Evolution of intestinal microbiome in a process of faecal microbiota transfer (FMT) in a patient with Clostridioides difficile infection: NGS analysis with different software programs

Abstract

Introduction: Clostridioides difficile infection (CDI) has become a global healthcare challenge due to increases in its incidence and mortality rates. Faecal microbiota transfer (FMT) is postulated as a protocol to prevent CDI recurrence.

Material and methods: A donor faecal sample and patient faecal samples (pre-FMT and post-FMT) were analysed. The r16S gene was amplified and sequenced by NGS, and its diversity and taxonomy composition were examined.

Results: Microbial richness increased in post-FMT samples, and the β diversity studies grouped the samples into two clusters. One included the non-pathological samples (donor and pre-FMT samples), and the other included the pathological sample. The results obtained by Qiime2 and Bioconductor were similar.

Conclusion: The analysis showed an increase in taxonomic diversity after the FMT, which suggests its usefulness. Moreover, these results showed that standardisation of bioinformatics analysis is key.

Keywords: Clostridioides difficile; Faecal microbiota transfer; Microbiota; NGS; Secuenciación masiva; Transferencia microbiota fecal.