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Rooney J, Rivera-de-Torre E, Li R, Mclean K, Price DR, Nisbet AJ, Laustsen AH, Jenkins TP, Hofmann A, Bakshi S, Zarkan A, Cantacessi C. Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions. Comput Struct Biotechnol J 2024; 23:1522-1533. [PMID: 38633385 PMCID: PMC11021794 DOI: 10.1016/j.csbj.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.
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Affiliation(s)
- James Rooney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ruizhe Li
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Kevin Mclean
- Moredun Research Institute, Penicuik Midlothian, United Kingdom
| | | | | | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Hofmann
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Somenath Bakshi
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Yang S, Guo Z, Sun J, Wei J, Ma Q, Gao X. Recent advances in microbial synthesis of free heme. Appl Microbiol Biotechnol 2024; 108:68. [PMID: 38194135 PMCID: PMC10776470 DOI: 10.1007/s00253-023-12968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024]
Abstract
Heme is an iron-containing porphyrin compound widely used in the fields of healthcare, food, and medicine. Compared to animal blood extraction, it is more advantageous to develop a microbial cell factory to produce heme. However, heme biosynthesis in microorganisms is tightly regulated, and its accumulation is highly cytotoxic. The current review describes the biosynthetic pathway of free heme, its fermentation production using different engineered bacteria constructed by metabolic engineering, and strategies for further improving heme synthesis. Heme synthetic pathway in Bacillus subtilis was modified utilizing genome-editing technology, resulting in significantly improved heme synthesis and secretion abilities. This technique avoided the use of multiple antibiotics and enhanced the genetic stability of strain. Hence, engineered B. subtilis could be an attractive cell factory for heme production. Further studies should be performed to enhance the expression of heme synthetic module and optimize the expression of heme exporter and fermentation processes, such as iron supply. KEY POINTS: • Strengthening the heme biosynthetic pathway can significantly increase heme production. • Heme exporter overexpression helps to promote heme secretion, thereby further promoting excessive heme synthesis. • Engineered B. subtilis is an attractive alternative for heme production.
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Affiliation(s)
- Shaomei Yang
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China.
| | - Zihao Guo
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Jiuyu Sun
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Jingxuan Wei
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Qinyuan Ma
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Xiuzhen Gao
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China.
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Ding X, Zheng Z, Zhao G, Wang L, Wang H, Wang P. Adaptive laboratory evolution for improved tolerance of vitamin K in Bacillus subtilis. Appl Microbiol Biotechnol 2024; 108:75. [PMID: 38194140 DOI: 10.1007/s00253-023-12877-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/10/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024]
Abstract
Menaquinone-7 (MK-7), a subtype of vitamin K2 (VK2), assumes crucial roles in coagulation function, calcium homeostasis, and respiratory chain transmission. The production of MK-7 via microbial fermentation boasts mild technological conditions and high biocompatibility. Nevertheless, the redox activity of MK-7 imposes constraints on its excessive accumulation in microorganisms. To address this predicament, an adaptive laboratory evolution (ALE) protocol was implemented in Bacillus subtilis BS011, utilizing vitamin K3 (VK3) as a structural analog of MK-7. The resulting strain, BS012, exhibited heightened tolerance to high VK3 concentrations and demonstrated substantial enhancements in biofilm formation and total antioxidant capacity (T-AOC) when compared to BS011. Furthermore, MK-7 production in BS012 exceeded that of BS011 by 76% and 22% under static and shaking cultivation conditions, respectively. The molecular basis underlying the superior performance of BS012 was elucidated through genome and transcriptome analyses, encompassing observations of alterations in cell morphology, variations in central carbon and nitrogen metabolism, spore formation, and antioxidant systems. In summation, ALE technology can notably enhance the tolerance of B. subtilis to VK and increase MK-7 production, thus offering a theoretical framework for the microbial fermentation production of other VK2 subtypes. Additionally, the evolved strain BS012 can be developed for integration into probiotic formulations within the food industry to maintain intestinal flora homeostasis, mitigate osteoporosis risk, and reduce the incidence of cardiovascular disease. KEY POINTS: • Bacillus subtilis was evolved for improved vitamin K tolerance and menaquinone-7 (MK-7) production • Evolved strains formed wrinkled biofilms and elongated almost twofold in length • Evolved strains induced sporulation to improve tolerance when carbon was limited.
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Affiliation(s)
- Xiumin Ding
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, China
- University of Science and Technology of China, Hefei, China
| | - Zhiming Zheng
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
| | - Genhai Zhao
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Li Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Han Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Peng Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
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Wu Y, Duan B, Lin Q, Liang Y, Du X, Zheng M, Zhu Y, Jiang Z, Li Q, Ni H, Li Z, Chen J. Fermentation of waste water from agar processing with Bacillus subtilis by metabolomic analysis. Appl Microbiol Biotechnol 2024; 108:15. [PMID: 38170310 DOI: 10.1007/s00253-023-12891-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/01/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024]
Abstract
Fungal infection has become a major threat to crop loss and affects food safety. The waste water from agar processing industries extraction has a number of active substances, which could be further transformed by microorganisms to synthesize antifungal active substances. In this study, Bacillus subtilis was used to ferment the waste water from agar processing industries extraction to analyze the antifungal activity of the fermentation broth on Alternaria alternata and Alternaria spp. Results showed that 25% of the fermentation broth was the most effective in inhibited A. alternata and Alternaria spp., with fungal inhibition rates of 99.9% and 96.1%, respectively, and a minimum inhibitory concentration (MIC) was 0.156 μg/mL. Metabolomic analysis showed that flavonoid polyphenols such as coniferyl aldehyde, glycycoumarin, glycitin, and procyanidin A1 may enhance the inhibitory activity against the two pathogenic fungal strains. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that polyphenols involved in the biosynthesis pathways of isoflavonoid and phenylpropanoid were upregulated after fermentation. The laser confocal microscopy analyses and cell conductivity showed that the cytoplasm of fungi treated with fermentation broth was destroyed. This study provides a research basis for the development of new natural antifungal agents and rational use of seaweed agar waste. KEY POINTS: • Bacillus subtilis fermented waste water has antifungal activity • Bacillus subtilis could transform active substances in waste water • Waste water is a potential raw material for producing antifungal agents.
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Affiliation(s)
- Yanyan Wu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
| | - Boyan Duan
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
| | - Qiaoyan Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
| | - Yingying Liang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
| | - Xiping Du
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, Fujian, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, Fujian, China
| | - Mingjing Zheng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, Fujian, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, Fujian, China
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, Fujian, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, Fujian, China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, Fujian, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, Fujian, China
| | - Qingbiao Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, Fujian, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, Fujian, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, Fujian, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, Fujian, China
- Xiamen Ocean Vocational College, Xiamen, 361021, Fujian, China
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China.
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021, Fujian, China.
- Research Center of Food Biotechnology of Xiamen City, Xiamen, 361021, Fujian, China.
| | - Jinfang Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, Fujian, China.
- College of Harbour and Coastal Engineering, Jimei University, Xiamen, 361021, Fujian, China.
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Ren K, Wang Q, Chen J, Zhang H, Guo Z, Xu M, Rao Z, Zhang X. Design-build-test of recombinant Bacillus subtilis chassis cell by lifespan engineering for robust bioprocesses. Synth Syst Biotechnol 2024; 9:470-480. [PMID: 38634000 PMCID: PMC11021899 DOI: 10.1016/j.synbio.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/03/2024] [Accepted: 04/07/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial cell factories utilize renewable raw materials for industrial chemical production, providing a promising path for sustainable development. Bacillus subtilis is widely used in industry for its food safety properties, but challenges remain in the limitations of microbial fermentation. This study proposes a novel strategy based on lifespan engineering to design robust B. subtilis chassis cells to supplement traditional metabolic modification strategies that can alleviate cell autolysis, tolerate toxic substrates, and get a higher mass transfer efficiency. The modified chassis cells could produce high levels of l-glutaminase, and tolerate hydroquinone to produce α-arbutin efficiently. In a 5 L bioreactor, the l-glutaminase enzyme activity of the final strain CRE15TG was increased to 2817.4 ± 21.7 U mL-1, about 1.98-fold compared with that of the wild type. The α-arbutin yield of strain CRE15A was increased to 134.7 g L-1, about 1.34-fold compared with that of the WT. To our knowledge, both of the products in this study performed the highest yields reported so far. The chassis modification strategy described in this study can Improve the utilization efficiency of chassis cells, mitigate the possible adverse effects caused by excessive metabolic modification of engineered strains, and provide a new idea for the future design of microbial cell factories.
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Affiliation(s)
- Kexin Ren
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Qiang Wang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Jianghua Chen
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Hengwei Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Zhoule Guo
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
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6
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Gao Y, Hu M, Meng W, Wen W, Zhang P, Fan B, Wang F, Li S. Study on the quality of soybean proteins fermented by Bacillus subtilis BSNK-5: Insights into nutritional, functional, safety, and flavor properties. Food Chem 2024; 443:138523. [PMID: 38286093 DOI: 10.1016/j.foodchem.2024.138523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
Microbial fermentation emerges as a promising strategy to elevate the quality of soybean proteins in food industry. This study conducted a comprehensive assessment of the biotransformation of four types of soybean proteins by Bacillus subtilis BSNK-5, a proteinase-rich bacterium. BSNK-5 had good adaptability to each protein. Soluble protein, peptides and free amino acids increased in fermented soybean proteins (FSPs) and dominant after 48-84 h fermentation, enhancing nutritional value. Extensive proteolysis of BSNK-5 also improved antioxidant and antihypertensive activities, reaching peak level after 48 h fermentation. Furthermore, excessive proteolysis effectively enhanced the generation of beneficial spermidine without producing toxic histamine after fermentation, and formed the flavor profile with 56 volatiles in 48 h FSPs. Further degradation of amino acids showed a positive correlation with off-flavors, particularly the enrichment of 3-methylbutanoic acid. These findings establish a theoretical foundation for regulating moderate fermentation by BSNK-5 to enabling the high-value utilization of soybean protein.
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Affiliation(s)
- Yaxin Gao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miao Hu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weimin Meng
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Wen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pengfei Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bei Fan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-products Processing, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengzhong Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-products Processing, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Shuying Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.
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Peng A, Yin G, Zuo W, Zhang L, Du G, Chen J, Wang Y, Kang Z. Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology. Synth Syst Biotechnol 2024; 9:223-233. [PMID: 38385150 PMCID: PMC10877136 DOI: 10.1016/j.synbio.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.
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Affiliation(s)
- Anqi Peng
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wenjie Zuo
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Luyao Zhang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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Li Y, Wangjiang T, Sun Z, Shi L, Chen S, Chen L, Guo X, Wu W, Xiong G, Wang L. Inhibition mechanism of crude lipopeptide from Bacillus subtilis against Aeromonas veronii growth, biofilm formation, and spoilage of channel catfish flesh. Food Microbiol 2024; 120:104489. [PMID: 38431332 DOI: 10.1016/j.fm.2024.104489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Aeromonas veronii is associated with food spoilage and some human diseases, such as diarrhea, gastroenteritis, hemorrhagic septicemia or asymptomatic and even death. This research investigated the mechanism of the growth, biofilm formation, virulence, stress resistance, and spoilage potential of Bacillus subtilis lipopeptide against Aeromonas veronii. Lipopeptides suppressed the transmembrane transport of Aeromonas veronii by changing the cell membrane's permeability, the structure of membrane proteins, and Na+/K+-ATPase. Lipopeptide significantly reduced the activities of succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) by 86.03% and 56.12%, respectively, ultimately slowing Aeromonas veronii growth. Lipopeptides also restrained biofilm formation by inhibiting Aeromonas veronii motivation and extracellular polysaccharide secretion. Lipopeptides downregulated gene transcriptional levels related to the virulence and stress tolerance of Aeromonas veronii. Furthermore, lipopeptides treatment resulted in a considerable decrease in the extracellular protease activity of Aeromonas veronii, which restrained the decomposing of channel catfish flesh. This research provides new insights into lipopeptides for controlling Aeromonas veronii and improving food safety.
