As far as bacteria are concerned, other living creatures are just another niche to exploit, which means that pretty much every animal and plant has a set of bacterial pathogens that come along with it. These bacteria have made the animal in question their speciality, and are highly adapted to live inside their hosts. While these bacteria often make the host ill, or less fit, or sometimes dead, the longer they live with their host, overall, the less they damage it. After all, it's no help to the bacteria if their home drops down dead right after they've moved in.
A great example of this appeared in PLoS Pathogens this month (reference 1), concerning the bacteria Wolbachia. These bacteria infect insects and other arthropods and are much beloved of journalists (well, compared to other insect bacteria at least) because one of their effects is to stop insects producing male offspring (so only female survive to pass on the bacterial genome), which gives journalists the opportunity to write silly headlines.
As well as passing from females onto their offspring, Wolbachia can also be transmitted horizontally, that is between insects in the same generation. In its normal host the Wolbachia is not hugely damaging (apart from removing all males from the population) but when transmitted to a new species it causes various unpleasant nervous system complications, often leading to death. Clearly, the bacteria are more virulent when they encounter a new species. However when the bacterial infection was closely examined, it was found that infected individuals of both species contained the same number of bacteria. It wasn't just that the new species couldn't respond to the infection, it was in fact the way they responded that was doing the damage.
As it turns out, the reason Wolbachia are more dangerous in new species isn't because the bacteria go wild in the unexplored territory, rather it's because the new host doesn't know how to deal with them. The insects that are used to dealing with the presence of the bacteria have developed ways to contain the infection, or just tolerate it. New species however, tend to panic, particularly as the bacteria tend to congregate in the gonads (sex organs) and the central nervous system, which even insects understand are bad places to have bacteria.
As the bacteria are found inside cells, the best way for an insect immune system to get rid of them, is by destroying the cells that house the bacteria. Which, as previously mentioned, are mainly the gonads and the central nervous system. When the Wolbachia get into a new species, the first response of the insect is to quickly and efficiently destroy any cells which have bacteria inside them. As a consequence the unfortunate insect basically destroys its own brain, leading to various unpleasant symptoms and death.
Even in insects, the immune system is vital to defend animals from bacterial, fungal, and viral attacks. However it's fascinating to see the cases where the immune system (even 'primitave' immune systems that consist of nothing more than infected cells quickly being removed) can lead to issues by over-reacting to a threat. The best response to the Wolbachia is for the insects to learn to deal with it, rather than to attempt to launch counter-attacks which can be damaging for the animal as a whole.
Reference 1:Le Clec'h W, Braquart-Varnier C, Raimond M, Ferdy JB, Bouchon D, & Sicard M (2012). High virulence of wolbachia after host switching: when autophagy hurts. PLoS pathogens, 8 (8) PMID: 22876183
Reference 2: (2004) Genome Sequence of the Intracellular Bacterium Wolbachia. PLoS Biol 2(3): e76. doi:10.1371/journal.pbio.0020076
Reference 3: Wernegreen JJ (2004) Endosymbiosis: Lessons in Conflict Resolution. PLoS Biol 2(3): e68. doi:10.1371/journal.pbio.0020068