Jermane Krishnan

Gut Microbiota

The terms “microbiota” and “microbiome” are frequently used interchangeably.  However, microbiota is defined as “a group or populations of  microbial organisms,” whereas microbiome is the catalogue of these microbiota and their genes.

The gut microbiota is implicated in the pathophysiology of a wide range of physical and psychological disorders. While research has provided insights into the mechanisms by which the microbiota influences health, much remains unknown or poorly understood.

Once overlooked, this component of the gastrointestinal (GI) tract is now getting a great deal of attention regarding its importance in optimal health. The food and supplements industries have bombarded advertising and sales of food and supplement products promoting “prebiotics,” “probiotics” and “fermented foods.” Yet, at this time science is only scratching the surface in understanding how to best apply knowledge of the microbiota to facilitate better health. This section will review what is currently “known” in an effort to guide patients in this new therapeutic world.

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Definitions and Terms Related to Pain

The Gut Microbiome

The widespread influence of the gut microbiome on many physiological and psychological processes is complex. It involves bi-directional communication between the gut and the brain, the hormone, immune and endocannabinoid systems as well as microbial production of neuroactive compounds.

It has been shown that the microbiome of people suffering from various medical conditions differs significantly from that of healthy controls. Research suggests  that altering a person’s microbiome through the use of probiotics, prebiotics, or dietary change can alleviate the symptoms and course of many medical conditions including pain.

The Human Microbiome Project (HMP), one of several international efforts, identifies and studies the microbiome in human health. Funded by the National Institute of Health (NIH) in 2008, the HMP has isolated and sequenced over 1,300 reference bacterial strains so far.

The microbiota includes trillions of microorganisms including bacteria, fungus and viruses which are distributed throughout the entire gastrointestinal tract. But different healthy people may have very different microbiomes depending on their diet and their lifestyle. There is considerable intra- and interpersonal variation in the composition of the microbiome because it is influenced by many, many factors including mode of delivery at birth and neonatal feeding, the aging process, dietary factors, geography, medications, and stress.


Changes in the Gut Microbiome with Age

Breast milk is the optimal food for infants as it meets all their nutritional and physiologic requirements. It contains protein, fat and carbohydrate, as well as iantibodies and endocannabinoids. Breast milk is not sterile – it contains more than 600 different species of bacteria including beneficial Bifidobacterium breve, B. adolescentis, B. longum, B. bifidum, and B. dentium

Because an infant’s diet is comprised of breast milk and formula, the microbiome has minimal diversity and with genes that promote metabolism of milk sugar (lactate). With the introduction of solid foods, by 3-years of age the bacterial composition of the gut microbiota is similar to that of an adult and remains stable until old age.  In terms of bacterial succession, the Bifidobacterium-dominated microbiota of the infant changes over time into the Bacteroidetes- and Firmicutes-dominated microbiota of the adult. This remains stable throughout adulthood in the absence of disturbances, such as long-term dietary changes or repeated use of antibiotics.

In older age groups, changes in oral and dental health, salivary function, digestive function and intestinal transit time affect the gut microbiota. Notable differences in the microbiota in elderly people compared to young adults include relative proportions of Bacteroidetes predominating in the elderly compared to higher proportions of Firmicutes in young adults. The elderly are also noted to have significant decreases in Bifidobacteria, Bacteriodes, and Clostridium cluster IV. However, there is marked variability among individuals ranging from 3 to 92% for Bacteroidetes and 7 to 94% for Firmicutes.

Decreased microbial diversity has been noted in individuals living in short- or long-term residential care compared to those living in the community, and this difference was associated with increased frailty, decreased diet diversity as well as increased inflammatory markers (serum TNF-α, IL-6, IL-8 and C-reactive protein).

Diet and the Gut Microbiome

Diet is one of the most relevant factors that influences the gut microbiome. Significant changes in the gut microbiota are associated with dietary alterations, especially with consumption of dietary fiber from fruits and vegetables. A varied diet is associated with a more diversified microbiome. 

Enrichment of the microbiome is associated with diets high in fruits, vegetables and fiber compared to a western diet rich in fat, sugars and animal protein, one with little fiber. When the microbiota associated with a strict vegetarian diet is compared with that of an omnivorous diet, the vegetarian microbiota has significantly less Bifidobacterium, Bacteroides, E. coli and Enterobacteriaceae species and lower stool pH compared with the omnivore microbiota.

Also, compared to an omnivore diet, a vegetarian diet is associated with a higher carbohydrate and fiber content in which the undigestible polysaccharides can be fermented into short chain fatty acids (SCFA) by the gut microbiota. Production of SCFA is associated with decreased gut pH. The fact that E. coli and Enterobacteriacea do not thrive in lower pH ranges (5.5–6.5) and that they prefer proteins as their energy source, may explain their lower counts in those eating a vegetarian diet.

