More than 400K MinION reads were obtained from three 1D/R9.5 runs of the rrn amplicon sequencing, obtained by amplification of the bacterial 16S-IT-23S gene markers from 24 human faecal DNA samples derived from subjects involved in a faecal microbiota transplantation (FMT) intervention. The long-read information was used to de novo assembly rrn to index and annotate in the rrn database and to perform a microbiota assessment at the species-level. Single-nucleotide variation analysis was also carried out to survey microbial species engraftment after FMT. Available data consist of albacore-basecalled pass fast5 files.