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Maktabdar M, Truelstrup Hansen L, Wemmenhove E, Gkogka E, Dalgaard P. Prevalence, characteristics, and selection of Bacillus cereus sub-groups from dairy products for challenge testing and predictive model development. J Food Prot 2024:100367. [PMID: 39357564 DOI: 10.1016/j.jfp.2024.100367] [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: 07/24/2024] [Revised: 09/24/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024]
Abstract
Prevalence, toxin gene profiles, lactose fermentation, and growth responses of B. cereus sensu lato sub-groups in various dairy and dairy alternative products and ingredients were studied to identify relevant isolates for challenge testing and model development to predict and manage growth responses. Out of 71 examined products or ingredients, 51 B. cereus s.l. isolates were obtained from 35 positive samples (49% prevalence). These 51 isolates along with 18 additional dairy isolates and 12 B. cereus s.l. reference strains were identified using MALDI-TOF. The 81 isolates were further characterized by panC sequencing, testing for cold shock and toxin genes (cspA; hbl, nhe, CytK and ces), lactose fermentation, and study of growth rates (µmax) under various conditions (45°C, 10°C, 6% NaCl, pH 5.1), resulting in 298 µmax-values. These conditions were selected to differentiate mesophilic and psychrotolerant strains and to identify tolerant isolates. Dairy powders (83%), pasteurized upconcentrated cheese whey (43%), and cheeses (42%) had the highest prevalences of B. cereus s.l. and the highest concentrations in positive samples (5-100 CFU/g or ml). The panC groups II, III, IV, VI, and VIII were detected among the dairy isolates, with 97% harbouring one or more toxin genes. Lactose fermentation was observed in 42% of isolates, with lactose-fermenting B. cereus s.l. isolates of panC groups III and IV dominant in dairy powders. Growth rates of B. cereus s.l. varied considerably, among and within panC groups of the dairy isolates. Based on the highest growth rates at 45°C, 10°C, 6 % NaCl, pH 5.1, panC group membership, toxin genes profiles, and lactose fermentation ability, two cocktails of "mesophilic" or "psychrotolerant" isolates were selected. These strain cocktails can be used in future challenge testing and predictive food microbiology studies to evaluate and manage growth of B. cereus s.l. in dairy products and ingredients.
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Affiliation(s)
- Maryam Maktabdar
- Food Microbiology and Hygiene, National Food Institute (DTU Food), Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Lisbeth Truelstrup Hansen
- Food Microbiology and Hygiene, National Food Institute (DTU Food), Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ellen Wemmenhove
- Arla Foods Ingredients Innovation Center, Arla Foods Ingredients, Nr. Vium, Denmark
| | | | - Paw Dalgaard
- Food Microbiology and Hygiene, National Food Institute (DTU Food), Technical University of Denmark, Kgs. Lyngby, Denmark
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2
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Finton M, Skeie SB, Aspholm ME, Franklin-Alming FV, Mekonnen YB, Kristiansen H, Porcellato D. Two-year investigation of spore-formers through the production chain at two cheese plants in Norway. Food Res Int 2024; 190:114610. [PMID: 38945575 DOI: 10.1016/j.foodres.2024.114610] [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: 02/17/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]
Abstract
Spore-forming bacteria are the most complex group of microbes to eliminate from the dairy production line due to their ability to withstand heat treatment usually used in dairy processing. These ubiquitous microorganisms have ample opportunity for multiple points of entry into the milk chain, creating issues for food quality and safety. Certain spore-formers, namely bacilli and clostridia, are more problematic to the dairy industry due to their possible pathogenicity, growth, and production of metabolites and spoilage enzymes. This research investigated the spore-forming population from raw milk reception at two Norwegian dairy plants through the cheesemaking stages until ripening. Samples were collected over two years and examined by amplicon sequencing in a culture independent manner and after an anaerobic spore-former enrichment step. In addition, a total of 608 isolates from the enriched samples were identified at the genus or species level using MALDI-TOF analysis. Most spore-forming isolates belong to the genera Bacillus or Clostridium, with the latter dominating the enriched MPN tubes of raw milk and bactofugate. Results showed a great variation among the clostridia and bacilli detected in the enriched MPN tubes. However, B. licheniformis and C. tyrobutyricum were identified in all sample types from both plants throughout the 2-year study. In conclusion, our results shed light on the fate of different spore-formers at different processing stages in the cheese production chain, which could facilitate targeted actions to reduce quality problems.
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Affiliation(s)
- Misti Finton
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Siv Borghild Skeie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Marina Elisabeth Aspholm
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | | | - Yohannes Beyene Mekonnen
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Hanne Kristiansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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3
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Hongchao D, Ma L, Xu Z, Soteyome T, Yuan L, Yang Z, Jiao XA. Invited review: Role of Bacillus licheniformis in the dairy industry- friends or foes? J Dairy Sci 2024:S0022-0302(24)00904-4. [PMID: 38851582 DOI: 10.3168/jds.2024-24826] [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: 02/25/2024] [Accepted: 05/07/2024] [Indexed: 06/10/2024]
Abstract
Bacillus licheniformis is one of the major spore-forming bacteria with great genotypic diversity in raw milk, dairy ingredients, final dairy products, and is found throughout the dairy processing continuum. Though being widely used as a probiotic strain, this species also serves as a potential risk in the dairy industry based on its roles in foodborne illness and dairy spoilage. Biofilm formation of B. licheniformis in combined with the heat resistance of its spores, make it impossible to prevent the presence of B. licheniformis in final dairy products by traditional cleaning and disinfection procedures. Despite the extensive efforts on the identification of B. licheniformis from various dairy samples, no reviews have been reported on both hazard and benefits of this spore-former. This review discusses the prevalence of B. licheniformis from raw milk to commercial dairy products, biofilm formation and spoilage potential of B. licheniformis, and its potential prevention methods. In addition, the potential benefits of B. licheniformis in the dairy industry were also summarized.
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Affiliation(s)
- Dai Hongchao
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, 225127 China; Jiangsu Key Laboratory of Zoonoses, Yangzhou, Jiangsu, 225009 China
| | - Lili Ma
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, 225127 China
| | - Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou 510640, China; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | - Thanapop Soteyome
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | - Lei Yuan
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, 225127 China; Jiangsu Key Laboratory of Zoonoses, Yangzhou, Jiangsu, 225009 China.
| | - Zhenquan Yang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, 225127 China
| | - Xin-An Jiao
- Jiangsu Key Laboratory of Zoonoses, Yangzhou, Jiangsu, 225009 China
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4
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Park SM, Rhee MS. Prevalence and phylogenetic traits of nitrite-producing bacteria in raw ingredients and processed baby foods: Potential sources of foodborne infant methemoglobinemia. Food Res Int 2024; 178:113966. [PMID: 38309914 DOI: 10.1016/j.foodres.2024.113966] [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: 08/05/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Nitrite, which has been mainly regarded as a chemical hazard, can induce infant methemoglobinemia. As for nitrite as a product of microbial metabolism, the contribution of the oral or gut microbiome has mostly received attention, whereas the role of nitrite-producing bacteria (NPBs) in food has been less elucidated. In this study, mesophilic NPBs were isolated from food samples (n = 320) composed of raw ingredients for weaning foods (n = 160; beetroot, broccoli, carrot, lettuce, rice powder, spinach, sweet potato, and honey) and processed baby foods (n = 160; cereal snack, cheese, yogurt, powdered infant formula, sorghum syrup, vegetable fruit juice, and weaning food). The phylogenetic diversity of the NPB strains was analyzed via 16S rRNA sequencing. All 15 food items harbored NPBs, with a prevalence of 71.9 % and 34.4 % for the raw ingredients and processed foods, respectively. The NPBs isolated from the foods were identified as Actinomycetota (Actinomycetes), Bacteroidota (Flavobacteriia, Sphingobacteriia), Bacillota (Bacilli), or Pseudomonadota (Alpha-, Beta-, and Gammaproteobacteria). Among the raw and processed foods, beetroot (85.0 %) and powdered infant formula (70.0 %) showed had the highest NPB prevalence (P > 0.05). Bacillota predominated in both types of food. The contamination source of Pseudomonadota, which was another major phylum present in the raw ingredients, was presumed to be the soil and endophytes in the seeds, whereas that of Bacillota was the manufacturing equipment used with the raw ingredients. Common species for probiotics, such as Lacticaseibacillus, Leuconostoc, Enterococcus, and Bacillus, were isolated and identified as NPBs. To our knowledge, this is the first study to reveal the taxonomical diversity and omnipresence of NPBs in food for babies. The results of this study highlight the importance of food-mediated microbiological risks of infant methemoglobinemia which are yet underrecognized.
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Affiliation(s)
- Sun Min Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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5
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Lücking G, Albrecht K, Märtlbauer E, Schauer K. Draft genome sequences of two thermophilic, spore-forming Aeribacillus pallidus strains isolated from dairy products. Microbiol Resour Announc 2024; 13:e0089623. [PMID: 38088573 DOI: 10.1128/mra.00896-23] [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: 09/22/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The presence of thermophilic spore-forming bacteria is challenging in industrial food processing. The presented genome sequences of Aeribacillus pallidus, isolated from raw milk and cocoa powder, provide insights into how to prevent damage to minimally processed foods and products with extended shelf life, such as milk products.
