What does it mean to have a ‘healthy gut?’

Healthy gut

Can you improve the health of your gut?

The phrase ‘healthy gut’ is used a lot in the health space at the moment. But what does this actually mean? And can you improve the health of your gut? I will address these questions in the following article.

First of all, let’s define some terminology. The gut refers to the human gastrointestinal tract or GI tract. This is composed of the stomach, the small intestines and the large intestines or colon.

You may have heard the term ‘gut microbiome’ when gut health is being discussed. The human GI tract is home to 1013-1014 microorganisms or microbes (that is between 100 000 000 000 000 – 1000 000 000 000 000). In fact there are over 10 times more bacterial cells in your gut than there are your own cells making up your body. The community of microbes living in your gut is referred to as the gut microbiota. The gut microbiota is mostly made up of bacteria, but viruses and fungi are also present. The total genome content of these microbes, meaning all of the genes carried by all of these microorganisms, is referred to as the gut microbiome. Thanks to advances in the ability to sequence DNA, scientists are now starting to understand just how important this complex community of microbes is to human health and disease.

Health benefits provided by the gut microbiota

The health benefits provided by the gut microbiota include preventing disease causing bacteria, breaking down toxic compounds, shaping the immune system (1), providing nutrients, the synthesis of vitamins, particularly vitamin B and K (2) and the production of important metabolites. Metabolites are the intermediates or end products of metabolism. The metabolites produced by the microbes in the gut make up one third of all the metabolites found in the human blood and these compounds have some very important functions. Short-chain fatty acids are the main metabolic end products produced by the gut microbiota.

What are short-chain fatty acids (SCFAs)?

The main end products produced from the fermentation of undigested carbohydrates by the microbes of the colon are the short-chain fatty acids (SCFAs) acetate, propionate and butyrate (3). Fermentation is a metabolic process that converts sugars to acids, gases or alcohol that often occurs when oxygen is lacking, known as an anaerobic environment.

One of the health effects of SCFAs in the human gut is lowering the pH making a more acidic environment. This stops the growth of disease causing bacteria and increases the absorption of some nutrients (3).

Another important function of SCFAs is maintaining the gut barrier function. Don’t worry – I will explain what this means. The gut barrier is a layer of cells lining the inside of the GI tract. This layer of cells, referred to as the intestinal epithelial cells, has two jobs: controlling the absorption of nutrients, electrolytes and water from the inside of the gut into the blood stream and preventing harmful substances, such as disease causing bacteria and toxins, entering the blood stream. The mucus produced by this layer of cells also helps maintain this barrier (4). SCFAs play a role in gut barrier function by providing a fuel source for the intestinal epithelial cells thereby increasing mucus production.

The cells of our colon, known as colonocytes, also use the SCFA butyrate as an energy source (5). The SCFAs that are not used by the colonocytes travel to the liver and will be used in gluconeogenesis (a metabolic pathway that produces glucose from non-carbohydrate substances) and lipid (fat) synthesis. So SCFAs provide an energy source for the human host.

SCFAs can even act as signalling molecules in the gut where they can influence appetite by changing the production of particular hormones. A study in 2003 showed that SCFAs can activate free fatty acid receptor (FFAR) 2 and 3 (6). These receptors are found on cells in the colon that secrete the appetite suppressing hormones peptide tyrosine tyrosine (PYY) and glucagon-like peptide (GLP)-1. Studies in rabbits and rats have shown that SFCAs increase the production of PYY and GLP-1 (7, 8). A recent study using human volunteers showed that the SCFA propionate, when delivered to the colon, increased the release of PYY and GLP-1 and prevented weight gain over a 24-week period (9). While there is still a lot more research needed in this area, these results suggest that the right combination of gut bacteria producing the right amounts of SCFAs could prevent obesity.

Diseases/conditions associated with disruptions to the gut microbiota

A major change in the gut microbial community is known as dysbiosis. Dysbiosis has been linked to a number of diseases and conditions in humans including the following:

Obesity and metabolic disorder

Obesity and the associated metabolic diseases, such as type 2 diabetes, were thought to be a result of a combination of genetics and life-style factors. It now seems that the gut microbiota is also playing a role. Studies in mice have shown evidence that the gut microbiota can influence obesity. Transfer of the microbiota from obese mice to mice with no microbiota caused weight gain and insulin resistance. This did not happen when the microbiota from lean mice were transferred to mice with no microbiota (10).

Inflammatory bowel disease and Irritable bowel syndrome

Major changes in the composition and the diversity of the gut microbiota have been found in patients with inflammatory bowel diseases (11). Currently it is thought that low levels of SCFAs, particularly butyrate, are causing the inflammation that is associated with inflammatory bowel disease (12).

Problems with the composition of the gut microbiota have also been found in patients with irritable bowel syndrome (IBS). IBS is different from inflammatory bowel disease as in this disorder there is no inflammation of the lining of the intestines and the symptoms are abdominal pain, diarrhea and/or constipation. Again it is thought that low levels of butyrate are involved, as well as increases in the gas hydrogen sulfide in the gut (13).

Mood and neurological disorders

Would you believe that the microbes in your gut can change your mood and your brain function? Dysbiosis has been linked to a range of mental illnesses including autism (14), stress (15), anxiety (16) and depression (17). How is this possible? The gut microbiota are able to influence the enteric nervous system (ENS) (18). The ENS is basically the brain of the gut and controls intestinal motility and sends signals to the central nervous system (CNS). The communication that occurs between the gut microbiota, the ENS and the CNS is referred to as the microbiota-gut-brain-axis.

One way that the gut microbiota can influence the ENS is through the production of neurotransmitters. Studies in mice have shown that bacteria found in the gut can affect the metabolism of tryptophan (19), an amino acid which is required for the synthesis of the neurotransmitter serotonin. Certain bacteria from the gut of mice and humans are even able to directly make serotonin (20). Serotonin has many effects in the body, including regulating mood, perception, fear, anger and appetite, so this suggests that our gut microbiota can directly influence our behaviour in a major way!

Also, chronic stress can disrupt the intestinal barrier. This disruption is known as ‘leaky gut’. When leaky gut occurs, parts of the outer protective layer of the bacterial cell, known as the cell wall, can leak into the blood stream and cause inflammatory responses. A study from 2012 showed that the leaking of bacterial cell wall components into the blood stream may play a role in causing chronic depression in people (21).

But it is not clear whether changes in the gut microbiota can cause neurological disorders OR if neurological disorders cause changes in the gut microbiota.

What makes up a healthy gut microbiota?

The human gut contains over 1 000 different bacterial species (22). It is not yet known which combinations of microbes make up the ideal ‘healthy gut’. However, high levels of diversity are thought to be important for a healthy, well-functioning gut microbial community (23) and several diseases of the human GI tract are associated with a reduction in microbial and genetic diversity (24). A diverse gut microbiota is necessary to ensure that we extract all of the nutrients out of our diet. Humans only produce less than 20 enzymes for the digestion of complex carbohydrates. Therefore, we rely on the microbiota in the digestive tract to break down the complex carbohydrate structures found in fruits and vegetables (25).

