TY - JOUR
T1 - Hiding in plain sight
T2 - Mining bacterial species records for phenotypic trait information
AU - Barberán, Albert
AU - Velazquez, Hildamarie Caceres
AU - Jones, Stuart
AU - Fierer, Noah
N1 - Funding Information:
This work was supported by grants to N.F. from the U.S. National Science Foundation (EAR 1331828 and DEB 1542653) and grants to S.J. from the U.S. National Science Foundation (DEB 1442230). We thank Paul Carini for critical feedback on earlier drafts of the manuscript. We also thank Sharon Bewick and those undergraduates at Johns Hopkins University, the University of Notre Dame, and the University of Colorado who helped compile the database. We declare that we have no conflicts of interest
Publisher Copyright:
© 2017 Barberán et al.
PY - 2017/7/1
Y1 - 2017/7/1
N2 - 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.
AB - 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.
KW - Phenotypes
KW - Phylogeny
KW - Salinity
KW - Traits
KW - pH
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U2 - 10.1128/mSphere.00237-17
DO - 10.1128/mSphere.00237-17
M3 - Article
AN - SCOPUS:85041456757
SN - 2379-5042
VL - 2
JO - mSphere
JF - mSphere
IS - 4
M1 - e00237-17
ER -