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Affiliation(s)
- Genia Lücking
- Chair of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich , Freising, Germany
| | - Klement Albrecht
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians University of Munich , Oberschleiβheim, Germany
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians University of Munich , Oberschleiβheim, Germany
| | - Kristina Schauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians University of Munich , Oberschleiβheim, Germany
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin , Dublin, Ireland
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6
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Kyrylenko A, Eijlander RT, Alliney G, de Bos ELV, Wells-Bennik MHJ. Levels and types of microbial contaminants in different plant-based ingredients used in dairy alternatives. Int J Food Microbiol 2023; 407:110392. [PMID: 37729802 DOI: 10.1016/j.ijfoodmicro.2023.110392] [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: 03/27/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/22/2023]
Abstract
In this study levels and types of microbial contaminants were investigated in 88 different plant-based ingredients including many that are used to manufacture dairy alternatives. Studied ingredients encompassed samples of pulses (pea, faba bean, chickpea, and mung bean), cereals/pseudocereals (oat, rice, amaranth and quinoa) and drupes (coconut, almond and cashew). The microbial analysis included: i) total viable count (TVC), ii) total aerobic mesophilic spore count (TMS), iii) heat resistant aerobic thermophilic spore count (HRTS), iv) anaerobic sulfite reducing Clostridium spore count (SRCS), and v) Bacillus cereus spore count (BCES). Microorganisms isolated from the counting plates with the highest sample dilutions were identified using 16S rRNA and MALDI-TOF MS analyses. Many of the investigated ingredients showed a high proportion of spores as part of their total aerobic mesophilic counts. In 63 % of the samples, the difference between TVC and TMS counts was 1 Log10 unit or less. This was particularly the case for the majority of pea isolates and concentrates, faba bean isolates, oat kernels and flakes, and for single samples of chickpea isolate, almond, amaranth, rice, quinoa, and coconut flours. Concentrations of TVC ranged between <1.0 and 5.3 Log10 CFU/g in different samples, and TMS varied between <1.0 and 4.1 Log10 CFU/g. Levels of HTRS, BCES and SRCS were generally low, typically around or below the LOD of 1.0 Log10 CFU/g. In total, 845 individual bacterial colonies were isolated belonging to 33 different genera. Bacillus licheniformis and B. cereus group strains were most frequently detected among Bacillus isolates, and these species originated primarily from pea and oat samples. Geobacillus stearothermophilus was the main species encountered as part of the HRTS. Among the Clostridium isolates, Clostridum sporogenes/tepidum were predominant species, which were mostly found in pea and almond samples. Strains with potential to cause foodborne infection or intoxication were typed using the PCR-based method for toxin genes detection. In the B. cereus group, 9 % of isolates contained the ces gene, 28 % contained hbl, 42 % cytK, and 69 % were positive for the nhe gene. Absence of the boNT-A and -B genes was confirmed for all isolated C. sporogenes/tepidum strains. Nearly all (98 %) B. licheniformis isolates were positive for the lchAA gene. Insight into the occurrence of microbial contaminants in plant-based ingredients, combined with knowledge of their key inactivation and growth characteristics, can be used for the microbial risk assessment and effective design of plant-based food processing conditions and formulations to ensure food safety and prevent spoilage.
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Affiliation(s)
- Alina Kyrylenko
- NIZO food research, Kernhemseweg 2, 6718 ZB Ede, the Netherlands; Wageningen University and Research, Food Microbiology, P.O. Box 17, 6700 AA Wageningen, the Netherlands.
| | | | - Giovanni Alliney
- NIZO food research, Kernhemseweg 2, 6718 ZB Ede, the Netherlands; Wageningen University and Research, Food Microbiology, P.O. Box 17, 6700 AA Wageningen, the Netherlands
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7
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Martin NH, Evanowski RL, Wiedmann M. Invited review: Redefining raw milk quality-Evaluation of raw milk microbiological parameters to ensure high-quality processed dairy products. J Dairy Sci 2023; 106:1502-1517. [PMID: 36631323 DOI: 10.3168/jds.2022-22416] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/17/2022] [Indexed: 01/11/2023]
Abstract
Raw milk typically has little bacterial contamination as it leaves the udder of the animal; however, through a variety of pathways, it can become contaminated with bacteria originating from environmental sources, the cow herself, and contact with contaminated equipment. Although the types of bacteria found in raw milk are very diverse, select groups are particularly important from the perspective of finished product quality. In particular, psychrophilic and psychrotolerant bacteria that grow quickly at low temperatures (e.g., species in the genus Pseudomonas and the family Enterobacteriaceae) and produce heat-stable enzymes, and sporeforming bacteria that survive processing hurdles in spore form, are the 2 primary groups of bacteria related to effects on processed dairy products. Understanding factors leading to the presence of these important bacterial groups in raw milk is key to reducing their influence on processed dairy product quality. Here we examine the raw milk microbiological parameters used in the contemporary dairy industry for their utility in identifying raw milk supplies that will perform well in processed dairy products. We further recommend the use of a single microbiological indicator of raw milk quality, namely the total bacteria count, and call for the development of a whole-farm approach to raw milk quality that will use data-driven, risk-based tools integrated across the continuum from production to processing and shelf-life to ensure continuous improvement in dairy product quality.
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Affiliation(s)
- N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
| | - R L Evanowski
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
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8
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Ouamba AJK, Gagnon M, LaPointe G, Chouinard PY, Roy D. Graduate Student Literature Review: Farm management practices: Potential microbial sources that determine the microbiota of raw bovine milk. J Dairy Sci 2022; 105:7276-7287. [PMID: 35863929 DOI: 10.3168/jds.2021-21758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/25/2022] [Indexed: 11/19/2022]
Abstract
Environmental and herd-associated factors such as geographical location, climatic conditions, forage types, bedding, soil, animal genetics, herd size, housing, lactation stage, and udder health are exploited by farmers to dictate specific management strategies that ensure dairy operation profitability and enhance the sustainability of milk production. Along with milking routines, milking systems, and storage conditions, these farming practices greatly influence the microbiota of raw milk, as evidenced by several recent studies. During the past few years, the increased interest in high-throughput sequencing technologies combined with culture-dependent methods to investigate dairy microbial ecology has improved our understanding of raw milk community dynamics throughout storage and processing. However, knowledge is still lacking on the niche-specific communities in the farm environment, and on the factors that determine bacteria transfer to the raw milk. This review summarizes findings from the past 2 decades regarding the effects of farm management practices on the diversity of bacterial species that determine the microbiological quality of raw cow milk.
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Affiliation(s)
- Alexandre J K Ouamba
- Département des Sciences des Aliments, Laboratoire de Génomique Microbienne, Université Laval, Québec, G1V 0A6, Canada; Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Saint-Hyacinthe, J2S 2M2, Canada.
| | - Mérilie Gagnon
- Département des Sciences des Aliments, Laboratoire de Génomique Microbienne, Université Laval, Québec, G1V 0A6, Canada; Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Saint-Hyacinthe, J2S 2M2, Canada
| | - Gisèle LaPointe
- Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Saint-Hyacinthe, J2S 2M2, Canada; Department of Food Science, University of Guelph, Guelph, N1G 2W1, Canada
| | - P Yvan Chouinard
- Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Saint-Hyacinthe, J2S 2M2, Canada; Département des Sciences Animales, Université Laval, Québec, G1V 0A6, Canada
| | - Denis Roy
- Département des Sciences des Aliments, Laboratoire de Génomique Microbienne, Université Laval, Québec, G1V 0A6, Canada; Regroupement de Recherche pour un Lait de Qualité Optimale (Op+Lait), Saint-Hyacinthe, J2S 2M2, Canada
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9
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Superheated steam effectively inactivates diverse microbial targets despite mediating effects from food matrices in bench-scale assessments. Int J Food Microbiol 2022; 378:109838. [PMID: 35863173 DOI: 10.1016/j.ijfoodmicro.2022.109838] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022]
Abstract
Sanitation in dry food processing environments is challenging due to the exclusion of water. Superheated steam (SHS) is a novel sanitation technique that utilizes high temperature steam to inactivate microorganisms. The high sensible heat of SHS prevents condensation on surfaces. Here we evaluated SHS thermal inactivation of various vegetative and spore forming bacteria and fungi and determined the effect of food matrix composition on SHS efficacy. Capillary tubes with vegetative cells (Salmonella, E. coli O157:H7, Listeria monocytogenes, or Enterococcus faecium), Aspergillus fischeri ascospores, or B. cereus spores (100 μL) were SHS treated at 135 ± 1 °C for 1 or 2 s. After 1 s, SHS achieved a reduction of 10.91 ± 0.63 log10 CFU/mL for vegetative cells, 2.09 ± 0.58 log10 ascospores/mL for A. fischeri, and 0.21 ± 0.10 log10 spores/mL for B. cereus. SHS treatment achieved significant reductions in vegetative cells and fungal ascospores (p < 0.05), however B. cereus spores were not significantly reduced after 2 s and were determined to be the most resistant of the cell types evaluated. Consequently, peanut butter compositions (peanut powder, oil, and water) and milk powder (whole and nonfat) inoculated with B. cereus spores on aluminum foil coupons (2 × 3 × 0.5 cm) were tested. The D161°C values for B. cereus spores ranged from 46.53 ± 4.48 s (6 % fat, 55 % moisture, aw: 0.927) to 79.21 ± 14.87 s (43 % fat, 10 % moisture, aw: 0.771) for various peanut butter compositions. Whole milk powder had higher D161°C (34.38 ± 20.90 s) than nonfat milk powder (24.73 ± 6.78 s). SHS (135 ± 1 °C) rapidly (1 s) inactivated most common vegetative bacterial cells; however B. cereus spores were more heat resistant. B. cereus spore inactivation was significantly affected by product composition (p < 0.05). Compared to the log-linear model (R2 0.81-0.97), the Weibull model had better fit (R2 0.94-0.99). Finally, the ease of peanut butter removal from surfaces increased while the ease of non-fat dry milk removal decreased with the increasing SHS treatment duration. However, allergen residues were detectable on surfaces regardless of SHS treatment. The findings from this study can inform the development of pilot-scale research on SHS.