Interestingly, major differences in the gut microbiome between Westerners and members of hunter-gatherer tribes have been observed. For example, the gut microbiota from the Hadza hunter-gatherer tribe from Tanzania is more diverse compared to urban living adults from Italy (26). The Hadza are one of the last remaining hunting-gathering communities in the world and live on a diet of wild foods including meat, honey, baobab (a fruit high in dietary fibre, vitamin C and polyphenols found in sub-Saharan Africa (27)), berries and tubers. One study has shown that a loss of diversity in the gut microbiota can result from a low fibre diet, such as a typical Western diet (28). The decrease in gut microbial diversity resulting from a typical Western diet could be a reason for the high rates of obesity and metabolic disorder in today’s population.

How can you maintain a healthy gut microbiota?

A number of factors can affect your gut microbiota including antibiotics, inflammation, ageing, GI tract motility and even the way you are born. However, it appears that diet has the greatest influence on the composition of the gut microbiota. So what can you include in your diet to promote a healthy gut microbiota?

One thing that stands out from the studies on diet and the gut microbiota is the influence of dietary fibre. Dietary fibre, particularly fibre that is classified as a prebiotic (29), appears to be important in maintaining a healthy and diverse gut microbiota (30). Prebiotics are defined as a selectively fermented ingredient that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health.

Finally, there is a method that is receiving attention at the moment that may gross you out, but is interesting. I am talking about feacal microbiota transplantation (FMT). Basically this means implanting the poop from a healthy person into the stomach, small intestine or large intestine of a sick person. FMT has been used successfully to treat infections with Clostridium difficile, which you may have heard referred to as C. diff. C. diff. is a nasty species of bacteria that causes severe diarrhea (31).

In the future, once we know more about what makes up the ideal healthy gut microbiota, ‘cocktails’ of beneficial bacteria may be a common method of treatment for a number of diseases and health conditions. But until then eating a diet rich in dietary fibre can help maintain a healthy gut.

  1. Ivanov, II, et al. (2008) Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell host & microbe 4(4):337-349.
  2. Hill MJ (1997) Intestinal flora and endogenous vitamin synthesis. European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation 6 Suppl 1:S43-45.
  3. Macfarlane GT & Macfarlane S (2012) Bacteria, colonic fermentation, and gastrointestinal health. Journal of AOAC International 95(1):50-60.
  4. Groschwitz KR & Hogan SP (2009) Intestinal barrier function: molecular regulation and disease pathogenesis. The Journal of allergy and clinical immunology 124(1):3-20; quiz 21-22.
  5. Pryde SE, Duncan SH, Hold GL, Stewart CS, & Flint HJ (2002) The microbiology of butyrate formation in the human colon. FEMS microbiology letters 217(2):133-139.
  6. Brown AJ, et al. (2003) The Orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids. The Journal of biological chemistry 278(13):11312-11319.
  7. Psichas A, et al. (2015) The short chain fatty acid propionate stimulates GLP-1 and PYY secretion via free fatty acid receptor 2 in rodents. International journal of obesity 39(3):424-429.
  8. Longo WE, et al. (1991) Short-chain fatty acid release of peptide YY in the isolated rabbit distal colon. Scandinavian journal of gastroenterology 26(4):442-448.
  9. Chambers ES, et al. (2015) Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults. Gut 64(11):1744-1754.
  10. Turnbaugh PJ, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444(7122):1027-1031.
  11. Damman CJ, Miller SI, Surawicz CM, & Zisman TL (2012) The microbiome and inflammatory bowel disease: is there a therapeutic role for fecal microbiota transplantation? The American journal of gastroenterology 107(10):1452-1459.
  12. Tedelind S, Westberg F, Kjerrulf M, & Vidal A (2007) Anti-inflammatory properties of the short-chain fatty acids acetate and propionate: a study with relevance to inflammatory bowel disease. World journal of gastroenterology 13(20):2826-2832.
  13. Matsunami M, et al. (2009) Luminal hydrogen sulfide plays a pronociceptive role in mouse colon. Gut 58(6):751-761.
  14. Kang DW, et al. (2013) Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PloS one 8(7):e68322.
  15. Bailey MT, et al. (2011) Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressor-induced immunomodulation. Brain, behavior, and immunity 25(3):397-407.
  16. Bercik P, et al. (2010) Chronic gastrointestinal inflammation induces anxiety-like behavior and alters central nervous system biochemistry in mice. Gastroenterology 139(6):2102-2112 e2101.
  17. Jiang H, et al. (2015) Altered fecal microbiota composition in patients with major depressive disorder. Brain, behavior, and immunity 48:186-194.
  18. Hyland NP & Cryan JF (2016) Microbe-host interactions: Influence of the gut microbiota on the enteric nervous system. Developmental biology.
  19. Wikoff WR, et al. (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proceedings of the National Academy of Sciences of the United States of America 106(10):3698-3703.
  20. Yano JM, et al. (2015) Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 161(2):264-276.
  21. Maes M, Kubera M, Leunis JC, & Berk M (2012) Increased IgA and IgM responses against gut commensals in chronic depression: further evidence for increased bacterial translocation or leaky gut. Journal of affective disorders 141(1):55-62.
  22. Rajilic-Stojanovic M & de Vos WM (2014) The first 1000 cultured species of the human gastrointestinal microbiota. FEMS microbiology reviews 38(5):996-1047.
  23. Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, & Relman DA (2012) The application of ecological theory toward an understanding of the human microbiome. Science 336(6086):1255-1262.
  24. Walker AW & Lawley TD (2013) Therapeutic modulation of intestinal dysbiosis. Pharmacol Res 69(1):75-86.
  25. Cantarel BL, Lombard V, & Henrissat B (2012) Complex carbohydrate utilization by the healthy human microbiome. PloS one 7(6):e28742.
  26. Schnorr SL, et al. (2014) Gut microbiome of the Hadza hunter-gatherers. Nature communications 5:3654.
  27. Coe SA, Clegg M, Armengol M, & Ryan L (2013) The polyphenol-rich baobab fruit (Adansonia digitata L.) reduces starch digestion and glycemic response in humans. Nutrition research 33(11):888-896.
  28. Sonnenburg ED, et al. (2016) Diet-induced extinctions in the gut microbiota compound over generations. Nature 529(7585):212-215.
  29. Gibson GR & Glenn R (2010) Dietary prebiotics: current status and new definition. Food Sci Technol Bull Funct Foods 7:1-19.
  30. Simpson HL & Campbell BJ (2015) Review article: dietary fibre-microbiota interactions. Alimentary pharmacology & therapeutics 42(2):158-179.
  31. Borgia G, Maraolo AE, Foggia M, Buonomo AR, & Gentile I (2015) Fecal microbiota transplantation for Clostridium difficile infection: back to the future. Expert opinion on biological therapy 15(7):1001-1014.

