Human Microbiome

Important Points:

  • Microbiome
  • Bacteria
  • Storage

Human Microbiome

We traditionally think of bacteria as dirty, something we want to keep outside of our bodies.  Intestinal bacteria are very important for digestion; they break complex fiber polysaccharides (sugar molecules connected to each other) into simple absorbable sugars by a process called fermentation, converting nutrients into calories.  The large intestine alone houses over 1400 species of bacteria numbering over 100 trillion.  In reality, the human body contains ten times more microbial cells than human cells, and the human body is dependent upon the genetic information encoded in these bacterial cells for specific metabolic pathways.

Our microbial partners have co-evolved with us, in a beneficial (symbiotic) relationship involving nutrient sharing.   The ability to store energy would be a beneficial attribute for ancient humans as they had variable access to food.  When nutrient dense food supply was available, their consumption and storage would benefit both them and their bacterial symbiotes later when food supplies were diminished. However, in modern, developed societies where there is ready access to large-portion, high-calorie diets, this “benefit” becomes a detriment, and we develop a previously rare condition called over-nutrition, over-storage, or obesity.

Obese individuals have a different mix of bacteria in their guts than thin people. The ratio of Firmicutes to Bacteroidetes (called the F/B ratio) is higher in obese people than in lean people, and it drops as those people lose weight. Both Firmicutes and Bacteroidetes bacteria are involved in complex polysaccharide breakdown, but Firmicutes are much more efficient than Bacteroidetes bacteria; therefore, having more Firmicutes bacteria in our gut makes more energy available leading to increased caloric intake and eventually obesity.  Firmicutes overload is also associated with slowed intestinal motility, commonly known as chronic constipation.

In studies of genetically identical twins, bacterial populations have been found to differ, depending on whether the twin is lean or obese, with much higher level of Firmicutes in the obese twins.  In obese patients undergoing gastric bypass surgery, colonic bacteria change to become more like those of normal-weight individuals after the operation, reducing their Firmicutes levels.

Antibiotic over utilization may also indiscriminately eradicate the beneficial bacteria in your gut along with the bad ones.  Conventional farmed meats are doped with antibiotics, with nearly 50-70% of all antibiotics produced in the United States used on healthy livestock to promote growth and weight gain in the animal feed.  Consuming these antibiotic-laden meats may be a significant factor enhancing growth and weight in the human population [obesity] as well.  Eating grass-fed and organically raised meats of all kinds can reduce this antibiotic intake.

The amazing thing to keep in mind is that you can rapidly – within 72 hours – change your gut bacteria to a healthy ratio simply by immediately eliminating refined carbohydrates and increasing your fiber intake.  Supplements of “get thin bacteria” will soon be available as well.


What can you eat to improve your gut flora and reduce inflammation?

Important Points:

  • Gastro Intestinal tract (GI)
  • Inflammation
  • Gut flora
  • Gut bacteria
  • Microbiome
  • Balance

What can you eat to improve your gut flora and reduce inflammation?

Your gut microbiome is made up of trillions of bacteria and other microorganisms — both friendly and unfriendly. Maintaining the right balance of bacteria in your gut is believed to improve digestion, reduce inflammation, decrease anxiety, and even improve brain function and mood. A healthy balance of gut bacteria is also said to boost metabolism, eliminate cravings, and help you shed unwanted weight. We will look at ways in which you can achieve this by the food you eat.

  • What functions happen in the gut?

Digestion: Carbohydrates the body is otherwise unable to process are fermented in the large intestine,where our friendly bacteria reside. Through this process they reduce gut inflammation, stimulate and improve metabolic function, and produce essential nutrients such as vitamin K.

Brain Health: Our gut prompts the production of several neurotransmitters, including serotonin; remarkably, 95% of serotonin is actually produced in our gut! Serotonin affects every part of your body and is viewed as a natural mood stabilizer regulating anxiety, happiness and mood. It is said that the way to a man’s heart is through the stomach. Is this why?

 Immunity: Approximately 70% of our immune system is situated in the gut. The beneficial flora our immune system is able to differentiate between friend and adversary and rebalance the immune system when it gets off-kilter.

  • How can we improve our gut health?

