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Khanal S, Kim TD, Begyn K, Duverger W, Kramer G, Brul S, Rajkovic A, Devlieghere F, Heyndrickx M, Schymkowitz J, Rousseau F, Broussolle V, Michiels C, Aertsen A. Mechanistic insights into the adaptive evolvability of spore heat resistance in Bacillus cereus sensu lato. Int J Food Microbiol 2024; 418:110709. [PMID: 38663147 DOI: 10.1016/j.ijfoodmicro.2024.110709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/09/2024] [Accepted: 04/13/2024] [Indexed: 05/27/2024]
Abstract
Wet heat treatment is a commonly applied method in the food and medical industries for the inactivation of microorganisms, and bacterial spores in particular. While many studies have delved into the mechanisms underlying wet heat killing and spore resistance, little attention has so far been dedicated to the capacity of spore-forming bacteria to tune their resistance through adaptive evolution. Nevertheless, a recent study from our group revealed that a psychrotrophic strain of the Bacillus cereus sensu lato group (i.e. Bacillus weihenstephanensis LMG 18989) could readily and reproducibly evolve to acquire enhanced spore wet heat resistance without compromising its vegetative cell growth ability at low temperatures. In the current study, we demonstrate that another B. cereus strain (i.e. the mesophilic B. cereus sensu stricto ATCC 14579) can acquire significantly increased spore wet heat resistance as well, and we subjected both the previously and currently obtained mutants to whole genome sequencing. This revealed that five out of six mutants were affected in genes encoding regulators of the spore coat and exosporium pathway (i.e. spoIVFB, sigK and gerE), with three of them being affected in gerE. A synthetically constructed ATCC 14579 ΔgerE mutant likewise yielded spores with increased wet heat resistance, and incurred a compromised spore coat and exosporium. Further investigation revealed significantly increased spore DPA levels and core dehydration as the likely causes for the observed enhanced spore wet heat resistance. Interestingly, deletion of gerE in Bacillus subtilis 168 did not impose increased spore wet heat resistance, underscoring potentially different adaptive evolutionary paths in B. cereus and B. subtilis.
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Affiliation(s)
- Sadhana Khanal
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Tom Dongmin Kim
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Katrien Begyn
- Research Unit Food Microbiology and Food Preservation (FMFP-UGent), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wouter Duverger
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, the Netherlands
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, the Netherlands
| | - Andreja Rajkovic
- Research Unit Food Microbiology and Food Preservation (FMFP-UGent), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Frank Devlieghere
- Research Unit Food Microbiology and Food Preservation (FMFP-UGent), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Marc Heyndrickx
- ILVO - Flanders Research Institute for Agriculture, Fisheries and Food, Technology and Food Science, Unit - Food Safety, Melle, Belgium; Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | | | - Chris Michiels
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium..
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Huang Y, Swarge BN, Roseboom W, Bleeker JD, Brul S, Setlow P, Kramer G. Integrative Metabolomics and Proteomics Allow the Global Intracellular Characterization of Bacillus subtilis Cells and Spores. J Proteome Res 2024; 23:596-608. [PMID: 38190553 PMCID: PMC10845140 DOI: 10.1021/acs.jproteome.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024]
Abstract
Reliable and comprehensive multi-omics analysis is essential for researchers to understand and explore complex biological systems more completely. Bacillus subtilis (B. subtilis) is a model organism for Gram-positive spore-forming bacteria, and in-depth insight into the physiology and molecular basis of spore formation and germination in this organism requires advanced multilayer molecular data sets generated from the same sample. In this study, we evaluated two monophasic methods for polar and nonpolar compound extraction (acetonitrile/methanol/water; isopropanol/water, and 60% ethanol) and two biphasic methods (chloroform/methanol/water, and methyl tert-butyl ether/methanol/water) on coefficients of variation of analytes, identified metabolite composition, and the quality of proteomics profiles. The 60% EtOH protocol proved to be the easiest in sample processing and was more amenable to automation. Collectively, we annotated 505 and 484 metabolites and identified 1665 and 1562 proteins in B. subtilis vegetative cells and spores, respectively. We also show differences between vegetative cells and spores from a multi-omics perspective and demonstrate that an integrative multi-omics analysis can be implemented from one sample using the 60% EtOH protocol. The results obtained by the 60% EtOH protocol provide comprehensive insight into differences in the metabolic and protein makeup of B. subtilis vegetative cells and spores.
