We're probably not going to switch to models from sprites for a while, as sprites are really fast to render, and they look the same in the top-down camera angle that we have. However, here are a few things I can think of:
1) Nucleus model. We actually have a bunch of nucleus models at the moment, but all of them don't work for various reasons. We have a sketch drawn by atrox in the current version, but it doesn't look very professional. If you do decide to work on this, the best idea would be to create a unit sphere in blender, texture it, and render with one sun light directly above to create a uniform shadow. Then I can just take your rendered square and put it on the nucleus. This post and the two beneath it have more information.
2) You can try creating a new flagellum model since the old one doesn't really fit with the new graphics and a lot of people seem to dislike it. This is the harder of the four as it involves adding a skeleton and doing some anything, which might be hard to export to ogre. Again, if you choose this one, you will have to bake all of your cycles/mudbox textures to an image and UV unwrap the flagella since things like SSS, volumetric shaders, and other cycles stuff don't translate well into Ogre. For transparency, you can use the alpha channel of your texture.
3) You could try modeling a toxin emitter if you want. Basically, it should be a spherical organelle that has an animation that causes a small sphere to "bud off" and move away in a straight line. When the smaller sphere touches the membrane we can spawn a compound cloud at that location and return back to the static model. Not sure how you would do that though. Metaballs would look the nicest, but I'm not sure if it's possible to import metaballs into Ogre. You should try Googling that if you want to give it a try. Alternatively, you can try your own interpretation of how agent secretors should work.
4) Finally, you can model a couple bacteria species for when we implement them into the game. There should be multiple species (hopefully with distinctively different shapes and colors so that the player can easily tell them apart). While this is arguably the most important modeling you can do, it will be a while until bacteria actually make it into the game and people see your work.
These are the 4 I can think of at the moment. Choose whichever you feel most comfortable and inspired to work on, and ask anyone if you have questions/comments/concerns.
Nice to have you join the team! Hope you have a lot of fun.