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Affiliation(s)
- Yali Li
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tianqi Wangjiang
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China; State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Sciences and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Zhida Sun
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liu Shi
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Sheng Chen
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Lang Chen
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Xiaojia Guo
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Wenjin Wu
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Guangquan Xiong
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Lan Wang
- Key Laboratory of Agricultural Products Cold Chain Logistics, Ministry of Agriculture and Rural Affairs, Institute of Agro-Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
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9
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Luo K, Guo Z, Liu Y, Li C, Ma Z, Tian X. Responses of growth performance, immunity, disease resistance of shrimp and microbiota in Penaeus vannamei culture system to Bacillus subtilis BSXE-1601 administration: Dietary supplementation versus water addition. Microbiol Res 2024; 283:127693. [PMID: 38490029 DOI: 10.1016/j.micres.2024.127693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/20/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
This study evaluated the effects of Bacillus subtilis BSXE-1601, applied either as dietary supplementation or water addition, on growth performance, immune responses, disease resistance of Penaeus vannamei, and microbiota in shrimp gut and rearing water. During the 42-day feeding experiment, shrimp were fed with basal diet (CO and BW group), basal diet supplemented with live strain BSXE-1601 at the dose of 1 × 109 CFU kg-1 feed (BD group) and 15 mg kg-1 florfenicol (FL group), and basal diet with strain BSXE-1601 added to water at the concentration of 1 × 107 CFU L-1 every five days (BW group). Results showed that dietary supplementation of strain BSXE-1601 significantly promoted growth performance of shrimp, both in the diet and water, enhanced disease resistance against Vibrio parahaemolyticus (P < 0.05). The BD and BW groups exhibited significant increases in acid phosphatase, alkaline phosphatase, lysozyme, peroxidase, superoxide dismutase activities, phenonoloxidase content in the serum of shrimp compared to the control (P < 0.05). Meanwhile, the expression of immune-related genes proPO, LZM, SOD, LGBP, HSP70, Imd, Toll, Relish, TOR, 4E-BP, eIF4E1α, eIF4E2 were significantly up-regulated compared to the control (P < 0.05). When added in rearing water, strain BSXE-1601 induced greater immune responses in shrimp than the dietary supplement (P < 0.05). Chao1 and Shannon indices of microbiota in rearing water were significantly lower in BD group than in the control. The microbiota in rearing water were significantly altered in BD, BW and FL groups compared to the control, while no significant impacts were observed on the microbiota of shrimp gut. When supplemented into the feed, strain BSXE-1601 obviously reduced the number of nodes, edges, modules in the ecological network of rearing water. The results suggested that dietary supplementation of BSXE-1601 could be more suitable than water addition in the practice of shrimp rearing when growth performance, non-specific immunity, disease resistance against V. parahaemolyticus in shrimp were collectively considered.
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Affiliation(s)
- Kai Luo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Zeyang Guo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China; Tropical Fisheries Research Institute of Sanya, Sanya 572018, PR China
| | - Yang Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Changlin Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Zhenhua Ma
- Tropical Fisheries Research Institute of Sanya, Sanya 572018, PR China.
| | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China.
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10
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Chen J, Cai R, Tang L, Wang D, Lv R, Guo C. Antagonistic activity and mechanism of Bacillus subtilis CG-6 suppression of root rot and growth promotion in Alfalfa. Microb Pathog 2024; 190:106616. [PMID: 38492826 DOI: 10.1016/j.micpath.2024.106616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
Root rot is a common disease, that severely affects the yield and quality of alfalfa. Biocontrol is widely used to control plant diseases caused by pathogenic fungi, however, biocontrol strains for alfalfa root rot are very limited. In this study, a Bacillus subtilis CG-6 strain with a significant biocontrol effect on alfalfa root rot was isolated. CG-6 secretes antibacterial enzymes and siderophore, phosphate solubilization and indoleacetic acid (IAA). The inhibition rate of strain CG-6 against Fusarium oxysporum was 87.33%, and it showed broad-spectrum antifungal activity. Inoculation with CG-6 significantly reduced the incidence of alfalfa root rot, the control effect of greenhouse cultivation reached 58.12%, and CG-6 treatment significantly increased alfalfa plant height, root length, fresh weight, and dry weight. The treatment with CG-6 significantly increased the levels of antioxidant enzymes (catalase, peroxidase, superoxide dismutase, and lipoxygenase) in alfalfa leaves by 15.52%-34.03%. Defensive enzymes (chitinase and β-1,3-glucanase) increased by 24.37% and 28.08%, respectively. The expression levels of regulatory enzyme genes (MsCAT, MsPOD, MsCu, Zn-SOD1, MsCu, Zn-SOD2, MsCu, Zn-SOD3, and MsLOX2) and systemic resistance genes (MsPR1, MsPDF1.2, and MsVSP2) increased by 0.50-2.85 fold, which were higher than those in the pathogen treatment group. Therefore, CG-6 could be used as a potential strain to develop biopesticides against alfalfa root rot.
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Affiliation(s)
- Jiaxin Chen
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Limin Development Zone, Harbin Normal University, No. 1 of Shida Road, Harbin 150025, China
| | - Run Cai
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Limin Development Zone, Harbin Normal University, No. 1 of Shida Road, Harbin 150025, China
| | - Lu Tang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Limin Development Zone, Harbin Normal University, No. 1 of Shida Road, Harbin 150025, China
| | - Dan Wang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Limin Development Zone, Harbin Normal University, No. 1 of Shida Road, Harbin 150025, China
| | - Ruiwei Lv
- Science and Technology Building, Heilongjiang Guohong Environmental Co., Ltd., No. 600 of Chuangxin Third Road, Songbei Zone, Harbin 150029, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Limin Development Zone, Harbin Normal University, No. 1 of Shida Road, Harbin 150025, China.
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11
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Zhu L, Xu Q, Liu W, Xu Q, Zhang L, Gao X, Cai J. Purification and characterization of an α-l-arabinofuranosidase, α-l-AFase, for hydrolyzed ginsenoside Rc from Bacillus subtilis. Protein Expr Purif 2024; 217:106432. [PMID: 38232795 DOI: 10.1016/j.pep.2024.106432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/27/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
Natural ginsenoside needs to be converted into rare ginsenoside before it can be readily absorbed into the bloodstream for action. In this study, an α-l-arabinofuranosidase (α-l-AFase) gene Bsafs2 was cloned from Bacillus subtilis (B. subtilis). Bsafs2 was ligated to the expression vector pET28a(+), and the expression vector was constructed and transformed into Escherichia coli (E. coli) BL21 heterologous recombinant expression to obtain α-l-AFase. α-l-AFase can hydrolyze at the C20 site of Ginsenoside Rc to obtain rare ginsenoside Rd. Studies on the enzymatic property showed that α-l-AFase had good tolerance to ethanol, glucose, and l-arabinose. The optimum temperature of α-l-AFase was 40 °C and pH = 5.5. Kinetic parameters Km of α-l-AFase for pNPαAraf and Ginsenoside Rc were 1.93 and 8.9 mmol/L, the Vmax were 26 and 154 μmol/min/mg, the Kcat were 24.14 and 1.48 S-1, respectively. This study provides the enzyme source for the biotransformation of Ginsenoside Rc.
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Affiliation(s)
- Ling Zhu
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, 655011, China
| | - Qingfang Xu
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, 655011, China
| | - Weiliang Liu
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, 655011, China
| | - Qihe Xu
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, 655011, China
| | - Lifang Zhang
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, 655011, China
| | - Xiu Gao
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, 655011, China.
| | - Jian Cai
- Yunnan Engineering Research Center of Fruit Wine, Qujing Normal University, Qujing, 655011, China.
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12
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Khosravi M, Avizeh R, Zayerzadeh A, Gharibi D, Razijalali M. Effect of Bacillus subtilis and Bacillus coagulans spores on induced allergic contact dermatitis in dogs. Vet Med Sci 2024; 10:e1410. [PMID: 38501344 PMCID: PMC10949178 DOI: 10.1002/vms3.1410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Probiotic strains have the potential to modulate immune responses, reduce intestinal inflammation, normalize intestinal mucosal function and decrease allergic reactions. OBJECTIVE This study aimed to investigate the effect of oral probiotic supplements containing Bacillus subtilis and Bacillus coagulans spores on clinical symptoms, haematological factors and immune responses to allergic contact dermatitis in dogs induced by dinitrochlorobenzene (DNCB). METHODS DNCB was injected subcutaneously into the scapular region of 20 healthy adult dogs of both sexes, divided into four groups, to induce experimental allergic contact dermatitis. Dogs in Group 1 received food without probiotics or medication. Oral prednisolone was administered to Group 2 for 30 days at a dosage of 0.25 mg/kg every other day. The dogs in Group 3 were treated with a combination of oral prednisolone and probiotics. The dogs in Group 4 were fed daily with a mixture of 109 B. subtilis and B. coagulans bacteria for 30 days. The immune system responses and related gene expression were analysed in the treated animals. RESULTS The administration of probiotics for 30 days resulted in a reduction in clinical symptoms and duration of wound repair. The probiotics treatment also significantly increased the serum bactericidal effects against Staphylococcus aureus and Escherichia coli. It enhanced both the classic and alternative activity of the complement, as well as lysozyme activity. Additionally, the probiotics led to higher total immunoglobulin levels and significant reductions in anti-trypsin and C-reactive protein levels. Furthermore, the expression of IgE, induction of interferon-gamma and IL-4 genes were also reduced. CONCLUSIONS According to the results, B. subtilis and B. coagulans can be further investigated as a viable alternative to corticosteroids in treating allergic contact dermatitis in dogs.
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Affiliation(s)
- Mohammad Khosravi
- Department of PathobiologyFaculty of Veterinary MedicineShahid Chamran University of AhvazAhvazKhuzestanIran
| | - Reza Avizeh
- Department of Clinical SciencesFaculty of Veterinary MedicineShahid Chamran University of AhvazAhvazKhuzestanIran
| | - Akram Zayerzadeh
- DVSc of Small Animal Internal MedicineFaculty of Veterinary MedicineShahid Chamran University of AhvazAhvazKhuzestanIran
| | - Darioush Gharibi
- Department of PathobiologyFaculty of Veterinary MedicineShahid Chamran University of AhvazAhvazKhuzestanIran
| | - Mohammad Razijalali
- Department of Clinical SciencesFaculty of Veterinary MedicineShahid Chamran University of AhvazAhvazKhuzestanIran
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13
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Khan Z, Tanoeyadi S, Jabeen N, Shafique M, Naz SA, Mahmud T. Molecular basis for the increased activity of ZMS-2 serine protease in the presence of metal ions and hydrogen peroxide. J Inorg Biochem 2024; 256:112566. [PMID: 38657303 DOI: 10.1016/j.jinorgbio.2024.112566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Serine proteases are important enzymes widely used in commercial products and industry. Recently, we identified a new serine protease from the desert bacterium Bacillus subtilis ZMS-2 that showed enhanced activity in the presence of Zn2+, Ag+, or H2O2. However, the molecular basis underlying this interesting property is unknown. Here, we report comparative studies between the ZMS-2 protease and its homolog, subtilisin E (SubE), from B. subtilis ATCC 6051. In the absence of Zn2+, Ag+, or H2O2, both enzymes showed the same level of proteolytic activity, but in the presence of Zn2+, Ag+, or H2O2, ZMS-2 displayed increased activity by 22%, 8%, and 14%, whereas SubE showed decreased activity by 16%, 12%, and 9%, respectively. In silico studies showed that both proteins have almost identical amino acid sequences and folding structures, except for two amino acids located in the protruding loops of the proteins. ZMS-2 contains Ser236 and Ser268, whereas SubE contains Thr236 and Thr268. Replacing Ser236 or Ser268 in ZMS-2 with threonine resulted in variants whose activities were not enhanced by Zn2+ or Ag+. However, this single mutation did not affect the enhancement by H2O2. This finding may be used as a basis for engineering better proteases for industrial uses.
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Affiliation(s)
- Zahoor Khan
- Department of Microbiology, University of Karachi, 75270, Pakistan; Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, United States
| | - Samuel Tanoeyadi
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, United States
| | - Nusrat Jabeen
- Department of Microbiology, University of Karachi, 75270, Pakistan
| | - Maryam Shafique
- Department of Microbiology, Federal Urdu University of Arts, Science and Technology, Karachi 75300, Pakistan
| | - Sehar Afshan Naz
- Department of Microbiology, Federal Urdu University of Arts, Science and Technology, Karachi 75300, Pakistan
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, United States.
