A practical guide on environmental genomics for prokaryotic systematics

Environmental shotgun sequencing can provide great insight into microbial community profiles, functional capabilities, and the recovery of metagenome-assembled genomes (MAGs) which represent individual microbiome members. Similarly, assembly of single-cell amplified genomes (SAGs) is possible through advances in microfluidics and sequencing techniques. These fields have experienced tremendous growth in the amount of data produced, the ongoing development of analytical tools, and ultimately, the number of genomes recovered lacking valid names. As most microbes are uncultivable and therefore incompatible with traditional naming requirements, sequence databases are filled with genomes of varying quality and without standardized nomenclature, hindering communication and data usability. Overcoming these limitations, the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) includes genome quality criteria and nomenclature standards to validly name uncultivated prokaryotes based on DNA sequence. Metagenomics and systematics can be overwhelming fields for new users, so here we provide a guide to help clarify topics and point out special considerations. These topics include metagenomic pipelines, genome quality assessment criteria, followed by taxonomy and trait prediction tools. Next, we cover source metadata, methods for abundance and occupancy measurement, and lastly, nomenclature and name registration. Community efforts to generate high-quality prokaryotic genomes with thorough descriptions and valid names are crucial for the future usability and communication of environmental genomic data.