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10
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Ibrahim AS, Hafiz NM, Saad MF. Prevalence of Bacillus cereus in dairy powders focusing on its toxigenic genes and antimicrobial resistance. Arch Microbiol 2022; 204:339. [PMID: 35589862 PMCID: PMC9120150 DOI: 10.1007/s00203-022-02945-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/31/2022]
Abstract
Bacillus cereus is a common environmental foodborne microorganism that is mainly found to harbor toxigenic genes with multiple antibiotic resistances and is linked to threatening the safety of dried milk in concern to powdered infant milk formula. In the current investigation, the mean value of B. cereus in 140 samples of powdered milk was 0.57 × 102 ± 0.182 × 102, 0.15 × 102 ± 0.027 × 102, 0.21 × 102 ± 0.035 × 102, and 0.32 × 102 ± 0.072 × 102 CFU/g in a percentage of 64.0 samples of whole milk powder, 43.3 of skim milk powder, 26.7 of powdered infant milk formula and 36.7 milk–cereal-based infant formula, respectively. The results revealed that B. cereus isolates were found to harbor toxigenic genes in the following percentages: 77.8, 2.0, 72.7, 16.2, and 67.7 for nhe, hbl, cytK, ces, and bceT, respectively. Despite all evaluated B. cereus strains were originated from dairy powders, they showed a significant difference (P < 0.05) in their harbored toxigenic cytK gene between whole and skim milk powders with powdered infant formula and milk–cereal-based infant formula, as well as between powdered infant formula and milk–cereal-based infant formula. All isolated B. cereus strains were resistant to cefoxitin, colistin sulfate, neomycin, trimethoprim–sulfamethoxazole, oxacillin, and penicillin. Based on the antimicrobial resistance of B. cereus strains to cephalothin, chloramphenicol, nalidixic acid, and tetracycline, there was a significant difference (P < 0.05) between powdered infant milk formula and whole milk powder strains. This survey is one of few studies proceeded in Egypt to determine the prevalence of toxigenic B. cereus strains in milk–cereal-based infant formula and powdered infant formula as well as skim milk powder.
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Affiliation(s)
- Aml S Ibrahim
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
| | - Nagah M Hafiz
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - M F Saad
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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11
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Yeak KYC, Perko M, Staring G, Fernandez-Ciruelos BM, Wells JM, Abee T, Wells-Bennik MHJ. Lichenysin Production by Bacillus licheniformis Food Isolates and Toxicity to Human Cells. Front Microbiol 2022; 13:831033. [PMID: 35197958 PMCID: PMC8859269 DOI: 10.3389/fmicb.2022.831033] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/03/2022] [Indexed: 12/20/2022] Open
Abstract
Bacillus licheniformis can cause foodborne intoxication due to the production of the surfactant lichenysin. The aim of this study was to measure the production of lichenysin by food isolates of B. licheniformis in LB medium and skimmed milk and its cytotoxicity for intestinal cells. Out of 11 B. licheniformis isolates tested, most showed robust growth in high salt (1M NaCl), 4% ethanol, at 37 or 55°C, and aerobic and anaerobic conditions. All strains produced lichenysin (in varying amounts), but not all strains were hemolytic. Production of this stable compound by selected strains (high producers B4094 and B4123, and type strain DSM13T) was subsequently determined using LB medium and milk, at 37 and 55°C. Lichenysin production in LB broth and milk was not detected at cell densities < 5 log10 CFU/ml. The highest concentrations were found in the stationary phase of growth. Total production of lichenysin was 4–20 times lower in milk than in LB broth (maximum 36 μg/ml), and ∼10 times lower in the biomass obtained from milk agar than LB agar. Under all conditions tested, strain B4094 consistently yielded the highest amounts. Besides strain variation and medium composition, temperature also had an effect on lichenysin production, with twofold lower amounts of lichenysin produced at 55°C than at 37°C. All three strains produced lichenysin A with varying acyl chain lengths (C11–C18). The relative abundance of the C14 variant was highest in milk and the C15 variant highest in LB. The concentration of lichenysin needed to reduce cell viability by 50% (IC50) was 16.6 μg/ml for Caco-2 human intestinal epithelial cells and 16.8 μg/ml for pig ileum organoids. Taken together, the presence of low levels (<5 log10 CFU/ml) of B. licheniformis in foods is unlikely to pose a foodborne hazard related to lichenysin production. However, depending on the strain present, the composition, and storage condition of the food, a risk of foodborne intoxication may arise if growth to high levels is supported and such product is ingested.
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Affiliation(s)
- Kah Yen Claire Yeak
- NIZO, Ede, Netherlands.,Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | | | | | - Jerry M Wells
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
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Gaballa A, Cheng RA, Trmcic A, Kovac J, Kent DJ, Martin NH, Wiedmann M. Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales. J Microbiol Methods 2021; 191:106350. [PMID: 34710512 DOI: 10.1016/j.mimet.2021.106350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Li F, Santillan-Urquiza E, Cronin U, O'Meara E, McCarthy W, Hogan SA, Wilkinson MG, Tobin JT. Assessment of the response of indigenous microflora and inoculated Bacillus licheniformis endospores in reconstituted skim milk to microwave and conventional heating systems by flow cytometry. J Dairy Sci 2021; 104:9627-9644. [PMID: 34127263 DOI: 10.3168/jds.2020-19875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/23/2021] [Indexed: 11/19/2022]
Abstract
Heat treatment is one of the most widely used processing technologies in the dairy industry. Its primary purpose is to destroy microorganisms, both pathogenic and spoilage, to ensure the product is safe and has a reasonable shelf life. In this study microwave volumetric heating (MVH) was compared with a conventional tubular heat exchanger (THE), in terms of the effects of each at a range of temperatures (75°C, 85°C, 95°C, 105°C, 115°C, and 125°C) on indigenous microflora viability and the germination of inoculated Bacillus licheniformis endospores in reconstituted skim milk. To assess the heat treatment-related effects on microbial viability, classical agar-based tests were applied to obtain the counts of 4 various microbiological groups including total bacterial, thermophilic bacterial, mesophilic aerobic bacterial endospore, and thermophilic aerobic bacterial endospore counts, and additional novel insights into cell permeability and spore germination profiles post-heat treatment were obtained using real-time flow cytometry (FC) methods. No significant differences in the plate counts of the indigenous microorganisms tested, the plate counts of the inoculated B. licheniformis, or the relative percentage of germinating endospores were observed between MVH- and THE-treated samples, at equal temperatures in the range specified above, indicating that both methods inactivated inoculated endospores to a similar degree (up to 70% as measured by FC and 5 log reduction as measured by plate counting for some treatments of inoculated endospores). Furthermore, increased cell permeability of indigenous microflora was observed by FC after MVH compared with THE treatment of uninoculated skim milk, which was reflected in lower total bacterial count at a treatment temperature of 105°C. This work demonstrates the utility of FC as a rapid method for assessing cell viability and spore inactivation for postthermal processing in dairy products and overall provides evidence that MVH is at least as effective at eliminating native microflora and inoculated B. licheniformis endospores as THE.
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Affiliation(s)
- F Li
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, P61 C996, Ireland
| | - E Santillan-Urquiza
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, P61 C996, Ireland
| | - U Cronin
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, V94 T9PX, Ireland
| | - E O'Meara
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, V94 T9PX, Ireland
| | - W McCarthy
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, P61 C996, Ireland
| | - S A Hogan
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, P61 C996, Ireland
| | - M G Wilkinson
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, V94 T9PX, Ireland
| | - J T Tobin
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, P61 C996, Ireland.
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14
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Delaunay L, Cozien E, Gehannin P, Mouhali N, Mace S, Postollec F, Leguerinel I, Mathot AG. Occurrence and diversity of thermophilic sporeformers in French dairy powders. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2020.104889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Martin NH, Torres-Frenzel P, Wiedmann M. Invited review: Controlling dairy product spoilage to reduce food loss and waste. J Dairy Sci 2020; 104:1251-1261. [PMID: 33309352 DOI: 10.3168/jds.2020-19130] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/16/2020] [Indexed: 01/30/2023]
Abstract
Food loss and waste is a major concern in the United States and globally, with dairy foods representing one of the top categories of food lost and wasted. Estimates indicate that in the United States, approximately a quarter of dairy products are lost at the production level or wasted at the retail or consumer level annually. Premature microbial spoilage of dairy products, including fluid milk, cheese, and cultured products, is a primary contributor to dairy food waste. Microbial contamination may occur at various points throughout the production and processing continuum and includes organisms such as gram-negative bacteria (e.g., Pseudomonas), gram-positive bacteria (e.g., Paenibacillus), and a wide range of fungal organisms. These organisms grow at refrigerated storage temperatures, often rapidly, and create various degradative enzymes that result in off-odors, flavors, and body defects (e.g., coagulation), rendering them inedible. Reducing premature dairy food spoilage will in turn reduce waste throughout the dairy continuum. Strategies to reduce premature spoilage include reducing raw material contamination on-farm, physically removing microbial contaminants, employing biocontrol agents to reduce outgrowth of microbial contaminants, tracking and eliminating microbial contaminants using advanced molecular microbiological techniques, and others. This review will address the primary microbial causes of premature dairy product spoilage and methods of controlling this spoilage to reduce loss and waste in dairy products.
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Affiliation(s)
- N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
| | - P Torres-Frenzel
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
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Gauvry E, Mathot AG, Couvert O, Leguérinel I, Coroller L. Effects of temperature, pH and water activity on the growth and the sporulation abilities of Bacillus subtilis BSB1. Int J Food Microbiol 2020; 337:108915. [PMID: 33152569 DOI: 10.1016/j.ijfoodmicro.2020.108915] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 07/15/2020] [Accepted: 10/04/2020] [Indexed: 11/27/2022]
Abstract
Spore-forming bacteria are implicated in cases of food spoilage or food poisoning. In their sporulated form, they are resistant to physical and chemical treatments applied in the food industry and can persist throughout the food chain. The sporulation leads to an increase in the concentration of resistant forms in final products or food processing equipment. In order to identify sporulation environments in the food industry, it is necessary to be able to predict bacterial sporulation according to environmental factors. As sporulation occurs after bacterial growth, a kinetic model of growth-sporulation was used to describe the evolution of vegetative cells and spores through time. The effects of temperature, pH and water activity on the growth and the sporulation abilities of Bacillus subtilis BSB1 were modelled. The values of the growth boundaries were used as inputs to predict these effects. The good description of the sporulation kinetics by growth parameters suggests that the impact of the studied environmental factors is the same on both physiological process. Suboptimal conditions for growth delay the appearance of the first spores, and spores appear more synchronously in suboptimal conditions for growth. The developed model was also applicable to describe the growth and sporulation curves in changing temperature and pH conditions over time.