Depleted microbial biodiversity of the gut microbiota in people consuming a Western diet is associated with increasing incidence of obesity, coronary vascular disease, metabolic syndrome and certain malignancies. The diversity of the gut microbiome may reflect a long-term link to the potential for disease development.


Physiological and Psychological Stress and the Gut Microbiome


Stress can be acute or chronic,  predictable and controllable or unpredictable and uncontrollable, mild or severe, and and the perception of stress may vary between people, but stress contributes to susceptibility to disease.

Physical and psychological stressors activate the hypothalamic-pituitary-adrenal (HPA) axis between the brain and the adrenal glands. This results in hormonal responses including release of cortisol and the catecholamines, noradrenaline and adrenaline. The GI tract and the gut microbiota are sensitive to stress and some gut bacteria respond to stress by release of neuroactive compounds which can influence the host physiology.

While high intensity exercise can be a physiological stressor that can lead to gastrointestinal distress manifest by nausea, vomiting and diarrhea, regular exercise has an anti-inflammatory effect.

Psychological Stress and the Gut Microbiome

The gut–brain axis is a two-way biochemical signaling process that takes place between the nervous system of the gastrointestinal tract and the central nervous system. The brain and the gut reciprocally influence each other’s expression, providing a conceptual framework in which psychological factors interplay with the gut as exemplified by functional GI disorders such as irritable bowel syndrome. Early life stressors (psychological, sexual and/or physical abuse) have been implicated as important contributors to the development of functional GI disorders and the gut microbiota is  particularly vulnerable to these stressors.

Research suggests that stress, whether acute or chronic, creates a dysbiotic gut microbiome which can induce anxiety and depression via metabolites produced by the gut microbiota that can modulate brain biochemistry and behavior. Neurotransmitter metabolism can be altered by the gut microbiota which may then affect depression or anxiety, suggesting the potential for treatment with probiotics, alone or as an adjuvant to traditional therapy.


Pharmaceuticals and the Gut Microbiome

The gut microbiota plays a large role in the metabolism of many common medications, for example by assisting in the conversion of inactive medications (e.g., prodrugs) and nutrients into active medications and nutrients. For example, foods such as fruits, vegetables, cereals and coffee contain conjugated hydroxycinnamates which are antioxidant and anti- inflammatory compounds that require activation by the gut microbiota.This begs the question as to whether variations in medication responses between people is due to alterations in their gut microbiome.

The gut has many mechanisms that protect against ingested pathogens including the gut microbiota as well as an acidic gastric environment, optimal bile flow and propulstion through the gut. The gut microbiota protects against pathogens by competing for binding sites, competing for requirements, and by release of inhibitory molecules. But when these protective mechanisms are disrupted, an imbalance in the gut microbiota can occur.


Antibiotics and the Gut Microbiome

Antibiotic therapies not only target specific microorganisms causing an infection, but they also the impact the microbial communities in the gut. Most antibiotics have broad-spectrum activity so they can be used to treat many diseases but the gut microbiota are also affected, with a potentially negative effect that may persist long after the antibiotics have been discontinued. Antibiotics can also trigger the growth of antibiotic-resistant bacteria strains which can act as a reservoir for resistance genes in the gut microenvironment.

Decreased diversity in the microbiome typically follows antibiotic treatment and some healthful bacteria are lost from the community indefinitely. which can leave detrimental effects. The antibiotic spectrum of activity and dose will influence the shift in gut microbiota composition and can lead to increased colonization and infection by opportunistic organisms such as Clostridium difficile and Candida albicans. Antibiotic-induced changes can also include alterations in the metabolites produced by the microbiota such as short-chain fatty acids. Short-chain fatty acids (SCFA) are beneficial for gut health because they serve as a primary food source for the microbiota and they are involved with water and electrolyte absorption and they help to maintain the intestinal barrier (see Leaky Gut).

In summary, a dysregulated, imbalanced gut microbime, whether induced by stress, antibiotics or other conditions can result in disruption of the immune system and lead to increased susceptibility to disease.

Dysregulation of the Gut Microbiota

Small Intestinal Bacterial Overgrowth (SIBO)

Small intestinal bacterial overgrowth (SIBO) is an example of a pathologic condition associated with dysregulation and impairment of the gut microbiota. SIBO is a condition in which the presence of excessive numbers of bacteria in the small bowel causes gastrointestinal symptoms including abdominal pain, bloating, gas, distention, flatulence, and diarrhea, present in more than two- thirds of SIBO patients. Some patients may also complain of fatigue and poor concentration

In severe cases, nutritional deficiencies including vitamin B12, vitamin D, and iron deficiencies can occur. However, no single symptom can be specifically attributed to SIBO. Symptoms often masquerade as other diagnoses such as IBS, functional diarrhea, functional dyspepsia, or bloating. This is due in part to the varied presentation of patients with SIBO and the number of underlying risk factors that can lead to SIBO. SIBO has been linked to diseases such as irritable bowel syndrome (IBS), inflammatory bowel diseases (IBD) including Crohn’s and ulcerative colitis, cirrhosis, fatty liver, postgastrectomy syndrome, and a variety of other conditions.

