ArticleScientific reports2016
Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- An ecological-evolutionary perspective on the genomic diversity and habitat preferences of theMicrobial genomics · 2025Article
- An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota.bioRxiv : the preprint server for biology · 2024Article
- Comparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogenMicrobial genomics · 2024Article
- Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning.Scientific reports · 2022Article
- Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation.Nature communications · 2021Article
- Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey.Microbial genomics · 2021Article
- Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential.BMC genomics · 2021Article
- A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration.BMC microbiology · 2021Article
- A pan-genome method to determine core regions of theF1000Research · 2021Article
- The Great ESKAPE: Exploring the Crossroads of Bile and Antibiotic Resistance in Bacterial Pathogens.Infection and immunity · 2020Review
- Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species.BMC genomics · 2020Article
- Combined Transcriptome Sequencing ofFrontiers in microbiology · 2020Article
- The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation.Scientific data · 2019Article
- In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions.Microbial cell factories · 2019Article
- CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design.BMC bioinformatics · 2018Article
- Fermentation products in the cystic fibrosis airways induce aggregation and dormancy-associated expression profiles in a CF clinical isolate of Pseudomonas aeruginosa.FEMS microbiology letters · 2018Article
- SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.Bioinformatics (Oxford, England) · 2018Article
- Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio.Genome biology and evolution · 2018Article
- In silico engineering ofPeerJ · 2018Article
- Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate.Biotechnology and bioengineering · 2017Article
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Authors and funding
7 authors.
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Abstract
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.
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