The present invention relates to a method for preparing a fecal 5 microbiota sample of a donor subject. Said method includes the following steps: a) collecting at least one fecal microbiota sample from the donor subject； b) within a period of less than 5 minutes after collecting the sample, placing said sample obtained in step a) in an oxygen-tight collection device； c) mixing the sample obtained in step b) with at least one aqueous saline 10 solution containing at least one cryoprotectant and/or a filling agent； d) optionally, filtering the mixture obtained in step c), in particular by means of a filter comprising pores having a diameter of less than or equal to 0.7 mm, preferably less than or equal to 0.5 mm； and e) storing the mixture obtained in step c) or d) by freezing said mixture at a temperature 15 of between -15°C and -100°C. Steps b) to e) are carried out in anaerobiosis.