Proactive ways to improve our gut health:

  • Proper digestion: When we eat, we need to make sure that proper digestion takes place. The key to proper digestion is making sure we absorb all our food. How can we optimize our absorption? We can start by turning off the T.V., putting aside all our work, and sitting down at the table, so that all our energy can be focused on eating and digestion. Food is meant to be enjoyed, so chew and taste it!
  • Re-establish gut bacteria: Probiotics and fermented food, such as sauerkraut, kimchi and miso are the key to reestablishing the good bacteria in your gut. Eating plenty of whole plant foods, packed with fiber is another critical part of nourishing a healthy microbiota. Warning! Gluten-free foods and even a lot of salads can actually be low in fiber. To support the growth of good bacteria, probiotics aim to consume certain prebiotics, such as: almonds, bananas, garlic and onion, which will help to feed those friendly bacteria in your gut.
  • Take an anti-Inflammatory diet: Aim for fresh food or one-ingredient foods such as fruits, vegetables, legumes, lean meat or dairy and minimize processed foods. Omega 3 is a beneficial anti-inflammatory nutrient, so try incorporating salmon, walnuts, chia seeds or flax seeds into your diet. To spice up soups, stews, or stir fries, add turmeric as it is another amazing anti-inflammatory food.
  • What should you eat to boost your Gut Health?

Foods that boost your microbiome:

  • Eat more prebiotics

Scientists have identified a few species among the many trillions of microbes that live in your intestines playing a crucial role in gut health and maintaining a balanced immune system. Your dietary intake is vital to allowing these species to flourish and to preventing imbalances that can lead to disease. Prebiotics provide a good food source for certain populations of healthy gut bacteria, such as bifidobacteria, which, in turn, prevent intestinal inflammation. Studies have shown that prebiotics can be particularly beneficial for obese people, as they reduce insulin and cholesterol levels, while lowering the risk of heart disease and diabetes. Prebiotics can be bought as supplements or taken in naturally by eating asparagus, leeks, bananas, garlic and Jerusalem artichoke.

  • Focus on fiber and wholegrains

Western diets tend to be rich in fat and sugar with most of our food coming from only Twelve plant and five animal species. However, following a diet rich in high-fiber foods such as apples, artichokes, blueberries, chickpeas, lentils, peas and beans can limit the growth of harmful bacteria and stimulate Bifidobacterium, lactobacilli and another healthy species called Bacteroidetes.

  • Take fermented products

Fermented foods such as kimchi, kefir, kombucha, natural yoghurts and fermented soya bean milk have been shown to promote the abundance of healthy gut bacteria and reduce the levels of enterobacteriaceae, a family of bacteria linked to a number of chronic diseases. Natural yoghurt enriched with bifidobacteria has also been found to alleviate lactose intolerance in children and adults, while yoghurts enhanced with lactobacilli have had some beneficial results in patients with inflammatory bowel disease. Avoid flavored yoghurts, which tend to contain high levels of sugar.

  • Ensure you take some polyphenols

Polyphenols are plant compounds that are mainly digested by gut bacteria and are associated with a variety of benefits including a reduction in blood pressure, cholesterol and oxidative stress. They are found in almonds, blueberries and broccoli as well as in green tea, cocoa and red wine. The types of polyphenols found in cocoa are linked to changes in the microbiome that reduce inflammation and triglyceride levels.

  • Avoid artificial sweeteners at all costs

Artificial sweeteners such as aspartame are commonly used in food as replacements for sugar. Aspartame specifically has been found to alter gut bacteria in human and animal studies, and these changes appear to result in elevated blood sugar levels and increased susceptibility to metabolic disease.

  • Breastfeed your baby

 Our microbiome is continually developing during our first two years of life. A number of studies have shown that babies who are breastfed for six months develop a much healthier gut compared with those who are fed with formula. Children who have been breastfed are also less prone to allergies, obesity, leukemia and diabetes; this is thought to be linked to the microbiome.

  • Go vegetarian

Several studies have suggested that vegetarian diets may be good for the microbiome, with findings indicating that a largely plant-based diet decreases the levels of disease-causing bacteria such as E coli and Enterobacteriaceae. This may be particularly beneficial for obese people with type 2 diabetes or hypertension. One small study found that obese people who switched to a vegetarian diet had reduced levels of potentially harmful bacteria as well as lower levels of cholesterol and inflammation after one month.