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Affiliation(s)
- Yixuan Huang
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bhagyashree N. Swarge
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Winfried Roseboom
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jurre D. Bleeker
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter Setlow
- Department
of Molecular Biology and Biophysics, UConn
Health, Farmington, Connecticut 06030-3305, United States
| | - Gertjan Kramer
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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Lyu F, Zhang T, Gui M, Wang Y, Zhao L, Wu X, Rao L, Liao X. The underlying mechanism of bacterial spore germination: An update review. Compr Rev Food Sci Food Saf 2023; 22:2728-2746. [PMID: 37125461 DOI: 10.1111/1541-4337.13160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 05/02/2023]
Abstract
Bacterial spores are highly resilient and universally present on earth and can irreversibly enter the food chain to cause food spoilage or foodborne illness once revived to resume vegetative growth. Traditionally, extensive thermal processing has been employed to efficiently kill spores; however, the relatively high thermal load adversely affects food quality attributes. In recent years, the germination-inactivation strategy has been developed to mildly kill spores based on the circumstance that germination can decrease spore-resilient properties. However, the failure to induce all spores to geminate, mainly owing to the heterogeneous germination behavior of spores, hampers the success of applying this strategy in the food industry. Undoubtedly, elucidating the detailed germination pathway and underlying mechanism can fill the gap in our understanding of germination heterogeneity, thereby facilitating the development of full-scale germination regimes to mildly kill spores. In this review, we comprehensively discuss the mechanisms of spore germination of Bacillus and Clostridium species, and update the molecular basis of the early germination events, for example, the activation of germination receptors, ion release, Ca-DPA release, and molecular events, combined with the latest research evidence. Moreover, high hydrostatic pressure (HHP), an advanced non-thermal food processing technology, can also trigger spore germination, providing a basis for the application of a germination-inactivation strategy in HHP processing. Here, we also summarize the diverse germination behaviors and mechanisms of spores of Bacillus and Clostridium species under HHP, with the aim of facilitating HHP as a mild processing technology with possible applications in food sterilization. Practical Application: This work provides fundamental basis for developing efficient killing strategies of bacterial spores in food industry.
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Affiliation(s)
- Fengzhi Lyu
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, China Agricultural University, Beijing, China
| | - Tianyu Zhang
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, China Agricultural University, Beijing, China
| | - Meng Gui
- Fisheries Science Institute Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongtao Wang
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, China Agricultural University, Beijing, China
| | - Liang Zhao
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, China Agricultural University, Beijing, China
| | - Xiaomeng Wu
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, China Agricultural University, Beijing, China
| | - Lei Rao
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, China Agricultural University, Beijing, China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetable Processing of Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-Thermal Processing, China Agricultural University, Beijing, China
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Setlow P, Christie G. New Thoughts on an Old Topic: Secrets of Bacterial Spore Resistance Slowly Being Revealed. Microbiol Mol Biol Rev 2023; 87:e0008022. [PMID: 36927044 PMCID: PMC10304885 DOI: 10.1128/mmbr.00080-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
The quest for bacterial survival is exemplified by spores formed by some Firmicutes members. They turn up everywhere one looks, and their ubiquity reflects adaptations to the stresses bacteria face. Spores are impactful in public health, food safety, and biowarfare. Heat resistance is the hallmark of spores and is countered principally by a mineralized gel-like protoplast, termed the spore core, with reduced water which minimizes macromolecular movement/denaturation/aggregation. Dry heat, however, introduces mutations into spore DNA. Spores have countermeasures to extreme conditions that are multifactorial, but the fact that spore DNA is in a crystalline-like nucleoid in the spore core, likely due to DNA saturation with small acid-soluble spore proteins (SASPs), suggests that reduced macromolecular motion is also critical in spore dry heat resistance. SASPs are also central in the radiation resistance characteristic of spores, where the contributions of four spore features-SASP; Ca2+, with pyridine-2,6-dicarboxylic acid (CaDPA); photoproduct lyase; and low water content-minimize DNA damage. Notably, the spore environment steers UV photochemistry toward a product that germinated spores can repair without significant mutagenesis. This resistance extends to chemicals and macromolecules that could damage spores. Macromolecules are excluded by the spore coat which impedes the passage of moieties of ≥10 kDa. Additionally, damaging chemicals may be degraded or neutralized by coat enzymes/proteins. However, the principal protective mechanism here is the inner membrane, a compressed structure lacking lipid fluidity and presenting a barrier to the diffusion of chemicals into the spore core; SASP saturation of DNA also protects against genotoxic chemicals. Spores are also resistant to other stresses, including high pressure and abrasion. Regardless, overarching mechanisms associated with resistance seem to revolve around reduced molecular motion, a fine balance between rigidity and flexibility, and perhaps efficient repair.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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