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Sodhozai AR, Bibi S, Rabia M, Jadoon M, Akhtar H, Ali N. From Growth Inhibition to Ultrastructural Changes: Toxicological Assessment of Lambda Cyhalothrin and Fosetyl Aluminium against Bacillus subtilis and Pseudomonas aeruginosa. Environ Res 2024:118958. [PMID: 38640987 DOI: 10.1016/j.envres.2024.118958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/30/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
In modern agricultural practices, agrochemicals and pesticides play an important role in protecting the crops from pests and elevating agricultural productivity. This strategic utilization is essential to meet global food demand due to the relentless growth of the world's population. However, the indiscriminate application of these substances may result in environmental hazards and directly affect the soil microorganisms and crop production. Considering this, an in vitro study was carried out to evaluate the pesticides' effects i.e. lambda cyhalothrin (insecticide) and fosetyl aluminum (fungicide) at lower, recommended, and higher doses on growth behavior, enzymatic profile, total soluble protein production, and lipid peroxidation of bacterial specimens (Pseudomonas aeruginosa and Bacillus subtilis). The experimental findings demonstrated a concentration-dependent decrease in growth of both tested bacteria, when exposed to fosetyl aluminum concentrations exceeding the recommended dose. This decline was statistically significant (p <.000). However, lambda cyhalothrin at three times of recommended dose induces 10 % increase in growth of Pseudomonas aeruginosa (P. aeruginosa) and 76.8 % decrease in growth of Bacillus subtilis (B. subtilis) respectively as compared to control. These results showed the stimulatory effect of lambda cyhalothrin on P. aeruginosa and inhibitory effect on B. subtilis. Pesticides induced notable alterations in biomarker enzymatic assays and other parameters related to oxidative stress among bacterial strains, resulting in increased oxidative stress and membrane permeability. Generally, the maximum toxicity of both (P. aeruginosa and B. subtilis) was shown by fosetyl aluminum, at three times of recommended dose. Fosetyl alumimium induced morphological changes like cellular cracking, reduced viability, aberrant margins and more damage in both bacterial strains as compared to lambda cyhalothrin when observed under scanning electron microscope (SEM). Conclusively the, present study provide an insights into a mechanistic approach of pyrethroid insecticide and phosphonite fungicide induced cellular toxicity towards bacteria.
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Affiliation(s)
- Asma Rabbani Sodhozai
- Department of Microbiology, Faculty of Biological Sciences , Quaid-I-Azam University Islamabad 45320, Pakistan.
| | - Safia Bibi
- Department of Microbiology, Faculty of Biological Sciences , Quaid-I-Azam University Islamabad 45320, Pakistan.
| | - Mahwish Rabia
- Department of Statistics, Faculty of Natural Sciences, Quaid-I-Azam University Islamabad 45320, Pakistan.
| | - Muneeba Jadoon
- Department of Microbiology, Faculty of Biological Sciences , Quaid-I-Azam University Islamabad 45320, Pakistan.
| | - Hafsah Akhtar
- Department of Microbiology, Comsat University Lahore, Pakistan.
| | - Naeem Ali
- Department of Microbiology, Faculty of Biological Sciences , Quaid-I-Azam University Islamabad 45320, Pakistan.
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15
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Tan W, Miao Q, Jia X, Liu Y, Li S, Yang D. Research Progress on the Assembly of Large DNA Fragments. Chembiochem 2024; 25:e202400054. [PMID: 38477700 DOI: 10.1002/cbic.202400054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Synthetic biology, a newly and rapidly developing interdisciplinary field, has demonstrated increasing potential for extensive applications in the wide areas of biomedicine, biofuels, and novel materials. DNA assembly is a key enabling technology of synthetic biology and a central point for realizing fully synthetic artificial life. While the assembly of small DNA fragments has been successfully commercialized, the assembly of large DNA fragments remains a challenge due to their high molecular weight and susceptibility to breakage. This article provides an overview of the development and current state of DNA assembly technology, with a focus on recent advancements in the assembly of large DNA fragments in Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. In particular, the methods and challenges associated with the assembly of large DNA fragment in different hosts are highlighted. The advancements in DNA assembly have the potential to facilitate the construction of customized genomes, giving us the ability to modify cellular functions and even create artificial life. It is also contributing to our ability to understand, predict, and manipulate living organisms.
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Affiliation(s)
- Wei Tan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Qing Miao
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Xuemei Jia
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Ying Liu
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
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Muñoz-Gutierrez V, Cornejo FA, Schmidt K, Frese CK, Halte M, Erhardt M, Elsholz AKW, Turgay K, Charpentier E. Bacillus subtilis remains translationally active after CRISPRi-mediated replication initiation arrest. mSystems 2024; 9:e0022124. [PMID: 38546227 PMCID: PMC11019786 DOI: 10.1128/msystems.00221-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Initiation of bacterial DNA replication takes place at the origin of replication (oriC), a region characterized by the presence of multiple DnaA boxes that serve as the binding sites for the master initiator protein DnaA. This process is tightly controlled by modulation of the availability or activity of DnaA and oriC during development or stress conditions. Here, we aimed to uncover the physiological and molecular consequences of stopping replication in the model bacterium Bacillus subtilis. We successfully arrested replication in B. subtilis by employing a clustered regularly interspaced short palindromic repeats interference (CRISPRi) approach to specifically target the key DnaA boxes 6 and 7, preventing DnaA binding to oriC. In this way, other functions of DnaA, such as a transcriptional regulator, were not significantly affected. When replication initiation was halted by this specific artificial and early blockage, we observed that non-replicating cells continued translation and cell growth, and the initial replication arrest did not induce global stress conditions such as the SOS response.IMPORTANCEAlthough bacteria constantly replicate under laboratory conditions, natural environments expose them to various stresses such as lack of nutrients, high salinity, and pH changes, which can trigger non-replicating states. These states can enable bacteria to (i) become tolerant to antibiotics (persisters), (ii) remain inactive in specific niches for an extended period (dormancy), and (iii) adjust to hostile environments. Non-replicating states have also been studied because of the possibility of repurposing energy for the production of additional metabolites or proteins. Using clustered regularly interspaced short palindromic repeats interference (CRISPRi) targeting bacterial replication initiation sequences, we were able to successfully control replication initiation in Bacillus subtilis. This precise approach makes it possible to study non-replicating phenotypes, contributing to a better understanding of bacterial adaptive strategies.
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Affiliation(s)
- Vanessa Muñoz-Gutierrez
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Manuel Halte
- Humboldt-Universität zu Berlin, Institute of Biology – Molecular Microbiology, Berlin, Germany
| | - Marc Erhardt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology – Molecular Microbiology, Berlin, Germany
| | | | - Kürşad Turgay
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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17
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Yang W, Yuan Y, He L, Fan H. Single-cell analysis reveals microbial spore responses to sodium hypochlorite. J Biophotonics 2024:e202400015. [PMID: 38613161 DOI: 10.1002/jbio.202400015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Pollution from toxic spores has caused us a lot of problems because spores are extremely resistant and can survive most disinfectants. Therefore, the detection of spore response to disinfectant is of great significance for the development of effective decontamination strategies. In this work, we investigated the effect of 0.5% sodium hypochlorite on the molecular and morphological properties of single spores of Bacillus subtilis using single-cell techniques. Laser tweezers Raman spectroscopy showed that sodium hypochlorite resulted in Ca2+-dipicolinic acid release and nucleic acid denaturation. Atomic force microscopy showed that the surface of treated spores changed from rough to smooth, protein shells were degraded at 10 min, and the permeability barrier was destroyed at 15 min. The spore volume decreased gradually over time. Live-cell imaging showed that the germination and growth rates decreased with increasing treatment time. These results provide new insight into the response of spores to sodium hypochlorite.
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Affiliation(s)
- Weiming Yang
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong, China
- School of Information and Optoelectronic Science and Engineering, South China Normal University, Guangzhou, Guangdong, China
| | - Yufeng Yuan
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong, China
| | - Lin He
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong, China
| | - Haihua Fan
- School of Information and Optoelectronic Science and Engineering, South China Normal University, Guangzhou, Guangdong, China
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18
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Shu HY, Chen CC, Ku HT, Wang CL, Wu KM, Weng HY, Liu ST, Chen CL, Chiu CH. Complete genome sequence of Bacillus halotolerans F29-3, a fengycin-producing strain. Microbiol Resour Announc 2024; 13:e0124623. [PMID: 38451104 PMCID: PMC11008187 DOI: 10.1128/mra.01246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Bacillus halotolerans F29-3, a Gram-positive bacterium, is recognized for its synthesis of the antifungal substance fengycin. This announcement introduces the complete genome sequence and provides insights into the genetic products related to antibiotic secondary metabolites, including non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and NRPS/PKS combination.
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Affiliation(s)
- Hung-Yu Shu
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Hsin-Tzu Ku
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Keh-Ming Wu
- Bioinformatics Department, Welgene Biotech Co., Ltd., Taipei, Taiwan
| | - Hui-Ying Weng
- Biomedical Industry Ph.D. Program, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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Xie Z, Yun Y, Yu G, Zhang X, Zhang H, Wang T, Zhang L. Bacillus subtilis alleviates excessive apoptosis of intestinal epithelial cells in intrauterine growth restriction suckling piglets via the members of Bcl-2 and caspase families. J Sci Food Agric 2024. [PMID: 38597265 DOI: 10.1002/jsfa.13525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 02/15/2024] [Accepted: 04/10/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The intestine is a barrier resisting various stress responses. Intrauterine growth restriction (IUGR) can cause damage to the intestinal barrier via destroying the balance of intestinal epithelial cells' proliferation and apoptosis. Bacillus subtilis has been reported to regulate intestinal epithelial cells' proliferation and apoptosis. Thus, the purpose of this study was to determine if B. subtilis could regulate intestinal epithelial cells' proliferation and apoptosis in intrauterine growth restriction suckling piglets. RESULTS Compared with the normal birth weight group, the IUGR group showed greater mean optical density values of Ki-67-positive cells in the ileal crypt (P < 0.05). IUGR resulted in higher ability of proliferation and apoptosis of intestinal epithelial cells, by upregulation of the messenger RNA (mRNA) or proteins expression of leucine rich repeat containing G protein coupled receptor 5, Caspase-3, Caspase-7, β-catenin, cyclinD1, B-cell lymphoma-2 associated agonist of cell death, and BCL2 associated X (P < 0.05), and downregulation of the mRNA or protein expression of B-cell lymphoma-2 and B-cell lymphoma-2-like 1 (P < 0.05). However, B. subtilis supplementation decreased the mRNA or proteins expression of leucine rich repeat containing G protein coupled receptor 5, SPARC related modular calcium binding 2, tumor necrosis factor receptor superfamily member 19, cyclinD1, Caspase-7, β-catenin, B-cell lymphoma-2 associated agonist of cell death, and Caspase-3 (P < 0.05), and increased the mRNA expression of B-cell lymphoma-2 (P < 0.05). CONCLUSION IUGR led to excessive apoptosis of intestinal epithelial cells, which induced compensatory proliferation. However, B. subtilis treatment prevented intestinal epithelial cells of IUGR suckling piglets from excessive apoptosis. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Zechen Xie
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Yang Yun
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Ge Yu
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Xin Zhang
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Hao Zhang
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Tian Wang
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Lili Zhang
- College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, China
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20
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Lin YT, Hung YC, Chen LH, Lee KT, Han YS. Effects of adding Bacillus subtilis natto NTU-18 in paste feed on growth, intestinal morphology, gastrointestinal microbiota diversity, immunity, and disease resistance of Anguilla japonica glass eels. Fish Shellfish Immunol 2024; 149:109556. [PMID: 38608848 DOI: 10.1016/j.fsi.2024.109556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Japanese eel, Anguilla japonica, holds significant importance in Taiwanese aquaculture. With the intensification of eel farming, the impact of Edwardsiella tarda has become increasingly severe. Consequently, the abusive use of antibiotics has risen. Bacillus subtilis natto NTU-18, a strain of Bacillus with a high survival rate in feed processing, plays a crucial role in promoting intestinal health through competitive rejection, enhancing immune responses against bacterial pathogens, and improving intestinal health by modulating gastrointestinal microbiota to produce beneficial metabolites of mice and grass carp, Ctenopharyngodon idella. This study investigated the effects of different proportions (control, 0.25 %, 0.5 %, 1 %, and 2 %) of B. subtilis natto NTU-18 added to paste feed on the growth performance, intestinal morphology, and microbiota, expression of immune-related genes, and resistance to E. tarda in Japanese glass eel. The results indicated that the growth performance of all groups with B. subtilis natto NTU-18 added was significantly higher than that of the control group and did not impact the villi morphology. The expression of immune-related genes in the kidney, specifically HSP70 and SOD, was significantly higher from 0.5 % and above than the control; however, no significant differences were observed in CAT, POD, and HSP90. In the liver, significant differences were found in HSP70 and IgM above 0.25 % compared to the control group, with no significant differences in SOD, CAT, POD, and HSP90 among all groups. Additionally, intestinal microbiota analysis revealed that the 2 % additional group had significantly lower diversity than other groups, with Cetobacterium as the dominant species. The challenge test observed that the survival rates of the 0.5 % and 1 % groups were significantly higher. This research suggests that adding 0.5 % and 1 % of B. subtilis natto NTU-18 to the diet is beneficial for Japanese glass eel's immunity, growth performance, and disease resistance.
