Donor-dependent Fecal Microbiota Transplantation Efficacy Against Necrotizing Enterocolitis in Preterm Pigs

Abstract

BackgroundFecal microbiota transplantation (FMT) has shown high cure rates against recurrent Clostridioides difficile infection regardless of donor microbiota characteristics, whereas the clinical response of FMT in inflammatory bowel disease appears to be donor-dependent. We recently showed that FMT from healthy suckling piglet donors to newborn preterm piglets decreased the risk of necrotizing enterocolitis (NEC), a serious gastrointestinal disease of preterm infants, but could not replicate this finding in a follow-up study using phenotypically similar donors. This gave us the opportunity to directly investigate the microbiota dynamics of clinically efficient FMT. In this experiment, preterm piglets (n=38) were randomly allocated to receive control saline or FMT from inferior (FMT1) or superior donors (FMT2) by rectal administration. All animals were fed infant formula for four days to induce NEC-like lesions before necropsy and gut pathological evaluation. Donor and recipient colonic microbiotas were analyzed by 16S rRNA gene amplicon sequencing and shotgun metagenomics.ResultsAlthough the two donor microbiotas closely resembled one another, only FMT2 recipients had improved body growth and lower intestinal permeability relative to control, and were protected against NEC. Both FMT groups had shifted colon microbiota composition relative to CON, with increased lactobacilli relative abundance, but FMT2 recipients had a higher lactobacilli abundance relative to FMT1. Limosilactobacillus reuteri and Lactobacillus crispatus strains of FMT recipients showed high phylogenetic similarity with their respective donors, indicating successful engraftment. Further, NEC severity was positively associated with Clostridoides difficile, Clostridium perfringens and Enterococcus faecium abundance, while Lmb. reuteri and Lb. crispatus negatively correlated with diarrhea severity. Genome-resolved analysis indicated a higher gut replication rate of lactobacilli in FMT2 recipients, and identified specific glycosaminoglycan-degrading Bacteroides in the superior donor.ConclusionsFMT efficacy against NEC is donor-dependent, and introduced lactobacilli manifest strain-level differences with respect to colonizing recipients. Using shotgun metagenomics, we traced the engrafted strains back from donors and identified donor-specific microbes of potential importance. This may accelerate our understanding of optimal donor selection for clinical FMT.

Necrotizing enterocolitis: Bench to bedside approaches and advancing our understanding of disease pathogenesis

“…Pigs share many features of anatomy and physiology with humans, rendering them one of the more popular choices when exploring NEC pathogenesis. Additionally, the piglet's larger size affords the ability to study preterm neonates (148,149). Piglets are a good model for testing preclinical drugs, effects of various diet formulations, and pathological manifestation on NEC (150).…”

Current therapy option for necrotizing enterocolitis: Practicalities and challenge

“…Even though FMT has shown promising properties in preventing NEC, FMT is associated with safety concerns because no screening method will be able to exclude transfer of an infectious agent from the donor. Yan et al suggest that the guts of recipients had higher levels of pathogenic signatures from Escherichia coli and Salmonella enterica, which may be a risk factor (68). Oral FMT administration increases lethal sepsis incidence and overall mortality by exposing the proximal gut to potentially pathogenic organisms (66).…”

“…To improve the safety of FMT, Fecal filtrate transplantation (FFT) and FMT sterilization by ultraviolet radiation are techniques that remove the bacterial component from donor feces by sterile filtration (69,70). Most studies found that fecal donors are mainly 10-day-old healthy piglets (66,68,69). However, there are no standard procedures for selecting donors in NEC animal models.…”