Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
Abstract
:1. Introduction
2. Results
2.1. Reduction in Bacterial Growth of E. coli and S. aureus Caused by L. rhamnosus SCB0119
2.2. Effects of CFS on the Production of Intracellular ATP and Reactive Oxygen Species in E. coli and S. aureus
2.3. Changes in Cell Morphology and Structure of E. coli and S. aureus Caused by CFS
2.4. Transcriptomic Analysis of E. coli and S. aureus Cells in Response to CFS
3. Discussion
4. Material and Methods
4.1. Bacterial Strains and Culture Condition
4.2. Preparation of Cell-Free Culture Supernatants and Cells of L. rhamnosus SCB0119
4.3. Determination of the Antibacterial Activity of L. rhamnosus SCB0119
4.4. Minimum Inhibitory Concentrations of CFS against E. coli and S. aureus
4.5. Growth Curve of E. coli and S. aureus after Treatment with CFS
4.6. Scanning Electron Microscopy and Transmission Electron Microscopy
4.7. Concentrations of Alkaline Phosphatase and Intracellular ATP
4.8. Assay for Outer Membrane Permeability and Inner Membrane Integrity
4.9. Assays for Membrane Potential, pH Gradient, and Reactive Oxygen Species
4.10. Transcriptome Sequencing and Analysis
4.11. qRT-PCR
4.12. Data Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
CFS | cell-free culture supernatant |
LB | Luria Bertani |
MICs | minimum inhibitory concentrations |
SEM | scanning electron microscopy |
TEM | transmission electron microscopy |
AKP | alkaline phosphatase |
NPN | 1-N-phenylnaphthylamine |
PI | propidium iodide |
ΔΨ | membrane potential |
ΔpH | pH gradient |
ROS | reactive oxygen species |
DEGs | differentially expressed genes |
GO | gene ontology |
KEGG | Kyoto encyclopedia of genes and genomes |
MRS | De Man Rogosa Sharpe |
PBS | phosphate buffer saline |
FPKM | fragments per kilobase per million fragments mapped |
ATCC | American Type Culture Collection |
SD | standard deviation |
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Gene ID | RPKM Control | RPKM CFS | log2 Ratio | Gene Annotation |
---|---|---|---|---|
Fatty acid degradation | ||||
C7A06_RS17240 | 9.40 ± 0.16 | 2.62 ± 0.05 | −1.83961 | adhP; alcohol dehydrogenase AdhP |
Biosynthesis of amino acids | ||||
C7A06_RS27640 | 4.88 ± 1.53 | 21.23 ± 2.32 | 2.119947 | ilvN; acetolactate synthase small subunit |
C7A06_RS27645 | 5.18 ± 0.68 | 24.79 ± 0.65 | 2.259582 | ilvI; acetolactate synthase 3 large subunit |
C7A06_RS27660 | 17.62 ± 0.97 | 58.19 ± 0.51 | 1.723499 | leuA; 2-isopropylmalate synthase |
C7A06_RS27665 | 15.63 ± 2.17 | 48.10 ± 7.45 | 1.621654 | leuB; 3-isopropylmalate dehydrogenase |
C7A06_RS30700 | 15.96 ± 0.02 | 155.56 ± 1.24 | 3.284926 | lysC; lysine-sensitive aspartokinase 3 |