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Affiliation(s)
- Yen-Ting Lin
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chen Hung
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Li-Han Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Kung-Ta Lee
- Department of Biochemical Science & Technology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
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21
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Abedi AH, Adhami HR, Mousavi Ghahfarrokhi SS, Mirmasoumi M, Amin M. Bacillus subtilis stimulates plant growth and production of bioactive components in saffron. Nat Prod Res 2024:1-6. [PMID: 38598323 DOI: 10.1080/14786419.2024.2340045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024]
Abstract
The effects of B. subtilis on the morphology and physiology of saffron were investigated using two types of soils. Three different bacterial suspensions were applied at 14-day intervals to treat saffron. Morphological attributes were recorded, and the amounts of α-crocin and safranal in the stigma extracts were quantified. The longest stigma, petal, and leaf were observed in the treated groups with 105 and 108 cfu/ml. The highest weight of stigma per corm belonged to the treated groups with 102 cfu/ml in unsterile soil and 105 and 108 cfu/ml in sterile soil. Treatment with 102 and 108 cfu/ml caused a significant increase in safranal production in sterile and unsterile peat/perlite. While treatment with 105 and 108 cfu/ml in sterile peat/perlite and exposure to 102 cfu/ml in unsterile peat/perlite soil resulted in an increase in α-crocin. The data showed that B. subtlis triggers the morphological and physiological processes in saffron.
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Affiliation(s)
- Amir-Hossein Abedi
- Faculty of Pharmacy, International Campus, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid-Reza Adhami
- Department of Pharmacognosy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Sadeq Mousavi Ghahfarrokhi
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Pharmaceutical Microbiology Group, Pharmaceutical Quality Assurance Research Center, The Institute of Pharmaceutical Sciences (TIPS, Tehran University of Medical Sciences, Tehran, Iran)
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Masoud Mirmasoumi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mohsen Amin
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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22
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Warneke R, Herzberg C, Daniel R, Hormes B, Stülke J. Control of three-carbon amino acid homeostasis by promiscuous importers and exporters in Bacillus subtilis: role of the "sleeping beauty" amino acid exporters. mBio 2024; 15:e0345623. [PMID: 38470260 PMCID: PMC11005379 DOI: 10.1128/mbio.03456-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
The Gram-positive model bacterium Bacillus subtilis can acquire amino acids by import, de novo biosynthesis, or degradation of proteins and peptides. The accumulation of several amino acids inhibits the growth of B. subtilis, probably due to misincorporation into cellular macromolecules such as proteins or peptidoglycan or due to interference with other amino acid biosynthetic pathways. Here, we studied the adaptation of B. subtilis to toxic concentrations of the three-carbon amino acids L-alanine, β-alanine, and 2,3-diaminopropionic acid, as well as the two-carbon amino acid glycine. Resistance to the non-proteinogenic amino acid β-alanine, which is a precursor for coenzyme A biosynthesis, is achieved by mutations that either activate a cryptic amino acid exporter, AexA (previously YdeD), or inactivate the amino acid importers AimA, AimB (previously YbxG), and BcaP. The aexA gene is very poorly expressed under most conditions studied. However, mutations affecting the transcription factor AerA (previously YdeC) can result in strong constitutive aexA expression. AexA is the first characterized member of a group of amino acid exporters in B. subtilis, which are all very poorly expressed. Therefore, we suggest to call this group "sleeping beauty amino acid exporters." 2,3-Diaminopropionic acid can also be exported by AexA, and this amino acid also seems to be a natural substrate of AerA/AexA, as it can cause a slight but significant induction of aexA expression, and AexA also provides some natural resistance toward 2,3-diaminopropionic acid. Moreover, our work shows how low-specificity amino acid transporters contribute to amino acid homeostasis in B. subtilis.IMPORTANCEEven though Bacillus subtilis is one of the most-studied bacteria, amino acid homeostasis in this organism is not fully understood. We have identified import and export systems for the C2 and C3 amino acids. Our work demonstrates that the responsible amino acid permeases contribute in a rather promiscuitive way to amino acid uptake. In addition, we have discovered AexA, the first member of a group of very poorly expressed amino acid exporters in B. subtilis that we call "sleeping beauty amino acid exporters." The expression of these transporters is typically triggered by mutations in corresponding regulator genes that are acquired upon exposure to toxic amino acids. These exporters are ubiquitous in all domains of life. It is tempting to speculate that many of them are not expressed until the cells experience selective pressure by toxic compounds, and they protect the cells from rare but potentially dangerous encounters with such compounds.
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Affiliation(s)
- Robert Warneke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
| | - Richard Daniel
- Center for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Björn Hormes
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
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Soltan MA, Shewita RS, Matroud OA, Alkeridis LA, Sayed S, Shukry M, El-Shobokshy SA. Lignocellulose and probiotic supplementation in broiler chicken diet: effect on growth performance, digestive health, litter quality, and genes expression. Poult Sci 2024; 103:103735. [PMID: 38652957 DOI: 10.1016/j.psj.2024.103735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Three hundred one-day-old Avian 48 broiler chicks were used to investigate the effect of lignocellulose (LC) and probiotic supplementation in broiler chicken diet on growth performance, digestive health, litter quality, and some gene expression. Experimental treatments consisted of 3 × 2 factorial arrangements with 3 levels of LC without or with probiotics to formulate 6 experimental groups. Groups 1, 2, and 3 were fed on the basal diet with dietary LC inclusion at 0, 0.5, and 1.0%, respectively, while groups 4, 5, and 6 were fed on the previously mentioned design with Bacillus subtilis at 100 gm/ton. The results revealed that Dietary LC inclusion nonsignificantly (P ≥ 0.05) reduced body weight (BW), body weight gain (BWG), and feed intake. Meanwhile, B. subtilis supplementation improved BW and BWG and enhanced the effect of LC on the broilers' weight. The group fed a 0.5% LC and B. subtilis-supplemented diet recorded the best (P ≥ 0.05) BW, BWG, FCR, PER, EEU, and PI. LC and or B. subtilis supplementation improved carcass traits of broiler (higher dressing% with lower abdominal fat% compared with a control group), intestinal health, and absorptive capacity. LC potentiates the effect of B. subtilis supplementation in broilers' diet in modulating intestinal microflora (lowered (P ≥ 0.05) cecal Coliform and increased Lactobacillus counts), the highest Coliform counts were recorded in group fed 0.5 or 1.0% LC plus B. subtilis. LC at 0.5 or 1.0% and or B. subtilis supplementation reduced (P ≥ 0.05) litter moisture% at the 2nd, 4th, and 6th wk compared to the control group. Dietary inclusion of LC and or B. subtilis supplementation significantly (P < 0.001) up-regulated hepatic growth-related genes (growth hormone receptor (GHR) and insulin growth factor1 (IGF-1)) and antioxidant-related genes (superoxide dismutase 1 (SOD1), glutathione peroxidase (GPX1) and uncoupling protein (UCP) and down-regulated (P < 0.001) splenic toll-like receptor 4 (TLRP) gene expression while had no significant effect on splenic interleukin 8 (IL8) and tumor necrosis factor (TNF) with the best-obtained results with 1.0% followed by 0.5% LC with B. subtilis supplementation. We concluded that dietary LC and/or B. subtilis supplementation positively affected the growth performance, feed efficiency, carcass quality, intestinal absorptive capacity and health, litter quality and growth, and antioxidant and immune-related gene expression.
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Affiliation(s)
- Mosaad A Soltan
- Department of Nutrition and Veterinary Clinical Nutrition, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt
| | - Ramdan S Shewita
- Department of Nutrition and Veterinary Clinical Nutrition, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt
| | - Omaima A Matroud
- Department of Nutrition and Veterinary Clinical Nutrition, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt
| | - Lamya Ahmed Alkeridis
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Samy Sayed
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; Department of Science and Technology, University College-Ranyah, Taif University, 21944 Taif, Saudi Arabia
| | - Mustafa Shukry
- Department of Physiology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.
| | - Set A El-Shobokshy
- Department of Nutrition and Veterinary Clinical Nutrition, Faculty of Veterinary Medicine, Alexandria University, Alexandria 21944, Egypt
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24
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Sun HZ, Li Q, Shang W, Qiao B, Xu QM, Cheng JS. Combinatorial metabolic engineering of Bacillus subtilis for de novo production of polymyxin B. Metab Eng 2024; 83:123-136. [PMID: 38582143 DOI: 10.1016/j.ymben.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Polymyxin is a lipopeptide antibiotic that is effective against multidrug-resistant Gram-negative bacteria. However, its clinical development is limited due to low titer and the presence of homologs. To address this, the polymyxin gene cluster was integrated into Bacillus subtilis, and sfp from Paenibacillus polymyxa was expressed heterologously, enabling recombinant B. subtilis to synthesize polymyxin B. Regulating NRPS domain inhibited formation of polymyxin B2 and B3. The production of polymyxin B increased to 329.7 mg/L by replacing the native promoters of pmxA, pmxB, and pmxE with PfusA, C2up, and PfusA, respectively. Further enhancement in this production, up to 616.1 mg/L, was achieved by improving the synthesis ability of 6-methyloctanoic acid compared to the original strain expressing polymyxin heterologously. Additionally, incorporating an anikasin-derived domain into the hybrid nonribosomal peptide synthase of polymyxin increased the B1 ratio in polymyxin B from 57.5% to 62.2%. Through optimization of peptone supply in the fermentation medium and fermentation in a 5.0-L bioreactor, the final polymyxin B titer reached 962.1 mg/L, with a yield of 19.24 mg/g maltodextrin and a productivity of 10.02 mg/(L·h). This study demonstrates a successful approach for enhancing polymyxin B production and increasing the B1 ratio through combinatorial metabolic engineering.
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Affiliation(s)
- Hui-Zhong Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qing Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Wei Shang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin 300387, China.
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
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25
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Qi N, Zhan X, Milmine J, Chang KH, Li J. A novel thermophilic strain of Bacillus subtilis with antimicrobial activity and its potential application in solid-state fermentation of soybean meal. Microbiol Spectr 2024; 12:e0278423. [PMID: 38376165 DOI: 10.1128/spectrum.02784-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/09/2023] [Indexed: 02/21/2024] Open
Abstract
Soybean meal (SBM) is the most important source of plant protein in animal feeds, containing around 41%-48% crude protein. Nevertheless, 70%-80% of these proteins is allergenic antigens that can have adverse implications for the gastrointestinal well-being of animals, especially to young animals. Microbial fermentation is one of the most cost-effective strategies used to reduce allergenic antigens from plant sources. In this study, we report the isolation and characterization of a novel probiotic Bacillus subtilis "L5" strain from lake mud. L5 demonstrated remarkable temperature tolerance across a broad temperature spectrum, thriving at 25°C, 37°C, and 50°C. In addition, antimicrobial assay revealed that L5 exhibits strong antimicrobial activity against Escherichia coli, effectively reducing or eliminating the growth of Gram-negative bacteria in SBM when fermented with L5. When applied to SBM fermentation, L5 efficiently reduced SBM antinutritional factors such as glycinin, β-conglycinin, trypsin inhibitor, phytic acid, neutral detergent fiber, and acid detergent fiber, which in turn results in an increase in crude protein content and the free amino acid concentration. Our findings on the probiotic and fermentation capabilities of L5 suggest that this novel bacterium has dual functions that make it a strong candidate for improving the nutrient values of feed via its role in fermentation.IMPORTANCESoybean meal (SBM), containing 41%-48% crude protein, is the most important source of plant protein in animal feeds. Unfortunately, 70%-80% of the proteins in SBM is allergenic antigens including trypsin inhibition, β-conglycinin, and conglycinin, which negatively affect intestine health and function. Microbial solid-state fermentation methods have been applied to animal feeds for decades, to eliminate antinutritional factors. Here, a novel potential probiotic Bacillus subtilis "L5" strain with high enzymatic activity and antimicrobial activity will be a great help to improve the quality and reproducibility of SBM fermentation.