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Affiliation(s)
- Emilie Gauvry
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Anne-Gabrielle Mathot
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Olivier Couvert
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Ivan Leguérinel
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France
| | - Louis Coroller
- Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, UMT ALTER'IX, F-29000 Quimper, France.
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17
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Ribeiro-Júnior JC, Tamanini R, Alfieri AA, Beloti V. Effect of milk bactofugation on the counts and diversity of thermoduric bacteria. J Dairy Sci 2020; 103:8782-8790. [PMID: 32828509 DOI: 10.3168/jds.2020-18591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/03/2020] [Indexed: 11/19/2022]
Abstract
The objective of this work was to determine the effect of milk bactofugation on the counts and microbial diversity of mesophilic (MT), psychrotrophic (PT), and thermophilic (TT) thermoduric bacteria and its potential as a technological method to remove spoilage microorganisms resistant to pasteurization. Different batches of raw milk from 69 dairy farms divided into sets in 3 bulk tanks (A, B, C) were evaluated at different times during the technological process. As the raw milk was preheated (∼55°C) immediately before bactofugation (10,000 × g), the effect of bactofugation was estimated by comparing the counts in raw, preheated, and bactofuged milk. This centrifugation was sufficient to reduce the isolation of 88% of the MT in preheated milk. For PT, it was possible to verify a reduction of 72.5% in batch C. The TT were not recovered at higher detection limits (<5 cfu/mL). For diversity, 310 isolates were identified using a molecular approach; 15 species of contaminating thermoduric bacteria were identified from raw and preheated milk, and only 6 species were recovered in bactofuged milk. Only MT were recovered from the bactofuged milk, mainly the species Lysinibacillus fusiformis (61.7%) and Bacillus licheniformis (12.3%). Both species are known to be endospore-forming psychrotrophs and have proteolytic or lipolytic activity. The bactofugation of raw milk reduced the number of isolates of B. licheniformis, Bacillus toyonensis, Micrococcus aloeverae, and Aestuariimicrobium kwangyangense by 33, 43, 86, and 92%, respectively, and reduced the isolates of Macrococcus caseolyticus, Lysinibacillus varians, Carnobacterium divergens, Microbacterium hominis, Kocuria indica, Micrococcus yunnanensis, Gordonia paraffinivorans, Bacillus invictae, and Kocuria kristinae to undetectable levels. The results of this study indicate that bactofugation can be applied by the dairy industry to reduce pasteurization-resistant microorganisms in combination with prophylactic measures to prevent the contamination of raw milk by spores and vegetative forms of bacteria.
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Affiliation(s)
- J C Ribeiro-Júnior
- National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Federal University of Tocantins, Araguaína, Tocantins, Brazil 77804-970.
| | - R Tamanini
- National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Federal University of Tocantins, Araguaína, Tocantins, Brazil 77804-970
| | - A A Alfieri
- National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Federal University of Tocantins, Araguaína, Tocantins, Brazil 77804-970
| | - V Beloti
- National Institute of Science and Technology for the Dairy Production Chain (INCT - Leite), Federal University of Tocantins, Araguaína, Tocantins, Brazil 77804-970
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18
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Benahmed M, Leguerinel I, Moussa‐Boudjemaa B. Biodiversity, spoilage capacity and heat resistance of mesophilic aerobic spores isolated from milk powders marketed in Algeria. INT J DAIRY TECHNOL 2020. [DOI: 10.1111/1471-0307.12715] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meryem Benahmed
- Laboratoire de Microbiologie Appliquée à l'Agroalimentaire et à l'Environnement (LAMAABE) Faculté des SNV/STU Université de Tlemcen BP119 13000 Tlemcen Algeria
- Centre universitaire de Ain‐Témouchent route de Sidi Bel‐Abbès N°101 46000 Ain‐Témouchent Algeria
| | - Ivan Leguerinel
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne EA 3882 UMT ALTER'IX Université de Brest F‐29000 Quimper France
| | - Boumedine Moussa‐Boudjemaa
- Laboratoire de Microbiologie Appliquée à l'Agroalimentaire et à l'Environnement (LAMAABE) Faculté des SNV/STU Université de Tlemcen BP119 13000 Tlemcen Algeria
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19
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Li F, Hunt K, Buggy AK, Murphy KM, Ho QT, O'Callaghan TF, Butler F, Jordan K, Tobin JT. The effects of sequential heat treatment on microbial reduction and spore inactivation during milk processing. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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McHugh AJ, Feehily C, Fenelon MA, Gleeson D, Hill C, Cotter PD. Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder. mSystems 2020; 5:e00226-20. [PMID: 32265313 PMCID: PMC7141888 DOI: 10.1128/msystems.00226-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 11/20/2022] Open
Abstract
Microorganisms from the environment can enter the dairy supply chain at multiple stages, including production, milk collection, and processing, with potential implications for quality and safety. The ability to track these microorganisms can be greatly enhanced by the use of high-throughput DNA sequencing (HTS). Here HTS, both 16S rRNA gene amplicon and shotgun metagenomic sequencing were applied to investigate the microbiomes of fresh mid- and late-lactation milk collected from farm bulk tanks, collection tankers, milk silos, skimmed milk silos, a cream silo, and powder samples to investigate the microbial changes throughout a skim milk powder manufacturing process. 16S rRNA gene analysis established that the microbiota of raw milks from farm bulk tanks and in collection tankers were very diverse but that psychrotrophic genera associated with spoilage, Pseudomonas and Acinetobacter, were present in all samples. Upon storage within the whole-milk silo at the processing facility, the species Pseudomonas fluorescens and Acinetobacter baumannii became dominant. The skimmed milk powder generated during the mid-lactation period had a microbial composition that was very different from that of raw milk; specifically, two thermophilic genera, Thermus and Geobacillus, were enriched. In contrast, the microbiota of skimmed milk powder generated from late-lactation milk more closely resembled that of the raw milk and was dominated by spoilage-associated psychrotrophic bacteria. This study demonstrates that the dairy microbiota can differ significantly across different sampling days. More specifically, HTS can be used to trace microbial species from raw milks through processing to final powdered products.IMPORTANCE Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.
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Affiliation(s)
- Aoife J McHugh
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Mark A Fenelon
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Cork, Ireland
| | - David Gleeson
- Teagasc Animal and Grassland Research and Innovation Centre, Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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Vidic J, Chaix C, Manzano M, Heyndrickx M. Food Sensing: Detection of Bacillus cereus Spores in Dairy Products. BIOSENSORS 2020; 10:E15. [PMID: 32106440 PMCID: PMC7146628 DOI: 10.3390/bios10030015] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/14/2020] [Accepted: 02/22/2020] [Indexed: 12/21/2022]
Abstract
Milk is a source of essential nutrients for infants and adults, and its production has increased worldwide over the past years. Despite developments in the dairy industry, premature spoilage of milk due to the contamination by Bacillus cereus continues to be a problem and causes considerable economic losses. B. cereus is ubiquitously present in nature and can contaminate milk through a variety of means from the farm to the processing plant, during transport or distribution. There is a need to detect and quantify spores directly in food samples, because B. cereus might be present in food only in the sporulated form. Traditional microbiological detection methods used in dairy industries to detect spores show limits of time (they are time consuming), efficiency and sensitivity. The low level of B. cereus spores in milk implies that highly sensitive detection methods should be applied for dairy products screening for spore contamination. This review describes the advantages and disadvantages of classical microbiological methods used to detect B. cereus spores in milk and milk products, related to novel methods based on molecular biology, biosensors and nanotechnology.
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Affiliation(s)
- Jasmina Vidic
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Carole Chaix
- Institut des Sciences Analytiques, UMR 5280 CNRS, Université de Lyon, Université Claude Bernard Lyon 1, F-69100 Villeurbanne, France;
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, via Sondrio 2/A, 33100 Udine, Italy;
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, B-9090 Melle, Belgium;
- Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
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Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways. mSphere 2020; 5:5/1/e00739-19. [PMID: 31969477 PMCID: PMC7407005 DOI: 10.1128/msphere.00739-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk. Paenibacillus is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of Paenibacillus spp., we first used rpoB allelic typing data for a preexisting collection of 1,228 Paenibacillus species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented rpoB allelic types in the collection revealed that these isolates represent 21 different Paenibacillus spp., with P. odorifer being the predominant species. Further genomic characterization of P. odorifer isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all P. odorifer isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6°C, suggesting that psychrotolerance is conserved in P. odorifer. Overall, our data suggest that Paenibacillus spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage. IMPORTANCE Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.
