Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information

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 bacteria...

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Autores principales:	Albert Barberán, Hildamarie Caceres Velazquez, Stuart Jones, Noah Fierer
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	pH phenotypes phylogeny salinity traits Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/6c6dd96201ee443c87b6a8647ec87403
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spelling	oai:doaj.org-article:6c6dd96201ee443c87b6a8647ec874032021-11-15T15:22:04ZHiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172379-5042https://doaj.org/article/6c6dd96201ee443c87b6a8647ec874032017-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00237-17https://doaj.org/toc/2379-5042ABSTRACT 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. IMPORTANCE Cultivation in the laboratory is key for understanding the phenotypic characteristics, growth requirements, metabolism, and environmental preferences of bacteria. However, oftentimes, phenotypic information is not easily 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). We demonstrate how this database can be used to link bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and environmental preferences. The phenotypic database can be freely accessed (https://doi.org/10.6084/m9.figshare.4272392 ), and we have included instructions for researchers interested in adding new entries or curating existing ones.Albert BarberánHildamarie Caceres VelazquezStuart JonesNoah FiererAmerican Society for MicrobiologyarticlepHphenotypesphylogenysalinitytraitsMicrobiologyQR1-502ENmSphere, Vol 2, Iss 4 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	pH phenotypes phylogeny salinity traits Microbiology QR1-502
spellingShingle	pH phenotypes phylogeny salinity traits Microbiology QR1-502 Albert Barberán Hildamarie Caceres Velazquez Stuart Jones Noah Fierer Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
description	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. IMPORTANCE Cultivation in the laboratory is key for understanding the phenotypic characteristics, growth requirements, metabolism, and environmental preferences of bacteria. However, oftentimes, phenotypic information is not easily 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). We demonstrate how this database can be used to link bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and environmental preferences. The phenotypic database can be freely accessed (https://doi.org/10.6084/m9.figshare.4272392 ), and we have included instructions for researchers interested in adding new entries or curating existing ones.
format	article
author	Albert Barberán Hildamarie Caceres Velazquez Stuart Jones Noah Fierer
author_facet	Albert Barberán Hildamarie Caceres Velazquez Stuart Jones Noah Fierer
author_sort	Albert Barberán
title	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
title_short	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
title_full	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
title_fullStr	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
title_full_unstemmed	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
title_sort	hiding in plain sight: mining bacterial species records for phenotypic trait information
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/6c6dd96201ee443c87b6a8647ec87403
work_keys_str_mv	AT albertbarberan hidinginplainsightminingbacterialspeciesrecordsforphenotypictraitinformation AT hildamariecaceresvelazquez hidinginplainsightminingbacterialspeciesrecordsforphenotypictraitinformation AT stuartjones hidinginplainsightminingbacterialspeciesrecordsforphenotypictraitinformation AT noahfierer hidinginplainsightminingbacterialspeciesrecordsforphenotypictraitinformation
_version_	1718428076114706432

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information

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