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Strawberry and coconut ‘ice cream’ with low carb coconut cookie dough chunks

Strawberry and coconut ice creamThis dessert is soooo good, yet healthy too. What makes this dessert healthy? Well, my friends, this ‘ice cream’ is made with only frozen strawberries, coconut milk, shredded coconut and is sweetened with the low-calorie sugar alcohol erythritol (read all about why this is my sweetener of choice in my recent post “Which sweeteners are the healthiest to use?”).

This ingredient list means that my version of ice cream contains no refined carbohydrates, contains dietary fibre and has medium-chain fatty acids, which, according to the scientific literature, are metabolized more rapidly than long-chain fatty acids.

But the best part about this dessert is the chunks of delicious low carb coconut cookie dough. Again this cookie dough contains no refined carbohydrates and is high in dietary fibre.

Dietary fibre is important as it helps to feed the beneficial bacteria in your gastrointestinal tract. A recent study conducted by the husband and wife research team from the Department of Microbiology and Immunology at Stanford University, Erica and Justin Sonnenburg, showed that a diet low in dietary fibre, or Microbiota-accessible carbohydrates (MACs), decreases the diversity of the gut microbiota in mice. Reintroducing MACs in to the diet can reverse this loss in diversity. However, after multiple generations, this loss in diversity could not be recovered by diet alone (1). So what does this mean? The Sonnenburgs speculate that generations of a highly processed, highly refined, low-fibre modern diet are contributing to the loss of diversity in the human gut microbiota and may be responsible for the increase in many preventable health problems that are common in today’s society. You can attempt to stop this by eating more whole foods, which retain their fibre component.

You will have to freeze the strawberries, coconut and cookie dough a few hours in advance, so be prepared if you want to make this dessert. I believe it is worth the preparation. Your taste buds and your gut bacteria will be happy!

Strawberry and coconut ‘ice cream’ with low carb coconut cookie dough chunks

Makes 2 small serves


Strawberry and coconut ‘ice cream’

1 cup of strawberries, washed, tops removed and frozen

1 cup coconut milk, frozen in ice cube trays

Extra ½ cup coconut milk

½ tablespoon of erythritol (I use Natvia which is a blend of erythritol with a small percentage of stevia)

½ teaspoon coconut essence

3 tablespoons shredded coconut

Low carb coconut cookie dough

1 cup desiccated coconut

3 tablespoons coconut milk

2 tablespoons coconut flour

½ teaspoon coconut essence

½ tablespoon erythritol


Ice cube trays

Sharp knife

Chopping board

Measuring cups and spoons

Food processor

Cling wrap


  • Freeze the strawberries and coconut milk for at least two hours.
  • Add the frozen strawberries, frozen coconut milk, extra coconut milk, coconut essence and erythritol to the food processor.
  • Process until the ‘ice cream’ is smooth and has a fairly even consistency.
  • Add in the shredded coconut and process briefly to mix through. Divide the ice cream between two bowls and freeze for 30 – 60 minutes before serving (don’t let it get too hard).
  • For the cookie dough, add all the ingredients to the food processor and process until a firm ball forms.
  • Lay a sheet of cling wrap onto a chopping board.
  • Remove the ball of cookie dough from the food processor and place it onto the cling wrap.
  • Roll the cookie dough into a long, thick log with your hands.
  • Wrap the cookie dough in cling wrap and freeze for at least one hour.
  • Chop the cookie dough into chunks and place on top of the Strawberry and coconut ‘ice cream’
  1. Sonnenburg ED, et al. (2016) Diet-induced extinctions in the gut microbiota compound over generations. Nature 529(7585):212-215

Exercise has a beneficial effect on the diversity of the human gut microbiota

Human-gut-bacteriaI have an interest in the human gut microbiome and the influence that the composition of this dynamic ecosystem has on human health and disease. As such, I am always keeping an eye out for interesting studies and articles relating to the gut microbiome and/or microbiota. The following article was particularly intriguing to me as a molecular microbiologist and as an amateur athlete: ‘Exercise and associated dietary extremes impact on gut microbial diversity’ published in 2014 in the journal Gut (1).

The adult gut microbiota contains up to 100 trillion microorganisms, including at least 1000 different species of known bacteria. Humans have coevolved with these microbes for thousands of years and the bacteria in our gut play very important roles in digestion, development of the immune system and protection against some infectious agents. Advances in DNA sequencing technology have greatly expanded our ability to identify the microorganisms in the human gut and to understand the complex interplay between these microbes and our own cells.

Diversity of the gut microbiota has been associated with good health status. On the other hand, a loss of gut microbial diversity has been linked to a range of disease states including Crohn’s disease, ulcerative colitis, irritable bowel syndrome and infection with Clostridium difficile (2-5). Furthermore, obese people have fewer types of microbes in their guts than lean people (6, 7). Reduced diversity of the gut microbiota during infancy has been associated with an increased risk for the development of allergies in children (8).

Although it is known that diet plays a huge role in shaping the gut microbiota, the impact of exercise has received much less attention. The above study is one of only a few that has investigated the impact of exercise on the gut microbiota and is the only study conducted on humans to date. This study looked at the faecal microbiota of a professional rugby team while in a regulated environment of a preseason camp. The microbiota was compared to two control groups: one matched for athlete size with a comparable body mass index (BMI) and another group matched for age and gender. It should be noted that the average BMI of the elite rugby players in this study was 29.1, which is considered overweight and almost in the obese category.

Athletes were found to have greater gut microbiota diversity when compared to the control groups. The elite athletes also had lower inflammatory markers despite elevated levels of plasma creatine kinase, a marker of extreme exercise, and had improved metabolic markers. The athletes had a greater intake of dietary protein which also likely influenced gut microbiota diversity.

The findings from this study are that exercise and diet impact gut microbial diversity. It appears that microbiota diversity is an indicator of health, so if you are considering starting an exercise regime or getting back into sport in the new year then hopefully this study will motivate you. Exercise will not only improve your fitness and cardiovascular health, but it may also enhance the diversity of the microbes in your gut.

  1. Clarke SF, et al. (2014) Exercise and associated dietary extremes impact on gut microbial diversity. Gut 63(12):1913-1920.
  2. Dicksved J, et al. (2008) Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. The ISME journal 2(7):716-727.
  3. Frank DN, et al. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences of the United States of America 104(34):13780-13785.
  4. Carroll IM, et al. (2011) Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome. American journal of physiology. Gastrointestinal and liver physiology 301(5):G799-807.
  5. Chang JY, et al. (2008) Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea. The Journal of infectious diseases 197(3):435-438.
  6. Ley RE, Turnbaugh PJ, Klein S, & Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444(7122):1022-1023.
  7. Turnbaugh PJ, Backhed F, Fulton L, & Gordon JI (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell host & microbe 3(4):213-223.
  8. Bisgaard H, et al. (2011) Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. The Journal of allergy and clinical immunology 128(3):646-652 e641-645.


