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Microbiomes: Its Benefits in the Human Body

  • Microbiomes – Colonies of Helpful Micro-Organisms that May Improve Your Health

    Microbiomes – Little bugs? Germs? Viruses? What are they and will they hurt or help me? I am going to answer all these questions for you and more. Find out why healthy amounts of this bad bacteria may actually be good for you


    Microbiomes must sound awful especially to self-professed germ-a-phobes. Many people do confuse microbiomes to germs, but they are not actually germs. They aren’t something you can bleach away regularly, nor should you want to.

    Ever heard the saying, the enemy of my enemy is my friend? Well, this is the case with microbiomes. 

    Human Microbiomes – super small in size yet they take up a big role in our bodies. So small, the trillions of human microbiomes take up about 1-3% of our bodies total body mass and so large of a concept in our health that scientists refer to the human microbiomes as our “second brain”. 

    • Microbiomes are like a neighborhood of diverse people, houses, and cultures all getting along and performing unique functions.


    • Like a diverse culture, microbiomes are dynamic in behavior, they adapt to any circumstance, climate, and host. 


    • Microbiomes can live anywhere and occupy other things aside from humans. The human microbiome is one kind of collection or community of microorganisms.


    • We begin collecting microbes the moment we are born.

    Who is leading the study on human microbiomes?

    Microbiomes and related research have grown to cover a wide platform because it is a fascinating subject. Genetic scientists are enamored with the idea of the many applications and conditions associated with the microbiomes. Because of this, you can easily find microbiomes at the helm of many clinical studies.

    However, taking the lead on microbiome research is a project called the HMP, or Human Microbiome Project. This project began in 2008 and was granted a 150 Million dollar research budget. Of note, several GI specialists also currently studying microbiomes in varying capacities and populations regarding the role of microbiomes and gut health.

    What are human microbiomes/microbes?

    Scientifically speaking, Microbiomes is a community of organisms including certain bacteria forms, viruses, or fungi that occupy a particular environment.  Basically, microbiomes make up their own ecosystem or community on the space where they colonize. This space can be on a human, animal, or other environment. For example, the body houses trillions of microbiomes. There are ocean microbiomes, earth (soil) microbiomes, and even atmospheric microbiomes.

    Where - Where do microbes in the gut come from?

    Microbes in the gut or sometimes referred to as gut flora are the microbiota living within the intestine. The acid is too high for most bacteria to reside in the stomach. These gut microbes are comprised of more than 1,000 different species of bacteria. Sounds gross, we know. But these microbes are actually a big part of maintaining good gut health.

    When - When did microbiomes become such a hot topic?

    Microbiomes became interesting around the 1990s. They have become a hot topic because they are linked to immune health. The microbiome has been found to be essential to human development. The role they play within the body is significantly more advanced than previously thought. Research has indicated the microbiome is unique to each human and provides insight as to genetically inherited diseases or conversely immunity against certain diseases. 

    What is Gut Flora? Is it the same as Microbiomes? 

    The words gut health, gut flora, probiotics, digestive health products get lost in translation, so Let’s clarify it: Gut health is defined by having a balanced gut flora.

    Because the medical community has embraced the knowledge that good gut bacteria is essential to optimal health, we are seeing a surge of product offerings, services, and also information that has boosted visibility for microbiomes. 

    Gut Flora is defined as the microbiota (community of human microbiomes or microorganisms, therefore Gut Flora cannot be identified the same as Microbiomes and here is why – Gut Microbes or the Microbiota of the Intestines is representative of one of many different microbiomes.

    As mentioned above, a microbiome is like a neighborhood and can occupy different hosts or cities. But for all intents and purposes, when you see things that discuss the Human Gut Flora, it is referring to the microbiota existing within that specific human intestinal housing area. 

    So, you my friend have a unique intestinal microbiome different than anyone else! This means your microbiome constituents will always be unique to you.  Primarily, because the microbiome alters its state depending on the conditions of the host.

    This is what makes fecal transplants so successful. They have the ability to help other “neighborhoods” achieve a healthy, diverse balance of bacteria to offset the disease.

    Why do we believe microbiomes are linked to so many diseases and illnesses?

