Exploring donor difference in neonatal fecal microbiota transplantation

Using a controlled preterm piglet model, we found rectal fecal microbiota transplantation manifested clinically and microbiologically in a donor-dependent manner. Metagenomic analysis revealed strain-level phylogenetic separation of the engrafted lactobacilli strains according to the donors.

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Fecal microbiota transplantation (FMT) shows high cure rates (90% on average) in treating Clostridioides difficile infection1, the success of which is even not decided by a specific donor2. This overwhelming success encouraged researchers to expand the list of FMT use. Unfortunately, donor difference appears when FMT is applied to multi-factorial diseases, e.g., inflammatory bowel disease, and metabolic syndrome.

Necrotizing enterocolitis (NEC) is a devasting neonatal bowel disease implicated by immune imbalance, exogenous intake (e.g., formula feeding), gut dysbiosis, and other factors. First reported in the early 1800s3, NEC has an incidence of up to 7% among infants born preterm4. For very-low-birth-weight infants, the mortality rate can go up to 10-30%, which has not improved for years despite the aid of antibiotics or probiotics4.

We have found that FMT could reduce NEC incidence in preterm piglets while inhibiting mucosal pro-inflammatory TLR4 signaling5. However, in a follow-up study, we could not replicate the finding with a donor collected from another farm. This gave us a chance to explore the donor difference in FMT efficiency in a controlled environment.

Fecal donor material was obtained from two different groups of term piglets (Donor 1 and 2) and rectally administered to preterm piglets born at 90% gestational age on one and two days of life. The completed graphic was created with BioRender.com in an academic license.
Fig. 1. A schematic illustration of the study design. Fecal donor material was obtained from two different groups of term piglets (Donor 1 and 2) and rectally administered to preterm piglets born at 90% gestational age on one and two days of life. The completed graphic was created with BioRender.com in an academic license.

As shown in Fig. 1, the two donors were collected from two different specific pathogen-free herds. Preterm piglets at 90% gestation age, as recipients, received rectal FMT of the two donors or sterile saline in their first two days of life. Although the two donor communities showed comparably similar bacterial diversity and composition at the genus level, they differed in their efficiency in protecting the gastrointestinal tract of recipient piglets. Relative to the other, Donor 2 showed a superior effect in preventing NEC incidence and ameliorating diarrhea symptoms among preterm piglets (Fig. 2a). Meanwhile, the metagenomic analysis revealed that the administered donor is the driving factor in shaping the gut microbiome structure of recipients (Fig. 2b). Relative to sham-treated animals, a significant increase in lactobacilli and reductions in Enterobacteriaceae were found in the gut of FMT recipients, especially among those receiving the effective donor.

Fig. 2. Donor-dependent host response and gut microbiome shift in recipient piglets. The radar plots (a) show donor-dependent prevention against gastrointestinal necrosis and diarrhea in recipients, and the db-RDA biplot (b) suggests the recipient gut microbiome shifts were mainly decided by the received donors. 

Interestingly, the lactobacilli engraftment showed a distinct donor-dependent tendency. The lactobacilli population from Donor 2 seemed to have more efficient colonization (Fig. 3a) and propagation (Fig. 3b) in the gut after FMT. Phylogenetic tracing indicated a clear strain-level separation between the engrafted lactobacilli, which consistently corresponded to the given donors. A logical inference is that the variation of stains in donors affected the bacterial colonization in recipients, and in turn the clinical response.

Fig. 3. Donor-dependent lactobacilli engraftment and phylogenetic separation in the recipient piglets. The colonization (a), replication rate (b), and phylogenetic similarity of lactobacilli in recipients were decided by the received donors.

Due to the risk of antibiotic resistance and uncertainty regarding the effects of probiotic treatment, FMT could be a promising direction for microbiome-targeted therapy. Donor choice is considered essentially necessary in FMT as accumulated evidence disclosed the super donor phenomenon in treating polygenic diseases including NEC. Donor species richness is reported to be a crucial factor for the success of FMT treatment in inflammatory bowel disease6. In this study, the discrepant efficiency from two comparable donors, at least suggested donor diversity could not alone ensure a favorable outcome of FMT. Looking into the donor composition, we found the strain-level variation between donors might affect the bacterial engraftment and therefore the treatment results. The lactobacilli strains from the two donors showed phylogenetic differences and differed in inhabiting the gut of recipients.  The effective donor led to efficient engraftment of lactobacilli in rapid replication rate, greatly inhibiting pathogens e.g., Enterobacteriaceae overgrowth, and reducing the potential gastrointestinal disorders. Moreover, a glycosaminoglycans-degrading Bacteroides genome was recovered from the effective donor, which possibly contributed to pathogen resistance through competing for binding sites along the host gut epithelial extracellular matrix. Besides, we noticed increased pathogenetic signatures of Escherichia coli and Salmonella enterica in the gut of recipients receiving either of the donors. The transferred pathogens didn’t violate the FMT outcome of the efficient donor but initiated high sepsis cases in another oral FMT study5. This again highlights the importance of donor selection in FMT therapy.

By 

Yan Hui, Anders Brunse, Dennis Sandris Nielsen

Read the full paper at: https://www.nature.com/articles/s41522-022-00310-2

Bibliography

  1. Osman, M. et al. Donor Efficacy in Fecal Microbiota Transplantation for Recurrent Clostridium difficile: Evidence From a 1,999-Patient Cohort. Open Forum Infectious Diseases 3, (2016).
  2. Kassam, Z., Lee, C. H., Yuan, Y. & Hunt, R. H. Fecal Microbiota Transplantation for Clostridium difficile Infection: Systematic Review and Meta-Analysis. American Journal of Gastroenterology 108, 500–508 (2013).
  3. Obladen, M. Necrotizing Enterocolitis - 150 Years of Fruitless Search for the Cause. Neonatology 96, 203–210 (2009).
  4. Neu, J. & Walker, W. A. Necrotizing Enterocolitis. New England Journal of Medicine 364, 255–264 (2011).

Yan Hui

Postdoc, University of Copenhagen

Yan Hui is now a postdoc at the University of Copenhagen, mainly working with microbial genomic data. Under the supervision of Prof. Dennis Sandris Nielsen and Prof. Per Torp Sangild, he obtained a Ph.D. degree in microbiology with a focus on bioinformatic analysis of the preterm gut microbiome. In the past years, he has shown considerable expertise in analyzing second and third-generation sequencing data and multivariate analysis on microbiome data, creating/contributing to several open-source bioinformatics tools on GitHub (https://github.com/yanhui09).