The Human Microbiome and Microbiota

Within and on the human body, there is an entire ecosystem. We are, in fact, never alone…


What is the Human Microbiota?

A host of microorganisms, mostly bacteria, for the most part live in harmony with us and even benefit us. An example of this is the bacteria that live in our large intestine that produce vitamin K, which we then absorb into our blood from the large intestine. The bacteria in our large intestine also breakdown waste materials; those things we ate that we cannot easily digest. In return, the bacteria get to live in a sheltered, food-rich, warm environment. This relationship is a positive symbiotic relationship. This natural flora that lives in and on our bodies is called the microbiota. Different areas of the body will play host to different microorganisms depending on their requirements and in exchange will do different things for us. One of the things that beneficial bacteria will do for us is to inhabit and “occupy sites in the body and create an environment that inhibits colonisation by other organisms.” An example of this environmental modification is that done by lactobacilli, which lowers the pH, making the environment unfriendly to pathogens.

There is significant evidence to support our relatively new understanding that a healthy microbiota is a collection of “microbes in and on the body that normally do not cause disease and can actually provide protection against harmful microbes.” 30 This understanding is new because “the science of microbiology dates back only two hundred years” 31 to when Robert Koch discovered the bacteria that causes anthrax in 1876. So, bacteria, or germs, became the enemy and we undertook great efforts to kill them. More recently, the benefits of bacteria have been recognised and are now being researched. After killing so many microorganisms, it is only now that we begin to understand that we need them as much as, if not more than, they need us. While we are only just scratching the surface, new research is published almost weekly, from all over the world, so much so that it is hard to keep up with the reading. The variety and number of microorganisms are mind-boggling. Just counting the microbes, we are carrying around with us; they outnumber our cells ten to one.


What is the Human Microbiome?

The microbiome is the term used for the collective genomes belonging to the communities of microorganisms that live in the human gut. The microbiome is different from the microbiota as it is the name used to describe all the genes inside the members of the microbiota.


What is a Probiotic?

The word “probiotic” comes from the Latin root word, “pro” meaning “for” and the Greek root, “bios” meaning “life”. They are microorganisms that assist you in life. More technically, probiotics “are live microbial cultures applied to or ingested that are intended to exert a beneficial effect.” According to The International Scientific Association for Probiotics and Prebiotics Consensus Statement on the scope and appropriate use of the term probiotic, the Food and Agriculture Organisation and the World Health Organisation, the definition of a probiotic is “live microorganisms which when administered in adequate amounts confer a health benefit on the host.”

One example of a probiotic would be certain lactic acid bacteria (LAB) that, when ingested, can relieve the symptoms of diarrhoea. 36 Another example is “the use of LAB (lactic acid bacteria) to prevent surgical wound infection caused by Staphylococcus aureus.” Yet another example is found in an article in the Journal of Dairy Research which showed evidence of a “protective effect of feeding milk fermented with a mixture of Lactobacillus casei sp. and Lb. acidophilus sp. against Salmonella typhimurium infection.” The summary stated that “Milk fermented with this mixture could be used as an immunobiological method to prevent gastrointestinal infection.”39 This method of use is not the same as a cure once you have a disease, but rather a method of prevention to ensure you do not get sick in the first place.


What is a Prebiotic?

According to the Merriam Webster online dictionary, a prebiotic is “a substance and especially a carbohydrate (such as inulin) that is nearly or wholly indigestible and that when consumed (as in food) promotes the growth of beneficial bacteria in the digestive tract.” The definition has been recently updated by the International Scientific Association for Probiotics and Prebiotics to “a substrate that is selectively utilised by host microorganisms conferring a health benefit” allowing for a wider range of substances and locations outside the gut. 41 Probiotics are often administered with prebiotics, and this can increase the effectiveness of the probiotic.

While there is a lot of work going on in laboratories all over the world in the development of functional food, prebiotics can be obtained naturally from sources like vegetables, fruit, and grains consumed in our daily lives.” 42 In my view, I like to eat real food for my nutrition, not use something created to replace real food. A diet high in resistant starch, complex carbohydrates and fibre gives you all the prebiotics you need. Perfect examples of these high-quality foods are fruits, vegetables, whole grains, and legumes.


What is a Symbiotic?

Symbiotics are a combination of probiotics and prebiotics in a package. They are a fusion of probiotic and prebiotic products that helps in enhancing the survival and the implantation of live microbial dietary supplements in the gut.” Eating fermented foods eliminates the need to take such supplements under normal conditions. The exception would be someone with a specific medical condition requiring supplementation for acute or chronic situations or where fermented foods are not appropriate for medical reasons.


What is a Postbiotic?

Postbiotic is a relatively new term and accounts for those products that the bacteria make during their lifecycle, which are beneficial to the host. Another word often used in the place of a postbiotic is a metabolite. The difference is that you can have a metabolite that is not a postbiotic, as there is no evidence it is beneficial to you, or you can have a postbiotic metabolite, where the evidence supports that there is a benefit.

The shortcut around fermented food is to take a probiotic pill, but this is not good enough. It is not just the bacteria that are helpful to human health; it is also the compounds they produce during their life cycle and how they interact with our bodies. So, fermented foods are better for you because they are full of probiotic microorganisms, but that is not the whole story. Fermented foods are also better for you because of what these microorganisms do to the food, the compounds they create, how they interact with your body and how they make the nutrients more bioavailable.


How can Diet affect your Microbiome?

In a healthy person, there is a balanced microbiome where probiotic bacteria, those that benefit our life, live in harmony. These bacteria have the prebiotics that they need to flourish, which they obtain from the foods we eat, such as complex carbohydrates, resistant starches, and fibre. We derive these from a mostly plant-based diet. Following a high-quality diet increases your beneficial bacteria. A low-quality diet decreases the beneficial bacteria, throwing your system out of balance, resulting in dysbiosis, which is the name for an imbalance in gut bacteria, and contributing to the numerous health challenges faced by people on a typical western diet.

A low-quality diet would contain large amounts of highly processed foods, added sugar, alcohol, and saturated fats. A high-quality diet would be rich in fruits, vegetables, legumes, and whole grains, including fermented foods.

Author: Valerie Pearson

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