Author:
Weimann Aaron,Mooren Kyra,Frank Jeremy,Pope Phillip B.,Bremges Andreas,McHardy Alice C.
Abstract
AbstractThe number of sequenced genomes is growing exponentially, profoundly shifting the bottleneck from data generation to genome interpretation. Traits are often used to characterize and distinguish bacteria, and are likely a driving factor in microbial community composition, yet little is known about the traits of most microbes. We describe Traitar, the microbial trait analyzer, which is a fully automated software package for deriving phenotypes from the genome sequence. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis and enzymatic activities. Furthermore, it suggests protein families associated with the presence of particular phenotypes. Our method uses L1-regularized L2-loss support vector machines for phenotype assignments based on phyletic patterns of protein families and their evolutionary histories across a diverse set of microbial species. We demonstrate reliable phenotype assignment for Traitar to bacterial genomes from 572 species of 8 phyla, also based on incomplete single-cell genomes and simulated draft genomes. We also showcase its application in metagenomics by verifying and complementing a manual metabolic reconstruction of two novel Clostridiales species based on draft genomes recovered from commercial biogas reactors. Traitar is available athttps://github.com/hzi-bifo/traitar.
Publisher
Cold Spring Harbor Laboratory
Reference63 articles.
1. Binning metagenomic contigs by coverage and composition
2. Functional overlap of the Arabidopsis leaf and root microbiota
3. Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes
4. Boser, B.E. , Guyon, I.M. , and Vapnik, V.N. (1992). A training algorithm for optimal margin classifiers. Paper presented at: Proceedings of the fifth annual workshop on computational learning theory (Association for Computing Machinery).
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献