Rapid and accurate identification of pathogens is critical to provide the appropriate treatment for patients suffering from certain gastrointestinal conditions. This has in particular been the case for acute diarrheal illness, for which identification of the causative agents still greatly relies on conventional microbiology techniques such as culturing of stool samples . However, although culture-based methods are rapid, sensitive, and specific, they are often designed around a presence/absence criterion, i.e., to detect microbial organisms that are usually absent in health and present in disease. Traditional clinical microbiology methods are less able to detect potential gut microbiota imbalances, i.e. aberrant ratios of multiple non-pathogenic, health-associated microorganisms in the setting of chronic conditions. One of the main reasons is that most intestinal commensals are hard to culture and can only be recovered under specialized technical conditions . Recent advancements in amplification and next-generation sequencing (NGS) techniques, in particular applied to the bacterial and archaeal ribosomal RNA encoding genes (16S rRNA genes) have overcome this problem, are increasingly used in the clinical microbiology lab , and have enormously expanded our knowledge of microbiome composition .