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Martin NH, Kent DJ, Evanowski RL, Zuber Hrobuchak TJ, Wiedmann M. Bacterial spore levels in bulk tank raw milk are influenced by environmental and cow hygiene factors. J Dairy Sci 2019; 102:9689-9701. [DOI: 10.3168/jds.2019-16304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/29/2019] [Indexed: 11/19/2022]
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24
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Dettling A, Doll E, Wedel C, Hinrichs J, Scherer S, Wenning M. Accurate quantification of thermophilic spores in dairy powders. Int Dairy J 2019. [DOI: 10.1016/j.idairyj.2019.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Gagnon M, Hamelin L, Fréchette A, Dufour S, Roy D. Effect of recycled manure solids as bedding on bulk tank milk and implications for cheese microbiological quality. J Dairy Sci 2019; 103:128-140. [PMID: 31677843 DOI: 10.3168/jds.2019-16812] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022]
Abstract
The dairy farm environment influences the raw milk microbiota and consequently affects milk processing. Therefore, it is crucial to investigate farm management practices such as the bedding materials. The aim of this study was to evaluate the effect of recycled manure solids (RMS) as bedding material on bulk tank milk and microbiological implications for cheese quality. Bulk tank samples were collected from 84 dairy farms using RMS or straw bedding. The use of RMS did not influence thermophilic and mesophilic aerobic viable counts from spores. However, straw-milk samples gave higher values for mesophilic anaerobic spore-forming bacteria (0.44 log cfu/mL) than RMS-milk samples (0.17 log cfu/mL). The presence of thermoresistant lactic acid bacteria was not increased in milk from farms using RMS. Nevertheless, taxonomic profiles of thermoresistant bacteria isolated were different between the 2 types of milk. More Enterococcus faecalis and Streptococcus spp. were identified in RMS-milk samples. Thermoresistant enterococci and streptococci could easily end up in cheese. Therefore, milk proteolytic activities of these isolates were tested. Neither Streptococcus spp. nor Enterococcus faecium isolates exhibited proteolytic activities, whereas 53% of E. faecalis showed some. Also, only 1 vancomycin-resistant enterococcus was detected. Survival of selected RMS-milk samples isolates (3 E. faecalis and 1 Streptococcus thermophilus) was evaluated during a model Cheddar cheese manufacture. Although those strains survived well, they did not modify the acidification curve of milk. However, they might cause organoleptic defects during cheese maturing.
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Affiliation(s)
- Mérilie Gagnon
- Département des sciences des aliments, Laboratoire de génomique microbienne, Université Laval, 2440, boulevard Hochelaga, Québec QC G1V 0A6, Canada; Regroupement de recherche pour un lait de qualité optimale (Op+Lait), 3200, rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Laurie Hamelin
- Département des sciences des aliments, Laboratoire de génomique microbienne, Université Laval, 2440, boulevard Hochelaga, Québec QC G1V 0A6, Canada; Regroupement de recherche pour un lait de qualité optimale (Op+Lait), 3200, rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Annie Fréchette
- Regroupement de recherche pour un lait de qualité optimale (Op+Lait), 3200, rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada; Département de pathologie et microbiologie, Faculté de médecine vétérinaire, Université de Montréal, C. P. 5000, Saint-Hyacinthe, QC J2S 7C6, Canada
| | - Simon Dufour
- Regroupement de recherche pour un lait de qualité optimale (Op+Lait), 3200, rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada; Département de pathologie et microbiologie, Faculté de médecine vétérinaire, Université de Montréal, C. P. 5000, Saint-Hyacinthe, QC J2S 7C6, Canada
| | - Denis Roy
- Département des sciences des aliments, Laboratoire de génomique microbienne, Université Laval, 2440, boulevard Hochelaga, Québec QC G1V 0A6, Canada; Regroupement de recherche pour un lait de qualité optimale (Op+Lait), 3200, rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada.
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Li F, Hunt K, Van Hoorde K, Butler F, Jordan K, Tobin JT. Occurrence and identification of spore-forming bacteria in skim-milk powders. Int Dairy J 2019. [DOI: 10.1016/j.idairyj.2019.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Rossi GAM, Silva HO, Aguilar CEG, Rochetti AL, Pascoe B, Méric G, Mourkas E, Hitchings MD, Mathias LA, de Azevedo Ruiz VL, Fukumasu H, Sheppard SK, Vidal AMC. Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil. FEMS Microbiol Lett 2019; 365:4780294. [PMID: 29390131 DOI: 10.1093/femsle/fnx283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/23/2017] [Indexed: 12/20/2022] Open
Abstract
The genomes of 262 Bacillus cereus isolates were analyzed including 69 isolates sampled from equipment, raw milk and dairy products from Brazil. The population structure of isolates showed strains belonging to known phylogenetic groups II, III, IV, V and VI. Almost all the isolates obtained from dairy products belonged to group III. Investigation of specific alleles revealed high numbers of isolates carrying toxin-associated genes including cytK (53.62%), hblA (59.42%), hblC (44.93%), hblD (53.62%), nheA (84.06%), nheB (89.86%) and nheC (84.06%) with isolates belonging to groups IV and V having significant higher prevalence of hblACD and group IV of CytK genes. Strains from dairy products had significantly lower prevalence of CytK and hblACD genes compared to isolates from equipment and raw milk/bulk tanks. Genes related to sucrose metabolism were detected at higher frequency in isolates obtained from raw milk compared to strains from equipment and utensils. The population genomic analysis demonstrated the diversity of strains and variability of putative function among B. cereus group isolates in Brazilian dairy production, with large numbers of strains potentially able to cause foodborne illness. This detailed information will contribute to targeted interventions to reduce milk contamination and spoilage associated with B. cereus in Brazil.
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Affiliation(s)
- Gabriel Augusto Marques Rossi
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ. Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Via de acesso Paulo Castellane, s/n, CEP 14884-900 Jaboticabal, São Paulo, Brazil
| | - Higor Oliveira Silva
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ. Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Via de acesso Paulo Castellane, s/n, CEP 14884-900 Jaboticabal, São Paulo, Brazil
| | - Carlos Eduardo Gamero Aguilar
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ. Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Via de acesso Paulo Castellane, s/n, CEP 14884-900 Jaboticabal, São Paulo, Brazil
| | - Arina Lázaro Rochetti
- Departamento de Medicina Veterinária, Avenida Duque de Caxias Norte 225, Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos (FZEA), CEP 13635-900 Pirassununga, São Paulo, Brazil
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, 4 South, Lab 0.39, Claverton Down, BA2 7AY Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, 4 South, Lab 0.39, Claverton Down, BA2 7AY Bath, UK
| | - Evangelos Mourkas
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, 4 South, Lab 0.39, Claverton Down, BA2 7AY Bath, UK
| | | | - Luis Antonio Mathias
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ. Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Via de acesso Paulo Castellane, s/n, CEP 14884-900 Jaboticabal, São Paulo, Brazil
| | - Vera Letticie de Azevedo Ruiz
- Departamento de Medicina Veterinária, Avenida Duque de Caxias Norte 225, Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos (FZEA), CEP 13635-900 Pirassununga, São Paulo, Brazil
| | - Heidge Fukumasu
- Departamento de Medicina Veterinária, Avenida Duque de Caxias Norte 225, Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos (FZEA), CEP 13635-900 Pirassununga, São Paulo, Brazil
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, 4 South, Lab 0.39, Claverton Down, BA2 7AY Bath, UK
| | - Ana Maria Centola Vidal
- Departamento de Medicina Veterinária, Avenida Duque de Caxias Norte 225, Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos (FZEA), CEP 13635-900 Pirassununga, São Paulo, Brazil
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Awasti N, Anand S, Djira G. Sporulating behavior of Bacillus licheniformis strains influences their population dynamics during raw milk holding. J Dairy Sci 2019; 102:6001-6012. [DOI: 10.3168/jds.2018-15613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/23/2019] [Indexed: 01/09/2023]
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Murphy SI, Kent D, Martin NH, Evanowski RL, Patel K, Godden SM, Wiedmann M. Bedding and bedding management practices are associated with mesophilic and thermophilic spore levels in bulk tank raw milk. J Dairy Sci 2019; 102:6885-6900. [PMID: 31202649 DOI: 10.3168/jds.2018-16022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/24/2019] [Indexed: 11/19/2022]
Abstract
Mesophilic and thermophilic spore-forming bacteria represent a challenge to the dairy industry, as these bacteria are capable of surviving adverse conditions associated with processing and sanitation and eventually spoil dairy products. The dairy farm environment, including soil, manure, silage, and bedding, has been implicated as a source for spores in raw milk. High levels of spores have previously been isolated from bedding, and different bedding materials have been associated with spore levels in bulk tank (BT) raw milk; however, the effect of different bedding types, bedding management practices, and bedding spore levels on the variance of spore levels in BT raw milk has not been investigated. To this end, farm and bedding management surveys were administered and unused bedding, used bedding, and BT raw milk samples were collected from dairy farms (1 or 2 times per farm) across the United States over 1 yr; the final data set included 182 dairy farms in 18 states. Bedding suspensions and BT raw milk were spore pasteurized (80°C for 12 min), and mesophilic and thermophilic spores were enumerated. Piecewise structural equation modeling analysis was used to determine direct and indirect pathways of association among farm and bedding practices, levels of spores in unused and used bedding, and levels of spores in BT raw milk. Separate models were constructed for mesophilic and thermophilic spore levels. The analyses showed that bedding material had a direct influence on levels of spores in unused and used bedding as well as an indirect association with spore levels in BT raw milk through used bedding spore levels. Specific bedding and farm management practices as well as cow hygiene in the housing area were associated with mesophilic and thermophilic spore levels in unused bedding, used bedding, and BT raw milk. Notably, levels of spores in used bedding were positively related to those in unused bedding, and used bedding spore levels were positively related to those in BT raw milk. The results of this study increase the understanding of the levels and ecology of mesophilic and thermophilic spores in raw milk, emphasize the possible role of bedding as a source of spores on-farm, and present opportunities for dairy producers to reduce spore levels in BT raw milk.
