Under that definition, humans make a species. Horses make a species, donkeys make a species, but mules do not. Apparently in the world of Star Trek, Klingons and humans make a species: Worf (Klingon) had a child with a half-human/half-Klingon woman, and Tom Paris (human) had a child with a half-human/half-Klingon woman. Not sure about Vulcans and Romulans...obviously they can mate, but I'm not sure Spock himself can have children, perhaps we'll find out in a future movie. In Futurama, Kiff reproduced with Leela.
As to the concept of a human as a "super-organism", the problem with bacteria being part of the equation is that they do not transmit their replicator payload through the germ-line transmission vector. They are not integrated into the next generation in whole or in part. Via the concept of the extended phenotype they may alter and extend their environment to improve their chance of success (and often mothers and children have the same bacteria flora), but it's better to think of it as symbiosis (or in the worst case, parasitism) than true "super-organism" reproduction. (Me thinks!)