FMT exhibits high cure rates (90% in average) when used to treat overgrowth of one specific pathogen, Cl. difficile, in the gut [54]. The success of FMT in rCDI treatment is not affected by a specific donor [55]. In a cohort compromising of 1999 FMT recipients and 28 donors, the rCDI cure rate was found to be high for all donors [54]. Encouraged by this overwhelming success, researchers have extended the use of FMT in a range of diseases characterized by GM dysbiosis e.g. IBD [56] and metabolic syndrome [57]. Contrarily, the super donor phenomenon appears to exist in FMT treatments of these diseases e.g. Crohn’s disease [16], ulcerative colitis [17, 18], irritable bowel syndrome [19], type-2 diabetes [57]. Accordingly, we found NEC prevention among preterm piglet FMT recipients to be donor dependent. Recipients of the superior donor feces (FMT2) showed no NEC cases relative to 23% NEC incidence in recipients of the inferior donor feces and 42% in the CON group. Moreover, FMT2 piglets exhibited improved gut function (e.g. barrier, digestion) and body weight gain.
A superior donor appears to be more essential for FMT use in multifactorial disease such as IBD and NEC, which result from complex interactions between host immune response, host genetics, GM, and exogenous intake e.g. formula feeding. Gut dysbiosis is implicated in the etiology and development of these diseases but none is considered to be solely induced by overgrowth of one specific microbe as rCDI. Given the existing redox potentials in gut [58], a preterm GM is usually characterized by relatively low microbial diversity and prolonged dominance of facultative anaerobes e.g. Enterobacter, Enterococcus and Staphylococcus, but delayed colonization by obligate anaerobes e.g. Bifidobacterium and Bacteroides [59]. This might provide favorable gastrointestinal condition of high NEC risk. Herein, we noticed that the donor-dependent phenomenon not only existed in the host response but also was reflected in the shifted recipient GM. Higher Shannon index and more lactobacilli but much less Cl. difficile, C. perfringens and E. faecium were found in the colon of FMT2 piglets receiving the superior donor feces.
Pathogen resistance is a noted advantage provided by GM [60], which is also expected to provide protection against NEC. Using Pearson’s correlation analysis, we found the shifted abundance of Cl. difficile and C. perfringens and E. faecium positively linked with increased pathological severity and gut inflammation. Although we cannot causally link these species with NEC, we still note that efficient FMT may inhibit the colonization of opportunistic pathogens. Consistently, functional profiling of GM indicated the FMT2 group contained much less microbial genes encoding staphyloferrin synthesis, but more genes associated with lysine and acetate biosynthesis in the gut. Staphyloferrin is high-affinity siderophore excreted by S. aureus to acquire iron to proliferate [61]. This mechanism is employed by some pathogens to scavenge sequestrated iron from host and plays an essential role in bacterial virulence [62]. Reduction of these genetic elements suggested a declined risk of invasive gastroenteritis by Staph. aureus. Lysine, considered to be an essential amino acid, is found recently to be produced partially by GM and then absorbed by host [63]. GM-mediated amino acid metabolism could be essential for neonates given the high accretion of body protein. A disrupted GM, e.g. suppressed by antibiotics, is linked to decreased protein synthesis rate in gut [64]. Orally administrated lysine is also reported to ameliorate diarrhea symptoms in a rodent model [65]. Besides, the superior Donor 2 resulted in recipient GM with higher capacity for acetate production, which is in accordance with the reported increase of SCFA production using the same donor [20].
Donor species richness is reported to determine FMT success among IBD patients [16]. In this study, the two donor microbiotas had similar alpha diversity and composition but resulted in different alpha diversity, composition and clinical response after transplantation. Hence, microbial richness alone may not ensure the FMT efficiency. Our data suggest that even strain-level variation may play an important role and affect the bacterial engraftment. The two donors had comparable lactobacilli composition, however lactobacilli colonized recipients in a donor-dependent manner. Phylogenetic analysis indicated different strains of Lmb. reuteri and Lb. crispatus existed between the donors. Identified by PanPhlAn, Lmb. reuteri strains from the superior donor (Donor 2) conferred more drug resistance genes such as colistin resistance protein EmrB. The strain-level variation likely made the Lmb. reuteri from Donor 2 more robust to cope with environmental challenges and led to a higher replication rate of lactobaclli in the gut. Besides, MAG-level analysis indicated that Donor 2 contained specific Bacteroides e.g. B. vulgatus conferring heparan and keratan sulfate utilization genes. Heparan and keratan sulfate are two major classes of GAGs on mammalian epithelial cells, which play a fundamental role in mutualistic bacteria adhesion [65, 66] as well as bacterial infectivity of pathogens. Given the high genome coverage of these MAGs solely in the superior donor, we suspected the GAG-degrading Bacteriodes might facilitate bacterial engraftment including lactobacilli and also competitively exclude other GAG-binding pathogens [68]. Bacteroides are considered as next-generation probiotics for their ubiquitous GAG-degrading capacity [66] and production of anti-inflammatory lipopolysaccharide [69]. Gavage of B. vulgatus is reported to alleviate murine endotoxemia by suppressing lipopolysaccharide production in gut [70]. One multi-donor FMT trial has also indicated that increased Bacteroides in donor stool is associated with ulcerative colitis remission in recipients [71].
Although rectal FMT showed promising properties in terms of preventing NEC, we also noticed increased pathogenetic signatures from Escherichia coli and Salmonella enterica in recipient guts. This highlights the risk of potential transmission of infectious agents during FMT, which also explains previously high sepsis cases through oral administration [20]. Even though the transferred enteropathogens did not violate the preventive effect of rectal FMT here, they might become a risk factor [72].