Evaluating microbial determinants of donor efficacy to translate faecal microbiota transplantation from research to clinical practice

After becoming an established therapy for recurrent Clostridioides difficile infection (rCDI), faecal microbiota transplantation (FMT) has been investigated also in non-communicable disorders, including IBD, IBS, metabolic syndrome, neurological disease and others.1 While the transfer of a healthy biomass appears to be effective regardless of its composition in rCDI (which is an example of acute, elementary dysbiosis), increasing evidence suggests that the clinical success of FMT in chronic disorders is influenced by several factors, including donor microbiome composition2 or FMT working protocols,3 and that these effects may be mediated by the engraftment capacity of the donor microbiome into the recipient gut.4 Haifer et al5 have published in the latest issue of Gut a subanalysis of a recent randomised trial (the LOTUS trial) of FMT for UC,6 where they had observed a significant variability of clinical efficacy between the…

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Dicembre 2022

Microbial determinants of effective donors in faecal microbiota transplantation for UC

Objective
Faecal microbiota transplantation (FMT) has variable efficacy in treating UC. Recently, oral lyophilised FMT was found to induce remission in patients with UC, with one donor having 100% efficacy compared with a second donor (36% efficacy). We characterised differences in the gut microbiota of these two donors with the aim of improving FMT donor selection.

Design
Faecal samples from the two donors were collected over a period of 44 (donor 1) or 70 (donor 2) weeks. The microbiome and metabolome were profiled using shotgun metagenomics and untargeted metabolomics

Results
Gut microbiome long-term stability was highly evident in the effective donor. Donor microbiota species evenness was a robust feature associated with clinical efficacy across two clinical trials of FMT in UC, leading to increased donor species engraftment in patients. Alpha diversity and beta diversity of donor gut microbiotas significantly differed. 90 bacterial species and one archaeon were differentially abundant between donors, 44 of which were >0.1% in relative abundance. 17/44 species were enriched in the effective donor, 11 of which (64.7%) were assembled into high-quality genomes that were prevalent (≥75% samples) in that donor, and six showed evidence of engraftment in patients. Taxonomic differences between donors translated to substantial microbial functional differences that were validated using metabolomics.

Conclusion
Donor microbiota stability and species evenness were identified as novel metrics that were associated with therapeutic efficacy in UC, beyond individual microbial species or metabolites. These metrics may represent community resilience that translates to better engraftment in the host.

Trial registration number
ACTRN12619000611123.

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Dicembre 2022

Advancing human gut microbiota research by considering gut transit time

Accumulating evidence indicates that gut transit time is a key factor in shaping the gut microbiota composition and activity, which are linked to human health. Both population-wide and small-scale studies have identified transit time as a top covariate contributing to the large interindividual variation in the faecal microbiota composition. Despite this, transit time is still rarely being considered in the field of the human gut microbiome. Here, we review the latest research describing how and why whole gut and segmental transit times vary substantially between and within individuals, and how variations in gut transit time impact the gut microbiota composition, diversity and metabolism. Furthermore, we discuss the mechanisms by which the gut microbiota may causally affect gut motility. We argue that by taking into account the interindividual and intraindividual differences in gut transit time, we can advance our understanding of diet–microbiota interactions and disease-related microbiome signatures, since these may often be confounded by transient or persistent alterations in transit time. Altogether, a better understanding of the complex, bidirectional interactions between the gut microbiota and transit time is required to better understand gut microbiome variations in health and disease.

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Dicembre 2022