A bacteria scanner

A technology goal: to create a scanner capable of probing the bacterial population at a variable depth within tissue. How could you probe without damaging tissue? Maybe with a thin enough glass tube, you could sample many bacteria, while killing a only a few tissue cells. For example, a thin glass tube with small pores and an internal thread or "sponge". You insert the tube into tissue, pull back on the thread- to get a fresh sample,  then pull back a little more to isolate the sample, then remove the tube. Later, pull the thread more to expose the samples.