Low carb bibimbap

Given that my article entitled “Everything you always wanted to know about fermented foods” has just been published on the informative blog Science-Based Medicine I thought that I would re-post this older post on how to make low carb bibimbap. It is a very tasty way to use kimchi .

I have not actually holidayed in South Korea. I have only stopped at the airport a number of times on transit to other parts of the world. But every time I stop at Incheon International Airport in Seoul, South Korea, I head straight for the food court to get a big bowl of bibimbap. If you are not familiar with bibimbap it is a signature Korean dish meaning ‘mixed rice’. It is served as a bowl of warm white rice topped with various seasoned vegetables, and a delicious and spicy sauce containing sunchang gochujang, (a Korean hot pepper paste made from red chilli, glutinous rice, fermented soybeans and salt) soy sauce and sesame oil. A fried egg and beef are also often added to this dish. I also love to top it with kimchi. Kimchi is a traditional fermented Korean side dish made of vegetables, most commonly napa cabbage, with a variety of seasonings, the most common including brine, scallions, spices, ginger, chopped radish, garlic, shrimp sauce and fish sauce.

Bibimbap is actually a very nutritious meal, however, I normally limit refined carbohydrates in my diet, so I set out to make a low carbohydrate, simpler version. This is not a dish that I would consider making on a week night, unless I had the seasoned vegetables and marinated meat left over from the weekend. I suggest that if you are going to prepare this meal, leave it to the weekend.

Bibimbap step 14

The nutritional components of bibimbap

As I was writing this post, I did a little bit of research into the components of bibimbap and came across the reported health benefits of kimchi. As it is a fermented product, I assumed that the bacteria contained within it were likely to be beneficial by adding variety to your existing gut microbial community, known as the microbiome. The predominant lactic acid bacteria involved in the fermentation process of kimchi include Weissella, Lactobacillus, Leuconostoc and Pedicoccus species (1 – 3). I came across a number of studies reporting various health benefits of kimchi including cancer prevention (4 – 7) and anti-obesity effects (8 – 10). Now don’t get me wrong, I am not saying that kimchi is going to cure cancer, and I also noticed that one of these studies was supported by the Globalization of Korean Food R and D program (slightly suspicious), but including this nutritious, fermented food as a part of your diet may have benefits to your long-term health.

I also discovered that sesame seeds and sesame oil contain a range of vitamins and minerals, including calcium, magnesium, iron and vitamin B (in the whole seed only) and, interestingly, contain some of the group of natural compounds known as lignans. Sesame lignans include sesamin, sesamolin and sesaminol (11). There has been quite a bit of research into these lignans and studies have shown that the lignans display antioxidative properties, meaning these compounds can scavenge free radicals which can lead to life style disease such as circulatory disorders and aging (12 – 14) and may have serum lipid-lowering effects in experimental animals and humans. One recent study entitled Comparative Effects of Sesame Seeds Differing in Lignan Contents and Composition on Fatty Acid Oxidation in Rat Liver looked at groups of 6 – 7 rats starting with the same average body weight fed different experimental diets for 16 days. These experimental diets contained the same protein, fat, and fibre content, and mineral and vitamin composition, but either did not contain sesame or contained 200g/kg of one of 4 different variety of sesame. The results showed that those rats feed the diets containing sesame seeds had significantly increased levels of various hepatic enzymes involved in fatty acid oxidation and significantly decreased levels of enzymes involved in fatty acid synthesis. Serum triacylglycerol (type of lipid or fat) concentrations were significantly lower in the groups of rats fed the diets containing sesame seeds compared to the rats fed the control diet without sesame seeds. However, this study found that hepatic or liver cholesterol levels were higher in the rats fed the diets with sesame seeds and that after the 16 days there was no significant difference in the body weight of the rats in each group (15). I am not going to go into any more detail about the health benefits of sesame seeds and oil, but I found these antioxidant and serum lipid-lowering properties of the lignans quite interesting. Again, I am not declaring sesame seeds as a cure for disease, part as a part of whole food diet, consisting predominantly of vegetables and quality protein, sesame seeds may have benefits to your long term health.

In addition to the kimchi and sesame seeds served with bibimbap, the vitamins and minerals from the fresh and seasoned vegetables and the protein and fat from the meat and eggs make this a very nutritious and tasty meal so head down to your local Asian grocery store and get cooking!

Low carbohydrate bibimbap

Makes 2 large serves with a small amount left over (could be made into a third serve with an extra egg)



250 grams lean mince

1 tablespoon soy sauce

1 tablespoon sesame oil

½ brown onion

1 clove garlic, minced

Seasoned spinach

250 grams fresh spinach

1 tablespoon shallots, finely chopped

1 teaspoon garlic, minced

1 tablespoon roasted sesame seeds

1 tablespoon soy sauce

½ tablespoon sesame oil

Seasoned bean sprouts

125 grams mung bean sprouts

1 tablespoon shallots, finely chopped

1 teaspoon garlic, minced

1 tablespoon roasted sesame seeds

1 tablespoon soy sauce

½ tablespoon sesame oil

Bibimbap sauce

2 tablespoons Sunchang gochujang

1 tablespoon sesame oil

1 teaspoon honey

1 tablespoon water

1 tablespoon roasted sesame seeds

1 teaspoon white vinegar

1 clove garlic, minced

Seasoned mushrooms

½ tablespoon sesame oil

1 tablespoon shallots, finely sliced

1 cup mushroom, thinly sliced

½ clove garlic, minced

1 tablespoon soy sauce

½ teaspoon ground ginger

Water for cooking

1 carrot, peeled

1 Lebanese cucumber

2 eggs, fried

Kimchi to serve (see Note below)

2 cups cauliflower rice


Step 1 – Take a trip to your local Asian supermarket and purchase Sunchang gochujang (I like the brand Daesang), kimchi, sesame oil, sesame seeds and bean sprouts.

Bibimbap step 1

Step 2 – Marinate your meat by combining the mince with the soy sauce, sesame oil, onion and garlic.

Bibimbap step 2

Step 3 – Pour yourself a drink. It makes the process more enjoyable.

Step 4 – Roast 4 tablespoons of sesame seeds in a dry non-stick frying pan, stirring often.

Bibimbap step 4

Step 5 – Mince all the garlic and shallots.

Bibimbap step 5

Step 6 – Prepare the bibimbap sauce by combining the gochujang, sesame oil, honey, water, roasted sesame seeds, white vinegar and garlic into a small bowl and mix well.