For example, in a patient with chronic pancreatitis, it may be difficult to conclude whether diarrhea results from pancreatic enzyme insufficiency or from coexistent SIBO. Similarly, in patients with Crohn’s disease, particularly those having undergone surgery, symptoms of abdominal pain, boating, and diarrhea could result from SIBO vs that of active inflammation, bile acid malabsorption, or postoperative strictures.

Several conditions such as intestinal dysmotility, altered GI anatomy, immune deficiencies, and reduced stomach acidity are predisposing factors for the development of SIBO.

While reduced stomach acidity can be a result of Helicobacter pylori colonization and aging, many people also take medications such as proton pump inhibitors (PPIs) to reduce their gastric acidity for stress ulcer prevention or gastric esophageal reflux disease (GERD).  PPIs are known to alter the gut microbiota in 50% of patients on long-term treatment withPPIs. Although PPI duration is related to incidence of SIBO, there is a lack of knowledge regarding the appropriate or safe duration for taking PPIs.

Given the protective role gastric acidity has in regards to protecting against ingested pathogens, it is plausible that prolonged use of gastric acid suppressants may contribute to the incidence of SIBO and patients should be judicious in their use.

There are no universally accepted treatment approaches to treatment for SIBO. There are mixed reports of effectiveness for treatment with diet, antibiotics, probiotics and fecal transplantation.



The impact of the gut microbiome on health and disease is currently one of the most stimulating areas of medicine. Learning more about the gut microbiome  may provide new treatment options for many conditions and diseases currently resistant to effective management including fibromyalgia, irritable bowel disease, Crohn’s, ulcerative colitis and autism.

The medical world is just beginning to learn about the gut microbiome,  its role in dietary intake and disease development, and the effect of probiotic supplementation on various disease states.



Gut Microbiota

Gut Microbiota Overviews

  1. The Gut Microbiome- What we do and don’t know – 2015
  2. The role of the microbiome for human health- from basic science to clinical applications – 2018
  3. Influence of diet on the gut microbiome and implications for human health – 2017
  4. Man and the Microbiome- A New Theory of Everything? – PubMed 2019


Gut Microbiota – Pain

  1. Stress and the Microbiota–Gut–Brain Axis in Visceral Pain – Relevance to Irritable Bowel Syndrome – 2016
  2. The Role of the Gastrointestinal Microbiota in Visceral Pain – PubMed 2017
  3. Gut microbiota regulates neuropathic pain – potential mechanisms and therapeutic strategy – 2020
  4. Pain and Opioid-Induced Gut Microbial Dysbiosis – 2022


Gut Microbiota – Fibromyalgia

  1. Gut–Pain Connection Reaffirmed by Microbiome Differences in Fibromyalgia Patients and Controls – 2019


Gut Microbiota – Psychiatric Disorders

  1. Disentangling What We Know About Microbes and Mental Health – 2019

Gut Microbiota – Small Intestinal Bacterial Overgrowth (SIBO)

  1. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth – 2019



Probiotics – Overviews

  1. Role of Probiotics in Human Gut Microbiome-Associated Diseases – 2019

Probiotics – Foods


Probiotics – IBD (Inflammatory Bowel Diseases)

  1. Cellular and Molecular Therapeutic Targets in Inflammatory Bowel Disease—Focusing on Intestinal Barrier Function – 2019


Probiotics – IBS

  1. Stress and the Microbiota–Gut–Brain Axis in Visceral Pain – Relevance to Irritable Bowel Syndrome – 2016
  2. Adherence to the pro-inflammatory diet in relation to prevalence of irritable bowel syndrome – 2019
  3. The Evolving Role of Gut Microbiota in the Management of Irritable Bowel Syndrome – An Overview of the Current Knowledge – 2020


Probiotics – Infections

  1. Prevention of respiratory syncytial virus infection with probiotic lactic acid bacterium Lactobacillus gasseri SBT2055 – 2019
  2. Probiotics and Paraprobiotics in Viral Infection – Clinical Application and Effects on the Innate and Acquired Immune Systems – 2018
  3. Probiotics in respiratory virus infections – 2014


Probiotics – Pain

  1. Lactobacillus paracasei S16 Alleviates Lumbar Disc Herniation by Modulating Inflammation Response and Gut Microbiota – 2021.pdf
  2. Visceral pain – gut microbiota, a new hope? – 2019