Released on May 25, 2023
Back to episode listWe are back to discussing systematics and SeqCode, a nomenclatural code for prokaryotes described from sequence data.
Marike Palmer, a postdoctoral researcher in the School of Life Sciences at the University of Nevada, Las Vegas, and Miguel Rodriguez, an Assistant Professor of Bioinformatics at the University of Innsbruck in the Departments of Microbiology and the Digital Science Center (DiSC), shared insights on this topic.
Palmer and Rodriguez discussed SeqCode, the nomenclature code specifically devised for prokaryotes described from sequence data. This code aims to provide a nomenclature system for previously uncultivated organisms. Palmer emphasized that the impetus for SeqCode was the need to accommodate previously uncultivated organisms under a specific nomenclature code. The SeqCode was designed to allow any peer-reviewed publication to propose names. Authors can choose from three validation paths within the SeqCode, encouraging collaboration with curriculum teams to ensure optimum descriptions, names, etymology, and solidification.
Rodriguez elaborated on the governance of the SeqCode, which is publicly accessible for anyone interested in joining the SeqCode community. The governance structure comprises an executive board, committees, and working groups, with some co-opted members, while others are chosen by ballot. The Isme Society provides support as an umbrella organization for the SeqCode.
Palmer and Rodriguez emphasized that SeqCode is not a competing code but rather a parallel one that complements existing systems by accommodating previously uncultivated organisms. They noted that most scientists culture prokaryotes to advance knowledge through physiology experiments rather than for naming purposes. This new system is a product of long-term collaborative efforts, uniting various viewpoints and philosophies.
The discussion highlighted practical requirements under SeqCode, including standards for genome sequence data completeness and contamination levels. Although the 16S rRNA gene sequence is not mandatory, it's recommended for accuracy in cross-talk between different taxonomies. They stressed the importance and challenges of naming microorganisms, aiming for a system inclusive of all microorganisms—both cultivated and uncultivated.
SeqCode advocates for high-quality genomes as control types to ensure the system's integrity. Recognizing the challenge of obtaining complete genomes for certain organisms, like obligate intracellular parasites, obtaining housekeeping genes was suggested as a solution. They tackled the technical issue of estimating completeness or contamination for many taxa, with Palmer confirming that registering a name on the SeqCode registry necessitates adding such estimates.
In summary, the conversation highlighted the importance and challenges of naming microorganisms, emphasizing collaboration within the scientific community to create an inclusive system. Despite inherent challenges, this is an ongoing process with scientists working towards a system that is accurate, practical, and beneficial for all.