The Guide stem appears in Metroid Prime in the Canyon Cavern located in the Tallon Overworld. It appears to be nothing more than a stalk with a glowing orange bulb on it. It is seen hanging on tree roots that descend underground. It seems to thrive in dark areas like the Saturnine. According to the Logbook, it is a "Pervasive indigenous species of bioluminescent weed."
"Species: Guide stem. Pervasive indigenous species of bioluminescent weed."