![\"\"](\"https:\/\/renewable-carbon.eu\/news\/media\/2026\/03\/1-s2.0-S0167779926000491-gr1.jpg\")
Section snippets<\/h3>\n\n\n\n<\/div>\n\n\n\nMultistress challenges in industrial Bacillus<\/em> spp.<\/h3>\n\n\n\nIndustrial Bacillus<\/em> strains encounter multiple overlapping stresses during fermentation, including heat, pH fluctuations, oxidative bursts, osmotic shocks, and toxic metabolites, which often act together to limit growth and productivity [1]. For example, sudden heat spikes oxidize proteins, while solvents exacerbate acid sensitivity. Osmotic shifts strain energy and redox pathways, limiting synthesis and secretion. System-level evaluations of microbial cell factories confirm that such<\/p>\n\n\n\nSynergistic stress interactions<\/h3>\n\n\n\n
Single-stress engineering fails in industrial settings. Acid, solvent, heat, and osmotic stresses interact, destabilizing membranes, oxidizing proteins, and draining energy. Stress combinations are nonlinear; the cumulative effect is often greater than the sum of the individual insults.<\/p>\n\n\n\n
Industrial and agricultural relevance<\/h3>\n\n\n\n
Multistress tolerance in Bacillus<\/em> strains reduces the need for buffering, cooling, and additional supplementation. Robust Bacillus<\/em> minimizes downtime, improves productivity, and lowers costs. Outside<\/p>\n\n\n\nTechnological enablers of resilience-by-design<\/h3>\n\n\n\n
Genome-scale perturbation and modular engineering tools, including CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)\/Cas9 (CRISPR-associated protein 9) [9], CRISPR interference (CRISPRi) [7], and base editing [10], and dedicated toolkits such as SubtiToolKit [11], enable systematic exploration of stress-tolerance determinants in Bacillus<\/em>. Coupled with single-cell, multiomics, and dynamic metabolomics analyses, these platforms reveal population heterogeneity, transient metabolic <\/p>\n\n\n\nDesign principles and predictive engineering<\/h3>\n\n\n\n
Engineering stress-resilient Bacillus<\/em> requires a unified design principle that integrates proteostasis, translation, and metabolism, rather than a patchwork of isolated optimizations. High-resolution genotype\u2013phenotype maps, coupled with multiomics data and AI-driven inference, now enable in silico<\/em> prediction of synergistic regulators, metabolic nodes, and transporters that confer resilience without compromising productivity. Transfer learning across Bacillus<\/em>species further enhances predictive <\/p>\n\n\n\nConcluding remarks and future perspectives<\/h3>\n\n\n\n
Next-generation\u00a0Bacillus<\/em>\u00a0platforms will transcend traditional fermentation, supporting applications from precision agriculture to environmental remediation and synthetic consortia stabilization. Engineered strains capable of withstanding harsh soils, detoxifying pollutants, or stabilizing microbial communities exemplify the shift from reactive to predictive biodesign. Resilience-by-design represents more than just a stress-tolerance strategy\u2014it establishes a blueprint for adaptive, intelligent,\u00a0…<\/p>\n\n\n\n<\/div>\n\n\n\nAcknowledgments<\/h3>\n\n\n\n
This work was supported by the\u00a0National Key Research and Development Program of China\u00a0(2025YFA0921800), the\u00a0Strategic Priority Research Program of the Chinese Academy of Sciences\u00a0(XDA0510300), and the\u00a0National Natural Science Foundation of China\u00a0(32100046). …<\/p>\n\n\n\n
<\/div>\n\n\n\nReferences<\/h3>\n\n\n\n
1. Lee, J.A. …<\/p>\n\n\n\n
Factors affecting the competitiveness of bacterial fermentation<\/strong><\/p>\n\n\n\nTrends Biotechnol.<\/em> 2023; 41<\/strong>:798-816<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n2. Kim, G.B. …<\/p>\n\n\n\n
Comprehensive evaluation of the capacities of microbial cell factories<\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2025; 16<\/strong>:2869<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n3. Zhu, M. …<\/p>\n\n\n\n
