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Nakano M. An improved DNA extraction method for detecting Bacillus subtilis spores in spiked foods and beverages. Int J Food Microbiol 2023; 401:110280. [PMID: 37327536 DOI: 10.1016/j.ijfoodmicro.2023.110280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/24/2023] [Accepted: 06/03/2023] [Indexed: 06/18/2023]
Abstract
Bacillus and Paenibacillus spp. are essential aerobic spoilage bacteria in various food industry sectors. Spoilage from microorganisms occurs at many points throughout food production systems. Due to their complex wall structures, spores can resist heat, radiation, chemical agents, and enzymatic treatments. An alkaline lysis and mechanical disruption combination method was developed and evaluated to counter this. This combination method effectively improved DNA extraction from B. subtilis spore cells spiked into food (solid) and beverages (liquid milk and coffee) at concentrations down to 102 CFU/mL or g when spiked into food matrices and drinks. Released DNA recoveries were 27 % and 25 % for potato salad and 38 % and 36 % for whole corn spiked at 106 and 103 CFU/mL concentrations. Conversely, there was a low recovery for wheat flour (10 % and 8.8 %) and milk powders (12 % and 25 %) at 106 and 103 CFU/mL spiked concentrations. The combination method provides rapid, specific, reliable, and accurate signature sequences identification for the detection and presence confirmation of psychrophilic and psychrotolerant spoilage spore cells, improving food spoilage assessments and food control applications.
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Affiliation(s)
- Miyo Nakano
- Division of Food Science, Toyo Institute of Food Technology, 23-2, 4-chome, Minami-hanayashiki, Kawanishi, Hyogo 666-0026, Japan.
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Carroll LM, Cheng RA, Wiedmann M, Kovac J. Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond. Crit Rev Food Sci Nutr 2021; 62:7677-7702. [PMID: 33939559 DOI: 10.1080/10408398.2021.1916735] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex that contains numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is thus essential for informing public health and food safety efforts. However, taxonomic classification of these organisms is challenging. Numerous-often conflicting-taxonomic changes to the group have been proposed over the past two decades, making it difficult to remain up to date. In this review, we discuss the major nomenclatural changes that have accumulated in the B. cereus s.l. taxonomic space prior to 2020, particularly in the genomic sequencing era, and outline the resulting problems. We discuss several contemporary taxonomic frameworks as applied to B. cereus s.l., including (i) phenotypic, (ii) genomic, and (iii) hybrid nomenclatural frameworks, and we discuss the advantages and disadvantages of each. We offer suggestions as to how readers can avoid B. cereus s.l. taxonomic ambiguities, regardless of the nomenclatural framework(s) they choose to employ. Finally, we discuss future directions and open problems in the B. cereus s.l. taxonomic realm, including those that cannot be solved by genomic approaches alone.
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Affiliation(s)
- Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
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Muras A, Romero M, Mayer C, Otero A. Biotechnological applications of Bacillus licheniformis. Crit Rev Biotechnol 2021; 41:609-627. [PMID: 33593221 DOI: 10.1080/07388551.2021.1873239] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus licheniformis is a Gram positive spore-forming bacterial species of high biotechnological interest with numerous present and potential uses, including the production of bioactive compounds that are applied in a wide range of fields, such as aquaculture, agriculture, food, biomedicine, and pharmaceutical industries. Its use as an expression vector for the production of enzymes and other bioproducts is also gaining interest due to the availability of novel genetic manipulation tools. Furthermore, besides its widespread use as a probiotic, other biotechnological applications of B. licheniformis strains include: bioflocculation, biomineralization, biofuel production, bioremediation, and anti-biofilm activity. Although authorities have approved the use of B. licheniformis as a feed additive worldwide due to the absence of toxigenic potential, some probiotics containing this bacterium are considered unsafe due to the possible transference of antibiotic resistance genes. The wide variability in biological activities and genetic characteristics of this species makes it necessary to establish an exact protocol for describing the novel strains, in order to evaluate its biotechnological potential.
