Gut Microbiome: What You Need to Know

gut microbiome and gut health - Linden Botanicals

Here’s what you need to know about the gut microbiome, gut health, and overall immune system health.


The gut microbiome refers to microorganisms such as viruses, bacteria, fungi, and protozoa that reside in the gastrointestinal tract. These microorganisms include normal flora, commensal flora, and pathogenic flora.

Several studies have tried to explore the interaction between gut microbiota and the host, including potential effects on the immune system and metabolism. Furthermore, current investigations reveal that the gut microbiota plays a key role in the absorption of nutrients and minerals, enzyme synthesis, and short-chain fatty acids production.

Classification of the Human Gut Microbiome

The gut microbiome is classified into many groups referred to as Phyla. Primarily, there are four types of phyla:

  1. Bacteriodetes
  2. Actinobacteria
  3. Proteobacteria
  4. Firmicutes

Although the majority of the bacteria are found in the gastrointestinal tract, bacteria are also known to colonize various parts of the human body, including the placenta, skin, vagina, and oral cavity. Predominant anaerobic bacteria are found in the colon.

There are 20,000 eukaryotic genes in the human body and up to 3.3 million prokaryotic genes in the gut microbiota. The development and alteration of the human microbiome are determined by various factors, including infant feeding methods, birthing, medications, environment, comorbid diseases, and diet.

What Is the Work of the Gut Microbiome?

The gut microbiome offers significant benefits for the fermentation of endogenous interstitial mucus and dietary fibers. The fermentation, in turn, enhances the growth of microorganisms that produce gases and SCFAs (short chain fatty acids). The main SFCAs produced include:

  • Acetate
  • Butyrate
  • Propionate

Butyrate offers the primary energy source for colonocytes and can induce apoptosis among cancer cells. It can also activate the gluconeogenesis of the intestines and energy homeostasis. It aids epithelial cells to consume large oxygen amounts.

Propionate is taken up to the liver to regulate gluconeogenesis. Acetate is a primary metabolite that promotes the growth of other bacteria.

Role of the Gut Microbiome in Diseases and Health Conditions

The term dysbiosis refers to the process of altering the microbial community resulting in a decrease in the numbers and diversity of the commensal bacteria. Scientific evidence has shown a relationship between dysbiosis of the gut and health conditions including metabolic syndromes, inflammatory bowel disease, cancer, and obesity.

  1. Irritable Bowel Syndrome (IBS)

Dietary changes, antibiotics, and probiotics can alter the gut microbiome. A study describing the relationship between dietary interventions low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) and changes in the gut microbiota shows overwhelming evidence in the reduction of putatively healthy microorganisms (e.g., clostridium cluster XIVa that is involved in the production of butyrate).

  1. Inflammatory Bowel Syndrome (IBD)

Inflammatory bowel syndrome (IBD) refers to the abnormal inflammation of the gut which occurs due to genetic and environmental risk factors.

Recent studies on overweight people point towards gut microbiota dysbiosis, which is characterized by low diversity. A UK study reveals that the Christensenella genus is rare among obese people. Akkermansia spp correlates with low-fat deposits. The dysbiosis of the gut microbiota results in diet-induced obesity, metabolic complications, altered gut hormone regulation, and immune dysregulation.

Herbal Teas and Extracts That Offer Support

The gut microbiome serves as a fundamental tool for human health. It would be difficult for humans to survive without gut microbiota. This microbiome begins to diversify as we grow older.

Studies now 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 herbal 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 may help 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, 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 up the bacterial biofilm in nasal and gut passages.

Further, a recent study 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 study’s 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.

To learn more, we recommend starting with Digestion 101, which highlights 7 strategies for dealing with digestive problems.

Digestion 101 Best Teas for Digestion Shop Now

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