Necrotizing enterocolitis (NEC) is a life-threatening gastrointestinal disorder afflicting preterm infants, which is currently unpreventable. Fecal microbiota transplantation (FMT) is a promising preventive therapy, but the transfer of pathogenic microbes or toxic compounds raise concern. Removal of bacteria from donor feces by micropore filtering may reduce this risk of bacterial infection, while residual bacteriophages could maintain the NEC-preventive effects. We aimed to assess preclinical efficacy and safety of fecal filtrate transplantation (FFT). Using fecal material from healthy suckling piglets, we compared rectal FMT administration (FMT, n = 16) with cognate FFT by either rectal (FFTr, n = 14) or oro-gastric administration (FFTo, n = 13) and saline (CON, n = 16) in preterm, cesarean-delivered piglets as models for preterm infants. We assessed gut pathology and analyzed mucosal and luminal bacterial and viral composition using 16S rRNA gene amplicon and meta-virome sequencing. Finally, we used isolated ileal mucosa, coupled with RNA-Seq, to gauge the host response to the different treatments. Oro-gastric FFT completely prevented NEC, which was confirmed by microscopy, whereas FMT did not perform better than control. Oro-gastric FFT increased viral diversity and reduced Proteobacteria relative abundance in the ileal mucosa relative to control. An induction of mucosal immunity was observed in response to FMT but not FFT. As preterm infants are extremely vulnerable to infections, rational NEC-preventive strategies need incontestable safety profiles. We show in a clinically relevant animal model that FFT, as opposed to FMT, efficiently prevents NEC without any recognizable side effects.

坏死性小肠结肠炎 (NEC) 是一种影响早产儿的危及生命的胃肠道疾病，目前无法预防。粪便微生物群移植（FMT）是一种很有前途的预防性疗法，但病原微生物或有毒化合物的转移引起了人们的关注。通过微孔过滤从供体粪便中去除细菌可以降低这种细菌感染的风险，而残留的噬菌体可以保持 NEC 预防效果。我们旨在评估粪便滤液移植（FFT）的临床前疗效和安全性。使用来自健康哺乳仔猪的粪便材料，我们比较了直肠 FMT 给药 (FMT, n  = 16) 与直肠 (FFTr, n  = 14) 或口胃给药 (FFTo, n = 13) 和生理盐水 (CON, n = 16) 在早产、剖宫产仔猪中作为早产儿的模型。我们使用 16S rRNA 基因扩增子和元病毒组测序评估了肠道病理学并分析了粘膜和腔内细菌和病毒的组成。最后，我们使用分离的回肠黏膜和 RNA-Seq 来衡量宿主对不同治疗的反应。口胃 FFT 完全阻止了 NEC，显微镜证实了这一点，而 FMT 的表现并不比对照好。与对照相比，口胃 FFT 增加了病毒多样性并降低了回肠黏膜中变形菌的相对丰度。观察到响应于 FMT 而不是 FFT 的黏膜免疫诱导。由于早产儿极易受到感染，因此合理的 NEC 预防策略需要无可争议的安全性。