Herbal Safety


Gut Microbiome

Part of the Clinical Practicum series on WholisticMatters designed to bring you clinical information for your practice.

 Gut Health

The gut microbiome constitutes bacteria, viruses, yeast, and parasites that reside in the gut. There is an estimated 100 trillion organisms that live in the gut, and more than 1,000 subspecies have been identified to date. The majority of bacteria in the gut reside in the large intestine and are involved in every aspect of gut function, performing many tasks that are essential to life.

The functions of the microbiome are expansive and include assisting with digestion and absorption, protecting against pathogenic organisms, regulating and training the immune system, and synthesizing essential vitamins that humans are not able to produce.

Adapted from: Laukens, Debby & Brinkman, Brigitta & Raes, Jeroen & de vos, martine & Vandenabeele, Peter. (2015). Heterogeneity of the gut microbiome in mice: Guidelines for optimizing experimental design. FEMS microbiology reviews. 40. 10.1093/

The major functions of the microbiome can be divided into three major parts:

  • Protect: against pathogens and overgrowth of potential pathogens by crowding out or displacing noxious organisms.
  • Structure: barrier fortification, strengthening of tight junctions between intestinal cells, and development of a healthy immune system capable of appropriately responding to harmful and benign stimuli.
  • Metabolism: synthesis of vitamins and fermentation of non-digestible dietary fiber to produce short chain fatty acids (SCFAs), which are important for nutrition and energy for intestinal cells. SCFAs have also been implicated in ant-inflammatory modulation and satiety signaling.

Microbes in the gut fall into three major categories:

  1. Symbionts represent different organisms that live together. Microbes are sub-divided into mutualistic (both organisms benefit), commensals (one benefits, the other is unaffected), and parasitic (one benefits, the other is harmed). The majority of the gut microbiome is composed of commensal or ‘friendly’ organisms that provide balance in gut ecology.
  2. Pathobionts represent organisms that have the capability to cause harm to the host under the right environmental circumstances in which they are allowed to overgrow. An example of a pathobiont is dificile overgrowth and infection in the setting of antibiotic wipeout of commensals. Pathobionts may also be associated with chronic inflammatory conditions.
  3. Pathogens cause harm to the host and produce disease. These are classical organisms that cause acute infection.

Image Reference: Sekirov, I., et al., Gut Microbiota in Health and Disease. Physiological Reviews, 2010. 90(3): p. 859-904.

There are four major phyla (the taxonomic rank below kingdom) that constitute the majority of microbes in the gut: bacteroidetes, firmicutes, actinobacteria, and proteobacteria. Ecological shifts in the relative proportion of bacteria in these four phyla may be one factor that leads to initiation of disease. “Dysbiosis” is the scientific term used to describe alterations in the gut microbiome that lead to initiation of disease. Dysbiosis represents an imbalance in the microbial ecosystem that leaves it vulnerable to overgrowth of pathobionts and pathogens, compromise of gut barrier function, inflammation, and changes in metabolic functions.

There are multiple types of dysbiosis:

  • Loss of good bacteria, or a known keystone taxon (a group of organisms that form a unit)
  • Loss of microbial diversity
  • Shifts in metabolic capacity, usually a result of growing more bad bacteria that harvest excess energy from food
  • Blooms of pathogens, such as yeast overgrowth or parasites
  • Displacement of bacteria from the large to small intestine (small intestinal bacterial overgrowth (SIBO))

Dysbiosis can be triggered by antibiotics – often the primary culprit – which can lead to a wipe out of a significant proportion of commensal bacteria, and it can take years to repopulate the gut. Other triggers of dysbiosis include poor nutrition, chronic stress, alcohol use, medications like proton-pump inhibitors (PPIs), nonsteroidal anti-inflammatory drugs (NSAIDs), and steroids. There is tremendous focus on the role of poor lifestyle choices as a trigger for gut dysbiosis, which has downstream implications for developing immune and metabolic diseases.

Clinically, symptoms of gut dysbiosis vary tremendously from person to person and may include:

  • Frequent gas, bloating, belching
  • Loose stools, diarrhea, constipation
  • Acid reflux
  • Unexplained weight gain and/or difficult weight loss
  • Irritable bowel syndrome (IBS)
  • Irritable bowel disease (IBD)
  • Anxiety
  • Depression and/or frequent low mood
  • Halitosis (chronic bad breath)
  • Brain fog
  • Joint pain
  • Skin conditions (acne, eczema, psoriasis)
  • Low energy and chronic fatigue
  • Diagnosis of an autoimmune condition (such as Hashimoto’s thyroiditis or rheumatoid arthritis)
  • Allergies and food sensitivities
  • Chronic yeast or fungal infections

There is emerging research on microbial signatures that can assist with diagnosis of gut dysbiosis. This research is in its infancy, but many companies have developed novel testing of the microbiome and its health using some limited sequencing platforms and measurement of gut dysbiosis. The microbiome research space is rapidly evolving, and there are likely to be many different iterations of this platform before it reaches conventional medicine.

In using a functional medicine approach to diagnosing dysbiosis, patterns are analyzed and clinical correlation is used to determine risk profile for gut dysbiosis. There is no “gold standard” test, and multiple testing platforms may be used to ascertain the health of the gut microbiome. Criteria to consider when testing include:

  • Microbial diversity score
  • Change in the ratio of Bacteroidetes and firmicutes
  • Depletion of keystone taxa
  • Low levels of beneficial bacteria (Bifidobacterium and lactobacillus)
  • High levels of pathogens or potential pathogens (bacteria, parasites, yeast)
  • Low levels of short chain fatty acids, an important metabolic product of good bacteria

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