Clostridium difficile

Often abbreviated to C. difficile or just C. diff. C. difficile can cause diarrhea and inflammation in infected patients, and spreads through a fecal-oral mechanism, generally the result of poor hygiene. Although C. difficile infections can respond poorly to antibiotics, recent research shows that fecal-microbiota transplants (FMT) can be effective. FMT involves transplanting fecal matter from a healthy donor into the infected patient’s gut in an effort to repopulate their microbiome. FMT is, however, an unusual approach.

Clostridium difficile (pronounced “closs-TRID-ee-um diff-ee-SEAL”) is from the genus (or group) Clostridium, other species of which are common and harmless occupants of the human gut. The genus name Clostridium comes from the Greek word klôstêr, which means “spindle”. Under a microscope, Clostridium bacteria have a cylinder-shape with a bulge at one end, resembling the spindles used in cloth weaving. The species name “difficile” is a form of the Latin adjective “difficilis,” because the organism proved problematic to isolate when it was first identified in 1935.

The main symptoms of Clostridium difficile infection are watery diarrhea, fever, loss of appetite, nausea, and abdominal pain. Treatment may involve the prescription of antibiotics, and the experimental and somewhat rare (but often surprisingly effective) use of fecal microbiome transplantation, in which specially-processed fecal matter from a healthy donor is transplanted into the patient’s gut in order to recolonize it with non-pathogenic bacteria.


1. Natalya Yutin and Michael Y. Galperin. (2013). A genomic update on clostridial phylogeny: Gram-negative spore-formers and other misplaced clostridia. Environ Microbiol, 15(10), 2631–2641. 

2. Pant, C., Deshpande, A., Altaf, M. A., Minocha, A., Sferra, T. J., & Altaf, M. A. (2013). Clostridium difficile infection in children : a comprehensive review. Current Medical Research and Opinion, 29(8), 967–984. 

3. Cohen, N. A., Ami, R. Ben, Guzner-gur, H., Santo, M. E., Halpern, Z., & Maharshak, N. (2015). Fecal Microbiota Transplantation for Clostridium difficile-Associated Diarrhea. IMAJ, 17(August), 510–515. 

4. Clostridium review on the Center for Disease Control and Prevention (CDC) website. http://www.cdc. gov/HAI/organisms/cdiff/Cdiff_faqs_HCP.html#a9

Welcome to uBiome!

We are the world’s first effort to map the human microbiome with citizen science. Our sequencing service provides information and tools for you to explore the populations of bacteria that live on and inside your body.

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Based on research from the NIH Human Microbiome Project, we've perfected the technology to perform large-scale microbiome studies. The knowledge we'll gain may (one day) empower people to live healthier and accelerate our understanding of the world around us. For the individual, we leverage this technology to help you better understand your own microbiome. Here's what you can learn:



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