From microbial community structure to metabolic inference using paprica

Abstract

Summary: Microbial taxonomic marker gene studies using 16S rRNA gene amplicon sequencing provide an understanding of microbial community structure and diversity; however, it can be difficult to infer the functionality of microbes in the ecosystem from these data. Here, we show how to predict metabolism from phylogeny using the paprica pipeline. This approach allows resolution at the strain and species level for select regions on the prokaryotic phylogenetic tree and provides an estimate of gene and metabolic pathway abundance.For complete details on the use and execution of this protocol, please refer to Erazo and Bowman (2021).

Keywords

• Bioinformatics
• Genomics
• Metabolism
• Microbiology
• Systems biology
• Evolutionary biology