Causes of weakened immune system? (snuffles flare-up)

As some of you may know my Boris has had problems with snuffles on and off since September, he's not had any symptoms since around Xmas but now they have recently come back. He's currently on Septrin which he gets twice daily, and it seems to slowly be taking effect, but I'm wondering what might have caused him to have a "relapse".

I know snuffles and other respiratory infections is usually caused by bacteria (pasteurella) and that these usually take over when the immune system is weakened, but that's the bit I can't work out. I don't know what could possibly have weakened his immune system. I've been thinking very hard and come up with some possible causes, I just need to know if they seem relevant at all or way too far-fetched.

1. Stress due to spring fever (which I obviously can't prevent)
2. Change in diet (lack of pellets really, as I ran out and couldn't get more straight away, so they went about a week without them)
3. Me not cleaning their room enough (Don't get me wrong it's never been filthy, but they had a cage in there that was difficult to clean out properly, I have now removed this and replaced it with another one)

Any thoughts? :wave:

It could also be change in weather, temperature, humidity...

Ive always thought its a bacteria called Pasteurella......as well as whats been mentioned.

Lily-Shane had terrible spine problems, her lung tissue going into the spinal humps.Picture an ECG...her spine went up and down like that.
This was contributory Im sure to her shocking runny nose....all her oesophagus and pipes in different places.

Well, they live in the basement. The humidity was checked when we moved in and apparently it's unusually low, so that's probably not it (although can't be sure). The temperature could potentially have been an underlying cause but I don't think there have been any major changes to be honest. It's pretty cold in there all year round. Hmm. :?

ETA: Perhaps I should change the thread title as what I really wonder is what could cause their immune systems to weaken, rather than what causes the actual condition...