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Gut Health 101: What is the Microbiome?

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Gut Health 101: What is the Microbiome?

Postby Spiritwind » Thu Oct 17, 2019 2:41 pm

I have recently been inspired to look more into the importance of the microbiome, as I was reflecting on the many ways we have been comprised.

Published Dec 22, 2016 - by Dr. Edward Group
Gut Health 101: What Is the Microbiome? ... icrobiome/

The human body is a complex, interconnected ecosystem and the gut is where your body interacts the most with the outside world. Your gut acts as the frontline of your immune system, as it is constantly exposed to new microbes and molecules that come from the things you eat and drink. The processes that take place in the gut are involved in the central nervous system, brain, and even influence your mood. But you can’t begin a discussion about the gut’s importance without discussing the organisms that live there.

So, What Is the Microbiome?
The collection of microbes that live in and on the human body is known as the microbiota.[1] The microbiome refers to the complete set of genes within these microbes. Microbial genes significantly influence how the body operates and even outnumber human genes by a ratio of 100:1.[2] Each of us has a unique microbiota and a unique microbiome. The microbes that live in your body are determined by what you're exposed to and these colonies are constantly in flux. Geography, health status, stress, diet, age, gender, and everything you touch all affect the composition of your microbiota.[3]

Public Health, Germ Theory, & the Microbiome
Scientists have known about microorganisms for hundreds of years. In 1673, Antony van Leeuwenhoek wrote to the Royal Society of London about his discovery of tiny “animalcules” with the use of his “microscopes.” Leeuwenhoek found microbes almost everywhere he looked,[4] but the discovery was largely ignored until the 1870s when their role in the cause and spread of disease was observed. Previously, doctors believed that bad air caused disease. Robert Koch proved that tiny microorganisms were responsible. His discovery solidified the validity of germ theory — the idea that certain microbes cause specific diseases.[5]

Germ theory created a scientific rationale for cleanliness that became the precursor to it becoming a moral and social imperative. People began bathing daily. Soap, once considered a luxury, became a basic household necessity. Doctors and surgeons started washing their hands and sanitizing their instruments.[6] New laws led to public health initiatives that limited the spread of disease and saved lives.[6]

Until recently, scientists focused almost solely on how pathogenic microbes negatively affect humans. There has since been a realization that some microorganisms are actually beneficial to human health.[7] More attention is now given to the microbiome and its role in health and immunity.[8] Launched in 2008, The Human Microbiome Project (HMP) was created to better understand the relationship between health, disease, and the microbiome.[9]

The Makeup of the Microbiome
The microbiota is comprised of a dizzying number of microorganisms. Bacteria make up the bulk — about 30-50 trillion cells.[10] The human body itself contains about 37 trillion human cells.[11] It may be disconcerting to think of yourself as mostly microbial cells, but, by weight, you’re definitely mostly human as microbial cells are significantly smaller than human cells. Bacterial cells range from 0.2-10 microns (micrometers) across; human cells range from 10-100 microns.[12] For reference, the average dust mite, which is microscopic, is 200-300 microns wide.

If you’ve seen the oft-quoted 10:1 ratio (10 microbes to 1 human cell), you might be surprised to learn that it was actually just an estimate that circulated throughout academic and scientific resources as fact. It is now regarded as academic urban legend.[13]

It's believed that humans carry about three pounds of bacteria in their intestines.[14] Everyone's individual microbiome is as unique as their fingerprint and comprised of hundreds of different types of bacteria.[15] The specific number of bacteria cells varies throughout the day and is always turning over.[16]

Although bacteria account for most of the mass of the microbiota, viruses are actually the most abundant inhabitants.[8, 17] We tend to think of viruses as harmful, but that’s not always the case. The viruses found in the gut are primarily bacteriophages, meaning that they infect gut bacteria cells but they don't necessarily harm them. Rather, they have a symbiotic relationship. Viruses can quickly transfer genes — beneficial genes. So, if new bacteria are introduced to your gut, either through diet or probiotics, the viral cells can help the bacteria thrive by transferring the genetic code.[18]

The Role of the Human Microbiota
The role of the microbiome is so central to the body’s operations that it essentially acts as an organ.[18] The microbiome impacts aging, digestion, the immune system, mood, and cognitive function.