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Affiliation(s)
- Nanshan Qi
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
- Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Xiaoshu Zhan
- Department of Animal Biosciences, University of Guelph, Guelph, Canada
- Department of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Joshua Milmine
- Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Kai-Hsiang Chang
- Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Julang Li
- Department of Animal Biosciences, University of Guelph, Guelph, Canada
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Ferrero-Bordera B, Bartel J, van Dijl JM, Becher D, Maaß S. From the outer space to the inner cell: deconvoluting the complexity of Bacillus subtilis disulfide stress responses by redox state and absolute abundance quantification of extracellular, membrane, and cytosolic proteins. Microbiol Spectr 2024; 12:e0261623. [PMID: 38358275 DOI: 10.1128/spectrum.02616-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding cellular mechanisms of stress management relies on omics data as a valuable resource. However, the lack of absolute quantitative data on protein abundances remains a significant limitation, particularly when comparing protein abundances across different cell compartments. In this study, we aimed to gain deeper insights into the proteomic responses of the Gram-positive model bacterium Bacillus subtilis to disulfide stress. We determined proteome-wide absolute abundances, focusing on different sub-cellular locations (cytosol and membrane) as well as the extracellular medium, and combined these data with redox state determination. To quantify secreted proteins in the culture medium, we developed a simple and straightforward protocol for the absolute quantification of extracellular proteins in bacteria. We concentrated extracellular proteins, which are highly diluted in the medium, using StrataClean beads along with a set of standard proteins to determine the extent of the concentration step. The resulting data set provides new insights into protein abundances in different sub-cellular compartments and the extracellular medium, along with a comprehensive proteome-wide redox state determination. Our study offers a quantitative understanding of disulfide stress management, protein production, and secretion in B. subtilis. IMPORTANCE Stress responses play a crucial role in bacterial survival and adaptation. The ability to quantitatively measure protein abundances and redox states in different cellular compartments and the extracellular environment is essential for understanding stress management mechanisms. In this study, we addressed the knowledge gap regarding absolute quantification of extracellular proteins and compared protein concentrations in various sub-cellular locations and in the extracellular medium under disulfide stress conditions. Our findings provide valuable insights into the protein production and secretion dynamics of B. subtilis, shedding light on its stress response strategies. Furthermore, the developed protocol for absolute quantification of extracellular proteins in bacteria presents a practical and efficient approach for future studies in the field. Overall, this research contributes to the quantitative understanding of stress management mechanisms and protein dynamics in B. subtilis, which can be used to enhance bacterial stress tolerance and protein-based biotechnological applications.
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Affiliation(s)
- Borja Ferrero-Bordera
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
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Garcia-Diosa JA, Grundmeier G, Keller A. Effect of DNA Origami Nanostructures on Bacterial Growth. Chembiochem 2024; 25:e202400091. [PMID: 38299762 DOI: 10.1002/cbic.202400091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/02/2024]
Abstract
DNA origami nanostructures are a powerful tool in biomedicine and can be used to combat drug-resistant bacterial infections. However, the effect of unmodified DNA origami nanostructures on bacteria is yet to be elucidated. With the aim to obtain a better understanding of this phenomenon, the effect of three DNA origami shapes, i.e., DNA origami triangles, six-helix bundles (6HBs), and 24-helix bundles (24HBs), on the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis is investigated. The results reveal that while triangles and 24HBs can be used as a source of nutrients by E. coli and thereby promote population growth, their effect is much smaller than that of genomic single- and double-stranded DNA. However, no effect on E. coli population growth is observed for the 6HBs. On the other hand, B. subtilis does not show any significant changes in population growth when cultured with the different DNA origami shapes or genomic DNA. The detailed effect of DNA origami nanostructures on bacterial growth thus depends on the competence signals and uptake mechanism of each bacterial species, as well as the DNA origami shape. This should be considered in the development of antimicrobial DNA origami nanostructures.
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Affiliation(s)
- Jaime Andres Garcia-Diosa
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
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28
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Dierksheide KJ, Li GW. A historical sequence deletion in a commonly used Bacillus subtilis chromosome integration vector generates undetected loss-of-function mutations. Microbiology (Reading) 2024; 170. [PMID: 38602388 DOI: 10.1099/mic.0.001455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Since the 1980s, chromosome-integration vectors have been used as a core method of engineering Bacillus subtilis. One of the most frequently used vector backbones contains chromosomally derived regions that direct homologous recombination into the amyE locus. Here, we report a gap in the homology region inherited from the original amyE integration vector, leading to erroneous recombination in a subset of transformants and a loss-of-function mutation in the downstream gene. Internal to the homology arm that spans the 3' portion of amyE and the downstream gene ldh, an unintentional 227 bp deletion generates two crossover events. The major event yields the intended genotype, but the minor event, occurring in ~10 % of colonies, results in a truncation of ldh, which encodes lactate dehydrogenase. Although both types of colonies test positive for amyE disruption by starch plating, the potential defect in fermentative metabolism may be left undetected and confound the results of subsequent experiments.
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Affiliation(s)
- K Julia Dierksheide
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Chmykh Y, Nadeau JL. The use of fluorescence lifetime imaging (FLIM) for in situ microbial detection in complex mineral substrates. J Microsc 2024; 294:36-51. [PMID: 38230460 DOI: 10.1111/jmi.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/16/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
Abstract
The utility of fluorescence lifetime imaging microscopy (FLIM) for identifying bacteria in complex mineral matrices was investigated. Baseline signals from unlabelled Bacillus subtilis and Euglena gracilis, and Bacillus subtilis labelled with SYTO 9 were obtained using two-photon excitation at 730, 750 and 800 nm, identifying characteristic lifetimes of photosynthetic pigments, unpigmented cellular autofluorescence, and SYTO 9. Labelled and unlabelled B. subtilis were seeded onto marble and gypsum samples containing endolithic photosynthetic cyanobacteria and the ability to distinguish cells from mineral autofluorescence and nonspecific dye staining was examined in parallel with ordinary multichannel confocal imaging. It was found that FLIM enabled discrimination of SYTO 9 labelled cells from background, but that the lifetime of SYTO 9 was shorter in cells on minerals than in pure culture under our conditions. Photosynthetic microorganisms were easily observed using both FLIM and confocal. Unlabelled, nonpigmented bacteria showed weak signals that were difficult to distinguish from background when minerals were present, though cellular autofluorescence consistent with NAD(P)H could be seen in pure cultures, and phasor analysis permitted detection on rocks. Gypsum and marble samples showed similar autofluorescence profiles, with little autofluorescence in the yellow-to-red range. Lifetime or time-gated imaging may prove a useful tool for environmental microbiology. LAY DESCRIPTION: The standard method of bacterial enumeration is to label the cells with a fluorescent dye and count them under high-power fluorescence microscopy. However, this can be difficult when the cells are embedded in soil and rock due to fluorescence from the surrounding minerals and dye binding to ambiguous features of the substrate. The use of fluorescence lifetime imaging (FLIM) can disambiguate these signals and allow for improved detection of bacteria in environmental samples.
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Affiliation(s)
- Yekaterina Chmykh
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Jay L Nadeau
- Department of Physics, Portland State University, Portland, Oregon, USA
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Freire V, Condón S, Gayán E. Impact of sporulation temperature on germination of Bacillus subtilis spores under optimal and adverse environmental conditions. Food Res Int 2024; 182:114064. [PMID: 38519157 DOI: 10.1016/j.foodres.2024.114064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/13/2024] [Accepted: 01/25/2024] [Indexed: 03/24/2024]
Abstract
Bacillus subtilis spores are important food spoilage agents and are occasionally involved in food poisoning. In foods that are not processed with intense heat, such bacterial spores are controlled by a combination of different hurdles, such as refrigeration, acidification, and low water activity (aw), which inhibit or delay germination and/or growth. Sporulation temperature has long been regarded as a relevant factor for the assessment of germination in chemically defined media, but little is known about its impact on food preservation environments. In this study, we compared germination dynamics of B. subtilis spores produced at optimal temperature (37 °C) with others incubated at suboptimal (20 °C) and supraoptimal (43 °C) temperatures in a variety of nutrients (rich-growth medium, L-alanine, L-valine, and AGFK) under optimal conditions as well as under food-related stresses (low aw, pH, and temperature). Spores produced at 20 °C had a lower germination rate and efficiency than those incubated at 37 °C in all the nutrients, while those sporulated at 43 °C displayed a higher germination rate and/or efficiency in response to rich-growth medium and mostly to L-alanine and AGFK under optimal environmental conditions. However, differences in germination induced by changes in sporulation temperature decreased when spores were activated by heat, mainly due to the greater benefit of heat for spores produced at 20 °C and 37 °C than at 43 °C, especially in AGFK. Non-heat-activated spores produced at 43 °C still displayed superior germination fitness under certain stresses that had considerably impaired the germination of the other two populations, such as reduced temperature and aw. Moreover, they presented lower temperature and pH boundaries for the inhibition of germination in rich-growth medium, while requiring a higher NaCl concentration threshold compared to spores obtained at optimal and suboptimal temperature. Sporulation temperature is therefore a relevant source of variability in spore germination that should be taken into account for the accurate prediction of spore behaviour under variable food preservation conditions with the aim of improving food safety and stability.
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Affiliation(s)
- Víctor Freire
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Santiago Condón
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Elisa Gayán
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain.
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31
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Zeng W, Liu Y, Shu L, Guo Y, Wang L, Liang Z. Production of ultra-high-molecular-weight poly-γ-glutamic acid by a newly isolated Bacillus subtilis strain and genomic and transcriptomic analyses. Biotechnol J 2024; 19:e2300614. [PMID: 38581093 DOI: 10.1002/biot.202300614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
Poly-γ-glutamic acid (γ-PGA) is a microbial-derived polymer with molecular weight (Mw) from 104 to 107 Da, and the high-Mw (> 7.0 × 105 Da) or ultra-high-Mw (> 5.0 × 106 Da) γ-PGA has important application value as a tissue engineering material, as a flocculant, and as a heavy metal remover. Therefore, how to produce these high-Mw γ-PGAs with low cost and high efficiency has attracted wide attention. In this study, a γ-PGA producer was isolated from the natural environment, and identified and named Bacillus subtilis GXD-20. Then, the ultra-high-Mw (> 6.0 × 106 Da) γ-PGA produced by GXD-20 was characterized. Interestingly, GXD-20 could produce γ-PGA at 42°C, and exhibited a γ-PGA titer of up to 22.29 ± 0.59 g L-1 in a 5-L fermenter after optimization of the fermentation process. Comparative genomic analysis indicated that the specific protein sequence and subcellular localization of PgdS (a γ-PGA-degrading enzyme) were closely related to the ultra-high-Mw of γ-PGA. Transcriptomic analysis revealed that the high γ-PGA titer at 42°C was mainly related to the high expression of genes encoding enzymes for sucrose transportation and utilization, nitrogen transportation, endogenous glutamate synthesis, and γ-PGA synthesis. These results provide new insights into the production of ultra-high-Mw γ-PGA by Bacillus at high temperatures.
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Affiliation(s)
- Wei Zeng
- Key Laboratory of Biochemistry and Molecular Biology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Yuanyuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Lin Shu
- Key Laboratory of Biochemistry and Molecular Biology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, Guangxi, China
| | - Yin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Linye Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Zhiqun Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Bassu G, Laurati M, Fratini E. Transition from active motion to anomalous diffusion for Bacillus subtilis confined in hydrogel matrices. Colloids Surf B Biointerfaces 2024; 236:113797. [PMID: 38431996 DOI: 10.1016/j.colsurfb.2024.113797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/06/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
We investigate the motility of B. subtilis under different degrees of confinement induced by transparent porous hydrogels. The dynamical behavior of the bacteria at short times is linked to characteristic parameters describing the hydrogel porosity. Mean squared displacements (MSDs) reveal that the run-and-tumble dynamics of unconfined B. subtilis progressively turns into sub-diffusive motion with increasing confinement. Correspondingly, the median instantaneous velocity of bacteria decreases and becomes more narrowly distributed, while the reorientation rate increases and reaches a plateau value. Analyzing single-trajectories, we show that the average dynamical behavior is the result of complex displacements, in which active, diffusive and sub-diffusive segments coexist. For small and moderate confinements, the number of active segments reduces, while the diffusive and sub-diffusive segments increase. The alternation of sub-diffusion, diffusion and active motion along the same trajectory can be described as a hopping ad trapping motion, in which hopping events correspond to displacements with an instantaneous velocity exceeding the corresponding mean value along a trajectory. Different from previous observations, escape from local trapping occurs for B. subtilis through active runs but also diffusion. Interestingly, the contribution of diffusion is maximum at intermediate confinements. At sufficiently long times transport coefficients estimated from the experimental MSDs under different degrees of confinement can be reproduced using a recently proposed hopping and trapping model. Finally, we propose a quantitative relationship linking the median velocity of confined and unconfined bacteria through the characteristic confinement length of the hydrogel matrix. Our work provides new insights for the bacterial motility in complex media that mimic natural environments and are relevant to important problems like sterilization, water purification, biofilm formation, membrane permeation and bacteria separation.