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Affiliation(s)
- S I Murphy
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - D Kent
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - R L Evanowski
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - K Patel
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul 55108
| | - S M Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul 55108
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
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30
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Salazar JK, Carstens CK, Ramachandran P, Shazer AG, Narula SS, Reed E, Ottesen A, Schill KM. Metagenomics of pasteurized and unpasteurized gouda cheese using targeted 16S rDNA sequencing. BMC Microbiol 2018; 18:189. [PMID: 30453904 PMCID: PMC6245907 DOI: 10.1186/s12866-018-1323-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 10/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The microbiome of cheese is diverse, even within a variety. The metagenomics of cheese is dependent on a vast array of biotic and abiotic factors. Biotic factors include the population of microbiota and their resulting cellular metabolism. Abiotic factors, including the pH, water activity, fat, salt, and moisture content of the cheese matrix, as well as environmental conditions (temperature, humidity, and location of aging), influence the biotic factors. This study assessed the metagenomics of commercial Gouda cheese prepared using pasteurized or unpasteurized cow milk or pasteurized goat milk via 16S rDNA sequencing. RESULTS Results were analyzed and compared based on milk pasteurization and source, spatial variability (core, outer, and under the rind), and length of aging (2-4 up to 12-18 months). The dominant organisms in the Gouda cheeses, based on percentage of sequence reads identified at the family or genus levels, were Bacillaceae, Lactococcus, Lactobacillus, Streptococcus, and Staphylococcus. More genus- or family-level (e.g. Bacillaceae) identifications were observed in the Gouda cheeses prepared with unpasteurized cow milk (120) compared with those prepared with pasteurized cow milk (92). When assessing influence of spatial variability on the metagenomics of the cheese, more pronounced differences in bacterial genera were observed in the samples taken under the rind; Brachybacterium, Pseudoalteromonas, Yersinia, Klebsiella, and Weissella were only detected in these samples. Lastly, the aging length of the cheese greatly influenced the number of organisms observed. Twenty-seven additional genus-level identifications were observed in Gouda cheese aged for 12-18 months compared with cheese only aged 2-4 months. CONCLUSIONS Collectively, the results of this study are important in determining the typical microbiota associated with Gouda cheese and how the microbiome plays a role in safety and quality.
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Affiliation(s)
- Joelle K Salazar
- Division of Food Processing Science and Technology, Office of Food Safety, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Christina K Carstens
- Division of Food Processing Science and Technology, Office of Food Safety, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Padmini Ramachandran
- Division of Microbiology, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, MD, USA
| | - Arlette G Shazer
- Division of Food Processing Science and Technology, Office of Food Safety, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Sartaj S Narula
- Illinois Institute of Technology, Institute for Food Safety and Health, Bedford Park, IL, USA
| | - Elizabeth Reed
- Division of Microbiology, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, MD, USA
| | - Andrea Ottesen
- Division of Microbiology, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, MD, USA
| | - Kristin M Schill
- Division of Food Processing Science and Technology, Office of Food Safety, U. S. Food and Drug Administration, Bedford Park, IL, USA.
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31
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Mesophilic Sporeformers Identified in Whey Powder by Using Shotgun Metagenomic Sequencing. Appl Environ Microbiol 2018; 84:AEM.01305-18. [PMID: 30076196 DOI: 10.1128/aem.01305-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/31/2018] [Indexed: 01/19/2023] Open
Abstract
Spoilage and pathogenic spore-forming bacteria are a major cause of concern for producers of dairy products. Traditional agar-based detection methods employed by the dairy industry have limitations with respect to their sensitivity and specificity. The aim of this study was to identify low-abundance sporeformers in samples of a powdered dairy product, whey powder, produced monthly over 1 year, using novel culture-independent shotgun metagenomics-based approaches. Although mesophilic sporeformers were the main target of this study, in one instance thermophilic sporeformers were also targeted using this culture-independent approach. For comparative purposes, mesophilic and thermophilic sporeformers were also tested for within the same sample using culture-based approaches. Ultimately, the approaches taken highlighted differences in the taxa identified due to treatment and isolation methods. Despite this, low levels of transient, mesophilic, and in some cases potentially pathogenic sporeformers were consistently detected in powder samples. Although the specific sporeformers changed from one month to the next, it was apparent that 3 groups of mesophilic sporeformers, namely, Bacillus cereus, Bacillus licheniformis/Bacillus paralicheniformis, and a third, more heterogeneous group containing Brevibacillus brevis, dominated across the 12 samples. Total thermophilic sporeformer taxonomy was considerably different from mesophilic taxonomy, as well as from the culturable thermophilic taxonomy, in the one sample analyzed by all four approaches. Ultimately, through the application of shotgun metagenomic sequencing to dairy powders, the potential for this technology to facilitate the detection of undesirable bacteria present in these food ingredients is highlighted.IMPORTANCE The ability of sporeformers to remain dormant in a desiccated state is of concern from a safety and spoilage perspective in dairy powder. Traditional culturing techniques are slow and provide little information without further investigation. We describe the identification of mesophilic sporeformers present in powders produced over 1 year, using novel shotgun metagenomic sequencing. This method allows detection and identification of possible pathogens and spoilage bacteria in parallel. Strain-level analysis and functional gene analysis, such as identification of toxin genes, were also performed. This approach has the potential to be of great value with respect to the detection of spore-forming bacteria and could allow a processor to make an informed decision surrounding process changes to reduce the risk of spore contamination.
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32
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Microbiota of milk powders and the heat resistance and spoilage potential of aerobic spore-forming bacteria. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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33
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Driehuis F, Wilkinson JM, Jiang Y, Ogunade I, Adesogan AT. Silage review: Animal and human health risks from silage. J Dairy Sci 2018; 101:4093-4110. [PMID: 29685279 DOI: 10.3168/jds.2017-13836] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/16/2017] [Indexed: 11/19/2022]
Abstract
Silage may contain several agents that are potentially hazardous to animal health, the safety of milk or other animal food products, or both. This paper reviews published literature about microbial hazards, plant toxins, and chemical hazards. Microbial hazards include Clostridium botulinum, Bacillus cereus, Listeria monocytogenes, Shiga toxin-producing Escherichia coli, Mycobacterium bovis, and various mold species. High concentrations of C. botulinum in silage have been associated with cattle botulism. A high initial concentration of C. botulinum spores in forage in combination with poor silage fermentation conditions can promote the growth of C. botulinum in silage. The elevated pH level that is generally associated with aerobic deterioration of silage is a major factor influencing concentrations of L. monocytogenes, Shiga toxin-producing E. coli, and molds in silage and may also encourage survival and growth of M. bovis, the bacterium that causes bovine tuberculosis. Soil is a major source of B. cereus spores in silage; growth of this bacterium in silage appears to be limited. Hazards from plant toxins include pyrrolizidine, tropane and tropolone alkaloids, phytoestrogens, prussic acid, and mimosine, compounds that exist naturally in certain plant species that may contaminate forages at harvesting. Another group of toxins belonging to this category are ergot alkaloids, which are produced by endophytic fungal species in forages such as tall fescue grass, sorghum, and ryegrass. Varying effects of ensiling on the degradation of these plant toxins have been reported. Chemical hazards include nitrate, nitrite, and toxic oxide gases of nitrogen produced from nitrate and high levels of butyric acid, biogenic amines, and ammonia. Chemical and microbiological hazards are associated with poorly fermented silages, which can be avoided by using proper silage-making practices and creating conditions that promote a rapid and sufficient reduction of the silage pH and prevent aerobic deterioration.
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Affiliation(s)
- F Driehuis
- NIZO Food Research, PO Box 20, NL-6710 BA Ede, the Netherlands.
| | - J M Wilkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Y Jiang
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32608
| | - I Ogunade
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32608
| | - A T Adesogan
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville 32608
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34
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Doyle CJ, O'Toole PW, Cotter PD. Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain. Front Microbiol 2018; 9:1507. [PMID: 30026740 PMCID: PMC6041559 DOI: 10.3389/fmicb.2018.01507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/18/2018] [Indexed: 11/25/2022] Open
Abstract
Anaerobic sporeformers, specifically spoilage and pathogenic members of the genus Clostridium, are a concern for producers of dairy products, and of powdered dairy products in particular. As an alternative to testing for individual species, the traditional, and still current, approach to detecting these sporeformers, including non-spoilage/non-pathogenic species, in dairy products has involved testing for a sulphite reducing phenotype [Sulphite reducing Clostridia (SRCs)] under anaerobic conditions. This phenotype is conserved throughout the Order Clostridia. Unfortunately, however, this phenotype is exhibited by other sulphite reducing bacteria (SRBs) also, potentially leading to potential for false positives. Here, this risk was borne out through the identification of several SRBs from industry samples that were identified as Proteus mirabilis and various Bacillus/Paenibacillus sp. Genome wide comparison of a number of representative SRCs and SRBs was employed to determine phylogenetic relationships, especially among SRCs, and to characterize the genes responsible for the sulphite reducing phenotype. This screen identified two associated operons, i.e., asrABC in SRCs, and cysJI in Bacillus/Paenibacillus spp. and P. mirabilis. This screen identified spp. belonging to sensu stricto, Lachnospiraceae and Cluster XIV of the Clostridia all producing the SRC phenotype. This study highlights the inaccuracy of the industry standard SRC test but highlights the potential to generate an equivalent molecular test designed to detect the genes responsible for this phenotype in clostridia.
