Plain language summary
The microbiome and its effects on health have received plenty of attention and research. A lot less is known about the virome, the collection of viruses in and on our bodies. This pilot observational study looked at the connection between the viruses and bacteria in the guts of patients with Clostridium difficile infection (CDI), compared to healthy controls, and changes and treatment outcomes observed after faecal microbiota transplantation (FMT) compared to vancomycin treatment. The study showed that, compared to healthy household controls, people with CDI had significant viral dysbiosis, in particular higher abundance but lower diversity, richness and evenness of the bacteriophage (a virus that infects bacteria) Caudovirales, the most abundant intestinal bacteriophage in humans. FMT changed both, the composition of the microbiome as well as the virome, whilst antibiotic treatment did not affect the bacteriophage composition. Treatment outcome with FMT depended on changes in Caudivirales. Although a small pilot study, according to the authors, this is the biggest study into the importance of intestinal viruses, and their correlation with the microbiome, in disease and for treatment outcomes. The authors point out that, as this was an observational study, it is not possible to ascertain whether the altered virome is a cause or a consequence of the disease.
Abstract
OBJECTIVE Faecal microbiota transplantation (FMT) is effective for the treatment of recurrent Clostridium difficile infection (CDI). Studies have shown bacterial colonisation after FMT, but data on viral alterations in CDI are scarce. We investigated enteric virome alterations in CDI and the association between viral transfer and clinical outcome in patients with CDI. DESIGN Ultra-deep metagenomic sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on stool samples from 24 subjects with CDI and 20 healthy controls. We longitudinally assessed the virome and bacterial microbiome changes in nine CDI subjects treated with FMT and five treated with vancomycin. Enteric virome alterations were assessed in association with treatment response. RESULTS Subjects with CDI demonstrated a significantly higher abundance of bacteriophage Caudovirales and a lower Caudovirales diversity, richness and evenness compared with healthy household controls. Significant correlations were observed between bacterial families Proteobacteria, Actinobacteria and Caudovirales taxa in CDI. FMT treatment resulted in a significant decrease in the abundance of Caudovirales in CDI. Cure after FMT was observed when donor-derived Caudovirales contigs occupied a larger fraction of the enteric virome in the recipients (p=0.024). In treatment responders, FMT was associated with alterations in the virome and the bacterial microbiome, while vancomycin treatment led to alterations in the bacterial community alone. CONCLUSIONS In a preliminary study, CDI is characterised by enteric virome dysbiosis. Treatment response in FMT was associated with a high colonisation level of donor-derived Caudovirales taxa in the recipient. Caudovirales bacteriophages may play a role in the efficacy of FMT in CDI. TRIAL REGISTRATION NUMBER NCT02570477.
Methodological quality
Allocation concealment
:
Not applicable
