Hiding in plain sight: Mining bacterial species records for phenotypic trait information

Albert Barberán, Hildamarie Caceres Velazquez, Stuart Jones, Noah Fierer

Research output: Contribution to journalArticlepeer-review

42 Scopus citations

Abstract

Cultivation in the laboratory is essential for understanding the phenotypic characteristics and environmental preferences of bacteria. However, basic phenotypic information is not readily accessible. Here, we compiled phenotypic and environmental tolerance information for > 5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) with all information made publicly available in an updatable database. Although the data span 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic strains from Proteobacteria (mainly Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes isolated from soils, marine habitats, and plants. Most of the routinely measured traits tended to show a significant phylogenetic signal, although this signal was weak for environmental preferences. We demonstrated how this database could be used to link genomic attributes to differences in pH and salinity optima. We found that adaptations to high salinity or high-pH conditions are related to cell surface transporter genes, along with previously uncharacterized genes that might play a role in regulating environmental tolerances. Together, this work highlights the utility of this database for associating bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and emphasizes the need for more comprehensive and consistent measurements of traits across a broader diversity of bacteria.

Original languageEnglish (US)
Article numbere00237-17
JournalmSphere
Volume2
Issue number4
DOIs
StatePublished - Jul 1 2017
Externally publishedYes

Keywords

  • Phenotypes
  • Phylogeny
  • Salinity
  • Traits
  • pH

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

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