It's a safe bet that there is no animal that could survive without its internal flora of microorganisms. Every moth, wildebeest, or aardvark bears a specialized community of germs, some of them so fitted to their host species that they are found nowhere else. When these animals vanish, their internal flora either find new hosts or go extinct. Most of them will die out. Some will find a convenient alternative organism to inhabit.
Humans are likely to be convenient fairly often.
Many of these organisms will be relatively benign. But some, like HIV, the Ebola virus, and hantavirus, will interfere violently with the workings of the human body. Less-deadly forms of the pathogens survive more reliably, thus reproducing more successfully, thus being selected for in an evolutionary sense. There is some evidence that HIV is becoming less-virulent with the passing decades, and you yourself may well harbor Ebola Reston, a benign strain of that frightening virus. As habitats are destroyed and their resident species obliterated, humans face the prospect of a series of plagues.