  • How to ensure your gut flora flourishes

The gastrointestinal tract is important to human health. In recent years, scientists have discovered that the GI system has an even bigger, more complex job than previously appreciated. It has been linked to numerous aspects of health that do not necessarily involve digestion, from immunity to emotional stress to chronic illnesses, including cancer and Type 2 diabetes.

There are trillions of bacteria found in the GI tract, which not only help us process food but also help our bodies maintain homeostasis and overall well-being. Experts say the key may lie in the microbiome—the makeup of bacteria and other microorganisms in the stomach and intestines or informally, the gut.

Research on the microbiome is still in its infancy. But studies have already found that certain environments, foods, and behaviors can influence gut health for better or worse. Fermented food sources—like yogurt, kefir, sauerkraut and kimchi—that have other nutritional benefits as well, should be considered in the front lines of influencing gut flora.

Finally, there are the cutting-edge ways in which doctors are beginning to manipulate the gut microbiome directly through Fecal transplants which introduce donor stool material containing healthy bacteria into the intestinal tract of a recipient, have been used to treat IBD as well as C. difficile, a dangerous infection that causes recurrent diarrhea. Researchers are also studying how bacteria-killing viruses can target strains of E. coli associated with Crohn’s disease. It is most beneficial to stick to natural food sources as much possible because a lot is still unknown about the microbiome and the effects of altering it.


  1. Healthline (2019): The Microbiome Diet: Can It Restore Your Gut Health? Retrieved from

  • Time (2019): Here’s Everything You Need to Know About Gut Health. Retrieved from

  • Food Yourself (2018): Gut Flora and How to Improve your Gut Health. Retrieved from

  • NCBI (2013): Strict vegetarian diet improves the risk factors associated with metabolic diseases by modulating gut microbiota and reducing intestinal inflammation. Retrieved from


Optimal Gut and intestinal microbiota in the prevention of metabolic inflammation

Important Points:

  • Microbiome
  • Inflammation
  • Gut Microbiota
  • Mediterranean diet

Optimal Gut and intestinal microbiota in the prevention of metabolic inflammation

If Hippocrates the father of modern medicine is to be believed, “All disease begins in the gut”. The gastrointestinal tract with its microbiota is a complex, open, and integrated ecosystem. It is widely accepted that healthy gut microbiota is essential for optimal health, and imbalance in the gut flora could lead to one being vulnerable to a large spectrum of infectious and non-communicable diseases including diabetes and obesity. There is an urgent need to develop efficient strategies to prevent and treat metabolic disorders such as diabetes and obesity. Let’s look at the implications of gut microbiota in diabesity and review ways of achieving optimal metabolic conditions.

  • What is Gut Microbiota and Gut Microbiome?

The gut microbiota is a collective term for the microbial community in the gut, whereas the gut microbiome is defined as the full collection of genes in the gut microbiota. The intestinal microbiota is known to be associated with metabolic syndrome and related comorbidities. Associated diseases including obesity, Type 2 Diabetes, and fatty liver disease (NAFLD/NASH) all seem to be linked to altered microbial composition; however, causality has not been proven yet. This points to the potential causal and personalized role of the human gut microbiota in obesity and Type 2 Diabetes is highly prioritized.

The gut microbiome contains an immense diversity of microorganisms, varying from bacteria as well as viruses, fungi, phages, protozoa, and archaea all colonizing our adult bodies. There is a proposed view that our microbiota is a microbial (endocrine) organ living symbiotically inside our gut which has led to a new perspective suggesting multiple lineages capable of communicating with each other and shaping host immune-metabolism in several ways. Some of the capabilities of this “organ” are:

  • The degradation of otherwise indigestible components of our diet
  • harvesting of energy and nutrients
  • shaping of the host immune system
  • maintaining the integrity of the gut mucosal barrier
  • xenobiotic metabolism

In this way, gut microbiota complements our biology in ways that are mutually beneficial.

The current research data regarding the precision/personalized nutrition suggest that dietary interventions, including administration of pre-, pro-, and syn-biotics, as well as antibiotic treatment should be individually tailored to prevent chronic diseases based on the genetic background, food and beverage consumption, nutrient intake, microbiome, metabolome, and other omic profiles.

