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Nucleic Acids Res. 2016 Dec 1;44(21):10074-10090. Epub 2016 Oct 24.

The landscape of microbial phenotypic traits and associated genes.

Author information

1
Division of Electronics, Ruder Boskovic Institute, 10000 Zagreb, Croatia.
2
Mediterranean Institute of Life Sciences, 21000 Split, Croatia.
3
Division of Electronics, Ruder Boskovic Institute, 10000 Zagreb, Croatia fran.supek@irb.hr.
4
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.
5
Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.

Abstract

Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text. Moreover, the ProTraits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in metagenomes. Notably, we find that gene synteny is highly predictive of many phenotypes, and highlight examples of gene neighborhoods associated with spore-forming ability. A global analysis of trait interrelatedness outlined clusters in the microbial phenotype network, suggesting common genetic underpinnings. Our extended set of phenotype annotations allows detection of 57 088 high confidence gene-trait links, which recover many known associations involving sporulation, flagella, catalase activity, aerobicity, photosynthesis and other traits. Over 99% of the commonly occurring gene families are involved in genetic interactions conditional on at least one phenotype, suggesting that epistasis has a major role in shaping microbial gene content.

PMID:
27915291
PMCID:
PMC5137458
DOI:
10.1093/nar/gkw964
[Indexed for MEDLINE]
Free PMC Article

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