Some of the bacteria in the gut produce enzymes that support digestion, especially the digestion of polysaccharides — healthy and complex sugars found in plant foods.[19] These bacteria also provide B vitamins, vitamin K, and short chain fatty acids. The microbiota also influences metabolic rate.[20]

A strong microbiome is the foundation of your immune system. When you were born, your gut was a clean slate, ready to learn.[21] Exposure to microbes provides the education that trains the immune system how to respond to different organisms. In this way, the immune system mediates the relationship between the body and the microbes it hosts.[21] Harmful organisms are dealt with, helpful organisms exist in harmony and contribute to good health overall.[22]

Research has also revealed the important role the microbiome has on mental health. There is a complex relationship between the gut and brain, called the gut-brain axis (GBA). The microbiota interacts with the central nervous system to regulate brain chemistry and mediate stress response, anxiety, and memory.[23]

How Is the Human Microbiota Formed?
It's generally agreed that the human body is first exposed to microbes during birth.[18, 24]

The makeup of the mother's microbiota changes during pregnancy and is extremely influential.[25] Babies born vaginally are colonized primarily by the Lactobacillus genus of bacteria. Newborns delivered by Caesarean section are exposed to skin microbes such as Staphylococcus, Corynebacterium, and Propionibacterium.[26] Whether the baby was born at home or the hospital can also affect the composition of the baby's microbiota.[3]

As babies grow, their microbiome will change. In the first few months of life, the body is colonized by relatively few species of microbes — only about 100. By the age of three, a child's microbiota possesses closer to 1,000 species of microbes and begins to resemble the microbiota of an adult. Puberty and, much later, menopause are two other life events that can significantly change the composition of the microbiota.[3]

The Bacteria in Your Gut Microbiome
Microbiome composition may vary throughout the intestines; most are concentrated in the large intestine. The bacteria in the average adult gut include Bifidobacterium, Lactobacillus, Bacteroides, Clostridium, Escherichia, Streptococcus, and Ruminococcus. Not only will diet influence the microbial composition of the microbiota, the microbiota influences the nutritional value of food.[27] Though specific bacteria vary, they share many of the same genes.[28]

Humans do not have the ability to produce the enzymes required to break down complicated nutrients. However, gut bacteria do have that ability and it's absolutely essential for proper digestion. Bacteria enable us to eat a diverse diet and receive a broad range of micronutrients and phytonutrients.[29]

Supporting the Microbiome
Your microbiome is constantly changing.[1] You rely on your microbiome for many processes, including digestion and immune system function; the stronger it is, the better off you'll be. To positively shape your microbiome, eat a diverse diet rich in complex carbohydrates and fiber.[30] Probiotic supplements can also help strengthen the microbiota. Choosing the best probiotic supplement is a whole other subject but, bottom line, the best probiotic supplements contain an assortment of probiotic strains and prebiotics. Prebiotics are food that help probiotics flourish.

I personally recommend FloraTrex™. It contains 25 different probiotic strains that support digestive health, mood, and promote a balanced microbiota; it provides prebiotics, too.
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Re: Gut Health 101: What is the Microbiome?

Postby Spiritwind » Sun Nov 03, 2019 6:38 pm

I went to hear a longer more in depth presentation by Nonia with Clearwater Cultures ( and now I am even more motivated to educate myself so I can incorporate this new understanding into my every day consciousness and thinking patterns. So I will most likely be adding to this thread as I go along. I learned a lot from her, more a different way of seeing than anything, but I liked it! I will write more as time permits. I’m always excited when I meet someone who is on fire for the simple reason of loving this earth, and wanting to help herself and her family heal in an increasingly toxic environment. They want us to be afraid, and feel helpless.

But the earth herself has the answers, if we can learn how to listen to her, and tune into her very real guidance. We, too, are her children, as long as we are in form, just like every other biological living thing here, and she can help restore us to a state of balance. This awareness has the potential to literally change the course we are on, if it were to come into a state of being common knowledge. But it flies in the face of what we have been taught to believe, and the “kill it or cut it out” mentality and attitude in so called modern medicine. Just remember, we humans have been on this planet for thousands of years before our current state of treating health issues came into common usage, and not many years at all since it became a “for profit” system. We are living proof that they were doing something right, or we would have died out and wouldn’t be here now.

Difference Between Microbiome and Microbiota ... icrobiota/

Key Difference – Microbiome vs Microbiota
Microorganisms are present everywhere. Their numbers are uncountable, and they live on and in animal bodies. It is estimated that around 100 trillion microbes are present in the human body. This number is ten times the number of human cells. Microbiota and microbiome are two terms used to describe these microorganisms. Microbiota refers to all types microorganisms present in a particular location. Human microbiota refers to the microorganisms present in and on the human body. The term microbiome is used to refer the entire genetic makeup of the microbiota. Human microbiome refers to the genetic composition of human microbiota. These two terms sometimes used interchangeably. However, it is important to recognize the difference between these two terms. The key difference between microbiome and microbiota is that microbiota includes the entire population of microorganisms that colonizes a particular location or organism while microbiome refers to the genetic makeup of the respective microbiota.

