Paleolithic cultures in the world to identify an ‘ideal’ microbiome, and discovered there was nothing uniform about them. What they discovered was that hunter-gatherer microbiome’s had greater bacterial diversity compared with Westerners, and this diversity conferred a benefit to the host 1. The further we move away from a traditional life-style, the less diversity our guts maintain. A reduction in bacterial diversity is linked to chronic disease such as bowel disease, inflammation, insulin resistance and obesity 2.
Current research links our microbiome with our environment. Children develop gut diversity when exposed to dirt, sunshine, exercise, animals and local food; the Earth’s ecosystem interfaces with our gut ecosystem. Protecting our natural environment, protects our species.
Core bacterial strains belong to six Genera: Faecalibacterium, Eubacterium, Clostridium, Blautia, Ruminococcus and Roseburia. These bacteria take on most of the workload of the gut, and having healthy numbers may be key to a healthy gut. These core bacteria are able to break down fibre to form butyrate, and they also convert other fatty acids from bacteria into Butyrate, called cross feeding. Enhancing these butyrate producing bacteria enhances metabolism and is key to a healthy gut 3.
Short Chain Fatty acids
Short chain fatty acids (SCFAs) such as Butyrate, acetate and propionate are the products of carbohydrate metabolism by bacteria in the gut 4 and contribute to health in many ways;
providing energy to the host
Producing anti inflammatory compounds
Influencing fat metabolism and satiety
Improving gut transit time
Maintaining the gut Ph and microbial balance 5
This suggests we should be more interested in the output of a healthy microbiome rather than which species are present. The Human Microbiome Project concluded that the metabolic output of a healthy gut was consistent, despite variation in bacteria 6. This is partly because more than one species can perform several roles in the gut.
A Dynamic Microbiome
Our microbiome is a dynamic environment, harbouring unique compositions which are constantly changing based on internal and external influences 7. Our bacterial communities work together like a team to maintain metabolic functions, making them very adaptable. They change rapidly due to dietary influences, and return to their original state afterwards 8. Modern day loss of core diversity from overuse of antibiotics, vaccines and anaesthetics makes it difficult for the gut to return to its original state, reducing resilience as the gut struggles to maintain homeostasis (balance).
Dysbiosis or imbalance has several features; reduced bacterial diversity, expansion of pathogens, changes in microbial composition ie. changes in increase or decrease in core strains 9. Loss of homeostasis leads to a collapse in the host-microbiome relationship and a decrease in barrier protection and increase in gut permeability, immune and metabolic imbalance.
The stability of the overall microbiome far outweighs the changing microbial composition. A healthy gut can withstand many microbial changes, without effecting its overall metabolic function.
Restoring the Microbiome
It is now well known that commercial probiotic strains aren’t commensal (original bacteria) and don’t make up a large percentage of gut bacteria. They aren’t seeding (staying), merely passing through the gut transiently 10. However, if the right strain is issued they can exert beneficial effects.
Lactobacillus Rhamnosus LGG
Some strain specific probiotics are clinically proven to restore the microbiome and improve its function, rather than just adding to it. An example is Lactobacillus Rhamnosus LGG, the world’s most researched strain of probiotic. Rhamnosus LGG promotes the growth and function of five out of six of the core strains. The functional benefits of this are increased Butyrate production and altered gene expression which allows the core bacteria to increase their flagella enabling them burrow through the thick mucous layer and distribute butyrate to the colon cells 11, 12, 13, 14.
Saccaromyces cerevisia (Boulardii)
It is the metabolic effect of S. Boulardii that makes it a superhero probiotic. Research shows that the greatest destructive factor for the gut microbiome is antibiotics 15. Multiple studies show that S. Boulardii reduces antibiotic-associated loss of bacteria and rapidly restores the microbiome, particularly core bacteria 16.
S. Boulardii spares butyrate producing bacteria, during and fully restores them after antibiotic therapy, therefore its no surprise that S. Boulardii increases butyrate production in people with a compromised microbiome 17, 18.
Bifidobacterium animals lactis (BB-12)
Bifidobacterium animals spp. Lactis (BB-12) is the most researched bifidobacterium in the world. Rather than promoting the growth of beneficial bacteria, BB-12 prevents the growth of pathogens by secreting antimicrobial chemicals preventing pathogens from adhering to the gut wall and preventing antibiotic associated diarrhea. In addition to pathogen inhibition, BB-12 enhances barrier function and immune interactions. BB-12 also improves bowel function and reduces the side-effects of antibiotics. BB-12 increases the body’s resistance to common respiratory infection’s and reduces the incidence of acute respiratory tract infections 19.
