Clostridioides difficile is an anaerobic bacteria. Not only does it thrive without oxygen, but oxygen is actually toxic to it. When exposed to oxygen it dies, leaving behind spores which can be thought of as really tiny hard-shelled nuts. They are dormant and very resilient.

These spores get into our digestive tract when we swallow contaminated food or air. When they reach the colon which has little oxygen, they germinate which is analogous to a seed nut sprouting.

Under normal circumstances our colon’s microbiome, a community of micro-organisms (bacteria, fungi, viruses, phages), crowds out the germinated C. difficile cells, preventing them from multiplying sufficiently to cause disease. Think of this like throwing out walnuts onto a messy overgrown lawn of grass and weeds. You probably won’t get any walnut trees.

Antibiotics are the foundation of modern medicine. They are used to cure otherwise potentially fatal bacterial infections of the bladder, kidney, skin, lungs, abdomen, and blood. They allow us to safely perform complex surgeries, organ transplants, chemotherapy for cancer, and treat autoimmune diseases where the body's immune system is compromised.

Unfortunately, antibiotics are also toxic to the bacteria in our colon, disrupting our microbiome, decreasing its ability to protect us from a C. difficile infection. This is analogous to plowing the aforementioned lawn, which kills some of the weeds and grass and loosens the soil so that the walnuts sprout and take root to make trees.