The microbiota consists of trillions of commensal bacteria that function largely to regulate human physiology. An individuals microbiota, or microflora is established at a young age and is largely dependent on things such as exposure to antibiotics directly after birth, or contact with a family pet as an infant, for example. Each person has a unique microbiota, however there are some Bacteroidetes and Firmicutes that are highly conserved in all individuals. Disruption of the microbiota that leads to changes in composition or structure is called dysbiosis. When a foreign pathogen, such as C. difficile as you mentioned, invades the gastrointestinal tract it competes for nutrient sources and space to colonize. The balance within the microbiota is delicate, therefore if the foreign pathogen successfully competes for carbon sources or uses microbiota metabolism byproducts, they are able to survive, colonize, and express their virulence genes. The expression of these genes allows for pathogenesis and disease symptoms of the invading bacteria. The sensitivity of an individuals microbiome to foreign pathogens is different for each person, however all humans have mechanisms to protect microbiome homeostasis. For example, a mucus layer in the GI tract functions to inhibit invasion of foreign pathogens, but it cannot protect against all pathogens. Many times, the ability of a pathogen to disrupt the microbiota is dependent on its ability to evade the host defenses, and utilize the nutrients available.
I would highly recommend the journal article listed below! It discusses in much greater detail the relationship between the microbiome and invading pathogens.
Microbiol Spectr. 2015 Jun;3(3). doi: 10.1128/microbiolspec.MBP-0001-2014. Enteric Pathogens Exploit the Microbiota-generated Nutritional Environment of the Gut. Pacheco AR(1), Sperandio V(1).