A fitness trade-off between growth and survival governed by Spo0A-mediated proteome allocation constraints in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\nSci. Adv.<\/em> 2023; 9<\/strong>:9733<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n4. Ou, X. …<\/p>\n\n\n\n
SecY translocon chaperones protein folding during membrane protein insertion<\/strong><\/p>\n\n\n\nCell.<\/em> 2025; 188<\/strong>:1912-1924<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n5. He, T.T. …<\/p>\n\n\n\n
A linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis<\/em><\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2023; 14<\/strong>:5722<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n6. Nadezhdin, E. …<\/p>\n\n\n\n
Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis<\/em> biofilms<\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2020; 11<\/strong>:950<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n7. Zhu, X. …<\/p>\n\n\n\n
Genome-wide CRISPRi screening of key genes for recombinant protein expression in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\nAdv. Sci.<\/em> 2024; 11<\/strong>, e2404313<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n8.<\/p>\n\n\n\n
Yan, Y. …<\/p>\n\n\n\n
Strain engineering of Bacillus coagulans<\/em> with high osmotic pressure tolerance for effective L-lactic acid production from sweet sorghum juice under unsterile conditions<\/strong><\/p>\n\n\n\nBioresour. Technol.<\/em> 2024; 400<\/strong>, 130648<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n9. Liu, Y. …<\/p>\n\n\n\n
A programmable CRISPR\/Cas9 toolkit improves lycopene production in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\nAppl. Environ. Microbiol.<\/em> 2023; 89<\/strong>, e0023023<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n10. Liu, Y. …<\/p>\n\n\n\n
Multiplex base editing of RBSs rewires Bacillus subtilis<\/em> metabolism for lycopene overproduction<\/strong><\/p>\n\n\n\nMetab. Eng.<\/em> 2026; 93<\/strong>:169-183<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n11. Caro-Astorga, J. …<\/p>\n\n\n\n
SubtiToolKit: a bioengineering kit for Bacillus subtilis<\/em> and Gram-positive bacteria<\/strong><\/p>\n\n\n\nTrends Biotechnol.<\/em> 2025; 43<\/strong>:1446-1469<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n12. Cui, H. …<\/p>\n\n\n\n
Enzyme specificity prediction using cross attention graph neural networks<\/strong><\/p>\n\n\n\nNature.<\/em> 2025; 647<\/strong>:639-647<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n13. Li, G. …<\/p>\n\n\n\n
Local flux coordination and global gene expression regulation in metabolic modeling<\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2023; 14<\/strong>:5700<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n14. Nyerges, A. …<\/p>\n\n\n\n
A swapped genetic code prevents viral infections and gene transfer<\/strong><\/p>\n\n\n\nNature.<\/em> 2023; 615<\/strong>:720-727<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n15. Zhang, K. …<\/p>\n\n\n\n
Multistress challenges in industrial Bacillus<\/em> spp.<\/h3>\n\n\n\nIndustrial Bacillus<\/em> strains encounter multiple overlapping stresses during fermentation, including heat, pH fluctuations, oxidative bursts, osmotic shocks, and toxic metabolites, which often act together to limit growth and productivity [1]. For example, sudden heat spikes oxidize proteins, while solvents exacerbate acid sensitivity. Osmotic shifts strain energy and redox pathways, limiting synthesis and secretion. System-level evaluations of microbial cell factories confirm that such<\/p>\n\n\n\nSynergistic stress interactions<\/h3>\n\n\n\n
Single-stress engineering fails in industrial settings. Acid, solvent, heat, and osmotic stresses interact, destabilizing membranes, oxidizing proteins, and draining energy. Stress combinations are nonlinear; the cumulative effect is often greater than the sum of the individual insults.<\/p>\n\n\n\n
Industrial and agricultural relevance<\/h3>\n\n\n\n