ABC transporters | ||||
C7A06_RS01665 | 14.27 ± 0.12 | 6.44 ± 0.43 | −1.14856 | nikE; nickel import ATP-binding protein NikE |
C7A06_RS01670 | 39.57 ± 0.39 | 15.70 ± 1.38 | −1.33379 | nikD; nickel import ATP-binding protein NikD |
C7A06_RS01675 | 43.38 ± 0.05 | 11.55 ± 1.74 | −1.90906 | nikC; nickel ABC transporter permease subunit NikC |
C7A06_RS01680 | 39.74 ± 2.21 | 10.25 ± 2.12 | −1.95437 | nikB; nickel ABC transporter permease subunit NikB |
C7A06_RS01685 | 10.05 ± 1.12 | 1.86 ± 0.26 | −2.43055 | nikA; nickel ABC transporter substrate-binding protein |
C7A06_RS01780 | 0.15 ± 0.08 | 1.01 ± 0.42 | 2.788886 | livH; ABC transporter permease LivH |
C7A06_RS01790 | 4.29 ± 0.27 | 14.90 ± 1.90 | 1.794947 | livG;ABC transporter ATP-binding protein LivG |
C7A06_RS24375 | 3.74 ± 0.98 | 1.53 ± 0.65 | −1.29111 | fepD; Fe3+ -siderophore ABC transporter permease |
Gene ID | RPKM Control | RPKM CFS | log2 Ratio | Gene Annotation |
---|---|---|---|---|
Fatty acid degradation | ||||
EKM74_RS11915 | 1832.07 ± 490.15 | 697.14 ± 121.09 | −1.39396 | adhP; alcohol dehydrogenase |
DNA replication | ||||
EKM74_RS04795 | 85.2 ± 44.94 | 39.85 ± 1.91 | −1.09611 | single-stranded DNA-binding protein |
Ribosome | ||||
EKM74_RS01000 | 77.06 ± 19.54 | 474.46 ± 30.77 | 2.622215 | accC; acetyl-CoA carboxylase biotin carboxylase subunit |
EKM74_RS01125 | 36.7 ± 12.69 | 642.43 ± 184.29 | 4.129847 | rpmG; 50S ribosomal protein L33 |
EKM74_RS01310 | 21.83 ± 0.96 | 168.95 ± 53.18 | 2.951911 | rpsT; 30S ribosomal protein S20 |
EKM74_RS01660 | 458.35 ± 97.45 | 2756.92 ± 263.1 | 2.588527 | rpmA; 50S ribosomal protein L27 |
EKM74_RS01670 | 102.05 ± 29.64 | 4057 ± 488.97 | 5.313122 | rplU; 50S ribosomal protein L21 |
EKM74_RS01855 | 19.42 ± 10.05 | 621.08 ± 94.23 | 4.999194 | rplT; 50S ribosomal protein L20 |
EKM74_RS01860 | 51.94 ± 21.24 | 5478.49 ± 45.03 | 6.720704 | rpmI; 50S ribosomal protein L35 |
EKM74_RS02080 | 80.66 ± 17.27 | 3451.94 ± 642.32 | 5.419314 | rpsD; 30S ribosomal protein S4 |
EKM74_RS05465 | 190.13 ± 11.18 | 3317.01 ± 500.37 | 4.124828 | rpsI; 30S ribosomal protein S9 |
EKM74_RS05470 | 150.17 ± 31.96 | 5880.76 ± 17.12 | 5.291357 | rplM; 50S ribosomal protein L13 |
EKM74_RS05495 | 122.74 ± 4.32 | 3341.82 ± 309.69 | 4.766903 | rplQ; 50S ribosomal protein L17 |
EKM74_RS05505 | 287.56 ± 78.6 | 2321.16 ± 704.2 | 3.01292 | rpsK; 30S ribosomal protein S11 |
EKM74_RS05510 | 582.25 ± 5.82 | 10,572.69 ± 1079.55 | 4.182553 | rpsM; 30S ribosomal protein S13 |
EKM74_RS05515 | 259.55 ± 26.92 | 8724.69 ± 798.78 | 5.071017 | rpmJ; 50S ribosomal protein L36 |
EKM74_RS05535 | 328.44 ± 51.85 | 2770.35 ± 239.31 | 3.076378 | rplO; 50S ribosomal protein L15 |
