TABLE 1.
Top differentially expressed genes (up and down) with |log2(fold change)| ≥ 1 and adjusted p-value < 0.05 in biofilms compared to the planktonic phenotype after 24 h of growth of UAS391, HEMRSA-15, and ST239-16.
| Gene annotation | UAS391 | HEMRSA-15 | ST239-16 | KEGG pathway |
| 24 h | ||||
| Chemotaxis protein | –2.36 | –3.33 | Staphylococcus aureus infection | |
| Lactate dehydrogenase | –2.31 | –2.45 | Pyruvate metabolism | |
| Hypothetical protein | –2.25 | No classified | ||
| Complement inhibitor | –2.21 | Staphylococcus aureus infection | ||
| Capsular biosynthesis protein | 2.4 | No classified | ||
| Carbamate kinase | 2.41 | 3.95 | Nitrogen metabolism | |
| Lantibiotic epidermin | 2.43 | Two-component system | ||
| GTP pyrophosphokinase | 2.45 | Purine metabolism | ||
| Ornithine carbamoyltransferase | 2.48 | 3.81 | Arginine biosynthesis | |
| Arginine deiminase | 2.98 | 3.66 | Arginine biosynthesis | |
| Cysteine protease | 3.98 | Peptidases | ||
| Cold-shock protein | 4.09 | 4.79 | Transcription | |
| Glutamyl endopeptidase | 4.41 | Quorum sensing | ||
| 48 h | ||||
| General stress protein | –6.37 | No classified | ||
| Glyceraldehyde-3-phosphate dehydrogenase | –5.69 | 3.33 | Glycolysis/Gluconeogenesis | |
| DNA-binding protein | –5.61 | 4.36 | No classified | |
| Cold-shock protein | –5.58 | 3.84 | Transcription | |
| Chaperone protein ClpB | –5.53 | 2.26 | Longevity regulating pathway | |
| Molecular chaperone DnaK | –5.46 | 3.09 | RNA degradation | |
| Acetoin reductase | –5.43 | 3.68 | Butanoate metabolism | |
| 50S ribosomal protein L28 | –5.42 | 5.51 | Ribosome | |
| Enolase | –5.35 | 3.64 | Glycolysis/Gluconeogenesis | |
| Quinol oxidase subunit 2 | –5.24 | 3.37 | Oxidative phosphorylation | |
| Siderophore biosynthesis protein SbnD | 2.05 | Transporters | ||
| Transposase | 2.15 | –6.89 | Replication and repair | |
| dUTP pyrophosphatase | 2.18 | Pyrimidine metabolism | ||
| Pseudouridine-5’-phosphate glycosidase | 2.24 | –1.13 | Pyrimidine metabolism | |
| 72 h | ||||
| General stress protein | –4.27 | –1.26 | No classified | |
| 50S ribosomal protein L28 | –3.58 | Ribosome | ||
| Lactate dehydrogenase | –3.42 | Glycolysis/Gluconeogenesis | ||
| Glyceraldehyde-3-phosphate dehydrogenase | –3.38 | Glycolysis/Gluconeogenesis | ||
| Preprotein translocase subunit SecY | –3.07 | Protein export | ||
| DNA-binding protein | –3.05 | No classified | ||
| Chaperone protein ClpB | –2.97 | Longevity regulating pathway | ||
| 50S ribosomal protein L22 | –2.95 | Ribosome | ||
| ATP:guanido phosphotransferase | –2.93 | No classified | ||
| 50S ribosomal protein L36 | –2.93 | Ribosome | ||
Blue signifies upregulation, purple downregulation (|log2(fold change)| ≥ 1 and padj < 0.05), and white cells indicate the UAS391 genes were not identified as differentially expressed (DEGs) in HEMRSA-15 and/or ST239-16. Two biological repeats were used for each phenotype in each strain across time points.