Microbial Malaise: How Can We Classify the Microbiome?

The names and lineages of microorganisms are critical to our understanding of the microbiome. However, microbial taxonomy and phylogeny are in perpetual flux, with emerging criteria being used to rename and reshape our views of the microbial world. Different candidate molecular and nonmolecular criteria are often broadly consistent with one another, which underpins the pluralistic approach to taxonomy. However, the taxonomic picture is clouded when underlying criteria are not in agreement, or when reference datasets contain erroneously named organisms. How does the shifting taxonomic landscape impact our interpretation of microbial communities, especially in the face of inconsistencies and errors? How can taxonomy be applied in a consistent way when different users have different requirements of the classifications that emerge? The key path forward involves finding ways to integrate conflicting taxonomic criteria, choosing the right units of analysis for microbiomic studies, and making molecular taxonomy transparent and accessible in a way that complements current genomic resources.

TrendsThe expanding field of microbiome analysis is heavily reliant on microbial classifications that derive both from hierarchical relationships and ad hoc groupings.Microbial taxonomy is in constant flux, with new types of evidence supplementing and supplanting older rules. Reclassifications based on new evidence may be slow to take hold, as is the case with many former members of the genus Clostridium.The emergence of molecular data, notably marker genes and sequenced genomes, has revolutionized the practice of microbial taxonomy. However, molecular data do not provide a completely consistent framework for classification, and questions remain about genome heterogeneity and its potential consequences.In focusing on microbes with defined but fluid taxonomic names and close matches in reference databases, microbiome analyses are missing potentially crucial sources of variation.