Bibimbap step 6

Step 7 – Julienne the carrots and cucumber.

Bibimbap step 7

Step 8 – Prepare the seasoned spinach. I used frozen spinach to make life easier. Thaw the frozen spinach in the microwave for 4 – 5 minutes. Mix in the shallots, garlic, roasted sesame seeds, soy sauce and sesame oil.

Bibimbap step 8

Step 9 – Prepare the bean sprouts by mixing the shallots, garlic, roasted sesame seeds, soy sauce and sesame oil through the fresh bean sprouts.

Bibimbap step 9

Step 10 – Prepare the cauliflower ‘rice’. In order to reduce the carbohydrates and calories in this dish I used cauliflower ‘rice’ instead of white rice. The cauliflower ‘rice’ still has the same texture as white rice and absorbs all the flavours of the bibimbap. Add 2 cups of cauliflower florets to a food processor and process until a rice-like texture has formed.

Bibimbap step 10

Step 11 – Prepare seasoned mushrooms. This step is my own addition to bibimbap. Traditionally, shitake mushrooms are used in this dish, but to be honest, I just don’t really like them. So instead I made these seasoned mushrooms. Add the sesame oil to a non-stick pan and cook the shallots until soft. Add the remaining ingredients and cook until the mushrooms are soft. Add water as required to prevent sticking.

Bibimbap step 11

Step 12 – Cook the marinated mince in a fry pan.

Bibimbap step 12

Step 13 – Fry the eggs. I prefer my yolk hard so I flipped the eggs, however, you can leave them sunny side up if you prefer a runny yolk.

Bibimbap step 13

Step 14 – Assemble the bibimbap by dividing the cauliflower ‘rice’ between 2 serving bowls. Top with the meat, seasoned spinach and bean sprouts, seasoned mushrooms, carrot, cucumber and the fried egg. Drizzle the bibimbap sauce over the top (see top photo).

Step 15 – Mix it all together and EAT!

Bibimbap step 15

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  2. Kim, M., Chun, J. Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis.(2005). Int J Food Microbiol. 103:91–6.
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How to make kimchi plus everything you always wanted to know about fermented foods

Kimchi daysFermented foods, such as sauerkraut and kombucha, have become increasingly popular in the health space at the moment. I have been making sauerkraut at home for several years in the belief that the bacteria responsible for the fermentation of the cabbage, lactic acid bacteria (LAB), predominantly Lactobacillus plantarum, would contribute to the diversity of my gut microbiota. As a research scientist in the field of bacterial pathogenesis, this made sense to me. Now that I have started this blog and have been writing more in depth articles about health related topics, I started thinking about what actual research has been conducted on the health benefits of fermented foods and do the bacteria within fermented foods actually survive the harsh conditions of the gastrointestinal tract, particularly the stomach? Hence I put together this review (supported by peer-reviewed science) about everything I always wanted to know regarding fermented foods.

What are fermented foods?

Fermentation is a predominantly anaerobic process, meaning without oxygen, carried out by microorganisms or cells in which sugars, such as glucose, are converted to other compounds, such as alcohol, for the purpose of energy production. Typically bacteria and yeast, which undergo lactic acid fermentation and ethanol fermentation, respectively, are used in the fermentation of foods. The unique flavours and textures of fermented foods are due to the different species of bacteria and yeast used.

Humans have fermented foods for thousands of years all throughout the world, with particular foods being unique to certain ethnic groups (1). Not only does the fermentation of foods add to the flavour and texture, but fermentation also improves the shelf-life of food. It is believed that fermentation processes were originally developed as a way to preserve fruit and vegetables during times of scarcity (2). The fermentation of food can occur spontaneously by the natural LAB surface microflora or by the use of a starter culture (3).

Types of fermented foods

Fermented diary

Lactic acid bacteria (LAB) are the main bacteria involved in the production of fermented dairy products, such as yoghurt, cheese and kefir milk, where they convert lactose (the main sugar in milk) to lactic acid. This results in an increased acidity making the growth of other microorganisms unfavourable. The most common LAB involved in the fermentation of dairy include members of the genera Lactobacillus, Streptococcus, Leuonostoc, Enterococcus and Lactococcus. Bifidobacteria are also included in fermented milk products. (4). Yoghurt is typically produced by using a culture of L. delbrueckii subp. bulgaricus and S. thermophiles (5).

During the fermentation of dairy a number of beneficial compounds are produced by the metabolic activity of LAB, propionibacteria, yeast and mould. The content of vitamin B-12, folic acid and biotin are enriched during the fermentation of milk by LAB (6). Conjugated linoleic acid (CLA), which I have previously discussed, is also increased in fermented milk (7). Bioactive peptides with reported antihypertensive, antimicrobial, antioxidative and immune-modulatory activities are released by the activity of LAB in fermented milk products (8). Galactooligosaccharide, which is synthesized by LAB from lactose, has a prebiotic effect on intestinal microbiota, meaning it promotes the growth of beneficial bacteria in the gut (9). In addition, yoghurt in particular is a rich source of dietary minerals, including calcium, magnesium, potassium, phosphorus and zinc (10). The concentration of these minerals is nearly 50% higher in yoghurt than in milk (11). The acidic environment created by fermentation with LAB can enhance the bioavailability of these minerals. Furthermore, yoghurt is also an excellent source of essential amino acids. The amount of free amino acids is increased due to the pre-digestion of milk proteins by the activity of bacterial cultures, allowing for better protein digestibility (12).

Harmful compounds, including mycotoxins and biogenic amines can also contaminate fermented dairy products, however, strict regulatory standards are set by international agencies for the monitoring of these substances and reliable methods to detect these compounds have been developed (13-16).

Large cohort studies conducted in the Netherlands, Sweden and Denmark found that fermented milk products were significantly associated with decreased disease states. These disease states includ bladder cancer, cardiovascular disease and periondontitis (17-19).


Kombucha has become a popular fermented beverage. It is a sweetened black tea fermented by a symbiotic colony of bacteria and yeast, meaning that both the bacteria and yeast live in close physical association and have a mutually beneficial relationship. The interaction of these microorganisms results in a floating cellulose layer on the surface of the fermented tea, which becomes thicker the longer it is fermented. The species that constitute the bacterial component of kombucha cultures are the acetic acid bacteria Acetobacter xylinum, A. xylinoides, Bacterium gluconicum, A. suboxydans, Gluconbacter liquefaciens, A. aceti and A. pasteruians and LAB including Lactobacillus bulgaricus (20).

The earliest known use of this beverage was by Dr. Kombu in 220BC who used it to cure the digestive troubles of Japan’s emperor (I did not make this up!) (21). The main metabolites found in kombucha are acetic acid, lactic, gluconic and glucuronic acids (22, 23). Kombucha also contains polyphenols, amino acids, vitamins and a variety of micronutrients (24).

