What is new and relevant for sequencing-based microbiome research? A mini-review

•Sample storage and nucleic acid isolation influence microbiota compositions.•Error-corrected amplicon sequence variants (ASVs) improve 16S rRNA analysis.•Contamination and host cells confound and complicate microbiota analysis.•Quantitative and active microbiota analyses can complement existing methods.•Open data and protocol sharing increases transparency and reproducibility.