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Affiliation(s)
- Gavino Bassu
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI)), Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Marco Laurati
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI)), Via della Lastruccia 3, Sesto Fiorentino 50019, Italy.
| | - Emiliano Fratini
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio per lo Sviluppo dei Sistemi a Grande Interfase (CSGI)), Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
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Parmar D, Rosado-Rosa JM, Shrout JD, Sweedler JV. Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods 2024; 224:21-34. [PMID: 38295894 DOI: 10.1016/j.ymeth.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/17/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.
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Affiliation(s)
- Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joenisse M Rosado-Rosa
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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Winther K, Kristensen C, Henriksen BL, Hansen LHB, Ryt-Hansen P, Vestergaard G, Skovgaard K, Sandvang D, Boll EJ, Williams AR, Larsen LE. Bacillus subtilis-597 induces changes in lung pathology and inflammation during influenza A virus infection in pigs. Vet Microbiol 2024; 291:110032. [PMID: 38430715 DOI: 10.1016/j.vetmic.2024.110032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
In recent years, it has become apparent that imbalances in the gastrointestinal system can impact organs beyond the intestine such as the lungs. Given the established ability of probiotics to modulate the immune system by interacting with gastrointestinal cells, our research aimed to investigate whether administering the probiotic strain Bacillus subtilis-597 could mitigate the outcome of influenza virus infection in pigs. Pigs were fed a diet either with or without the probiotic strain B. subtilis-597 for 14 days before being intranasally inoculated with a swine influenza A H1N2 strain (1 C.2 lineage). Throughout the study, we collected fecal samples, blood samples, and nasal swabs to examine viral shedding and immune gene expression. After seven days of infection, the pigs were euthanized, and lung and ileum tissues were collected for gene expression analysis and pathological examination. Our findings indicate that the administration of B. subtilis-597 exhibit potential in reducing lung lesions, possibly attributable to a general suppression of the immune system as indicated by reduced C-reactive protein (CRP) levels in serum, decreased expression of interferon-stimulated genes (ISGs), and localized reduction of the inflammatory marker serum amyloid A (SAA) in ileum tissue. Notably, the immune-modulatory effects of B. subtilis-597 appeared to be unrelated to the gastrointestinal microbiota, as the composition remained unaltered by both the influenza infection and the administration of B. subtilis-597.
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Affiliation(s)
- Katrine Winther
- Animal and Plant Health & Nutrition, Chr. Hansen A/S, Hoersholm, Denmark; Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Charlotte Kristensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Pia Ryt-Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Gisle Vestergaard
- Animal and Plant Health & Nutrition, Chr. Hansen A/S, Hoersholm, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Dorthe Sandvang
- Animal and Plant Health & Nutrition, Chr. Hansen A/S, Hoersholm, Denmark
| | - Erik Juncker Boll
- Animal and Plant Health & Nutrition, Chr. Hansen A/S, Hoersholm, Denmark
| | - Andrew R Williams
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Lars E Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Chen R, Liu N, Ren Y, Cui T. Transcriptomic and biochemical analysis of metabolic remodeling in Bacillus subtilis MSC4 under Benzo[a]pyrene stress. Chemosphere 2024; 353:141637. [PMID: 38462177 DOI: 10.1016/j.chemosphere.2024.141637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Polyaromatic benzo[a]pyrene (B[a]P) is a toxic carcinogenic environmental pollutant, and the use of microorganisms to remediate B[a]P contamination is considered to be one of the most effective strategies. However, there is still a gap in studying the metabolic remodeling of microorganisms under B[a]P stress. In this study, our systematically investigated the effects of B[a]P on the metabolism of Bacillus subtilis MSC4 based on transcriptomic, molecular and biochemical analyses. The results showed that in response to B[a]P stress, MSC4 formed more biofilm matrix and endospores, the structure of the endospores also was changed, which led to a reduction in their resistance and made them more difficult to germinate. In addition to an increase in glycolysis activity, the activities of tricarboxylic acid cycle, pentose phosphate pathway and the electron transport chain were decreased. B[a]P stress forced MSC4 to strengthen arginine synthesis, urea cycle, and urea decomposition, meanwhile, synthesize more ribonucleotides. The activity of DNA replication, transcription activities and the expression of multiple ribosomal protein genes were reduced. Moreover, all of the reported enzymes involved in B[a]P degradation showed decreased transcript abundance, and the degradation of B[a]P caused significant up-regulation of the gene expression of the acid inducible enzyme OxdC and the synthesis of acetoin. In addition, the cytotoxicity of B[a]P to bacteria was directly displayed in four aspects: increased intracellular level of reactive oxygen species (ROS), elevated cell membrane permeability, up-regulation of the cell envelope stress-sensing two-component system LiaRS, and downregulation of siderophores biosynthesis. Finally, B[a]P also caused morphological changes in the cells, with some cells exhibiting significant deformation and concavity. These findings provide effective research directions for targeted improvement the cellular activity of B[a]P-degrading strains, and is beneficial for further application of microorganisms to remediate B[a]P -contaminated soils.
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Affiliation(s)
- Rui Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Na Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Tangbing Cui
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, PR China.
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Zhang J, Wu Y, Li W, Xie H, Li J, Miao Y, Yang Z, Zhou Y, Wang X. Effects of a novel Bacillus subtilis GXYX crude lipopeptide against Salmonella enterica serovar Typhimurium infection in mice. Heliyon 2024; 10:e28219. [PMID: 38524560 PMCID: PMC10958701 DOI: 10.1016/j.heliyon.2024.e28219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024] Open
Abstract
The increased rate of antibiotic resistance strongly limits the resolution of Salmonella enterica serovar Typhimurium (S. Typhimurium) infection. Therefore, new strategies to control bacterial infections are urgently needed. Bacillus subtilis (B. subtilis) and its metabolites are desirable antibacterial agents. Here, we aimed to evaluate the antibacterial activity of the novel B. subtilis strain GXYX (No: PRJNA940956) crude lipopeptide against S. Typhimurium. In vitro, GXYX crude lipopeptides affected S. Typhimurium biofilm formation and swimming and attenuated the adhesion and invasion abilities of S. Typhimurium toward BHK-21 cells; in addition, it inhibited the mRNA expression of the filA, filC, csgA, and csgB genes, which are related to the adhesion and invasion ability of S. Typhimurium. In vivo, pretreatment with GXYX crude lipopeptide via intragastric administration improved the survival rate by 30%, which was related to reductions in organ bacterial loads and clinical signs in mice. Intragastric administration of GXYX crude lipopeptide significantly downregulated the mRNA levels of TNF-α, IL-1β, IL-12 and IL-6 in response to S. Typhimurium-induced inflammation compared with intraperitoneal injection. Moreover, it significantly improved the intestinal barrier-related gene (ZO-1, claudin-1, occludin-1) mRNA levels in intestinal tissue damaged by S. Typhimurium infection. In conclusion, GXYX crude lipopeptides were effective at reducing S. Typhimurium colonization, laying a foundation for the further development of novel antibacterial agents.
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Affiliation(s)
- Jingya Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yifan Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wei Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Honglin Xie
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jingyan Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yongqiang Miao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yefei Zhou
- Department of Life Science, Nanjing Xiaozhuang University, Nanjing, 211171, Jiangsu, China
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Han C, Song S, Cui C, Cai Y, Zhou Y, Wang J, Bei W, Zhang D, Guo W, Wang S. Strain-Specific Benefits of Bacillus Probiotics in Hybrid Grouper: Growth Enhancement, Metabolic Health, Immune Modulation, and Vibrio harveyi Resistance. Animals (Basel) 2024; 14:1062. [PMID: 38612301 PMCID: PMC11011011 DOI: 10.3390/ani14071062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
In the realm of modern aquaculture, the utilization of probiotics has gained prominence, primarily due to their ability to enhance growth, boost immunity, and prevent diseases in aquatic species. This study primarily investigates the efficacy of Bacillus subtilis strains, both host-derived and from other sources, in influencing fish growth, immunity, lipid metabolism, and disease resistance. Employing a 42-day feeding trial, we divided hybrid grouper into four distinct groups: a control group on a basal diet and three experimental groups supplemented with 1 × 108 CFU/g of different Bacillus subtilis strains-BS, 6-3-1, and HAINUP40. Remarkably, the study demonstrated that the 6-3-1 and HAINUP40 groups exhibited significant enhancements across key growth parameters: final body weight (FBW), weight gain rate (WGR), feed intake (FI), feed efficiency ratio (FER), and feed conversion ratio (FCR). The investigation into lipid metabolism revealed that the 6-3-1 strain upregulated seven metabolism-related genes, HAINUP40 affected four metabolism-related genes, and the BS strain influenced two metabolism-related genes, indicating diverse metabolic impacts by different strains. Further, a notable reduction in liver enzymes AST and ALT was observed across all supplemented groups, implying improved liver health. Noteworthy was the BS strain's superior antioxidative capabilities, positively affecting all four measured parameters (CAT, GSH-Px, MDA). In the sphere of immune-related gene expression, the BS strain significantly decreased the expression of both inflammation and apoptosis-related genes, whereas the HAINUP40 strain demonstrated an upregulation in these genes. The challenge test results were particularly telling, showcasing improved survival rates against Vibrio harveyi infection in the BS and 6-3-1 groups, unlike the HAINUP40 group. These outcomes highlight the strain-specific nature of probiotics and their varying mechanisms of action within the host. In conclusion, this study reveals that probiotic strains, varying by source, demonstrate unique, strain-specific effects in promoting growth and modulating immunity in hybrid grouper. This research highlights the promise of tailored probiotic applications in improving aquaculture practices. Such advancements contribute to more sustainable and efficient fish farming methods.
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Affiliation(s)
- Congjie Han
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Shizhen Song
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Congcong Cui
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Yan Cai
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Yongcan Zhou
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Jiawen Wang
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Weilie Bei
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Dongdong Zhang
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Weiliang Guo
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
| | - Shifeng Wang
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
- Collaborative Innovation Center of Marine Science and Technology, Hainan University, Haikou 570228, China
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Elhabal SF, Abdelaal N, Saeed Al-Zuhairy SAK, Elrefai MFM, Elsaid Hamdan AM, Khalifa MM, Hababeh S, Khasawneh MA, Khamis GM, Nelson J, Mohie PM, Gad RA, Rizk A, Kabil SL, El-Ashery MK, Jasti BR, Elzohairy NA, Elnawawy T, Hassan FE, El- Nabarawi MA. Green Synthesis of Zinc Oxide Nanoparticles from Althaea officinalis Flower Extract Coated with Chitosan for Potential Healing Effects on Diabetic Wounds by Inhibiting TNF-α and IL-6/IL-1β Signaling Pathways. Int J Nanomedicine 2024; 19:3045-3070. [PMID: 38559447 PMCID: PMC10981898 DOI: 10.2147/ijn.s455270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Background Diabetes Mellitus is a multisystem chronic pandemic, wound inflammation, and healing are still major issues for diabetic patients who may suffer from ulcers, gangrene, and other wounds from uncontrolled chronic hyperglycemia. Marshmallows or Althaea officinalis (A.O.) contain bioactive compounds such as flavonoids and phenolics that support wound healing via antioxidant, anti-inflammatory, and antibacterial properties. Our study aimed to develop a combination of eco-friendly formulations of green synthesis of ZnO-NPs by Althaea officinalis extract and further incorporate them into 2% chitosan (CS) gel. Method and Results First, develop eco-friendly green Zinc Oxide Nanoparticles (ZnO-NPs) and incorporate them into a 2% chitosan (CS) gel. In-vitro study performed by UV-visible spectrum analysis showed a sharp peak at 390 nm, and Energy-dispersive X-ray (EDX) spectrometry showed a peak of zinc and oxygen. Besides, Fourier transforms infrared (FTIR) was used to qualitatively validate biosynthesized ZnO-NPs, and transmission electron microscope (TEM) showed spherical nanoparticles with mean sizes of 76 nm and Zeta potential +30mV. The antibacterial potential of A.O.-ZnO-NPs-Cs was examined by the diffusion agar method against Gram-positive (Staphylococcus aureus and Bacillus subtilis) and Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa). Based on the zone of inhibition and minimal inhibitory indices (MIC). In addition, an in-silico study investigated the binding affinity of A.O. major components to the expected biological targets that may aid wound healing. Althaea Officinalis, A.O-ZnO-NPs group showed reduced downregulation of IL-6, IL-1β, and TNF-α and increased IL-10 levels compared to the control group signaling pathway expression levels confirming the improved anti-inflammatory effect of the self-assembly method. In-vivo study and histopathological analysis revealed the superiority of the nanoparticles in reducing signs of inflammation and wound incision in rat models. Conclusion These biocompatible green zinc oxide nanoparticles, by using Althaea Officinalis chitosan gel ensure an excellent new therapeutic approach for quickening diabetic wound healing.
