Jiri Hulcr and his colleagues launched the project to interest people in microbiology and teach them about the bacteria that is found on skin. Researchers opted for belly buttons because, as they said, "no one volunteers when we ask for armpit samples."
Seriously, however, the scientists noted that belly buttons are relatively isolated, making them a place where microbes are safe, and can grow easily. Of course, bacteria growing on folks with outies might dispute that. Bacteria on folks with innies have another advantage: few people wash the area with soap.
Additionally, since, as Hulcr said, "the belly button doesn't produce any special secretions or oils, such as other protected body parts, such as the nose or armpit, [...] the microflora inside the belly button is fairly representative of the rest of the body."
Volunteers are given a sterile cotton swab, and then are told to turn it around in their navel three times and place the swab in a vial. Scientists culture the bacteria, and once they have grown enough, they are photographed. The volunteers are given a sample number, so that they can view their bacteria online.
Participants also submit information about their habits and other details. For example, they are asked how often they wash their navels, their age, sex, ethnicity, and where they grew up, as well as whether they have an "innie" or an "outie."
Although the participants are anonymous, IDed only by a sample number, the researchers themselves submitted their own samples. Looking at some of the samples, one has to wonder if a potential date looked at them, they would change their mind.
Image Source: Belly Button Biodiversity Project