These strains also improve barrier integrity, support the immune system, interact with the nervous system producing broad spectrum benefits for the host. When it comes to choosing a probiotic, look for strains that have been tested in research, specific for the condition you are treating. Its also important to choose a good quality manufacturer and to store probiotics correctly to protect their strength and potency. Probiotics are vulnerable to heat and moisture.
Guidelines for taking probiotics:
probiotics can be taken at the same time as antibiotics 20, 21
Start taking probiotics on the same day as antibiotics
Separate probiotics from antibiotics by 2 hours
Take probiotics for a minimum of 3 weeks
Take probiotics for the duration of the antibiotic and for at least 2 weeks following (a minimum of 3weeks) 22, 233, 24
Probiotics are safe in breastfeeding, pregnancy, children and the elderly and with all medications
Diet and the Microbiome
Within twenty four hours the food you eat can be changing your gut microbiome 25. Its now thought that the way food changes the microbiota is more important to health than the amount of vitamins and minerals it contains. Proteins and fibre that pass digestion in the stomach and intestines become food for the microbes in the large intestine. They then produce short chain fatty acids, or harmful metabolites depending on what food has been eaten 26. This is how diet is crucial for good health.
Prebiotics are indigestible foods, like leeks and asparagus, that ensure the gut bacteria make SCFAs and encourage the growth of beneficial bacteria 27. Examples of prebiotics are inulin, FOS (fructo-oligo saccharides) and GOS (galacto-oligo saccharides) which feed the growth of F. Prauznitzii a butyrate producing bacteria 28.
Its now recognised that a wide variety of specific foods can also increase microbial diversity, increase SCFAs and benefit health. Resistant starch is one microbiota enhancing food which feeds Ruminococcus Bromii, an important species involved in cross feeding to maintain optimal gut fuel 29. Additional prebiotic foods include dietary fibre, polyphenols such as those found in blueberries and green tea, as well as ‘microbiotia accessible carbohydrates’ (MACs). (see infographic)
Microbiota Accessible Carbohydrates
MACs are carbohydrates, often found in dietary fibre and some animal tissue, that can be metabolically used by gut bacteria. Fibre is commonly thought of as being the first dietary consideration for gut health. However, its the MACs within the fibre that shape the microbial ecosystem 30. Studies by Erica and Justin Sonnenburg looked at the microbiome of mice on MAC deficient diets, and discovered they developed significant losses of microbial diversity. When successive generations also consumed MAC deficient diets, the loss of diversity continued and wasn’t recoverable with the introduction of fibre. This landmark study highlighted the dietary induced extinction of microbes passed from parents to offspring 31. Fibre consumption is essential for maintaining microbial diversity, which may irreversibly weaken the microbiome of future generations 32.
Consuming low fibre diets, especially low in fruit and vegetables, starves bowel microbes and forces them to turn on their environment for sustenance and degrade the mucous barrier in order to maintain their function 33. Low fibre diets increase the activity of mucous degrading bacteria and its subsequent loss, leading to increased immune activation and risk of bowel infection 34, 35.
While a plant based diet is essential for supporting the microbiome, numerous animal and human studies show diets high in animal fat and sugar and low in fibre may lead to the extinction of health promoting microbes 36. As an example, extremely low carbohydrate, low fibre diets reduce butyrate producing bacteria E. Rectalel and Roseburia 37. Diets high in animal fat increase the amount of inflammatory substances in the gut 38. Diets high in milk fat feed the growth of Bilophilia Wadsworthia associated with increased risk of colitis 39.
In summary, its crucial that people on low carbohydrate, low fibre diets increase their consumption of fruit and vegetables to protect the diversity and functionality of the microbiome. The typical Western high fat, low fibre diet needs to be replaced with fibre, polyphenols and prebiotic foods as needed by each individual.
Exercise and the microbiome
Studies on physical activity and diet reveal increased microbial diversity and composition in the stool of professional athletes compared to sedentary individuals 40. Athletes also have microbiomes with increased microbial functionality. For example, as well as increased SCFAs – acetate, propionate and butyrate, increased amino acid and carbohydrate metabolism occurred. These differences were associated with increased muscle turnover, fitness and overall health when compared with control groups. These findings demonstrate the importance of exercise improving the composition and function of the microbiome.
Spending time outdoors
Studies indicate that spending time outdoors, in nature with animals and playing team sports can enhance the type of bacteria living on and within us 41. Data collected from all corners of the globe comparing microbiomes confirm that these things are associated with wider microbial diversity, increasing our understanding of the impact of Westernisation on health and the need to address lifestyle factors as well as diet in order to achieve optimal gut health 42.
Gut Bacteria metabolise environmental toxins
Five core bacterial enzymes (including beta glucuronidase) produced by gut bacteria are involved in the metabolism of over 30 environmental contaminants including pesticides, metals, (mercury, lead, cadmium and arsenic), food additives and persistent organic pollutants (POPs) providing clear evidence that gut bacteria reduce toxins in the body 43. In addition, microbiome diversity and enzyme functions are affected by chemicals, pesticides, heavy metals and POPs which have all been shown to cause dysbiosis and provide a powerful link between environmental toxicity and intestinal and systemic diseases 44.