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Affiliation(s)
- Sammar Fathy Elhabal
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Mokattam, Cairo, Egypt
| | - Nashwa Abdelaal
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Mohamed Fathi Mohamed Elrefai
- Department of Anatomy, Histology, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
- Department of Anatomy and Embryology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | | | - Sandra Hababeh
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | | | - Gehad M Khamis
- Department of Clinical Pharmacology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Jakline Nelson
- Department of Microbiology and Immunology, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Passant M Mohie
- Department of Clinical Pharmacology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Rania A Gad
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Amira Rizk
- Food Science and Technology Department, Faculty of Agricultural, Tanta University, Tanta, Egypt
| | - Soad L Kabil
- Department of Clinical Pharmacology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Mohamed Kandeel El-Ashery
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University, Ras-Sedr, South Sinai, Egypt
| | - Bhaskara R Jasti
- Department of Pharmaceutics and Medicinal Chemistry, Thomas J. Long School of Pharmacy, University of the Pacific, Stockton, CA, USA
| | - Nahla A Elzohairy
- Air Force Specialized Hospital, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Mokattam, Cairo, Egypt
| | - Tayseer Elnawawy
- Department of Pharmaceutics, Egyptian Drug Authority, Cairo, Egypt
| | - Fatma E Hassan
- Medical Physiology Department, Faculty of Medicine, Cairo University, Giza, Egypt
- General Medicine Practice Program, Department of Physiology, Batterjee Medical College, Jeddah, Saudi Arabia
| | - Mohamed A El- Nabarawi
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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39
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Öktem A, Pranoto DA, van Dijl JM. Post-translational secretion stress regulation in Bacillus subtilis is controlled by intra- and extracellular proteases. N Biotechnol 2024; 79:71-81. [PMID: 38158017 DOI: 10.1016/j.nbt.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is a prolific producer of industrial enzymes that are effectively harvested from the fermentation broth. However, the high capacity of B. subtilis for protein secretion has so far not been exploited to the full due to particular bottlenecks, including product degradation by extracellular proteases and counterproductive secretion stress responses. To unlock the Bacillus secretion pathway for difficult-to-produce proteins, various cellular interventions have been explored, including genome engineering. Our previous research has shown a superior performance of genome-reduced B. subtilis strains in the production of staphylococcal antigens compared to the parental strain 168. This was attributed, at least in part, to redirected secretion stress responses, including the presentation of elevated levels of the quality control proteases HtrA and HtrB that also catalyse protein folding. Here we show that this relates to the elimination of two homologous serine proteases, namely the cytosolic protease AprX and the extracellular protease AprE. This unprecedented posttranslational regulation of secretion stress effectors, like HtrA and HtrB, by the concerted action of cytosolic and extracellular proteases has important implications for the biotechnological application of microbial cell factories. In B. subtilis, this conclusion is underscored by extracellular degradation of the staphylococcal antigen IsaA by both AprX and AprE. Extracellular activity of the cytosolic protease AprX is remarkable since it shows that not only extracellular, but also intracellular proteases impact extracellular product levels. We therefore conclude that intracellular proteases represent new targets for improved recombinant protein production in microbial cell factories like B. subtilis.
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Affiliation(s)
- Ayşegül Öktem
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Dicky A Pranoto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands.
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40
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Lilge L, Kuipers OP. A two-step regulatory circuit involving Spo0A-AbrB activates mersacidin biosynthesis in Bacillus subtilis. Int J Antimicrob Agents 2024; 63:107155. [PMID: 38527561 DOI: 10.1016/j.ijantimicag.2024.107155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Due to intramolecular ring structures, the ribosomally produced and post-translationally modified peptide mersacidin shows antimicrobial properties comparable to those of vancomycin without exhibiting cross-resistance. Although the principles of mersacidin biosynthesis are known, there is no information on the molecular control processes for the initial stimulation of mersacidin bioproduction. By using Bacillus subtilis for heterologous biosynthesis, a considerable amount of mersacidin could be produced without the mersacidin-specific immune system and the mersacidin-activating secretory protease. By using the established laboratory strain Bacillus subtilis 168 and strain 3NA, which is used for high cell density fermentation processes, in combination with the construction of reporter strains to determine the promoter strengths within the mersacidin core gene cluster, the molecular regulatory circuit of Spo0A, a master regulator of cell differentiation including sporulation initiation, and the global transcriptional regulator AbrB, which is involved in cell adaptation processes in the transient growth phase, was identified to control the initial stimulation of the mersacidin core gene cluster. In a second downstream regulatory step, the activator MrsR1, encoded in the core gene cluster, acts as a stimulatory element for mersacidin biosynthesis. These findings are important to understand the mechanisms linking environmental conditions and microbial responses with respect to the bioproduction of bioactive metabolites including antimicrobials such as mersacidin. This information will also support the construction of production strains for bioactive metabolites with antimicrobial properties.
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Affiliation(s)
- Lars Lilge
- Department of Molecular Genetics, University of Groningen, AG Groningen, The Netherlands; Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany.
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, AG Groningen, The Netherlands
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41
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Torres-García JR, Leonardo-Elias A, Angoa-Pérez MV, Villar-Luna E, Arias-Martínez S, Oyoque-Salcedo G, Oregel-Zamudio E. Bacillus subtilis Edible Films for Strawberry Preservation: Antifungal Efficacy and Quality at Varied Temperatures. Foods 2024; 13:980. [PMID: 38611287 PMCID: PMC11011878 DOI: 10.3390/foods13070980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Fungal infestations, particularly from Rhizopus stolonifer, pose significant post-harvest challenges for strawberries, compromising their shelf life and quality. Traditional preservation methods, including refrigeration, offer limited protection against such pathogens. This study introduces an innovative approach, utilizing edible films infused with Bacillus subtilis strains GOS 01 B-67748 and HFC 103, known for their antifungal properties. We demonstrate that these bioactive films not only inhibit fungal growth effectively but also enhance the preservation of strawberries at varying temperatures. The inclusion of Bacillus subtilis in edible films represents a significant advancement in extending the viability of strawberries, surpassing the efficacy of conventional methods. Our findings suggest a promising avenue for natural, safe food preservation techniques, aligning with current consumer preferences for additive-free products. This research contributes to the broader understanding of microbial-based food preservation strategies, offering potential applications across a range of perishable commodities.
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Affiliation(s)
- Jesús Rubén Torres-García
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, Justo Sierra 28, Col. Centro, Jiquilpan 59510, Michoacán, Mexico; (J.R.T.-G.); (A.L.-E.); (M.V.A.-P.); (E.V.-L.); (S.A.-M.)
- Investigadores por México, Consejo Nacional de Humanidades, Ciencias y Tecnología (CONAHCYT), México City 03940, Mexico
| | - Arnulfo Leonardo-Elias
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, Justo Sierra 28, Col. Centro, Jiquilpan 59510, Michoacán, Mexico; (J.R.T.-G.); (A.L.-E.); (M.V.A.-P.); (E.V.-L.); (S.A.-M.)
| | - María Valentina Angoa-Pérez
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, Justo Sierra 28, Col. Centro, Jiquilpan 59510, Michoacán, Mexico; (J.R.T.-G.); (A.L.-E.); (M.V.A.-P.); (E.V.-L.); (S.A.-M.)
| | - Edgar Villar-Luna
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, Justo Sierra 28, Col. Centro, Jiquilpan 59510, Michoacán, Mexico; (J.R.T.-G.); (A.L.-E.); (M.V.A.-P.); (E.V.-L.); (S.A.-M.)
| | - Sergio Arias-Martínez
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, Justo Sierra 28, Col. Centro, Jiquilpan 59510, Michoacán, Mexico; (J.R.T.-G.); (A.L.-E.); (M.V.A.-P.); (E.V.-L.); (S.A.-M.)
| | - Guadalupe Oyoque-Salcedo
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, Justo Sierra 28, Col. Centro, Jiquilpan 59510, Michoacán, Mexico; (J.R.T.-G.); (A.L.-E.); (M.V.A.-P.); (E.V.-L.); (S.A.-M.)
- Tecnológico Nacional de México, Instituto Tecnológico de Roque, Carretera Celaya—Juventino Rosas Km. 8, Celaya 38110, Guanajuato, Mexico
| | - Ernesto Oregel-Zamudio
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, Justo Sierra 28, Col. Centro, Jiquilpan 59510, Michoacán, Mexico; (J.R.T.-G.); (A.L.-E.); (M.V.A.-P.); (E.V.-L.); (S.A.-M.)
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42
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Willdigg JR, Patel Y, Arquilevich BE, Subramanian C, Frank MW, Rock CO, Helmann JD. The Bacillus subtilis cell envelope stress-inducible ytpAB operon modulates membrane properties and contributes to bacitracin resistance. J Bacteriol 2024; 206:e0001524. [PMID: 38323910 PMCID: PMC10955860 DOI: 10.1128/jb.00015-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
Antibiotics that inhibit peptidoglycan synthesis trigger the activation of both specific and general protective responses. σM responds to diverse antibiotics that inhibit cell wall synthesis. Here, we demonstrate that cell wall-inhibiting drugs, such as bacitracin and cefuroxime, induce the σM-dependent ytpAB operon. YtpA is a predicted hydrolase previously proposed to generate the putative lysophospholipid antibiotic bacilysocin (lysophosphatidylglycerol), and YtpB is the branchpoint enzyme for the synthesis of membrane-localized C35 terpenoids. Using targeted lipidomics, we reveal that YtpA is not required for the production of lysophosphatidylglycerol. Nevertheless, ytpA was critical for growth in a mutant strain defective for homeoviscous adaptation due to a lack of genes for the synthesis of branched chain fatty acids and the Des phospholipid desaturase. Consistently, overexpression of ytpA increased membrane fluidity as monitored by fluorescence anisotropy. The ytpA gene contributes to bacitracin resistance in mutants additionally lacking the bceAB or bcrC genes, which directly mediate bacitracin resistance. These epistatic interactions support a model in which σM-dependent induction of the ytpAB operon helps cells tolerate bacitracin stress, either by facilitating the flipping of the undecaprenyl phosphate carrier lipid or by impacting the assembly or function of membrane-associated complexes involved in cell wall homeostasis.IMPORTANCEPeptidoglycan synthesis inhibitors include some of our most important antibiotics. In Bacillus subtilis, peptidoglycan synthesis inhibitors induce the σM regulon, which is critical for intrinsic antibiotic resistance. The σM-dependent ytpAB operon encodes a predicted hydrolase (YtpA) and the enzyme that initiates the synthesis of C35 terpenoids (YtpB). Our results suggest that YtpA is critical in cells defective in homeoviscous adaptation. Furthermore, we find that YtpA functions cooperatively with the BceAB and BcrC proteins in conferring intrinsic resistance to bacitracin, a peptide antibiotic that binds tightly to the undecaprenyl-pyrophosphate lipid carrier that sustains peptidoglycan synthesis.
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Affiliation(s)
| | - Yesha Patel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | | | - Chitra Subramanian
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Matthew W. Frank
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Charles O. Rock
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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Akinsemolu AA, Onyeaka H, Odion S, Adebanjo I. Exploring Bacillus subtilis: Ecology, biotechnological applications, and future prospects. J Basic Microbiol 2024:e202300614. [PMID: 38507723 DOI: 10.1002/jobm.202300614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/28/2024] [Accepted: 02/17/2024] [Indexed: 03/22/2024]
Abstract
From its early identification by Christian Gottfried Ehrenberg to its current prominence in scientific research, Bacillus subtilis (B. subtilis) has emerged as a foundational model organism in microbiology. This comprehensive review delves deep into its genetic, physiological, and biochemical intricacies, revealing a sophisticated cellular blueprint. With the incorporation of advanced techniques such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 and integrative computational methodologies, the potential applications of B. subtilis span diverse sectors. These encompass its significant contributions to biotechnology, agriculture, and medical fields and its potential for aiding environmental cleanup efforts. Yet, as we move forward, we must grapple with concerns related to safety, ethics, and the practical implementation of our lab findings in everyday scenarios. As our understanding of B. subtilis deepens, it is evident that its contributions will be central to pioneering sustainable solutions for global challenges in the years to come.
