According to the spell description, at least on Google for 3.5,
You can comprehend and communicate with animals. You are able to ask questions of and receive answers from animals, although the spell doesn’t make them any more friendly or cooperative than normal.
The way I interpret this, the spell won't automatically make them friendly or cooperative, or automatically allow you to improve yourtheir mood. However, I don't see why that would stop you from conversing with them using the spell, to improve their mood with your words, which they can now understand due to the spell. Perhaps you could ask your DM if you can make a charisma check to see if you can talk them up to improve their mood.