Fecal virome is sufficient to reduce necrotizing enterocolitis

Abstract

Background: Fecal filtrate transfer (FFT, i.e. “sterile filtered” fecal matter) is gaining increasing attention as a safer alternative to traditional fecal microbiota transplantation (FMT) for treating gastrointestinal (GI) complications. Indeed, in the case of necrotizing enterocolitis (NEC), a life-threatening GI emergency occurring in preterm infants, FFT is superior to FMT in terms of both safety and efficacy when investigated in preterm piglets. Since fecal filtrate is virtually devoid of bacteria, prokaryotic viruses (bacteriophages) are assumed to mediate the beneficial effects by modulating the recipient gut microbiota. However, this assumption remains unproven. Results: To address this gap, we isolated the virome of donor feces from the residual postbiotic fluid with no loss of bacteriophage infective potential or bacteriophage spillover to the residual fluid. We then compared clinical and gut microbiota responses to these fractions with the parent FFT solution after transferring to NEC-susceptible preterm piglets. Importantly, transfer of isolated donor virome was equally effective as FFT in reducing the severity of NEC-like pathology, whereas the residual postbiotic fraction was ineffective. The bacterial compositional data corroborated clinical findings as virome transfer reduced the relative abundance of several NEC-associated pathogens e.g. Klebsiella pneumoniae and Clostridium perfringens. A viral metagenomics analysis indicated enrichment and diversification of recipient gut viral communities with concomitant constraining effect on bacterial composition in accordance with lytic phage predation of resident bacteria. Surprisingly, virome transfer but not residual postbiotic fluid was associated with suspected viral gastroenteritis as indicated by diarrhea, intestinal atrophy, and weight loss. Although virome sequencing did not reveal any obvious causative agent, we suggest that unidentified eukaryotic viruses are candidates responsible for these side effects. Conclusion: Using NEC as a relevant case for microbiota-directed therapy, we show that transfer of isolated fecal virome is sufficient to reduce pathogenic bacterial load and overall disease burden. However, we also highlight that receiving exogenous virome increases the risk of enteric virus infection. Despite diarrhea being a minor concern in the human infant context, future work should identify ways of eliminating eukaryotic viruses without losing treatment efficacy.

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments

“…These differently processed fecal viromes were evaluated in a C57BL/6J mouse C. difficile infection model [31] and compared with a saline solution, FMT (previously shown to effectively treat C. difficile infection in preclinical studies [32]), and untreated donor-filtrated feces (FVT-UnT). This proof-of-concept study represents an important first step towards developing safer and more consistent therapeutic approaches that can effectively target a wide range of gut-related diseases [12,13,16,19,[33][34][35], and potentially supplement FMT with phagemediated therapies.…”

“…This proof-of-concept study represents an important first step towards developing safer and more consistent therapeutic approaches that can effectively target a wide range of gut-related diseases [12,13,16,19,33–35], and potentially supplement FMT with phage-mediated therapies.…”