Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

@article{Seif2018GenomescaleMR,
  title={Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits},
  author={Yara Seif and Erol S. Kavvas and Jean-Christophe Lachance and James T. Yurkovich and Sean-Paul Nuccio and Xin Fang and Edward Catoiu and Manuela Raffatellu and Bernhard O. Palsson and Jonathan M. Monk},
  journal={Nature Communications},
  year={2018},
  volume={9}
}
Salmonella strains are traditionally classified into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) the Salmonella accessory metabolic network… Expand
High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
TLDR
This study provides a thoroughly updated metabolic reconstruction and new computable phenotypes for P. putida, which can be leveraged as a first step toward understanding the pan metabolic capabilities of Pseudomonas. Expand
Metabolic and genetic basis for auxotrophies in Gram-negative species
TLDR
This paper develops an algorithm (AuxoFind) using genome-scale metabolic reconstruction to predict auxotrophies and applies it to a series of available genome sequences of over 1,300 Gram-negative strains, and identifies 54 Auxotrophs, along with the corresponding metabolic and genetic basis, using a pangenome approach. Expand
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
TLDR
The present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. Expand
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
TLDR
The present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. Expand
Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates
TLDR
Recon reconstructs genome-scale metabolic models for 22 K. pneumoniae strains with various resistance profiles to different antibiotics, including two strains exhibiting colistin resistance isolated from Cairo, Egypt and uses the models to predict growth capabilities on 265 different sole carbon, nitrogen, sulfur, and phosphorus sources. Expand
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
TLDR
The authors extend their original Protocol used to generate a genome-scale metabolic model for a single strain to enable multi-strain models to be made, which can be used to study pan-metabolic capabilities and strain-specific differences across a species. Expand
Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens
TLDR
The current knowledge of genome-scale metabolic modeling in pathogen cells as well as pathogen host interaction systems and the promising applications in the extension of curative strategies against pathogens for global preventative healthcare are reviewed. Expand
Reconstructing organisms in silico: genome-scale models and their emerging applications.
TLDR
The overall development of GEMs and their applications are discussed, the evolution of the most complete GEM that has been developed to date is reviewed, and three emerging areas in genome-scale modelling of microbial phenotypes are explored: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses. Expand
Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets
TLDR
The growing number of sequenced genomes enables the study of secondary metabolite biosynthetic gene clusters (BGC) in phyla beyond well-studied soil bacteria and provides a guide to identify and understand PKS associated gene sets. Expand
Current status and applications of genome-scale metabolic models
TLDR
Current reconstructed GEMs are reviewed and discussed, including strain development for chemicals and materials production, drug targeting in pathogens, prediction of enzyme functions, pan-reactome analysis, modeling interactions among multiple cells or organisms, and understanding human diseases. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 85 REFERENCES
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
TLDR
Genome-scale analysis of multiple strains of a species can be used to define the metabolic essence of a microbial species and delineate growth differences that shed light on the adaptation process to a particular microenvironment. Expand
An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228
TLDR
The genome-scale metabolic reconstruction for K. pneumoniae presented here provides an experimentally validated in silico platform for further studies of this important industrial and biomedical organism. Expand
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
TLDR
A genome-scale metabolic network of Salmonella typhimurium LT2 that allows identification of networked metabolic pathways and generation of hypotheses about metabolism during infection, which might be used for the rational design of novel antibiotics or vaccine strains. Expand
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011
TLDR
The initial genome‐scale reconstruction of the metabolic network of Escherichia coli K‐12 MG1655 was assembled in 2000 and an update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. Expand
Genetic Characterization of the Galactitol Utilization Pathway of Salmonella enterica Serovar Typhimurium
TLDR
The first genetic characterization of galactitol degradation in Salmonella is provided, revealing novel insights into the regulation of this dissimilatory pathway. Expand
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity
TLDR
Genome-scale analysis of multiple strains of a species can be used to identify metabolic determinants of virulence and increase the understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world. Expand
Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution
TLDR
P phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, the loss of coding sequences with known metabolic functions, which leads to functional reduction and the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Expand
Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut
TLDR
Comparative genome analysis identifies a metabolic network that provides clues about the strategies for nutrient acquisition and utilization that are characteristic of gastrointestinal pathogens and suggests that it is part of a “business plan” for growth in the inflamed gastrointestinal tract. Expand
Patterns of genome evolution that have accompanied host adaptation in Salmonella
Significance Common features have been observed in the genome sequences of bacterial pathogens that infect few hosts. These “host adaptations” include the acquisition of pathogenicity islands ofExpand
Deletion of the gene encoding the glycolytic enzyme triosephosphate isomerase (tpi) alters morphology of Salmonella enterica serovar Typhimurium and decreases fitness in mice.
TLDR
It is shown for the first demonstration that tpiA is required for full in vivo fitness of a bacterial pathogen, and that it has a discernable impact on cell morphology, in Salmonella enterica serovar Typhimurium. Expand
...
1
2
3
4
5
...