Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models
Authors: Reygner Julie , Delannoy Johanne , Barba-Goudiaby Marie-Thérèse , Gasc Cyrielle , Levast Benoît , Gaschet Enora , Ferraris Laurent , Paul Stéphane , Kapel Nathalie , Waligora-Dupriet Anne-Judith , Barbut Frederic , Thomas Muriel , Schwintner Carole , Laperrousaz Bastien , Corvaïa Nathalie 
Published: April 2024

ABSTRACT

Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent
Clostridioides difficile
infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a “good” donor as well as the intrinsic variability of donor-derived products’ taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors’ feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products’ efficacy compared to corresponding single donor-derived products in
Salmonella
and
C. difficile
infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed
in vitro
growth inhibition assays of two extremely drug-resistant bacteria,
Enterococcus faecium
vanA and
Klebsiella pneumoniae
oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models.

IMPORTANCE

Growing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent
Clostridioides difficile
infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with
in vitro
and
in vivo
studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased
Salmonella
and
Clostridioides difficile
pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.