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Affiliation(s)
- Adenike A Akinsemolu
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
| | - Samuel Odion
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
- The Green Institute, Ondo, Ondo State, Nigeria
| | - Idris Adebanjo
- The Green Microbiology Lab, University of Birmingham, Birmingham, UK
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Ochi T, Oh K, Konishi H. Pylephlebitis Caused by Bacillus subtilis and Fusobacterium nucleatum. Intern Med 2024; 63:799-802. [PMID: 37438133 PMCID: PMC11009003 DOI: 10.2169/internalmedicine.2150-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/05/2023] [Indexed: 07/14/2023] Open
Abstract
A 90-year-old man presented with a 3-day history of general malaise. He was febrile (39.3°C) but the initial evaluation did not reveal the cause of the fever. After admission, Bacillus subtilis and Fusobacterium nucleatum were grown from multiple sets of blood cultures. In addition, contrast-enhanced computed tomography revealed thrombi in the portal vein and superior mesenteric vein; he was diagnosed with pylephlebitis. After receiving antimicrobial treatment and anticoagulation, the patient was cured. Pylephlebitis is a rare condition and may be the cause of unknown fevers. This is the first reported case of pylephlebitis caused by Bacillus subtilis.
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Affiliation(s)
- Tatsuya Ochi
- Department of General Internal Medicine, Kobe City Medical Center West Hospital, Japan
- Department of Emergency and Critical Care Medicine, Hyogo Emergency Medical Center, Japan
| | - Koji Oh
- Department of General Internal Medicine, Kobe City Medical Center West Hospital, Japan
| | - Hiroki Konishi
- Department of General Internal Medicine, Kobe City Medical Center West Hospital, Japan
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45
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Rocchi R, Zwinkels J, Kooijman M, Garre A, Smid EJ. Development of novel natto using legumes produced in Europe. Heliyon 2024; 10:e26849. [PMID: 38463896 PMCID: PMC10923668 DOI: 10.1016/j.heliyon.2024.e26849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Natto is a traditional Japanese fermented product consisting of cooked soybeans fermented with Bacillus subtilis var. natto. We assessed three different B. subtilis strains and investigated their impact on product quality aspects, such as microbial quality, textural quality (poly-γ-glutamate strand formation), free amino acids (FAA), and volatile organic compounds (VOCs), but also the vitamin K1, K2 and B1 content, and presence of nattokinase. Using Bayesian contrast analysis, we conclude that the quality attributes were influenced by both the substrate and strain used, without significant differences in bacterial growth between strain or substrate. Overall, all the tested European legumes, except for brown beans, are adequate substrates to produce natto, with comparable or higher qualities compared to the traditional soy. Out of all the tested legumes, red lentils were the most optimal fermentation substrate. They were fermented most consistently, with high concentrations of vitamin K2, VOCs, FAA.
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Affiliation(s)
- Rebecca Rocchi
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Jasper Zwinkels
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Merit Kooijman
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Alberto Garre
- Department of Agricultural Engineering & Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Spain
| | - Eddy J. Smid
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
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Martínez LE, Gómez G, Ramírez N, Franco B, Robleto EA, Pedraza-Reyes M. 8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis. Antioxidants (Basel) 2024; 13:332. [PMID: 38539865 PMCID: PMC10968225 DOI: 10.3390/antiox13030332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
The guanine oxidized (GO) system of Bacillus subtilis, composed of the YtkD (MutT), MutM and MutY proteins, counteracts the cytotoxic and genotoxic effects of the oxidized nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, the genetic inactivation of GO system potentiated mutagenesis (HPM), and subsequent hyperresistance, contributes to the damaging effects of hydrogen peroxide (H2O2) (HPHR). The mechanism(s) that connect the accumulation of the mutagenic lesion 8-OxoG with the ability of B. subtilis to evolve and survive the noxious effects of oxidative stress were dissected. Genetic and biochemical evidence indicated that the synthesis of KatA was exacerbated, in a PerR-independent manner, and the transcriptional coupling repair factor, Mfd, contributed to HPHR and HPM of the ΔGO strain. Moreover, these phenotypes are associated with wider pleiotropic effects, as revealed by a global proteome analysis. The inactivation of the GO system results in the upregulated production of KatA, and it reprograms the synthesis of the proteins involved in distinct types of cellular stress; this has a direct impact on (i) cysteine catabolism, (ii) the synthesis of iron-sulfur clusters, (iii) the reorganization of cell wall architecture, (iv) the activation of AhpC/AhpF-independent organic peroxide resistance, and (v) increased resistance to transcription-acting antibiotics. Therefore, to contend with the cytotoxic and genotoxic effects derived from the accumulation of 8-OxoG, B. subtilis activates the synthesis of proteins belonging to transcriptional regulons that respond to a wide, diverse range of cell stressors.
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Affiliation(s)
- Lissett E. Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Gerardo Gómez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Norma Ramírez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Bernardo Franco
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Eduardo A. Robleto
- School of Life Sciences, University of Nevada, Las Vegas, NV 89557, USA;
| | - Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
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Pan H, Wei L, Zhao H, Xiao Y, Li Z, Ding H. Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis. J Agric Food Chem 2024; 72:4834-4848. [PMID: 38401001 DOI: 10.1021/acs.jafc.3c06411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.
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Affiliation(s)
- Hang Pan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Longfeng Wei
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Hao Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Yang Xiao
- Institution of Supervision and Inspection Product Quality of Guizhou Province, Guiyang 550004, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Haixia Ding
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
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Wang B, van der Kloet F, Kes MBMJ, Luirink J, Hamoen LW. Improving gene set enrichment analysis (GSEA) by using regulation directionality. Microbiol Spectr 2024; 12:e0345623. [PMID: 38294221 PMCID: PMC10913524 DOI: 10.1128/spectrum.03456-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
To infer the biological meaning from transcriptome data, it is useful to focus on genes that are regulated by the same regulator, i.e., regulons. Unfortunately, current gene set enrichment analysis (GSEA) tools do not consider whether a gene is activated or repressed by a regulator. This distinction is crucial when analyzing regulons since a regulator can work as an activator of certain genes and as a repressor of other genes, yet both sets of genes belong to the same regulon. Therefore, simply averaging expression differences of the genes of such a regulon will not properly reflect the activity of the regulator. What makes it more complicated is the fact that many genes are regulated by different transcription factors, and current transcriptome analysis tools are unable to indicate which regulator is most likely responsible for the observed expression difference of a gene. To address these challenges, we developed the gene set enrichment analysis program GINtool. Additional features of GINtool are novel graphical representations to facilitate the visualization of gene set analyses of transcriptome data, the possibility to include functional categories as gene sets for analysis, and the option to analyze expression differences within operons, which is useful when analyzing prokaryotic transcriptome and also proteome data.IMPORTANCEMeasuring the activity of all genes in cells is a common way to elucidate the function and regulation of genes. These transcriptome analyses produce large amounts of data since genomes contain thousands of genes. The analysis of these large data sets is challenging. Therefore, we developed a new software tool called GINtool that can facilitate the analysis of transcriptome data by using prior knowledge of gene sets controlled by the same regulator, the so-called regulons. An important novelty of GINtool is that it can take into account the directionality of gene regulation in these analyses, i.e., whether a gene is activated or repressed, which is crucial to assess whether a regulon or functional category is affected. GINtool also includes new graphical methods to facilitate the visual inspection of regulation events in transcriptome data sets. These and additional analysis methods included in GINtool make it a powerful software tool to analyze transcriptome data.
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Affiliation(s)
- Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Frans van der Kloet
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Mariah B. M. J. Kes
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Joen Luirink
- Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Leendert W. Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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49
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Nguyen VDH, Huynh TNP, Nguyen TTT, Ho HH, Trinh LTP, Nguyen AQ. Expression and characterization of a lipase EstA from Bacillus subtilis KM-BS for application in bio-hydrolysis of waste cooking oil. Protein Expr Purif 2024; 215:106419. [PMID: 38110109 DOI: 10.1016/j.pep.2023.106419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
A lipase EstA from Bacillus subtilis KM-BS was expressed in Escherichia coli BL21 (DE3) cells. The recombinant enzyme achieved high activity (49.67 U/mL) with protein concentration of 1.29 mg/mL under optimal conditions at the large-scale expression of 6 h and post-induction time at 30 °C using 0.1 mM isopropyl-β-d-thiogalactopyranoside (IPTG). The optimal temperature and pH of the purified enzyme were at 45-55 °C and pH 8.0 - 9.0, respectively. Activity of the purified enzyme was stable in the presence of 1 mM Ca2+; stimulated by 1 mM Mg2+ and Mn2+, and inhibited by Fe3+. A significant amount of fatty acids was released during the hydrolysis of waste cooking oil under the catalysis of purified lipase, indicating that this recombinant lipase showed promise as a suitable candidate in industrial fields, particularly in biodiesel and detergent sector.
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Affiliation(s)
- Vinh D H Nguyen
- Khai Minh Technology Group - KMTG, Ho Chi Minh City, Viet Nam; Faculty of Biological Sciences, Nong Lam University, Ho Chi Minh City, Viet Nam
| | - Trang N P Huynh
- Khai Minh Technology Group - KMTG, Ho Chi Minh City, Viet Nam; Faculty of Biological Sciences, Nong Lam University, Ho Chi Minh City, Viet Nam
| | - Thao T T Nguyen
- Khai Minh Technology Group - KMTG, Ho Chi Minh City, Viet Nam; Faculty of Biological Sciences, Nong Lam University, Ho Chi Minh City, Viet Nam
| | - Hai H Ho
- Khai Minh Technology Group - KMTG, Ho Chi Minh City, Viet Nam; Faculty of Biological Sciences, Nong Lam University, Ho Chi Minh City, Viet Nam
| | - Ly T P Trinh
- Research Institute for Biotechnology and Environment, Nong Lam University, Ho Chi Minh City, Viet Nam; Faculty of Biological Sciences, Nong Lam University, Ho Chi Minh City, Viet Nam
| | - Anh Q Nguyen
- Khai Minh Technology Group - KMTG, Ho Chi Minh City, Viet Nam.
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Huang N, Jin X, Wen JT, Zhang YF, Yang X, Wei GY, Wang YK, Qin M. Biocontrol and Growth Promotion Potential of Bacillus subtilis CTXW 7-6-2 against Rhizoctonia solani that Causes Tobacco Target Spot Disease. Pol J Microbiol 2024; 73:29-38. [PMID: 38437465 PMCID: PMC10911660 DOI: 10.33073/pjm-2024-004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/19/2023] [Indexed: 03/06/2024] Open
Abstract
Fungal diseases form perforated disease spots in tobacco plants, resulting in a decline in tobacco yield and quality. The present study investigated the antagonistic effect of Bacillus subtilis CTXW 7-6-2 against Rhizoctonia solani, its ability to promote the growth of tobacco seedlings, and the expression of disease resistance-related genes for efficient and eco-friendly plant disease control. Our results showed that CTXW 7-6-2 had the most vigorous growth after being cultured for 96 h, and its rate of inhibition of R. solani growth in vitro was 94.02%. The volatile compounds produced by CTXW 7-6-2 inhibited the growth of R. solani significantly (by 96.62%). The fungal growthinhibition rate of the B. subtilis CTXW 7-6-2 broth obtained after high-temperature and no-high-temperature sterile fermentation was low, at 50.88% and 54.63%, respectively. The lipopeptides extracted from the B. subtilis CTXW 7-6-2 fermentation broth showed a 74.88% fungal growth inhibition rate at a concentration of 100 mg/l. Scanning and transmission electron microscopy showed some organelle structural abnormalities, collapse, shrinkage, blurring, and dissolution in the R. solani mycelia. In addition, CTXW 7-6-2 increased tobacco seedling growth and improved leaf and root weight compared to the control. After CTXW 7-6-2 inoculation, tobacco leaves showed the upregulation of the PDF1.2, PPO, and PAL genes, which are closely related to target spot disease resistance. In conclusion, B. subtilis CTXW 7-6-2 may be an efficient biological control agent in tobacco agriculture and enhance plant growth potential.
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Affiliation(s)
- Ning Huang
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
| | - Xin Jin
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
| | - Jin-Tao Wen
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
| | - Yi-Fei Zhang
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
| | - Xu Yang
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
| | - Guang-Yu Wei
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
| | - Yi-Kun Wang
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
| | - Min Qin
- Guizhou Province Tobacco Company Guiyang City Company, Guiyang, China
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