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Affiliation(s)
- Andrea Muras
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Romero
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Celia Mayer
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Otero
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Maier C, Hofmann K, Huptas C, Scherer S, Wenning M, Lücking G. Simultaneous quantification of the most common and proteolytic Pseudomonas species in raw milk by multiplex qPCR. Appl Microbiol Biotechnol 2021; 105:1693-1708. [PMID: 33527148 PMCID: PMC7880948 DOI: 10.1007/s00253-021-11109-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/17/2020] [Accepted: 01/11/2021] [Indexed: 12/26/2022]
Abstract
Abstract The heat-stable peptidase AprX, secreted by psychrotolerant Pseudomonas species in raw milk, is a major cause of destabilization and premature spoilage of ultra-high temperature (UHT) milk and milk products. To enable rapid detection and quantification of seven frequent and proteolytic Pseudomonas species (P. proteolytica, P. gessardii, P. lactis, P. fluorescens, P. protegens, P. lundensis, and P. fragi) in raw milk, we developed two triplex qPCR assays taking into account species-dependent differences in AprX activity. Besides five species-specific hydrolysis probes, targeting the aprX gene, a universal rpoB probe was included in the assay to determine the total Pseudomonas counts. For all six probes, linear regression lines between Cq value and target DNA concentration were obtained in singleplex as well as in multiplex approaches, yielding R2 values of > 0.975 and amplification efficiencies of 85–97%. Moreover, high specificity was determined using genomic DNA of 75 Pseudomonas strains, assigned to 57 species, and 40 other bacterial species as templates in the qPCR. Quantification of the target species and total Pseudomonas counts resulted in linear detection ranges of approx. 103–107 cfu/ml, which correspond well to common Pseudomonas counts in raw milk. Application of the assay using 60 raw milk samples from different dairies showed good agreement of total Pseudomonas counts calculated by qPCR with cell counts derived from cultivation. Furthermore, a remarkably high variability regarding the species composition was observed for each milk sample, whereby P. lundensis and P. proteolytica/P. gessardii were the predominant species detected. Key points • Multiplex qPCR for quantification of seven proteolytic Pseudomonas species and total Pseudomonas counts in raw milk • High specificity and sensitivity via hydrolysis probes against aprX and rpoB • Rapid method to determine Pseudomonas contamination in raw milk and predict spoilage potential Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11109-0.
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Affiliation(s)
- Christopher Maier
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany
| | - Katharina Hofmann
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany
| | - Christopher Huptas
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Siegfried Scherer
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany.,Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Mareike Wenning
- Bavarian Health and Food Safety Authority (LGL), Veterinärstr. 2, 85764, Oberschleißheim, Germany
| | - Genia Lücking
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany.
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Lv S, Zhang X, Feng Y, Jiang Q, Niu C, Yang Y, Wang X. Gut Microbiota Combined With Metabolomics Reveals the Repeated Dose Oral Toxicity of β-Cyclodextrin in Mice. Front Pharmacol 2021; 11:574607. [PMID: 33519440 PMCID: PMC7845417 DOI: 10.3389/fphar.2020.574607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022] Open
Abstract
Βeta-cyclodextrin (β-CD) with a hydrophobic cavity enables the formation of inclusion complexes with organic molecules. The formation of host–guest complexes makes the application of β-CD popular in many fields, but their interaction with organisms is poorly understood. In the present study, the effect of β-CD on gut microbiota (16S rRNA gene sequencing), serum metabolites (gas chromatography–mass spectrometry platform), and their correlation (Pearson correlation analysis) was investigated after 14 days repeated oral exposure in mice. β-CD did not significantly affect the α-diversity indexes, including Richness, Chao1, Shannon and Simpson indexes, but disturbed the structure of the gut bacteria according to the result of principal component analysis (PCA). After taxonomic assignment, 1 in 27 phyla, 2 in 48 classes, 3 in 107 orders, 6 in 192 families, and 8 in 332 genera were significantly different between control and β-CD treated groups. The serum metabolites were significantly changed after β-CD treatment according to the result of unsupervized PCA and supervised partial least squares-discriminant analysis (PLS-DA). A total of 112 differential metabolites (89 downregulated and 23 upregulated) were identified based on the VIP >1 from orthogonal PLS-DA and p <0.05 from Student’s t-test. The metabolic pathways, including ABC transporters, pyrimidine metabolism, purine metabolism, glucagon signaling pathway, insulin signaling pathway, and glycolysis/gluconeogenesis, were enriched by KEGG pathway analysis. Our study provides a general observation of gut microbiota, serum metabolites and their correlation after exposure to β-CD in mice, which will be helpful for future research and application of β-CD.
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Affiliation(s)
- Shuangyu Lv
- Institute of Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xiaomei Zhang
- Institute of Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yu Feng
- Institute of Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Qiying Jiang
- Institute of Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Chenguang Niu
- Key Laboratory of Clinical Resources Translation, The First Affiliated Hospital of Henan University, Kaifeng, China
| | - Yanjie Yang
- Institute of Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xinchun Wang
- Key Laboratory of Clinical Resources Translation, The First Affiliated Hospital of Henan University, Kaifeng, China
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Fraiture MA, Joly L, Vandermassen E, Delvoye M, Van Geel D, Michelet JY, Van Hoeck E, De Jaeger N, Papazova N, Roosens NH. Retrospective survey of unauthorized genetically modified bacteria harbouring antimicrobial resistance genes in feed additive vitamin B2 commercialized in Belgium: Challenges and solutions. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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