  • The gut and diet….

Diet is essential in the composition and the function of the gut microbiota. Microbiota alters rapidly when exposed to great and fast changes in diet. Short-term dietary changes such as switching between plant- and meat-based diets, or adding more than 30 grams of fiber per day to the diet, or following a diet with different fat/fiber content can change the human gut microbiota in function and composition significantly in 48 hours.

Fiber-enriched diets have been shown to improve insulin resistance in lean and in obese subjects with diabetes. However, only long-term dietary habits are effective in shaping the composition of the gut microbiota as short-term dietary interventions failed to change the major features and classification of the microbiota.

  • What is the impact of Gut Microbiome in Insulin Resistance and Type 2 Diabetes?

When there is low diversity in the gut microbiome, there is a higher prevalence of obesity, insulin resistance, non-alcoholic fatty liver disease (NAFLD), and low-grade inflammation. Furthermore, low bacterial diversity was characterized by pro-inflammatory properties, suggested by the reduction in butyrate-producing bacteria and the increase in mucin-degrading bacteria. These characteristics potentially impair the gut integrity causing low-grade inflammation through endotoxemia. This low-grade inflammation of visceral adipose tissue may provide a link between obesity and insulin resistance.

Ethnic differences between human populations may also affect microbiota composition. Karlsson et al. compared data of Type 2 Diabetes-associated metagenomes between Chinese and Swedish subjects with Type 2 Diabetes, which indicated that different intestinal bacterial species were involved in similar metabolic functions. The authors were also able to distinguish subjects with Type 2 Diabetes from healthy subjects, with a predictive power exceeding that of body mass index (BMI).

  • What is the effect of Gut Microbiota in Lipid Metabolism?

In recent decades, it has become clear that many metabolic, inflammatory, and innate immune mechanisms are also coordinated by (dietary-derived) lipids. The nutritional importance of dietary lipids is unequivocal.

Lipid accumulation in conjunction with low-grade inflammation is a pathophysiological hallmark of atherosclerosis. There is emerging evidence that the pathophysiology of atherosclerosis is related to interpersonal gut microbiome differences. Atherosclerosis seems to be related to TMAO, which is a new marker associated with increased risk of atherosclerosis and coronary artery disease.

Other key intestinal regulators of lipid and cholesterol metabolism are bile acids, which are involved in facilitating intestinal absorption and transport of diet-derived nutrients, vitamins, and lipids. Whereas bile production takes place in the liver (and is facilitated by products derived from lipid catabolism), 95% of all bile acids will be reabsorbed in the terminal ileum and subsequently re-absorbed by the liver, constituting the so-called enterohepatic circulation.

The intestinal microbiota is responsible for converting primary bile salt to secondary bile salts via bile acid de-hydroxylation. Although short courses of oral antibiotics affect intestinal microbiota composition and bile acid metabolism in humans, we found differential effects on glucose metabolism.      

  • What effect does the Gut Microbiome have on Appetite?

Obesity is defined as an imbalance between energy intake (usually food intake) and energy expenditure. The brain is a key regulator in detecting alterations in energy balance and induces behavioral and metabolic responses to correct these alterations. The hypothalamus plays an important role in regulation of both food intake as well as energy homeostasis, receiving hormonal and (vagal) neuronal information from the periphery.

Changing the gut microbiome composition with prebiotics has also been shown to affect portal vein levels of other hormones including GLP-1, which in turn affected food intake, followed by a decrease in body weight and fat mass.

  • What are the Microbial Signatures in Type 2 Diabetes and Obesity?

Dysbiosis, which is the disruption of normal microbiota, has been described to be involved in a large spectrum of diseases, including diabetes, obesity, and insulin resistance, through disturbing the energy balance. It has therefore been suggested that the modulation of microbiota, either directly (by antimicrobials, diet, prebiotics and/or probiotics, stool transplant, microbial-derived signaling molecules or metabolites) or indirectly (e.g., immunotherapy) may contribute to the therapeutic management of these pathologies.

  • What is the Influence of Diet on Gut Microbiota in Diabetes and Obesity?