Multistress tolerance in Bacillus<\/em> strains reduces the need for buffering, cooling, and additional supplementation. Robust Bacillus<\/em> minimizes downtime, improves productivity, and lowers costs. Outside<\/p>\n\n\n\nTechnological enablers of resilience-by-design<\/h3>\n\n\n\n
Genome-scale perturbation and modular engineering tools, including CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)\/Cas9 (CRISPR-associated protein 9) [9], CRISPR interference (CRISPRi) [7], and base editing [10], and dedicated toolkits such as SubtiToolKit [11], enable systematic exploration of stress-tolerance determinants in Bacillus<\/em>. Coupled with single-cell, multiomics, and dynamic metabolomics analyses, these platforms reveal population heterogeneity, transient metabolic <\/p>\n\n\n\nDesign principles and predictive engineering<\/h3>\n\n\n\n
Engineering stress-resilient Bacillus<\/em> requires a unified design principle that integrates proteostasis, translation, and metabolism, rather than a patchwork of isolated optimizations. High-resolution genotype\u2013phenotype maps, coupled with multiomics data and AI-driven inference, now enable in silico<\/em> prediction of synergistic regulators, metabolic nodes, and transporters that confer resilience without compromising productivity. Transfer learning across Bacillus<\/em>species further enhances predictive <\/p>\n\n\n\nConcluding remarks and future perspectives<\/h3>\n\n\n\n
Next-generation\u00a0Bacillus<\/em>\u00a0platforms will transcend traditional fermentation, supporting applications from precision agriculture to environmental remediation and synthetic consortia stabilization. Engineered strains capable of withstanding harsh soils, detoxifying pollutants, or stabilizing microbial communities exemplify the shift from reactive to predictive biodesign. Resilience-by-design represents more than just a stress-tolerance strategy\u2014it establishes a blueprint for adaptive, intelligent,\u00a0…<\/p>\n\n\n\n<\/div>\n\n\n\nAcknowledgments<\/h3>\n\n\n\n
This work was supported by the\u00a0National Key Research and Development Program of China\u00a0(2025YFA0921800), the\u00a0Strategic Priority Research Program of the Chinese Academy of Sciences\u00a0(XDA0510300), and the\u00a0National Natural Science Foundation of China\u00a0(32100046). …<\/p>\n\n\n\n
<\/div>\n\n\n\nReferences<\/h3>\n\n\n\n
1. Lee, J.A. …<\/p>\n\n\n\n
Factors affecting the competitiveness of bacterial fermentation<\/strong><\/p>\n\n\n\nTrends Biotechnol.<\/em> 2023; 41<\/strong>:798-816<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n2. Kim, G.B. …<\/p>\n\n\n\n
Comprehensive evaluation of the capacities of microbial cell factories<\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2025; 16<\/strong>:2869<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n3. Zhu, M. …<\/p>\n\n\n\n
A fitness trade-off between growth and survival governed by Spo0A-mediated proteome allocation constraints in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\nSci. Adv.<\/em> 2023; 9<\/strong>:9733<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n4. Ou, X. …<\/p>\n\n\n\n
SecY translocon chaperones protein folding during membrane protein insertion<\/strong><\/p>\n\n\n\nCell.<\/em> 2025; 188<\/strong>:1912-1924<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n5. He, T.T. …<\/p>\n\n\n\n
A linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis<\/em><\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2023; 14<\/strong>:5722<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n6. Nadezhdin, E. …<\/p>\n\n\n\n
Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis<\/em> biofilms<\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2020; 11<\/strong>:950<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n7. Zhu, X. …<\/p>\n\n\n\n
Genome-wide CRISPRi screening of key genes for recombinant protein expression in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\nAdv. Sci.<\/em> 2024; 11<\/strong>, e2404313<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n8.<\/p>\n\n\n\n