EKM74_RS05540 | 370.08 ± 105.31 | 13,564.79 ± 1089.74 | 5.195877 | rpmD; 50S ribosomal protein L30 |
EKM74_RS05545 | 183.9 ± 22.05 | 4254.61 ± 754.45 | 4.532035 | rpsE; 30S ribosomal protein S5 |
EKM74_RS05550 | 205.01 ± 26.43 | 9035.82 ± 328.78 | 5.461917 | rplR; 50S ribosomal protein L18 |
EKM74_RS05555 | 81.16 ± 4.22 | 1809.37 ± 428.25 | 4.478643 | rplF; 50S ribosomal protein L6 |
EKM74_RS05560 | 98.44 ± 3.27 | 3014.88 ± 247.03 | 4.93666 | rpsH; 30S ribosomal protein S8 |
EKM74_RS05570 | 126.29 ± 2.95 | 4279.22 ± 391.93 | 5.082565 | rplE; 50S ribosomal protein L5 |
EKM74_RS05575 | 138.6 ± 11.64 | 4600.35 ± 70.63 | 5.052719 | rplX; 50S ribosomal protein L24 |
EKM74_RS05580 | 181.27 ± 11.93 | 4136.6 ± 837.23 | 4.512211 | rplN; 50S ribosomal protein L14 |
EKM74_RS05585 | 140.46 ± 16.11 | 4981.9 ± 113.47 | 5.148408 | rpsQ; 30S ribosomal protein S17 |
EKM74_RS05590 | 154.79 ± 34.38 | 4723.29 ± 418.72 | 4.931395 | rpmC; 50S ribosomal protein L29 |
EKM74_RS05595 | 194.99 ± 8.39 | 3442.61 ± 618.09 | 4.142009 | rplP; 50S ribosomal protein L16 |
EKM74_RS05600 | 333.68 ± 100.38 | 6017.46 ± 493.68 | 4.172617 | rpsC; 30S ribosomal protein S3 |
EKM74_RS05605 | 267.84 ± 59.12 | 9325.05 ± 0.95 | 5.121682 | rplV; 50S ribosomal protein L22 |
EKM74_RS05610 | 210.47 ± 4.59 | 7349.55 ± 191.55 | 5.125963 | rpsS; 30S ribosomal protein S19 |
EKM74_RS05615 | 231.04 ± 32.27 | 4313.16 ± 576.59 | 4.222508 | rplB; 50S ribosomal protein L2 |
EKM74_RS05620 | 87.68 ± 7.24 | 1918.56 ± 543.34 | 4.451662 | rplW; 50S ribosomal protein L23 |
EKM74_RS05625 | 145.16 ± 12.67 | 3427.73 ± 563.02 | 4.561522 | rplD; 50S ribosomal protein L4 |
EKM74_RS05630 | 188.98 ± 15.87 | 7819.97 ± 221.75 | 5.37082 | rplC; 50S ribosomal protein L3 |
EKM74_RS05635 | 294.61 ± 86.56 | 9259.91 ± 978.26 | 4.97412 | rpsJ; 30S ribosomal protein S10 |
EKM74_RS07510 | 151.39 ± 9.3 | 705.28 ± 120.89 | 2.219912 | rplI; 50S ribosomal protein L9 |
EKM74_RS07590 | 114.58 ± 17.68 | 1144.54 ± 138.16 | 3.320336 | rpmH; 50S ribosomal protein L34 |
EKM74_RS10450 | 236.72 ± 37.3 | 7542.84 ± 237.11 | 4.993827 | rpsF; 30S ribosomal protein S6 |
EKM74_RS10460 | 55.84 ± 4.69 | 531.48 ± 99.45 | 3.250636 | rpsR; 30S ribosomal protein S18 |
EKM74_RS11530 | 51.86 ± 16.74 | 493.86 ± 62.28 | 3.251456 | rpmG; 50S ribosomal protein L33 |
EKM74_RS11545 | 230.05 ± 33.59 | 6745.81 ± 496 | 4.873994 | rplK; 50S ribosomal protein L11 |
EKM74_RS11550 | 89.54 ± 9.77 | 1345.42 ± 304.26 | 3.909295 | rplA; 50S ribosomal protein L1 |
EKM74_RS11560 | 75.58 ± 8 | 6432.15 ± 34.02 | 6.411134 | rplJ; 50S ribosomal protein L10 |
