Reproducible chemostat cultures to minimize eukaryotic viruses from fecal transplant material. ChemostatVirome

During the last decade it has become evident that () complex diseases such as metabolic syndrome, autoimmune diseases and colon cancer are associated with imbalances of gut microbiome (GM). This makes the GM an attractive therapeutic target for faecal microbiota transplantation (FMT). During FMT in addition to bacteria also archaea and prokaryotic as well as eukaryotic viruses are transferred. Recent studies indicate the role of bacteriophages for successful FMT. However, wider clinical application of FMT is unlikely due to donor variability and concerns of infection risks by bacteria and human viruses. To overcome these challenges, mouse cecal and human fecal material were propagated in chemostat cultures. Environmental conditions supported reproduction of bacteria, archaea, and phages, whilst multiplication of eukaryotic viruses was prevented by the absence of eukaryotic host cells. The results showed decrease of the median relative abundance of contigs of eukaryotic viruses from 0.2 % to below 0.01 %. The number of phage-assigned OTUs remained over 1000 x higher than these of eukaryotic viral OTUs after 5 volumes dilution. The corresponding bacterial virome profiles showed dilution rate dependency, a reproducibility between biological replicates, and maintained high diversity. The dominant viral taxa in mice cecal and human fecal matters were Petitvirales and Tubulavirales but the chemostat cultured phageomes contained mainly taxa from Caudoviricetes. This proof-of-concept cultivation approach may constitute the first step of developing novel therapeutic tools with low risk of infection from the donor material to target a broad spectrum of gut-related diseases.