Human Microbiome and Gut Health 101

human microbiome and gut health - Linden Botanicals

The human microbiome is linked to immune system health and gut health. Here’s what you should know.


Did you know that your body is filled with bacteria and fungi? Fortunately, you don’t necessarily need to be worried about these microbes, as most of them help keep our bodies healthy and alive.

Let’s board a train into the world of the human microbiome. The human body harbors a microbiota that contains between 10 trillion and 100 trillion microbial cells. A larger percentage of these microbial cells are primarily bacteria, fungi, and viruses. Since they are small in size, they contribute to only 3% of the body’s mass.

Microbial Diversity

The human microbiome is estimated to host up to 1,000 different microbial species. This diversity affirms the different microbial compositions, not only among human beings but also among different parts of the body.

Our bodies offer an array of conducive environments for the survival of microbes. Every body part has a unique ecosystem, which respective microbes have adapted depending on the characteristics of the body part in question. For instance, our hands and faces are often dry and exposed to immigrant microbes and elements. Armpits are moist, dark and warm, thus providing a conducive environment for bacterial growth. The gut microbiome hosts thousands of bacteria.

What Is the Role of the Human Microbiome?

Most microbes benefit humans by providing us with unique traits that we wouldn’t otherwise possess. For instance, the gut microbiome assists humans in breaking down foods and preventing the gastrointestinal tract from being colonized by pathogenic bacteria. In return, these microbes obtain nutrients for their growth from foods ingested by humans. Some microbes such as Staphylococcus, Klebsiella, Streptococcus, and Enterobacter are not pathogenic in their normal environments.

That said, these microbes are capable of becoming pathogenic under certain conditions. A perfect illustration of the relationship between human health, disease, and the human microbiome is the Clostridium difficile infection. When humans ingest antibiotics to treat pathogenic bacteria, they increase the number of C. difficile (a normal flora), which may result in cramping, nausea, and diarrhea.

When pathogenic microbes accumulate in the body, they can cause changes in the metabolic processes and gene activity, which in some instances may lead to abnormal responses in human immunity. Dysfunction of the microbiome may result in autoimmune conditions such as rheumatoid arthritis, diabetes, multiple sclerosis, fibromyalgia, and muscular dystrophy.

Gut microbes also regulate fat storage and aid in activating human cell genes that are usually involved in breaking down nutrients, creating blood vessels and absorbing nutrients. They may also replenish the gut lining. Native microorganisms compete with invading ones to prevent infections. Usually, our immune system is partially formed at birth, and our body’s interaction with both native and invading microbes helps to shape and strengthen immunity. Native microbes can help differentiate between symbiotic ones and invaders, hence helping the immune system become hardwired.

Preventing Pathogenic Invaders

Studies link a healthy human microbiome to a well-functioning immune system, as well as to other essential functions like sleep. The same research suggests that maintaining diversity of good flora in the microbiome is key to counteracting bad pathogenic invaders.

The human gut is a complex ecosystem operating a highly defended immune system. External pathogens rarely penetrate this system successfully, but the ones that do can compromise our health. In addition to sleep, exercise, and diet, drinking Phyllanthus niruri tea may help the body stop harmful pathogens from populating the gut.

Phyllanthus niruri, also known as Chanca Piedra and Stone Breaker, supports balanced immune system function, strengthening weak systems and calming overactive ones. As a result, it helps the body avoid damaging inflammation and auto-immune diseases. It supports a healthy human microbiome, selectively inhibiting the reproduction of pathogenic bacteria without affecting gut-friendly flora. In other words, Phyllanthus niruri, also known as Chanca Piedra and Stone Breaker, doesn’t harm friendly lacto-bacillus, but it does disadvantage other types of bacteria.

Bacterial biofilm is a complex microbiome structure containing several colonies that adhere to a surface. The cells are often embedded in an extracellular matrix that contains DNA, polysaccharides, and proteins. A study on the effect of bacterial biofilms against antibiotics revealed that biofilms are the leading cause of many recent infection persistence cases. The biofilm forms a barrier that inhibits the penetration of antibiotics and immune cells, causing resistance and pathogenesis. Cistus incanus tea is a powerful biofilm busting tea that breaks the bacterial biofilm in nasal and gut passages.

A recent article in Frontiers in Pharmacology addresses the benefits of Cistanche tubulosa extract, including the antidepressant-like effects of Cistanche tubulosa extract through restoration of gut microbiota homeostasis.

The authors note: “Growing evidence shows that neuropsychiatric disorders, such as depression, are linked with gut microbiome through the gut–brain axis. Cistanches Herba is well known for the treatment of “kidney-yang” deficiency in traditional Chinese medicine (TCM), and has been used for treatment of neurodegenerative diseases in recent years. … [T]hese results identify [Cistanche] as a potential treatment for depressive symptoms by restoring homeostasis of gut microbiota for microbiota–gut–brain axis disorders, opening new avenues in the field of neuropsychopharmacology.”

Finally, Terminalia chebula extract, also called Haritaki and Myrobalan, is also effective in nourishing the digestive system and thus supporting immune system health.

Human Microbiome and Immune Health

The human microbiome plays a significant role in our growth and development, nutritional health, and immune system health. As it turns out, the more you support your microbiome, the healthier and happier you may be.

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