1. Overview and Key Difference
2. What is Microbiota
3. What is Microbiome
4. Side by Side Comparison – Microbiome vs Microbiota in Tabular Form
5. Summary

What is Microbiota?
Microbiota refers to the entire population of microorganisms that colonize a particular location. All types of microorganisms including bacteria, viruses, fungi, archaea, and protozoans are addressed by the term microbiota. For example, human microbiota refers to the entire microbial population and viruses in and on the human body. Microbes are mainly present in human gastrointestinal tract and skin. The microbial population in the gastrointestinal tract of a human is known as gut microbiota. Gut microbiota is involved in human health and nutrition. Healthy gut microbiota is largely responsible for the overall health of the organism. Human gut microbiota is mainly composed of two major phyla named bacteriodetes and firmicutes. Earlier it was assumed that the gut microbiota contains 500-1000 species of microorganisms. However, recent studies have revealed that the collective human gut microbiota comprises of over 35000 bacterial species.

From a microbial and immunological perspective, microorganisms are considered as pathogens. Hence, host immune systems always tend to eliminate them from the body. However, the majority of the human gut microbiota contains nonpathogenic and cohabit microorganisms which are important in many ways to humans. The human gut commensal microbes support nutrient metabolism, drug metabolism, and intestinal barrier function, and prevent colonization of pathogenic microorganisms.

Human gut microbiota mainly comprises of anaerobic microorganisms. Hence, the analysis of gut microbiota was difficult. However, once the anaerobic culturing techniques were developed, it was identified that gut microbiota is dominated by Bacteroids, Clostridium, Bifidobacterium, etc.

There are several factors affecting the healthy gut microbiota. They are age of the human, diet, and antibiotics. Antibiotics are used to combat pathogenic microorganisms. However, due to their broad spectrum, antibiotics may also work against the normal microbiota in our gut.

What is Microbiome?
Microbiome refers to the genes or the genetic makeup of the microbiota. The collection of overall genes of the microbial community is considered under microbiome. Human microbiome refers to the complete genetic material of human microbiota. Compared to the human genome, human microbiome is considered as the second genome, and it contains 100 times genes than human genes.

Sometimes the word ‘microbiome’ is often used to refer the microbial population and the combined genetic material of the microorganisms in a particular environment.

The genes of microbiota interact with the human genome to function together, helping to improve human health and fight against diseases. These genes are involved in numerous beneficial functions such as supporting life such as digesting food, preventing disease-causing pathogens from invading the body, and synthesizing essential nutrients and vitamins.

Research carried out on microbiome have expressed that the human microbiome is a fundamental component of human physiology. Therefore, human microbiome is an important factor of human cellular activities. Changes in microbiome affect the normal function of the human body and disease development.
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Re: Gut Health 101: What is the Microbiome?

Postby Spiritwind » Sun Nov 03, 2019 6:41 pm


What is the difference between Microbiome and Microbiota?

Microbiome vs Microbiota
Microbiome is the entire collection of genetic material of microbiota in a particular location.
Microbiota is the entire microbial population in a particular location such as human body, animal body, etc.

Microbiome focuses on genes and genetic composition
Microbiota focuses on different types and species of microorganisms.

Importance of Human Microbiome and Microbiota
Microbiome is important to understand the collaborative function of microbiome with the human genome.
Microbiota is important in many aspects including nutrition, disease prevention, immune responses, etc

Summary – Microbiota vs Microbiome
The terms microbiota and microbiome are sometimes used interchangeably. However, there is a difference between microbiota and microbiome. Microbiota refers to the entire population of microorganisms colonized in a particular location. Microbiome refers to the genetic material of the microbiota of a particular location or the entire collection of genes of microbiota. This is the main difference between microbiome and microbiota.

1. Jandhyala, Sai Manasa, Rupjyoti Talukdar, Chivkula Subramanyam, Harish Vuyyuru, Mitnala Sasikala, and D. Nageshwar Reddy. “Role of the normal gut microbiota.” World Journal of Gastroenterology : WJG. Baishideng Publishing Group Inc, 07 Aug. 2015. Web. Available here. 16 June 2017
2. Ursell, Luke K., Jessica L. Metcalf, Laura Wegener Parfrey, and Rob Knight. “Defining the Human Microbiome.” Nutrition reviews. U.S. National Library of Medicine, Aug. 2012. Web. Available here. 16 June 2017
3. MacGill, Markus. “What is the gut microbiota? What is the human microbiome?”Medical News Today. MediLexicon International, 24 Mar. 2016. Web. Available here. 17 June 2017.
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