Antibiotics
The success of antibiotics saving millions of lives has come at a cost with lasting effects on microbial composition and function. World-wide use is associated with declining microbiome diversity and bacterial resistance 45. Studies show that the microbiome is resilient to short single courses of antibiotics 46, however the reality is that patients are exposed to multiple prescriptions over time 47. Antibiotic resistant infections are the result of over exposure to antibiotics due to their persistence in the environment and ongoing as in farm animals and crops. This is associated with a population wide decrease in biodiversity and increased antibiotic resistance 48.
Curcumin, Resveratrol and EGCg enhance the microbiome
Phytonutrients Curcumin, EGCg and Resveratrol are an important part of a Nutrigenetic protocol. As well as having positive effects on genetic expression in T21, cutting edge research shows that Curcumin, Resveratrol and EGCg have beneficial effects on the microbiome. These extraordinary phytonutrients have ‘prebiotic like’ effects through selectively enhancing beneficial bacteria and reducing inflammation and gut permeability 49, 51, 52.
In animal studies, Curcumin shifted the microbiome towards a lean composition while on a high fat diet, and reduced associated inflammation. It restored microbial diversity in rats who had gut composition changes from oestrogen deficiency. In mouse models with colitis, Curcumin increased butyrate abundance and increased T regulatory cells which are changes associated with reduced inflammation and restoring the gut barrier. Turmeric suppressed overgrowth of pathogenic species Clostridia and Rumminococcus and increased Lactobacillus species in mice 49. These effects on the gut barrier improve gut diversity and composition.
Resveratrol
Studies show that oxidative stress is chronically elevated in T21 due to an imbalance in the antioxidant pathway (overexpression of SOD1) 50. In addition, the gut can produce high amounts of oxidative stress from dysbiosis which leads to chronic inflammation, increased gut permeability, barrier dysfunction and expansion of unfavourable bacteria. This overproduction of free radicals by gut bacteria can cause DNA damage to cells leading to genetic instability 51. Chronic inflammation in the gut reduces the gut immune systems ability to maintain balance and this results in autoimmunity.
The polyphenol Resveratrol is a potent antioxidant, antibacterial, anti-obesity, anti inflammatory and anticancer agent in vitro and in vivo. It is a strong scavenger of reactive oxidative species (ROS). Polyphenols are considered to be the main antioxidants in the colon as others such as Vitamin E and C are absorbed in the small intestine 51.
Studies show that Resveratrol changes the microbiome decreasing pathogenic bacteria in vivo. The number of Bacteroides, Lactobacillus, Bifidobacterium and Akkermansia were significantly increased in Resveratrol fed animals while pathogenic Enterococcus and Escherichia Coli species decreased. Both Escherichia Coli and Enterococcus are associated with increased oxidative stress while Lactobacilli are associated with increased antioxidant capacity. Therefore Resveratrol alleviates oxidative stress and intestinal damage via its effect on gut microbes 51.
EGCg (Green tea)
Flavanols such as EGCg aren’t absorbed in the small intestine but are metabolised by bacteria in the colon. Populations of Bifidobacterium are increased in people consuming EGCg. Recently, EGCg has been found to inhibit the binding of Hepatitis C and Influenza virus to the cell surface. Enterovirus 71, Human Hepatitis B virus, Adenovirus, Epstein barr Virus and Herpes Simplex are also inhibited by EGCg 52.
EGCg exerts antibacterial activity against Staphylococcus, neutralising its toxins and inhibiting biofilm formation. EGCG inhibits Streptococcus Pyogenes, Bacillus spp. Clostridium Salmonella and Haemorrhagic E. coli. EGCg also has anti fungal activity against Candida albicans 53.
When mice were fed a high fat diet DNA damage was observed due to high levels of inflammation and reduced bacterial diversity, however EGCg supplementation reduced DNA damage reversing these effects and maintaining bacterial diversity 54.
The obesity related microbiome is characterised by less microbial diversity and altered metabolism. This is characterised by an increase in Firmicutes and reduced Bacteroidetes. Intervention with EGCg resulted in a decrease in Clostridia spp., increased Bacteroidetes increasing Bifidobacteria and Prevotella and better regulating energy metabolism in the body 54.
In summary, there are many key points to keep in mind when working towards optimising gut health. Diet, sunshine, dirt, exercise, polyphenols, fibre, animals and seasonal food go a log way to keeping your body healthy and disease free.
Healthy Diet Guidelines – Adult
Healthy Diet Guidelines – Child
Healthy Diet Guidelines – Baby
