Breaking down the role of the gut microbiome

When it comes to the human body, we are never truly alone. In fact, we share our bodies – specifically the surfaces of our skin, noses, mouths, vaginas for some of us and intestinal tracts – with a diverse and complex colony of microorganisms, called the microbiome. These microscopic ecosystems play host to trillions of bacteria, fungi, archaea and viruses, known collectively as microbiota, that comprise an estimated 500 to 1,000 different species.¹ ² ³ ⁴

Advances in biotechnology have supported a surge in research, including the National Institutes of Health’s Human Microbiome Project⁵, to understand the composition and function of the microbiome. Interest in the role of the microbiome in promoting human health and mitigating disease is at an all-time high.⁶

The gut microbiome plays a central role in keeping us healthy. This colony of microbiota lives within the large intestine, just beyond the anus and rectum⁷, and has been shown to enhance immunity, prevent colonization by harmful pathogens and form a protective barrier between the cells of the intestine walls and its contents.⁸ ⁹ ¹⁰ The gut microbiome, now considered a distinct and essential organ within the body,¹¹ is also connected to a wide range of diseases, such as obesity, inflammatory bowel disease, liver disease and infections to name a few.⁶ 

There is a relationship between the microbiota living within our gut and the human cells that make up the walls of the intestines. Everyone has their own diverse mix of microbiota,¹ ¹²  but the most prevalent phyla of organisms are Bacteroidetes and Firmicutes.¹³ ¹⁴ ¹⁵ While both of these phyla include beneficial and harmful species, the helpful ones play an important role in the microbiome’s protective function. Bacteroidetes, are gram-negative bacteria, some of which modulate the immune system and may have the ability to stop harmful pathogens.¹³ ¹⁶ ¹⁷ ¹⁸ Gram-positive Firmicutes are composed of helpful and harmful bacteria.² ¹⁷ Firmicutes are the most abundant and diverse bacterial gut species,² with functions that include anti-inflammatory effects¹⁹ ²⁰ ²¹ and fortification of the gut barrier (along with other bacteria).²² ²³ ²⁴

When the volume and diversity of microbiota are disrupted, an imbalance, called dysbiosis, occurs. Dysbiosis can be caused by diet, hygiene and other drug therapies, including antibiotics used to treat infections.⁸ ²⁵ ²⁶ Dysbiosis has been associated with a range of GI and non-GI diseases, including neurologic, metabolic, liver, inflammatory diseases and infections such as C. difficile.⁸ ²⁶ ²⁷ 

Classified as an urgent public health threat by the Centers for Disease Control and Prevention (CDC), C. difficile infection is a serious disease that may result in life-threatening medical emergencies, causing about half a million illnesses and nearly 30,000 deaths in the U.S. each year.²⁷ Because C. difficile infections are extremely contagious they can spread easily in communal settings and are the most common healthcare-associated infections in U.S. hospitals.²² ²⁸ ²⁹ The burden of these infections on the U.S. healthcare system is significant. In fact, two studies show 57% of Medicare patients with C. difficile infection were hospitalized at least twice a year, with each hospital stay lasting an average of 18 days. Total medical costs for Medicare patients with recurrent C. difficile infection ranged from $131,000 to $207,000.³⁰ ³¹

C. difficile infection is often the start of a vicious cycle of recurrence, and while antibiotics are the standard treatment for initial C. difficile infection, they fail to address the underlying dysbiosis associated with recurrence, increasing the likelihood of subsequent recurrences.³² ³³ ³⁴ In fact, studies have shown C. difficile infection recurs in up to 35% of cases within eight weeks of initial diagnosis. Moreover, up to 65% of those patients go on to experience additional recurrences.²⁰ ³⁵

To reduce the likelihood of recurrence, it is necessary to address dysbiosis. That means repopulating the gut microbiome with diverse and plentiful healthy microbiota.⁸ ²¹ ²² While probiotics are helpful for maintaining a healthy gut environment, they do not restore the microbiome by addressing dysbiosis.³⁶ ³⁷ ³⁸ The good news is that as scientists advance their understanding of the gut microbiome, they are shedding new light on ways to unlock its power to address serious diseases, including the vicious cycle of C. difficile infection recurrence.

To learn more about the gut microbiome, visit


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