Gastrointestinal microbiome: Evaluation of testing technologies

Advances in the field of microbiology made it possible to identify bacterial causative agents for a number of conditions in the foregut, such as chronic gastritis and peptic ulcer disease. Modern-era microbiome research requires a robust characterization of complex microbial communities in different ecosystems to disentangle their impact on host physiology in health and disease. The expansion toward sites like the esophagus with a low abundance of resident microbes remains challenging for both culture-dependent and -independent detection techniques. Exceptional culture conditions for fastidious organisms, the strict control for contamination, and the host nucleic acid background in genomic approaches are some of the factors to be considered. Recent advancements in next-generation sequencing of bacterial genomes, high-throughput bacterial culture coupled with state-of-the-art detection methods (“culturomics”), and bioinformatics pipelines to account for contaminants may enable to characterize microbial patterns in the esophagus and evaluate their association with diseases of this organ.