Not a lot of studies have been conducted on the health benefits of kombucha. However, I did discover that kombucha contains the compound D-saccharic acid-1,4-lactone (DSL). DSL is a derivative of D-glucaric or saccharic acid (25) and is known to possess antioxidative properties (26). The chronic hyperglycemia associated with diabetes mellitus results in oxidative stress due to the overproduction of reactive oxygen species causing tissue damage such as renal (kidney) injury (27). Studies investigating the effects of feeding DSL to diabetic rats found that DSL was able to reduce renal injury and oxidative stress in the kidney tissues. The authors of this study speculate that this is due to the ability of DSL to maintain intracellular antioxidant machineries, such as the antioxidant enzymes superoxide dismutase, catalase and glutathione reductase, at normal levels (28, 29).

Fermented vegetables

The fermentation of vegetables by LAB is recognized as a simple and valuable method to maintain and enhance the safety, nutritional quality and the shelf life of vegetables. This method is particularly important when access to fresh vegetables is limited.

The most commercially significant fermented vegetables are cabbage, in the form of sauerkraut and kimchi, cucumbers, in the form of pickles, and olives. Typically the fermentation of vegetables occurs spontaneously by the surface microbiota, however, starter cultures are also used. Starter cultures can speed up the fermentation process, ensure reliability of the final product, prevent the risk of fermentation failure and assist with the inhibition of spoilage and pathogenic microorganisms (30).

Lactic fermentation has been shown to enhance the nutritional value of foods, including vegetables. Lactic fermentation of maize, soybeans and sorghum (a grain) reduces the content of phytate, a well-known inhibitor of iron and zinc absorption (31). It has also been shown that fermentation of maize enhances the bioavailability iron (32). A recent study published in the European journal of Nutrition found that the reason for the increased bioavailability of iron in lactic-fermented vegetables compared to fresh vegetables is due to an increase in the concentration of hydrated ferric iron (Fe3+) which may be more favourable for iron absorption (33).

One of the metabolites produced by the LAB responsible for the fermentation of vegetables, known as bacteriocins (antimicrobial compounds which are discussed later), has attracted attention for their potential use as safe and natural food preservatives (34).

The impact of fermented foods and probiotics on the human gut microbiome and health

With our increasing understanding of the importance of the human gut microbiota and microbiome to health and disease, research in this field has focused on how the composition of this complex bacterial community is modulated (to clarify the gut microbiota is the microorganisms that inhabit the gut while the gut microbiome is the total genome content of the gut microbiota). Diet is one of the main factors that influence the human gut microbiota (35, 36). Many food-ingested bacteria are capable of transiently or temporarily integrating into the gut microbiota where they may have an impact on the composition and the activity of the resident gut microbial community. These food-ingested bacteria can be found in fermented foods and as probiotics. Probiotics are defined as the live microorganisms, when supplemented in adequate amounts as part of food, confer a health benefit on the host (37). The bacteria used to ferment foods can be considered probiotics. Recent research suggests that the human gut microbiome is made up of a core AND a variable commensal community and it seems that bacteria ingested via food contribute to this ‘variable microbiome’ (38).

As already discussed, LAB are the most widely used strains to ferment foods. Some LAB species are thought to be permanent inhabitants of the gastrointestinal (GI) tract while other species, such as L. plantarum, L. rhamonosus and L. paracasei appear to be transient colonizers (39). Some species of bifidobacteria, which are the dominant members of the microbiota of breast-fed babies (40) but make up only 1% of the total adult gut bacteria (41), are also typical members of the transient microbiota (42). Some species of bifidobacteria are used as probiotics. The propionibacteria, commonly used to make Swiss-type cheeses, are another common form of ingested microbes (43).

In order for ingested bacteria to have any sort of beneficial impact in the human intestinal system, they must first be able to survive within the food matrix. A number of factors can affect the probiotic viability in the food matrix, such as the acidity, oxygen availability, the concentration of sugars, the moisture content and the storage temperature (44).

Next these microbes must be able to withstand the very hostile environment of the human upper GI tract. After ingestion, the bacteria from fermented foods and probiotics initially passage through the stomach, which is very acidic (pH <3) and contains enzymes, such as pepsin, which break down proteins. Most ingested bacteria will not survive. Those bacteria that do happen to survive then enter the small intestine, where the pH rises to over 6, but they are exposed to bile and more digestive enzymes, such as pancreatin and lipase. Some bacterial strains can recover, and even grow in the small intestine before these cells continue on to the colon (45). Ingested bacteria must also be able to adhere to the gut epithelial cells of the human host in order to have any beneficial effects (46, 47).

Variation in the ability of probiotic strains to survive the human GI tract has been demonstrated. Studies subjecting various strains to conditions simulating the environment of the human GI tract found that strains of B. animalis, L. casei, L. rhamnosus and L. plantarum have the greatest resilience (45, 48-50).

Numerous clinical studies have been conducted investigating the impact of probiotics on human health. The reported beneficial effects of probiotic consumption include improvement of constipation, diarrhea, intestinal inflammatory conditions such as, Crohn’s disease, ulcerative colitis, irritable bowel syndrome and necrotizing enterocolitis (51), and the prevention of allergic disease in infants (52, 53). Furthermore, supplementation with probiotics has been shown to positively enhance immune system function (54-56), improve the symptoms of lactose intolerance, and can prevent infection with pathogenic or disease causing microorganisms (57). The mechanisms by which probiotics exert these benefits to humans are not yet totally clear. What the research tells us is that the intestinal epithelial cells of the GI tract are a very important part of the innate or non-specific immune system and act as a link to the adaptive or specific immune system. The intestinal epithelial cells are able to recognize many bacterial components and are the first point of contact for ingested microbes (58, 59). The latest research suggests that possible mechanisms for the health benefits of probiotics include outcompeting disease causing bacterial pathogens, inhibiting attachment of pathogens to host cells (60-62), strengthening the mucosal barrier (63), stimulation of anti-inflammatory cytokine production (cytokines are cell signalling proteins which are produced by a range of cells, importantly immune cells) (64, 65) and the production of antimicrobial substances, including bacteriocins (66), which are antimicrobials peptides that inhibit the growth of other bacteria, organic acids and hydrogen peroxide (67).

Products containing probiotics can come as either supplements, such as pills and capsules, or as foods. In 2009 it was estimated that the global probiotic supplement market was approximately $1.5 billion USD (68) and was predicted to expand to $32.6 billion by 2014 (69). It is estimated that the probiotic industry holds about a 10% share of the global functional food market (70). There seems to be agreement in the literature that at least 108 – 109 (100 000 000 – 1 000 000 000) viable cells must reach the intestine for health benefits to be achieved. This means that the product or food must contain 108 – 109 CFUs/serving (CFUs stands for colony forming units – when the product/food is plated, this amount of colonies must grow from 1 serving) (71-73). The traditional method of plating used to validate the amount of bacteria present in food is quite time-consuming, however, faster more reliable methods are becoming available. A study in 2013 published in the Journal of Applied Microbiology found between 107 and 108 CFU/ml of Lactobacillus delbrueckii subsp. bulgaricus within a commercial brand of yoghurt (Activia® from Danone). This strain was mentioned on the product’s package (74). Other studies have also found that commercial yoghurts do contain significant numbers of Lactobacillus species to confer potential health benefits (75).

