Organogenesis and animal adaptation upon loss of body parts are crucial events in regeneration of all traits, and both are uncovered areas in biology. The organogenesis of the mouth and anus during regeneration was studied in Eudrilus eugeniae. It was found that the earthworm regenerates a functional mouth and anus in six days. During the course of organogenesis, the earthworm adopts unique starvation behavior for 5 days, and the starvation triggers the gut microflora of E. eugeniae to produce riboflavin. One of the efficient riboflavin-producing bacteria, Bacillus endophyticus, confirmed through 16S rRNA sequencing, has been isolated from its gut. The symbiotic association provides shelter and nutrition to the bacterium and the earthworm in return gets riboflavin to maintain homeostasis during the starvation period of early regeneration.