The invention discloses a Bacillus methylotrophicus strain VJ4-1 of which the preservation number is CCTCC No:M 2012004. The invention provides a tobacco chaff extract prepared by using microbe Bacillus methylotrophicus and conducting biotransformation and an application of the chaff extract in tobacco. According to the invention, by applying the fermented and purified tobacco chaff extract in cigarettes, the extract is in harmony with the smoke, reduces miscellaneous gases, reduces the irritancy, obviously adding characteristic fragrance, enriches the tobacco aroma, and improves the tasting; the method has the advantages of simple process, mild reaction conditions, low pollution, high concentration of the products, simple extraction steps, clean production, environmentally friendly product, safety and reliability, wide sources of main raw materials, extremely low cost, and nature, and has an industrial production prospect.