For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica
Abstract
:1. Introduction
2. Results
2.1. Dataset Preparation
2.2. Pangenome Reconstruction
2.3. Host-Wise Characterization of Salmonella enterica Phylogeny
2.4. Revealing Host Specificity Determinants and Known Virulence Factors
2.5. Functional Annotation of Gene Groups
3. Discussion
4. Materials and Methods
4.1. Environments
4.2. Data Acquisition
4.3. Pangenome Reconstruction
4.4. Phylogenetic Analysis
4.5. Virulence and Specificity Factors Analysis
4.6. Functional Annotation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
MGEs | Mobile genetic elements |
CDC | Centers for Disease Control and Prevention |
LPS | Lipopolysaccharides |
T3SS | Type III secretion systems |
SCV | Salmonella-containing vacuole |
tcf | Typhi colonization factor |
BH | Benjamini-Hochberg |
SNP | Single nucleotide polymorphism |
BIC | Bayesian information criterion |
CI | Consistency index |
RI | Retention index |
VFDB | Virulence factor database |
GO | Gene Ontology |
MF | Molecular Functions |
BP | Biological Processes |
CC | Cellular Components |
pan-GWAS | Pangenome-wide associating method |
MDR | Multidrug resistance |
MFS | Major facilitator |
tra | Transfer operon |
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Merkushova, A.V.; Shikov, A.E.; Nizhnikov, A.A.; Antonets, K.S. For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica. Int. J. Mol. Sci. 2023, 24, 13670. https://doi.org/10.3390/ijms241813670
Merkushova AV, Shikov AE, Nizhnikov AA, Antonets KS. For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica. International Journal of Molecular Sciences. 2023; 24(18):13670. https://doi.org/10.3390/ijms241813670
Chicago/Turabian StyleMerkushova, Anastasiya V., Anton E. Shikov, Anton A. Nizhnikov, and Kirill S. Antonets. 2023. "For Someone, You Are the Whole World: Host-Specificity of Salmonella enterica" International Journal of Molecular Sciences 24, no. 18: 13670. https://doi.org/10.3390/ijms241813670