The DOF is a function of your f-stops. At f/2.8 (your widest aperture) your DOF is going to be very shallow. That is, if you focus on a polyp in front, the next one behind it will already begin to blur. If you wanted to include the polyps behind and have them in focus, you would start to close the aperature by going to f/4, f/5.6, f/8 etc. You would need to set the camera to aperture priority. However, the more you aperture closes, the less light lets in so your camera is going to compensate by slowing the shutter speed. Any movement is going to cause motion blur. You can fix this with a nice flash unit if your so inclined.
In the second photo, the polyps in front are OoF and the Ones in back are OoF. The one in the center is fine. So, you need to deside before you take the shot what you want the composure to be. Have an idea in your head what you want the picture to look like. If you want that polyp in focus, then the front ones are distracting and you can just crop them out in post processing. If you want the ones in front to be in focus, you probably need to back up a little. You may have been inside the minimum focal distance. Either that or focus on the front ones and shoot at f/8 or f/11.
Mike