Engraftment of bacteria after fecal microbiota transplantation is dependent on both frequency of dosing and duration of preparative antibiotic regimen

The gut microbiota has emerged as a key mediator of human physiology, and germ-free mice have been essential in demonstrating a role for the microbiome in disease. Preclinical models us-ing conventional mice offer the advantage of working with a mature immune system. However, optimal protocols for FMT engraftment in conventional mice are yet to be established.Conventional BALB/c mice were randomized to receive 3-day (3d) or 3-week (3w) antibiotic (ABX) regimen in their drinking water followed by 1 or 5-daily FMTs from a human donor. Fecal samples were collected longitudinally and characterized using 16S rRNA sequencing. Semi-targeted metabolomic profiling of fecal samples was done with LC-MS.Recovery of baseline diversity scores were greatest in the 3d groups, driven by re-emergence of mouse commensal microbiota. Greatest resemblance to donor microbiota was seen in the 3w+5-FMT group. Re-emergence of amplicon sequence variants (ASVs) from the mice at baseline was seen in all groups, while those related to the input material engrafted most robustly in the 3w+5-FMT group in two different strains of mice. Lastly, comparison of metabolomic profiles revealed distinct functional profiles by group.These results indicate successful model optimization and emphasize the importance of ABX du-ration and frequency of FMT dosing; the most stable and reliable colonization by donor ASVs was seen in the 3wk+5-FMT group.