The Human Microbiome


CDI Scope Clinical Trial Recurrent C Diff

The human microbiome is defined as the entire microbial community (bacteria, fungi, viruses and protozoa) present in the human body. The human microbiome aids in the development and maintenance of the immune system and metabolism among other important body functions.

The most dense and diverse microbial community in humans has been found in the gastrointestinal tract. Clinical and scientific studies show that disturbances to the gut microbiota known as “dysbiosis,”1 may be involved in many human conditions including inflammatory, metabolic, liver, neurological, and infectious diseases.

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Advances in understanding about the human microbiome may open the possibility to develop new microbiota-based drug therapies for challenging diseases. Large research projects including the Human Microbiome Project2 in the U.S. and the MetaHIT Project3 in Europe accelerated research on the human microbiome. Scientists are quickly learning the details of how these microbial communities interact and the roles they play in health and disease.

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What is C. difficile infection?

C. difficile infection (CDI) is a bacterial infection of the gut. In the US, CDI accounts for nearly 225,000 infections and approximately 12,800 deaths each year. It is believed that CDI is caused by a disruption of the normal, healthy balance of microorganisms (tiny living cells such as bacteria) in the gut after taking antibiotics. Many people with CDI are cured with a course of antibiotics but this is not the case for everyone. Some people have repeated episodes of severe diarrhea that resolve while the person is taking antibiotics, but the diarrhea typically returns when the antibiotics are stopped. This type of CDI is called “recurrent CDI”.


How is recurrent CDI treated?

For many years, doctors have treated people with recurrent CDI with a solution made of stool from healthy people. The goal of this treatment is to prevent recurrence of diarrhea by introducing a healthy mix of microorganisms to the gut. This therapy is called “fecal transplant”. Doctors have found that a fecal transplant can be an effective way to prevent recurrence of CDI. Doctors may use a procedure called colonoscopy to deliver the fecal transplant into the large bowel (last part of the intestines, also called colon). 

  1. Simon Carding, Kristin Verbeke, Daniel T. Vipond, Bernard M. Corfe & Lauren J. Owen (2015) Dysbiosis of the gut microbiota in disease, Microbial Ecology in Health and Disease, 26:1, DOI: 10.3402/mehd.v26.261912
  2. NIH Human Microbiome Project – Home (hmpdacc.org), accessed 19Sep2023
  3. Qin, J., Li, R., Raes, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010). https://doi.org/10.1038/nature08821