The Microbiome

A significant part of the health and function of the digestive tract is the commensal micro flora which is referred to as the human gut microbiome.  The microflora consists of viral, fungal, protozoans, archaea and bacteriophage flora that have beneficial roles. [2.56]

The human microbiome in the gut, lung, skin and other mucous membranes play a role in both health and disease has been researched extensively, demonstrating its involvement in almost every aspect of human biology including digestion, immunity and even central nervous system function. [2.3][2.4].  The microbiome also supports synthesis and release of antimicrobial peptides from different gastrointestinal cells. [2.57] Antimicrobial peptides are broad spectrum natural antimicrobials that have recently been considered as the Achille’s Heel of antimicrobial resistance. [2.58] [2.59] In other words, a healthy microbiome supports one of the body’s best defense mechanisms against antimicrobial resistance. This is a really cool and hot topic now in AMR.

​ Many factors can impact the health of the human gut microbiome. For example:

  • Diet and food additives [2.5]

  • Exercise and sleep [2.6]

  • Medications including NSAIDs, PPIs, metformin, antibiotics and others [2.7] [2.8]

  • Aging

  • Environmental toxicants

Imbalance of normal gut flora (often termed dysbiosis) can negatively alter the physiological processes that the microbiome is responsible for, leaving the body more susceptible to opportunistic infections. An altered gut microbiome also has been linked with gastrointestinal conditions such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), and wider systemic manifestations of disease such as obesity, type 2 diabetes, autoimmunity, mental health issues and allergy. [2.3]


One of the main contributing factors to imbalanced gut flora is the inappropriate use of antibiotics. Maintaining a healthful microbiome during antibiotic therapy can help reduce the risk of antimicrobial resistance.  This has been achieved with the use of probiotics along with antibiotics. [2.8]  Probiotics are often taken at opposite times to antibiotics.

    Key Points