    It is believed that imbalanced microbiomes or “communities” are associated with ill health. There has been strong correlative evidence between poor gut health and advanced disease such as Type 2 diabetes, inflammatory bowel disease, rheumatoid arthritis, and cirrhosis.

    Researchers are even studying microbiomes in association with other health problems such as depression and anxiety. There have even been fecal transplants performed where they implant the microbiome from a healthy intestine into that of a diseased intestine and the results were a corrective response to the disease over time, so we know conclusively that the microbiome is an integral component to gut health and immune function.

    How might microbiomes differ from person to person and what are the effects of these differences?

    Each microbiome or community of microbes are unique to each host or “human”. For example, the gut microbiome of an obese person and that of a lean person. A person with an autoimmune disease is thought to actually inherit microbiomes associated with that particular disease.

    How are some of the ways that microbiomes affect our health?

    Microbiomes can affect health in a myriad of different ways. Microbiomes in relation to gut health are linked to rheumatoid arthritis, obesity, and a vast array of autoimmune diseases. More interesting, microbiomes can change depending on changing health circumstances. In one of the studies conducted by the HMP (Human Microbiome Project) they found that nasal and gut microbiomes changed differently in response to an infection that those of patients with healthy receptor signaling. 

    There is a tendency to think of microbiomes only applying to gut health or gut flora and its applications towards obesity, or gastrointestinal disorders. However, the science tells us the microbiomes in our gut also directly impact our neurological health.

    In fact, we cite a very revealing study that paints a clear picture between depression or mood disorders and gut health. This fascinates researchers and gives much needed hope in this area as depression is of epidemic proportions and considered a crisis in both adults and teens. We are even seeing higher rates of children with depressive symptomology.

    Now, we know that the culprit could be related to poor diet I.e. gut health. The overall consensus among leading respected medical experts is that Microbiomes seem to play a comprehensive role in our overall health.

    How do we improve our microbiomes?

    You can eat your gut microbiome by eating fermented foods, yogurts, and increasing fiber intake. Gut health is associated by maintaining a healthy diet consisting of vegetables and fruits. Polyphenols (anti-oxidants) are also shown to assist in gut health.

    There is also evidence on supplementing with multispecies probiotics can assist in obtaining optimal levels of the necessary bacteria. This helps to achieve a balanced microbiome. This is especially true if one has been treated with antibiotics.

    Clinical Study: 

    A Randomized Controlled Study to test Multi-Species Probiotics on Cognitive Reactivity to Sad Mood

    This study involves 40 subjects and was conducted by a group of researchers from the Leiden Institute for Brain and Cognition. The study participants were given specialized tests to highlight the presence of any prior neurological disease or psychological function.

    They were required to be non-smokers and other health requirements to be eligible. They were randomized accordingly for the study and treated for four weeks. 20 of which received the placebo and the other 20 participants a daily 2g dose of probiotics referred to as Ecologic Probiotic based in the Netherlands. 

    This study came on the heels after much evidence circumventing the gut-brain axis which involves bi-directional highway of communication between the neural, endocrine, and immune pathways. In layman’s terms, scientists realized the strong link between the gut microbiome and brain health – specifically depression. 

    The goal of the study was to isolate the impact of altering the gut flora with probiotics and studying whether it impacted the study participants' ability to overcome sad mood or depression. 

    What they found and concluded was remarkable. Using a sophisticated scoring system, the study found the participants taking the probiotics experienced less sadness, aggression, rumination, and overall mental balance.

    From a layman’s perspective, the study revealed there was a significant reduction in depressive thoughts and known associated risks. No known adverse effects were reported.


    I have now explained how microbiomes basically act as buffer against a host of harmful pathogens. Although microbiomes are comprised of many forms of bacteria, we know they work synergistically towards improved health.

    Maintaining gut health is one of the best things you can do to keep advanced diseases at bay. More importantly, we can assess current health based on poor gut health symptomology. Questions to ask yourself might include: 

    • Are you getting the recommended amounts of fruits and vegetables in your diet? 
    • Do you suffer from constipation/diarrhea or other known gut ailments? 
    • Have you been on a course of antibiotics and suffered malnutrition symptoms or diarrhea?
    • Are you currently diagnosed with advanced disease or showing precursor signs and symptoms? 

    Do you think you have poor gut health? If so, what evidence or symptoms do you have that may be related to a poorly established microbiome?  

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