EKM74_RS11565 | 38.15 ± 13.06 | 2351.81 ± 364.44 | 5.945945 | rplL; 50S ribosomal protein L7/L12 |
EKM74_RS11590 | 185.09 ± 16.78 | 6759.64 ± 1120.81 | 5.190643 | rpsL; 30S ribosomal protein S12 |
EKM74_RS11595 | 156.22 ± 21.95 | 3889.22 ± 770.69 | 4.637864 | rpsG; 30S ribosomal protein S7 |
EKM74_RS14380 | 74.47 ± 6.98 | 956.98 ± 89.75 | 3.683755 | rpmF; 50S ribosomal protein L32 |
EKM74_RS15340 | 44.89 ± 6.07 | 387.7 ± 59.81 | 3.110434 | rpsP; 30S ribosomal protein S16 |
EKM74_RS15355 | 56.77 ± 3.55 | 839.03 ± 212.16 | 3.885462 | rplS; 50S ribosomal protein L19 |
EKM74_RS15435 | 112.72 ± 30.02 | 3718.42 ± 314.52 | 5.043867 | rpsB; 30S ribosomal protein S2 |
EKM74_RS15530 | 178.88 ± 2.05 | 2219.27 ± 90.62 | 3.633007 | rpsO; 30S ribosomal protein S15 |
Aminoacyl-tRNA biosynthesis | ||||
EKM74_RS02305 | 35.37 ± 21.65 | 401.03 ± 43.46 | 3.503254 | leuS; leucine-tRNA ligase |
EKM74_RS03605 | 63.4 ± 16.82 | 997.64 ± 109.83 | 3.975903 | gatB; Asp-tRNA (Asn)/Glu-tRNA (Gln) amidotransferase subunit |
EKM74_RS11370 | 90.84 ± 8.58 | 509.92 ± 53.53 | 2.488778 | lysS; lysine-tRNA ligase |
EKM74_RS11490 | 107.77 ± 37.9 | 605.02 ± 32.1 | 2.489052 | gltX; glutamate-tRNA ligase |
EKM74_RS14775 | 34.9 ± 14.25 | 239.53 ± 20.28 | 2.77887 | pheT; phenylalanine-tRNA ligase subunit beta |
EKM74_RS15105 | 30.17 ± 17.78 | 273.57 ± 29.78 | 3.180715 | ileS; isoleucine-tRNA ligase |
Oxidative phosphorylation | ||||
EKM74_RS04830 | 170.47 ± 3.15 | 3033.08 ± 240.81 | 4.153207183 | atpD; F0-F1 ATP synthase subunit beta |
EKM74_RS04840 | 97.18 ± 1.86 | 1251.21 ± 170.89 | 3.686521282 | atpA; F0-F1 ATP synthase subunit alpha |
EKM74_RS04855 | 241.14 ± 56.65 | 1679.25 ± 147.57 | 2.799862175 | atpE; F0-F1 ATP synthase subunit C |
EKM74_RS04860 | 239.15 ± 52.69 | 1550.63 ± 98.56 | 2.696892312 | atpB; F0-F1 ATP synthase subunit A |
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Peng, H.; Zhou, G.; Yang, X.-M.; Chen, G.-J.; Chen, H.-B.; Liao, Z.-L.; Zhong, Q.-P.; Wang, L.; Fang, X.; Wang, J. Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus. Int. J. Mol. Sci. 2022, 23, 15159. https://doi.org/10.3390/ijms232315159
Peng H, Zhou G, Yang X-M, Chen G-J, Chen H-B, Liao Z-L, Zhong Q-P, Wang L, Fang X, Wang J. Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus. International Journal of Molecular Sciences. 2022; 23(23):15159. https://doi.org/10.3390/ijms232315159
Chicago/Turabian StylePeng, Huan, Gang Zhou, Xi-Miao Yang, Guo-Jun Chen, Hai-Bin Chen, Zhen-Lin Liao, Qing-Ping Zhong, Li Wang, Xiang Fang, and Jie Wang. 2022. "Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus" International Journal of Molecular Sciences 23, no. 23: 15159. https://doi.org/10.3390/ijms232315159