Dr. Denef has shown that even bacteria with the same fingerprint can have slightly different genomic profiles, and that these different profiles can change the bacterial composition. To put the idea of small genetic differences leading to large changes in phenotype and ecology, consider that the genomes of humans and chimpanzees are 99.9% similar - but that differing 0.01% makes a world of difference. Do these types of difference matter in bacteria? The answer is a resounding yes. One all-too-common example of small differences within the same species is antibiotic resistance. Not all strains of Staphylococcus aureus (the bug that causes staph infections) are harmful, and most people's skin is permanently colonized with these bacteria to no ill effect. But if you get infected with MRSA - the drug resistant strain - it will lead to a medical emergency. However, if you compared the normal strain to the resistant stain using the same techniques we use to fingerprint bacteria, they'd come up as the same species.
Antibiotic resistance is the best example in bacteria that affect humans, and right now we just don't know how common these differences are in the bacteria living in our gut. They could be common, and they could have drastic effects (imagine if these kinds of differences caused irritable bowel syndrome!) or they could just end up being a scientific curiosity. But we won't know until we look.