The microbiome gains increasing attention not only in medical science but also even for lifestyle. Next generation sequencing allows quantifying even non-culturable bacteria. Consequently, from the guts comes the biggest resource of bacterial sequence information. The scientific as well as the popular press associates these communities to disease, characteristics of humans and even moods, which needs sophisticated bioinformatics, maybe even AI. Yet, the whole microbiota field faces hurdles in reproducibility and is confronted with doubts about reliability. Therefore, wet lab pipelines as well as bioinformatics require standardised workflows and quality control.