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Affiliation(s)
- Conor J Doyle
- Teagasc Food Research Centre, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
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35
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Reichler SJ, Trmčić A, Martin NH, Boor KJ, Wiedmann M. Pseudomonas fluorescens group bacterial strains are responsible for repeat and sporadic postpasteurization contamination and reduced fluid milk shelf life. J Dairy Sci 2018; 101:7780-7800. [PMID: 29960782 DOI: 10.3168/jds.2018-14438] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/11/2018] [Indexed: 01/18/2023]
Abstract
Postpasteurization contamination (PPC) of high temperature, short time-pasteurized fluid milk by gram-negative (GN) bacteria continues to be an issue for processors. To improve PPC control, a better understanding of PPC patterns in dairy processing facilities over time and across equipment is needed. We thus collected samples from 10 fluid milk processing facilities to (1) detect and characterize PPC patterns over time, (2) determine the efficacy of different media to detect PPC, and (3) characterize sensory defects associated with PPC. Specifically, we collected 280 samples of high temperature, short time-pasteurized milk representing different products (2%, skim, and chocolate) and different fillers over 4 samplings performed over 11 mo at each of the 10 facilities. Standard plate count (SPC) as well as total GN, coliform, and Enterobacteriaceae (EB) counts were performed upon receipt and after 7, 10, 14, 17, and 21 d of storage at 6°C. We used 16S rDNA sequencing to characterize representative bacterial isolates from (1) test days with SPC >20,000 cfu/mL and (2) all samples with presumptive GN, coliforms, or EB. Day-21 samples were also evaluated by a trained defect judging panel. By d 21, 226 samples had SPC >20,000 cfu/mL on at least 1 d of shelf life; GN bacteria were found in 132 of these 226 samples, indicating PPC. Crystal violet tetrazolium agar detected PPC with the greatest sensitivity. Spoilage due to PPC was predominantly associated with Pseudomonas (isolated from 101 of the 132 samples with PPC); coliforms and EB were found in 27 and 37 samples with spoilage due to PPC, respectively. Detection of Pseudomonas and Acinetobacter was associated with lower flavor scores; coagulated, fruity fermented, and unclean defects were more prevalent in d-21 samples with PPC. Repeat isolation of Pseudomonas fluorescens group strains with identical partial 16S rDNA sequence types was observed in 8 facilities. In several facilities, specific lines, products, or processing days were linked to repeat product contamination with Pseudomonas with identical sequence types. Our data show that PPC due to Pseudomonas remains a major challenge for fluid milk processors; the inability of coliform and EB tests to detect Pseudomonas may contribute to this. Our data also provide important initial insights into PPC patterns (e.g., line-specific contamination), supporting the importance of molecular subtyping methods for identification of PPC sources.
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Affiliation(s)
- S J Reichler
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - A Trmčić
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - K J Boor
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
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36
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Guimarães JT, Silva EK, Alvarenga VO, Costa ALR, Cunha RL, Sant'Ana AS, Freitas MQ, Meireles MAA, Cruz AG. Physicochemical changes and microbial inactivation after high-intensity ultrasound processing of prebiotic whey beverage applying different ultrasonic power levels. ULTRASONICS SONOCHEMISTRY 2018; 44:251-260. [PMID: 29680610 DOI: 10.1016/j.ultsonch.2018.02.012] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/13/2018] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
In this work, we investigated the effects of the ultrasonic power (0, 200, 400 and 600 W) on non-thermal processing of an inulin-enriched whey beverage. We studied the effects of high-intensity ultrasound (HIUS) on microbial inactivation (aerobic mesophilic heterotrophic bacteria (AMHB), total and thermotolerant coliforms and yeasts and molds), zeta potential, microstructure (optical microscopy, particle size distribution), rheology, kinetic stability and color. The non-thermal processing applying 600 W of ultrasonic power was comparable to high-temperature short-time (HTST) treatment (75 °C for 15 s) concerning the inactivation of AMHB and yeasts and molds (2 vs 2 log and 0.2 vs 0.4 log, respectively), although HIUS has reached a lower output temperature (53 ± 3 °C). The HIUS was better than HTST to improve beverage kinetic stability, avoiding phase separation, which was mainly attributed to the decrease of particles size, denaturation of whey proteins and gelation of polysaccharides (inulin and gellan gum). Thus, non-thermal processing by HIUS seems to be an interesting technology for prebiotic dairy beverages production.
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Affiliation(s)
- Jonas T Guimarães
- Department of Food Technology, Faculty of Veterinary, Fluminense Federal University, Niterói, RJ, Brazil
| | - Eric Keven Silva
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil.
| | - Verônica O Alvarenga
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Ana Letícia R Costa
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Rosiane L Cunha
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Monica Q Freitas
- Department of Food Technology, Faculty of Veterinary, Fluminense Federal University, Niterói, RJ, Brazil
| | - M Angela A Meireles
- School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Adriano G Cruz
- Department of Food, Federal Institute of Science and Technology of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Miller RA, Jian J, Beno SM, Wiedmann M, Kovac J. Intraclade Variability in Toxin Production and Cytotoxicity of Bacillus cereus Group Type Strains and Dairy-Associated Isolates. Appl Environ Microbiol 2018; 84:e02479-17. [PMID: 29330180 PMCID: PMC5835744 DOI: 10.1128/aem.02479-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/05/2018] [Indexed: 01/24/2023] Open
Abstract
While some species in the Bacillus cereus group are well-characterized human pathogens (e.g., B. anthracis and B. cereus sensu stricto), the pathogenicity of other species (e.g., B. pseudomycoides) either has not been characterized or is presently not well understood. To provide an updated characterization of the pathogenic potential of species in the B. cereus group, we classified a set of 52 isolates, including 8 type strains and 44 isolates from dairy-associated sources, into 7 phylogenetic clades and characterized them for (i) the presence of toxin genes, (ii) phenotypic characteristics used for identification, and (iii) cytotoxicity to human epithelial cells. Overall, we found that B. cereus toxin genes are broadly distributed but are not consistently present within individual species and/or clades. After growth at 37°C, isolates within a clade did not typically show a consistent cytotoxicity phenotype, except for isolates in clade VI (B. weihenstephanensis/B. mycoides), where none of the isolates were cytotoxic, and isolates in clade I (B. pseudomycoides), which consistently displayed cytotoxic activity. Importantly, our study highlights that B. pseudomycoides is cytotoxic toward human cells. Our results indicate that the detection of toxin genes does not provide a reliable approach to predict the pathogenic potential of B. cereus group isolates, as the presence of toxin genes is not always consistent with cytotoxicity phenotype. Overall, our results suggest that isolates from multiple B. cereus group clades have the potential to cause foodborne illness, although cytotoxicity is not always consistently found among isolates within each clade.IMPORTANCE Despite the importance of the Bacillus cereus group as a foodborne pathogen, characterizations of the pathogenic potential of all B. cereus group species were lacking. We show here that B. pseudomycoides (clade I), which has been considered a harmless environmental microorganism, produces toxins and exhibits a phenotype consistent with the production of pore-forming toxins. Furthermore, B. mycoides/B. weihenstephanensis isolates (clade VI) did not show cytotoxicity when grown at 37°C, despite carrying multiple toxin genes. Overall, we show that the current standard methods to characterize B. cereus group isolates and to detect the presence of toxin genes are not reliable indicators of species, phylogenetic clades, or an isolate's cytotoxic capacity, suggesting that novel methods are still needed for differentiating pathogenic from nonpathogenic species within the B. cereus group. Our results also contribute data that are necessary to facilitate risk assessments and a better understanding as to which B. cereus group species are likely to cause foodborne illness.
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Affiliation(s)
- Rachel A Miller
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Jiahui Jian
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Sarah M Beno
- 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, Cornell University, Ithaca, New York, USA
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Propensity for biofilm formation by aerobic mesophilic and thermophilic spore forming bacteria isolated from Chinese milk powders. Int J Food Microbiol 2017; 262:89-98. [DOI: 10.1016/j.ijfoodmicro.2017.09.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/27/2017] [Accepted: 09/24/2017] [Indexed: 02/08/2023]
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Masiello SN, Kent D, Martin NH, Schukken YH, Wiedmann M, Boor KJ. Longitudinal assessment of dairy farm management practices associated with the presence of psychrotolerant Bacillales spores in bulk tank milk on 10 New York State dairy farms. J Dairy Sci 2017; 100:8783-8795. [PMID: 28865849 DOI: 10.3168/jds.2017-13139] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/16/2017] [Indexed: 11/19/2022]
Abstract
The ability of certain spore-forming bacteria in the order Bacillales (e.g., Bacillus spp., Paenibacillus spp.) to survive pasteurization in spore form and grow at refrigeration temperatures results in product spoilage and limits the shelf life of high temperature, short time (HTST)-pasteurized fluid milk. To facilitate development of strategies to minimize contamination of raw milk with psychrotolerant Bacillales spores, we conducted a longitudinal study of 10 New York State dairy farms, which included yearlong monthly assessments of the frequency and levels of bulk tank raw milk psychrotolerant spore contamination, along with administration of questionnaires to identify farm management practices associated with psychrotolerant spore presence over time. Milk samples were first spore pasteurized (80°C for 12 min) and then analyzed for sporeformer counts on the initial day of spore pasteurization (SP), and after refrigerated storage (6°C) for 7, 14, and 21 d after SP. Overall, 41% of samples showed sporeformer counts of >20,000 cfu/mL at d 21, with Bacillus and Paenibacillus spp. being predominant causes of high sporeformer counts. Statistical analyses identified 3 management factors (more frequent cleaning of the bulk tank area, the use of a skid steer to scrape the housing area, and segregating problem cows during milking) that were all associated with lower probabilities of d-21 Bacillales spore detection in SP-treated bulk tank raw milk. Our data emphasize that appropriate on-farm measures to improve overall cleanliness and cow hygiene will reduce the probability of psychrotolerant Bacillales spore contamination of bulk tank raw milk, allowing for consistent production of raw milk with reduced psychrotolerant spore counts, which will facilitate production of HTST-pasteurized milk with extended refrigerated shelf life.