Yan, Y. …<\/p>\n\n\n\n
Strain engineering of Bacillus coagulans<\/em> with high osmotic pressure tolerance for effective L-lactic acid production from sweet sorghum juice under unsterile conditions<\/strong><\/p>\n\n\n\nBioresour. Technol.<\/em> 2024; 400<\/strong>, 130648<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n9. Liu, Y. …<\/p>\n\n\n\n
A programmable CRISPR\/Cas9 toolkit improves lycopene production in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\nAppl. Environ. Microbiol.<\/em> 2023; 89<\/strong>, e0023023<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n10. Liu, Y. …<\/p>\n\n\n\n
Multiplex base editing of RBSs rewires Bacillus subtilis<\/em> metabolism for lycopene overproduction<\/strong><\/p>\n\n\n\nMetab. Eng.<\/em> 2026; 93<\/strong>:169-183<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n11. Caro-Astorga, J. …<\/p>\n\n\n\n
SubtiToolKit: a bioengineering kit for Bacillus subtilis<\/em> and Gram-positive bacteria<\/strong><\/p>\n\n\n\nTrends Biotechnol.<\/em> 2025; 43<\/strong>:1446-1469<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n12. Cui, H. …<\/p>\n\n\n\n
Enzyme specificity prediction using cross attention graph neural networks<\/strong><\/p>\n\n\n\nNature.<\/em> 2025; 647<\/strong>:639-647<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n13. Li, G. …<\/p>\n\n\n\n
Local flux coordination and global gene expression regulation in metabolic modeling<\/strong><\/p>\n\n\n\nNat. Commun.<\/em> 2023; 14<\/strong>:5700<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n14. Nyerges, A. …<\/p>\n\n\n\n
A swapped genetic code prevents viral infections and gene transfer<\/strong><\/p>\n\n\n\nNature.<\/em> 2023; 615<\/strong>:720-727<\/p>\n\n\n\nGoogle Scholar<\/a><\/p>\n\n\n\n15. Zhang, K. …<\/p>\n\n\n\n
Synergistic stress interactions<\/h3>\n\n\n\n
Single-stress engineering fails in industrial settings. Acid, solvent, heat, and osmotic stresses interact, destabilizing membranes, oxidizing proteins, and draining energy. Stress combinations are nonlinear; the cumulative effect is often greater than the sum of the individual insults.<\/p>\n\n\n\n
Industrial and agricultural relevance<\/h3>\n\n\n\n
Multistress tolerance in Bacillus<\/em> strains reduces the need for buffering, cooling, and additional supplementation. Robust Bacillus<\/em> minimizes downtime, improves productivity, and lowers costs. Outside<\/p>\n\n\n\n Genome-scale perturbation and modular engineering tools, including CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)\/Cas9 (CRISPR-associated protein 9) [9], CRISPR interference (CRISPRi) [7], and base editing [10], and dedicated toolkits such as SubtiToolKit [11], enable systematic exploration of stress-tolerance determinants in Bacillus<\/em>. Coupled with single-cell, multiomics, and dynamic metabolomics analyses, these platforms reveal population heterogeneity, transient metabolic <\/p>\n\n\n\n Engineering stress-resilient Bacillus<\/em> requires a unified design principle that integrates proteostasis, translation, and metabolism, rather than a patchwork of isolated optimizations. High-resolution genotype\u2013phenotype maps, coupled with multiomics data and AI-driven inference, now enable in silico<\/em> prediction of synergistic regulators, metabolic nodes, and transporters that confer resilience without compromising productivity. Transfer learning across Bacillus<\/em>species further enhances predictive <\/p>\n\n\n\n Next-generation\u00a0Bacillus<\/em>\u00a0platforms will transcend traditional fermentation, supporting applications from precision agriculture to environmental remediation and synthetic consortia stabilization. Engineered strains capable of withstanding harsh soils, detoxifying pollutants, or stabilizing microbial communities exemplify the shift from reactive to predictive biodesign. Resilience-by-design represents more than just a stress-tolerance strategy\u2014it establishes a blueprint for adaptive, intelligent,\u00a0…<\/p>\n\n\n\n This work was supported by the\u00a0National Key Research and Development Program of China\u00a0(2025YFA0921800), the\u00a0Strategic Priority Research Program of the Chinese Academy of Sciences\u00a0(XDA0510300), and the\u00a0National Natural Science Foundation of China\u00a0(32100046). …<\/p>\n\n\n\n 1. Lee, J.A. …<\/p>\n\n\n\n Factors affecting the competitiveness of bacterial fermentation<\/strong><\/p>\n\n\n\n Trends Biotechnol.