Diet is one of the major lifestyle factors involved in the genesis, prevention and control of diabetes, obesity and other cardiometabolic diseases, being also strongly linked to changes in microbiota. Many reports have shown that the genetic susceptibility to obesity may have interacted with an obesogenic environment (e.g., a major shift in dietary patterns influencing the gut microbiota, a sedentary lifestyle and physical inactivity) in determining the obesity epidemic. To date, there are many popular diets including Mediterranean, gluten-free, vegan, Western, omnivore, vegetarian, AND most of these diets have been clearly linked to different microbiome profiles.

Following the industrial revolution, countries in the West underwent a nutritional transition from the traditional diet to a diet rich in heavily processed foods, fats, sugars, proteins, plus different additives, while remaining low in micronutrients and dietary fibers (also referred to as Western diet). These diets were deficient of dietary fibers, which are essential for gut health due to their role in stimulation of the growth and/or activity of certain beneficial microorganisms.

Conversely, people in traditional societies, with a fiber intake of almost 50–120 g/day harbor a much more diverse gut microbiota which indicates good health. SCFAs are found in lower amounts in individuals consuming a Western diet. Western diet was correlated with a decrease in the total bacterial load and in beneficial commensals. On the other hand, subjects consuming vegan and vegetarian diets which are rich in fermentable plant-based foods were reported to have a microbiota characterized by a lower abundance of Bacteroides sp. and Bifidobacterium sp.

The Mediterranean diet (vegetables, moderate consumption of poultry, olive oil, cereals, legumes, winenuts, fish and a low amount of red meat, dairy products, and refined sugars) provides beneficial effects through the elevated content in mono-unsaturated and poly-unsaturated fatty acids, as well as high levels of antioxidants, fibers and vegetable protein content. The gut microbiota in individuals receiving Mediterranean diet is characterized by a high colonization by Lactobacillus sp., Bifidobacterium sp., and Prevotella sp., and low levels of Clostridium sp, species which are associated with weight loss, improvement of the lipid profile, and decreased inflammation.

Dietary proteins have also been reported to be involved in shaping the microbiota. Individuals consuming a diet rich in beef had high levels of Bacteroides sp. and Clostridia and were low in Bifidobacterium adolescentis unlike individuals eating a meatless diet. Several studies have recently shown that diets including vegetarian whey/pea protein, and animal protein (meats, eggs, and cheese) are linked with microbial diversity. Consumption of animal-based protein was positively associated to a richness in bile-tolerant anaerobes, including Alistipes sp., Bilophila sp., and Bacteroides sp.

  • What is the Future Perspective on the Gut Microbiome?

Accumulating evidence suggests that gut microbiota plays a significant role in the initiation and progression of MS. The gut microbiota was proven to modulate plasma glucose, appetite, serum lipids and pro-inflammation. In addition, prebiotics or probiotics, which are widely used to manipulate the microbiota, can reduce low-grade intestinal inflammation and improve gut barrier integrity to reduce plasma glucose and serum lipid levels, induce weight loss, and decrease insulin resistance. Based on these current achievements, the gut microbiota may be a potential therapeutic target for MS, but clinical trials addressing the efficacy and efficiency of current or potential treatments on therapeutic applications in metabolic syndrome are needed.

Also, Individuals who are obese are likely to have an imbalance in gut microbiota composition. This possibility is a thrilling avenue for further research and possible novel treatment targets, however because most studies have been undertaken in animals, direct translation of the findings to human is limited.

Prebiotics or other newly identified beneficial bacterial strains are potential interventions that will be used for treatment in the near future, and it will be important to evaluate their efficacy. Similarly, interventional studies with metabolites of microbiota will be performed (including SCFA butyrate supplementation) to evaluate if this compound has similar effects on food intake, energy expenditure, and improved metabolic features in humans.

The modifiable effects of the human gut microbiota on the development of metabolic syndrome make its handling a promising therapeutic approach. Analyzing and mapping individual microbial composition on a metagenomic level provides insight into specific targets for treatment and contributes to personalized therapeutic interventions.


  • Frontiers in Nutrition: Gut Microbiota, Host Organism, and Diet Trialogue in Diabetes and Obesity. Retrieved from

  • NCBI (2018): The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes. Retrieved from

  • NCBI (2017): Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics