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I notice the little red fruit flies gathering around the food bowl in the cage, probably from the fruit I put out for the rats. Then they stick around and find the poop. Is there any way to get rid of them and stop them from coming back or is this just something that comes with feeding rats fruit?
 

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Fruit flies are the worst, I mean at least they aren't like big fat flies, but they are annoying. I suggest you wash out your food bowl really well after having fruit in it.

You could put out traps for them, but honestly traps seem to attract more. If you'd want to try a trap get a bottle or an empty jar fill the bottom with apple cider vinegar or red wine and add dish soap. After you do that seal the top with saran wrap (plastic wrap) and rubber band it on. Make tiny holes in the plastic wrap and viola! you have a trap. Be aware that this might attract more fruit flies in the end.

Another solution you could try is to do a major clean. Clean out your sinks (kitchen, bathroom, shower and or tub) wash out your trash can, and immediately wipe up any food debris. Also keep fruits and veggies in the fridge during this time. It's annoying, but in the end the fruit flies won't find anywhere they'd want to lay more eggs and they'll die off.
 

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Clean the whole cage out. Keep litter boxes and food areas cleaned out till they are all dead. Follow Kelsbels advice for the rest of the house as well.
 

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Oh boy, last summer I had really messy roommates and we had a full out war with the fruit flies... No matter how many times I asked the roommates to not keep old food in their room, I know they did because they flies just never left. I put drain cleaner in all my drains, took out the trash every day, set up traps, kept the rat cage as clean as I could. In the end, winter weather killed them all but it was not a fun time. I would suggest a full clean of everywhere food is kept, check behind the fridge and stove too.

I found that setting traps AWAY from where the problem was really helped. Apple cider vinegar with some fruit in the bottom of a cup with foil or plastic wrap on the top (with the holes poked in it).
 

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We get them every now and then from bananas we buy. If I leave a peal in the trash too long they pop up and infest us for a couple weeks. One thing I've found that helps is if you put a little bit of orange juice or lemonade in the bottom of a small bowl or mug it will attract them and they will usually drown in the bottom of it. Other then that you have to avoid leaving fruit out on the counter and keep peals/cores out of the trash for a couple weeks until they die off.
 
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