<\/em> 2023; 41<\/strong>:798-816<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 2. Kim, G.B. …<\/p>\n\n\n\n Comprehensive evaluation of the capacities of microbial cell factories<\/strong><\/p>\n\n\n\n Nat. Commun.<\/em> 2025; 16<\/strong>:2869<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 3. Zhu, M. …<\/p>\n\n\n\n A fitness trade-off between growth and survival governed by Spo0A-mediated proteome allocation constraints in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\n Sci. Adv.<\/em> 2023; 9<\/strong>:9733<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 4. Ou, X. …<\/p>\n\n\n\n SecY translocon chaperones protein folding during membrane protein insertion<\/strong><\/p>\n\n\n\n Cell.<\/em> 2025; 188<\/strong>:1912-1924<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 5. He, T.T. …<\/p>\n\n\n\n A linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis<\/em><\/strong><\/p>\n\n\n\n Nat. Commun.<\/em> 2023; 14<\/strong>:5722<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 6. Nadezhdin, E. …<\/p>\n\n\n\n Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis<\/em> biofilms<\/strong><\/p>\n\n\n\n Nat. Commun.<\/em> 2020; 11<\/strong>:950<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 7. Zhu, X. …<\/p>\n\n\n\n Genome-wide CRISPRi screening of key genes for recombinant protein expression in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\n Adv. Sci.<\/em> 2024; 11<\/strong>, e2404313<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 8.<\/p>\n\n\n\n Yan, Y. …<\/p>\n\n\n\n Strain engineering of Bacillus coagulans<\/em> with high osmotic pressure tolerance for effective L-lactic acid production from sweet sorghum juice under unsterile conditions<\/strong><\/p>\n\n\n\n Bioresour. Technol.<\/em> 2024; 400<\/strong>, 130648<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 9. Liu, Y. …<\/p>\n\n\n\n A programmable CRISPR\/Cas9 toolkit improves lycopene production in Bacillus subtilis<\/em><\/strong><\/p>\n\n\n\n Appl. Environ. Microbiol.<\/em> 2023; 89<\/strong>, e0023023<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 10. Liu, Y. …<\/p>\n\n\n\n Multiplex base editing of RBSs rewires Bacillus subtilis<\/em> metabolism for lycopene overproduction<\/strong><\/p>\n\n\n\n Metab. Eng.<\/em> 2026; 93<\/strong>:169-183<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 11. Caro-Astorga, J. …<\/p>\n\n\n\n SubtiToolKit: a bioengineering kit for Bacillus subtilis<\/em> and Gram-positive bacteria<\/strong><\/p>\n\n\n\n Trends Biotechnol.<\/em> 2025; 43<\/strong>:1446-1469<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 12. Cui, H. …<\/p>\n\n\n\n Enzyme specificity prediction using cross attention graph neural networks<\/strong><\/p>\n\n\n\n Nature.<\/em> 2025; 647<\/strong>:639-647<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 13. Li, G. …<\/p>\n\n\n\n Local flux coordination and global gene expression regulation in metabolic modeling<\/strong><\/p>\n\n\n\n Nat. Commun.<\/em> 2023; 14<\/strong>:5700<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 14. Nyerges, A. …<\/p>\n\n\n\n A swapped genetic code prevents viral infections and gene transfer<\/strong><\/p>\n\n\n\n Nature.<\/em> 2023; 615<\/strong>:720-727<\/p>\n\n\n\n Google Scholar<\/a><\/p>\n\n\n\n 15. Zhang, K. …<\/p>\n\n\n\nTechnological enablers of resilience-by-design<\/h3>\n\n\n\n
Design principles and predictive engineering<\/h3>\n\n\n\n
Concluding remarks and future perspectives<\/h3>\n\n\n\n
Acknowledgments<\/h3>\n\n\n\n
References<\/h3>\n\n\n\n