So do the bacteria within commercial yoghurts actually survive the treacherous journey through the human GI tract? A study involving 15 healthy volunteers between the ages of 24 and 46 looked at the effect of commercial yoghurt consumption containing probiotic LAB on the fecal bacterial community. The subjects were divided into 3 groups with one group consuming 110grams of yoghurt A, one group consuming 180ml of yoghurt B and the third group consuming 90 grams of yoghurt C. The subjects consumed one serve per day for 20 days. The labels of yoghurt A and B stated that these products contain a probiotic Lactobacillus strain, while yoghurt C did not state this on the label. The probiotic strains were detected in the feces of subjects consuming yoghurt A and B for up to 28 days after the first day of consumption. The study also detected changes in the populations of bacterial groups of the fecal microbiota in all three groups (76). This study showed that probiotic strains in yoghurt can survive the human GI tract, however, it seems that the consumption of yoghurt, and not just the presence of probiotics in the yoghurt, can influence the composition of bacterial groups in the fecal microbiota. Another study involving 36 subjects looked at the persistence of 4 probiotic strains administered as capsules, yoghurts or cheese at a dose of 1.9 – 5.0 x 109 CFUs. This study found that all four probiotic strains survived the GI tract and could be detected in fecal samples following consumption in all subjects. This study also found that the food matrix had an effect on the survival of 2 of the 4 strains, with the highest quantities recovered in the fecal samples from the yoghurt group (77). These studies suggest that probiotics present in yoghurt can survive the human GI tract provided that the bacteria are present in high enough numbers in the yoghurt to begin with.

On 24 April 2013, the First Global Summit on the Health Effects of Yoghurt was held. Keep in mind that sponsors of this event included the Dairy Research Institute and the Danone Institute, who may have vested interests. However, The Nutrition Society and The American Society of Nutrition were also sponsors. The conclusions from this summit were that there is accumulating preclinical, clinical and epidemiological evidence to support the health benefits associated with yoghurt consumption. Further research needs to be conducted to firmly establish these findings including investigations across the life span, from the very young to the old, randomized, placebo-controlled studies in healthy and diseased populations, more detailed descriptions of the types and doses of bacteria present in the yoghurt products being used in studies, assessment of the delivery matrix on the efficacy of probiotic bacteria, the effects of live compared to killed bacteria in yoghurt and studies into the mechanisms of yoghurt and/or probiotic bacteria on gut health and the microbiome (5).

So what about the health benefits of other fermented foods, such as vegetables? I will focus on kimchi as, eventually, I will be describing how to make this tasty fermented side dish. Kimchi has been consumed for about 2000 years in Korea. The most popular kimchi is baechu or chinese cabbage kimchi, which is generally made by LAB fermentation of beachu cabbage, radish, green onion, red pepper powder, garlic, ginger and fermented seafoods (78). Usually kimchi contains approximately 107 – 109 CFUs/gram of LAB. The LAB profile of kimchi actually changes during the fermentation process due to the pH. Leuconostoc mesenteroides is present during the early fermentation (pH 5.64 – 4.27) while Lactobacillus sakei dominates in the later stages of fermentation (pH 4.15) (79). Other LAB contributing to kimchi fermentation include Leu. citreum, Leu. gasicomitatum, L. brevis, L. curvatus, L. plantarum, Lactococcus lactis, Pediociccus pentosaceus, Weissella confusa and W. koreensis (80, 81).

Studies investigating the potential beneficial effects of the bacteria isolated from kimchi have found the following:

One of the LAB strains isolated from kimchi was found to have potent antioxidative activity (82). L. plantarum from kimchi has shown various immune-modulatory activities, such as the activation and stimulation of cytokine production in macrophages (a type of innate immune cell) from mice (83, 84). Furthermore, L. plantarum enhanced immune function when fed to mice (85, 86). LAB from kimchi was found to have antiobesity effects in rats (87, 88) and in mouse adipocytes (fat cells) (88). LAB isolated from kimchi has shown antimicrobial activities against a range of pathogenic bacteria (89, 90).

Again this raises the question of whether the LAB found in kimchi can survive the human GI tract? One study found that L. plantarum KC21 isolated from kimchi showed acid and bile tolerance and the ability to adhere to human intestinal cells (90). Another study found that human subjects who consumed 300grams/day of kimchi containing 108 CFU/gram of LAB for 2 weeks had significantly higher counts of fecal Lactobacillus species and Leuconostoc species during the kimchi intake period (91). These results suggest that if LAB is present in sufficient numbers in your kimchi then the bacteria will survive the journey through your GI tract and may confer health benefits.


My final thoughts after conducting this thorough analysis of the research are as follows: although further research needs to be conducted on probiotics, including those found in fermented foods, it is clear that these microorganisms have positive effects on human health. It also seems that the consumption of fermented foods can have a can confer these health benefits, if the bacteria are present in high enough numbers to begin with and have survived the storage conditions. Not only do the microbes themselves confer health benefits, but the fermentation process also enhances the nutritional qualities of the food. I will continue to enjoy fermented foods knowing that the microbes are beneficial for my health. However, I do suggest that you are wary of the high sugar content that is present in a lot of commercially available yoghurt and go for unsweetened and add you own stevia or a little bit of honey.

Now that we have established that fermented foods are good for your health, here is how to make kimchi.

As with most of my recipes, I am always looking for short cuts that reduce the preparation time without reducing the quality of the end product. Some methods for making kimchi that I came across online instruct you to soak the cabbage overnight, but in my experience this is not necessary. I soak the cabbage for one hour and the texture is perfect and the fermentation is successful.

Typically kimchi contains a seafood flavour, such as fish sauce or shrimp paste, however, I actually despise both of these ingredients and although I do enjoy traditional kimchi, I decided to have a go at making kimchi without the seafood flavour. I enjoyed the taste, so this version is actually vegan. I find the process of making kimchi enjoyable, it is tasty, there are health benefits associated with eating it, beyond the presence of the probiotics, and the total cost to make a huge jar, which keeps in the fridge, was about $3. Have a go at it this weekend. I will be posting some follow up recipes involving my homemade kimchi soon.

