Microbiota analysis in Eosinophilic Esophagitis: a comparison of bioinformatic pipelines and case-control group design

Eosinophilic esophagitis (EoE) is a rare condition characterized by eosinophilic infiltration of the esophagus, leading to a chronic inflammatory process that results in swallowing diculties. Diagnosing and treating EoE can be challenging due to the lack of a reliable non-invasive biomarker. Recent advancements in sequencing technologies have highlighted the role of the human microbiota in diseases exhibiting inflammatory patterns, suggesting its potential for providing new diagnostic and therapeutic insights. Sequencing data preprocessing is a crucial step in microbiome studies, yet it often lacks standardization, which can introduce biases and hinder the comparability of studies’ results. This study compared two processing pipelines: a custom-built pipeline that integrates various tools and an automated pipeline that utilizes KneadData, a wrapper tool that simplifies the process. After demonstrating the excellent trade-off achieved with KneadData, this research focused on the development of BioDonut, a straightforward pipeline designed to analyze paired-end shotgun metagenomics data from human microbiota studies, specifically based on fecal and saliva samples. BioDonut covers a comprehensive workflow, from initial preprocessing phases (such as quality filtering and decontamination) to several first-line downstream analyses. Finally, since BioDonut is intended for studies comparing microbiota composition between healthy and diseased individuals, a propensity score matching algorithm was developed to reduce biases introduced by confounders when designing case-control groups from volunteer participants. BioDonut is publicly available at github.com/strmrc/BioDonut.