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Background  Fecal microbiota transplantation (FMT) in patients with ulcerative colitis has shown variable efficacy depending on the protocol used. A previous randomized controlled trial reported that anaerobic preparation of donor stool contributes to improved efficacy. Despite the suggestion that viable obligate anaerobes would be decreased through aerobic handling, there have been only a limited number of reports on how these aerobic or anaerobic procedures affect the composition of viable microbiota in the fecal slurries used for FMT.    Methods  We adopted 16S and 23S rRNA-targeted reverse transcription-quantitative polymerase chain reaction to quantify viable bacteria in fecal slurries. This study utilized specific primers designed to detect obligate anaerobes (including  Clostridium coccoides  group,  C. leptum  subgroup,  Bacteroides fragilis  group,  Bifidobacterium ,  Atopobium  cluster, and  Prevotella ) and facultative anaerobes (including total lactobacilli,  Enterobacteriaceae ,  Enterococcus ,  Streptococcus,  and  Staphylococcus ). We then calculated the ratio change (RC) between before and after mixing, and compared the resulting values between anaerobic-prep and aerobic-prep in samples fixed immediately after blending (RC An0  vs. RC Ae0 ) and in samples maintained (under anaerobic or aerobic conditions) for 1 h after blending (RC An1  vs. RC Ae1 ).    Results  For most obligate anaerobes, the median RC tended to be less than 1, indicating that the number of obligate anaerobes was decreased by the blending procedure. However, in samples maintained for 1 h after blending, anaerobic-prep counteracted the decrease otherwise seen for the  C. coccoides  group and  B. fragilis  groups ( P  < 0.01 for both). The  C. leptum  subgroup also tended to show higher RC by anaerobic-prep than by aerobic-prep, although this effect was not statistically significant. Among facultative anaerobes,  Enterobacteriaceae ,  Enterococcus, and Staphylococcus  showed median RC values of more than 1, indicating that these organisms survived and even grew after mixing. Moreover, oxygen exposure had no significant influence on the survival of the facultative anaerobes.    Conclusions  The conditions under which the blending procedure was performed affected the proportion of live anaerobes in fecal slurries. The obligate anaerobes tended to be decreased by blending processes, but anaerobic-prep significantly mitigated this effect. Anaerobic-prep may improve the efficacy of FMT by permitting the efficient transfer of obligate anaerobes to patients with ulcerative colitis.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02325-9.

bmc microbiology

Stool preparation under anaerobic conditions contributes to retention of obligate anaerobes: potential improvement for fecal microbiota transplantation