Homemade kimchi


¾ wombok cabbage


3 tablespoons Korean red pepper powder (purchase this at your local Asian supermarket)

3 tablespoons soy sauce

1 large clove garlic, finely minced

3 cm fresh ginger, finely grated

3 tablespoons water

2 shallots (green part only), chopped


Chopping board

Sharp knife

Large mixing bowl

Colander or large strainer

Small mixing bowl


Large glass jar with lid for fermenting


  • Chop the wombok cabbage into quarters lengthwise and remove the core. Slice the cabbage into about 2 -3 cm thick strips and place the cabbage into a large bowl. Salt the cabbage and massage it with your hands until it begins to soften. Cover the cabbage with water and allow it to soak for at least one hour.Kimchi soaking cabbage
  • Keep ¼ cup of the salty water that the cabbage is soaking in. Place the cabbage into a colander or large strainer and rinse it well in water and drain it. Rinse the bowl that the cabbage was soaked in and place the cabbage back into the bowl after it has drained.
  • To make the paste combine the red pepper powder, soy sauce, garlic, ginger and water into the small mixing bowl and mix well. Add in the chopped shallots and mix.Kimchi paste
  • Add the kimchi paste to the cabbage and mix it into the cabbage. I found using clean hands is the easiest way to do this.

Kimchi cabbage mixed

  • Using your hands put the cabbage into a large glass jar, pressing the cabbage down firmly with each handful. The idea is to remove as much oxygen as possible to create the correct environment for the fermentation to occur. This process does get a bit messy.
  • Wipe the sides of the jar down and place the kimchi into a warm spot to ferment. I typically ferment my kimchi for 3 days, however, I believe that this would vary depending on the climate. I live on the Gold Coast in Queensland, Australia. Even in the middle of winter the temperature can reach 20°C, so if you live in a colder climate you may need to ferment it for longer. Taste the kimchi and continue fermenting until your desired taste is achieved.Kimchi day 0
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Cool article about the microbiome of an isolated tribe of hunter-gatherers living in the Amazon jungle

Yanomami_Woman_&_ChildI have a fascination with the human gut microbiome and the role this complex microbial community plays in health and disease. This is an emerging area, not only in the field of microbiology, but also in many areas of biomedical research. This topic appeals to me as a microbiologist and as a health nut. I came across this article published in Science Advances last month (April, 2015) entitled ‘The microbiome of uncontacted Amerindians’ by Clemente et al. This study investigates the fecal, oral and skin bacterial microbiome of members of an isolated Yanomami village, a seminomadic hunter-gather people inhabiting the Amazon jungle who have had no previously reported contact with western civilization.

The fecal microbiome of these isolated hunter-gatherers displayed the greatest diversity ever reported in any human group thus far. The bacterial species detected in the Yanomami samples varied from that of subjects from the U.S, with the Yanomami people having higher intestinal Bacteroidales S24-7, Mollicutes and Verrucomicrobia, members of the families Aeromonadaceae, Oxalobacteraceae, and Methanomassiliicoccaceae, and genera Phascolarctobacterium, Desulfovibrio, Helicobacter, Spirochaeta, and Prevotella. Some of these species, for example, Helicobacter, were completely absent in the feces of U. S. subjects (1).

Similar findings were obtained from a study that compared the gut microbial composition of children aged 1-6 years living in a rural African village to western European children of the same age. The diet of the children in the African village was that of a traditional rural African diet consisting of locally produced, cultivated and harvested grains, legumes and vegetables and occasional animal protein in the form of chicken and termites. A greater microbial richness and biodiversity was found in the African village children compared to the European children (2).

Diet is one of factors that can impact the diversity and composition of the human gut microbiome, along with age, disease states, mode of delivery at birth and antibiotic use. Therefore, these findings are not surprising considering the diet and lifestyle of the Yanomami people and the rural African children compared to the typical Western lifestyle and diet. The unprocessed, unrefined, high fibre, nutrient dense diet of the Yanomami people and African children is clearly having a positive impact on their gut microbiota

The gut microbiota is involved in the development of our immune system, the utilization of energy and nutrients from our diet and the prevention of the establishment of potentially harmful intestinal microbes. Therefore, having a greater diversity in the gut microbiome is likely to have a range of health benefits.

I came across this saying which I think is very appropriate ‘they are what we eat’ – ’they’ being the gut microbiota (3). So keep this in mind the next time you are reaching for that highly processed, packaged snack food. Is that the sort of fuel that is going to promote a diverse and rich microbiome?

  1. C. Clemente, E. C. Pehrsson, M. J. Blaser, K. Sandhu, Z. Gao, B. Wang, M. Magris, G. Hidalgo, M. Contreras,Ó.Noya-Alarcón, O. Lander, J.McDonald, M. Cox, J. Walter, P. L. Oh, J. F. Ruiz, S. Rodriguez, N. Shen, S. J. Song, J. Metcalf, R. Knight, G. Dantas, M. G. Dominguez-Bello. (2015). The microbiome of uncontacted Amerindians. Sci. Adv. 1: e1500183.
  2. Filippo, C. D., Cavalieri, D., Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G. and Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. PNAS. 107: 14691-14696.
  3. Hold, G. L. (2014). Western lifestyle: a ‘master’ manipulator of the intestinal microbiota? Gut. 63: 5-6.

Image of Yanomami woman and her child, June 1997 from Cmacauley

Scientific evidence that processed food is bad for you

I am not the only one who suspected that the highly processed Western diet has contributed to the increase in worldwide obesity and the diseases associated with obesity, known as metabolic syndrome*. A friend drew my attention to this article (thank you, Katie) published in Nature Letters (the top journal in science) in February of this year entitled Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome (1). Basically, the scientists behind this study showed that two emulsifiers, carboxymethylcellulose and polysorbate-80, commonly found in foods such as ice cream, altered mucus thickness, microbiota composition (the community of bacteria) and enhanced inflammation in the gut of mice. The scientists also showed that administration of the emulsifiers to the mice resulted in weight gain and an increase in fat mass. These effects occurred when mice were given the emulsifiers via drinking water and via food, and as little as 0.1% was sufficient to produce these effects. The authors state that the consumption of emulsifiers by humans is not something that is well evaluated, but the use of emulsifiers in many foods exceeds 1.0%.

Keep in mind that the mice in this study were fed these emulsifiers every day for 3 months. So I believe that the take home message here is that an excess of processed foods is clearly bad for your health. If you need some inspiration for recipes containing minimally processed ingredients then you are in the right place.

* Metabolic syndrome is diagnosed by the presence of diabetes, impaired fasting glucose, impaired glucose tolerance or insulin resistance, together with at least two of the following: hypertension, hyperlipidemia, central obesity and microalbuminuria (2). In other words, you are fat and sick!

  1. Chassaing, B., Koren, O., Goodrich, J. K., Poole A. C., Srinivasan, S., Ley, R. E. and Gewirtz1, A. T. (2015). Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature. doi:10.1038/nature14232.
  2. Bruce, K. D and Byrne, C. D. (2009). The metabolic syndrome: common origins of a multifactorial discussion. Postgrad Med J. 85:614–21.