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Affiliation(s)
- S N Masiello
- Milk Quality Improvement Program, Department of Food Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - D Kent
- Milk Quality Improvement Program, Department of Food Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - N H Martin
- Milk Quality Improvement Program, Department of Food Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - Y H Schukken
- Quality Milk Production Services, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - K J Boor
- Milk Quality Improvement Program, Department of Food Science, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data. Appl Environ Microbiol 2017. [PMID: 28625989 PMCID: PMC5561296 DOI: 10.1128/aem.01096-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but it can be particularly challenging due to the high genomic similarity within the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multilocus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B. cereus group isolates using nucleotide sequencing data. BTyper was applied to a set of 662 B. cereus group genome assemblies to (i) identify anthrax-associated genes in non-B. anthracis members of the B. cereus group, and (ii) identify assemblies from B. cereus group strains with emetic potential. With BTyper, the anthrax toxin genes cya, lef, and pagA were detected in 8 genomes classified by the NCBI as B. cereus that clustered into two distinct groups using k-medoids clustering, while either the B. anthracis poly-γ-d-glutamate capsule biosynthesis genes capABCDE or the hyaluronic acid capsule hasA gene was detected in an additional 16 assemblies classified as either B. cereus or Bacillus thuringiensis isolated from clinical, environmental, and food sources. The emetic toxin genes cesABCD were detected in 24 assemblies belonging to panC clades III and VI that had been isolated from food, clinical, and environmental settings. The command line version of BTyper is available at https://github.com/lmc297/BTyper. In addition, BMiner, a companion application for analyzing multiple BTyper output files in aggregate, can be found at https://github.com/lmc297/BMiner. IMPORTANCEBacillus cereus is a foodborne pathogen that is estimated to cause tens of thousands of illnesses each year in the United States alone. Even with molecular methods, it can be difficult to distinguish nonpathogenic B. cereus group isolates from their pathogenic counterparts, including the human pathogen Bacillus anthracis, which is responsible for anthrax, as well as the insect pathogen B. thuringiensis. By using the variety of typing schemes employed by BTyper, users can rapidly classify, characterize, and assess the virulence potential of any isolate using its nucleotide sequencing data.
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Gauvry E, Mathot AG, Leguérinel I, Couvert O, Postollec F, Broussolle V, Coroller L. Knowledge of the physiology of spore-forming bacteria can explain the origin of spores in the food environment. Res Microbiol 2017; 168:369-378. [DOI: 10.1016/j.resmic.2016.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/22/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
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Kilic T, Karaca B, Ozel BP, Ozcan B, Cokmus C, Coleri Cihan A. Biofilm characteristics and evaluation of the sanitation procedures of thermophilic Aeribacillus pallidus E334 biofilms. BIOFOULING 2017; 33:352-367. [PMID: 28426246 DOI: 10.1080/08927014.2017.1313412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/23/2017] [Indexed: 06/07/2023]
Abstract
The ability of Aeribacillus pallidus E334 to produce pellicle and form a biofilm was studied. Optimal biofilm formation occurred at 60 °C, pH 7.5 and 1.5% NaCl. Extra polymeric substances (EPS) were composed of proteins and eDNA (21.4 kb). E334 formed biofilm on many surfaces, but mostly preferred polypropylene and glass. Using CLSM analysis, the network-like structure of the EPS was observed. The A. pallidus biofilm had a novel eDNA content. DNaseI susceptibility (86.8% removal) of eDNA revealed its importance in mature biofilms, but the purified eDNA was resistant to DNaseI, probably due to its extended folding outside the matrix. Among 15 cleaning agents, biofilms could be removed with alkaline protease and sodium dodecyl sulphate (SDS). The removal of cells from polypropylene and biomass on glass was achieved with combined SDS/alkaline protease treatment. Strong A. pallidus biofilms could cause risks for industrial processes and abiotic surfaces must be taken into consideration in terms of sanitation procedures.
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Affiliation(s)
- Tugba Kilic
- a Faculty of Science, Biology Department , Ankara University , Ankara , Turkey
| | - Basar Karaca
- a Faculty of Science, Biology Department , Ankara University , Ankara , Turkey
| | - Beste Piril Ozel
- a Faculty of Science, Biology Department , Ankara University , Ankara , Turkey
| | - Birgul Ozcan
- b Faculty of Sciences and Letters, Biology Department , Mustafa Kemal University , Hatay , Turkey
| | - Cumhur Cokmus
- c Faculty of Agriculture and Natural Sciences, Molecular Biology and Genetics Department , Konya Food and Agriculture University , Konya , Turkey
| | - Arzu Coleri Cihan
- a Faculty of Science, Biology Department , Ankara University , Ankara , Turkey
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Gupta TB, Brightwell G. Farm level survey of spore-forming bacteria on four dairy farms in the Waikato region of New Zealand. Microbiologyopen 2017; 6. [PMID: 28256808 PMCID: PMC5552919 DOI: 10.1002/mbo3.457] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/10/2017] [Accepted: 01/25/2017] [Indexed: 11/09/2022] Open
Abstract
The aim of our study was to determine the occurrence and diversity of economically important spore-forming bacteria in New Zealand dairy farm systems. Farm dairy effluent (FDE) collected from Waikato dairy farms were tested for the presence of spore-forming bacteria, using a new culture-based methodology followed by genomic analysis. An enrichment step in which samples were inoculated in cooked meat glucose starch broth under anaerobic conditions, aided in the differential isolation of Bacillus and Clostridium species. Furthermore, the use of molecular methods such as ERIC genotyping, 16S rRNA gene sequence analysis identified different spore-forming bacteria present in FDE. C. sporogenes signature PCR gave further information on the phylogenetic relationship of the different Clostridium spp. isolated in this study. In total 19 Bacillus spp., 5 Paenibacillus spp. and 17 Clostridium spp. were isolated from farm dairy effluent. Sequence types similar to economically important food spoilage bacteria viz: C. butyricum, C. sporogenes and members of the Paenibacillus Genus were isolated from all four farms, whereas, sequence types similar to potential toxigenic, B. cereus, C. perfringens, C. butyricum, and C. botulinum were found on at least three of the farms. Sampling of farm dairy effluent provides a good indicator of farm level prevalence of bacterial load as it is used to irrigate dairy pasture in New Zealand. This study highlights the presence of various spore-forming bacteria in dairy waste water and indicates the implementation of good hygienic farm practices and dairy waste effluent management.
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Affiliation(s)
- Tanushree B Gupta
- Food Assurance and Meat Quality, Hopkirk Research InstituteAgResearch Limited, Massey University Campus, Palmerston North, New Zealand
| | - Gale Brightwell
- Food Assurance and Meat Quality, Hopkirk Research InstituteAgResearch Limited, Massey University Campus, Palmerston North, New Zealand
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McHugh AJ, Feehily C, Hill C, Cotter PD. Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products. Front Microbiol 2017; 8:109. [PMID: 28197144 PMCID: PMC5281614 DOI: 10.3389/fmicb.2017.00109] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/16/2017] [Indexed: 01/28/2023] Open
Abstract
With the abolition of milk quotas in the European Union in 2015, several member states including Ireland, Luxembourg, and Belgium have seen year on year bi-monthly milk deliveries to dairies increase by up to 35%. Milk production has also increased outside of Europe in the past number of years. Unsurprisingly, there has been a corresponding increased focus on the production of dried milk products for improved shelf life. These powders are used in a wide variety of products, including confectionery, infant formula, sports dietary supplements and supplements for health recovery. To ensure quality and safety standards in the dairy sector, strict controls are in place with respect to the acceptable quantity and species of microorganisms present in these products. A particular emphasis on spore-forming bacteria is necessary due to their inherent ability to survive extreme processing conditions. Traditional microbiological detection methods used in industry have limitations in terms of time, efficiency, accuracy, and sensitivity. The following review will explore the common spore-forming bacterial contaminants of milk powders, will review the guidelines with respect to the acceptable limits of these microorganisms and will provide an insight into recent advances in methods for detecting these microbes. The various advantages and limitations with respect to the application of these diagnostics approaches for dairy food will be provided. It is anticipated that the optimization and application of these methods in appropriate ways can ensure that the enhanced pressures associated with increased production will not result in any lessening of safety and quality standards.
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Affiliation(s)
- Aoife J McHugh
- Food Bioscience Department, Teagasc Food Research CentreCork, Ireland; School of Microbiology, University College CorkCork, Ireland
| | - Conor Feehily
- Food Bioscience Department, Teagasc Food Research CentreCork, Ireland; APC Microbiome InstituteCork, Ireland
| | - Colin Hill
- School of Microbiology, University College CorkCork, Ireland; APC Microbiome InstituteCork, Ireland
| | - Paul D Cotter
- Food Bioscience Department, Teagasc Food Research CentreCork, Ireland; APC Microbiome InstituteCork, Ireland
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Md Zain SN, Bennett R, Flint S. The Potential Source ofB. licheniformisContamination During Whey Protein Concentrate 80 Manufacture. J Food Sci 2017; 82:751-756. [DOI: 10.1111/1750-3841.13633] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/28/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Siti Norbaizura Md Zain
- Massey Inst. of Food Science and Technology; Massey Univ.; Private Bag 11 222 Palmerston North New Zealand
- Applied Science Faculty; UiTM Negeri Sembilan; Kuala Pilah campus, 72000 Kuala pilah Negeri Sembilan Malaysia
| | - Rod Bennett
- Massey Inst. of Food Science and Technology; Massey Univ.; Private Bag 11 222 Palmerston North New Zealand
| | - Steve Flint
- Massey Inst. of Food Science and Technology; Massey Univ.; Private Bag 11 222 Palmerston North New Zealand
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Martinez BA, Stratton J, Bianchini A. Isolation and genetic identification of spore-forming bacteria associated with concentrated-milk processing in Nebraska. J Dairy Sci 2016; 100:919-932. [PMID: 27988120 DOI: 10.3168/jds.2016-11660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/19/2016] [Indexed: 11/19/2022]
Abstract
Spore-forming bacteria are heat-resistant microorganisms capable of surviving and germinating in milk after pasteurization. They have been reported to affect the quality of dairy products by the production of enzymes (lipolytic and proteolytic) under low-temperature conditions in fluid milk, and have become a limiting factor for milk powder in reaching some selective markets. The objective of this research was to isolate and identify the population of spore-forming bacteria (psychrotrophic and thermophilic strains) associated with concentrated milk processing in Nebraska. During 2 seasons, in-process milk samples from a commercial plant (raw, pasteurized, and concentrated) were collected and heat-treated (80°C/12 min) to recover only spore-formers. Samples were spread-plated using standard methods agar and incubated at 32°C to enumerate mesophilic spore counts. Heat-treated samples were also stored at 7°C and 55°C to recover spore-formers that had the ability to grow under those temperature conditions. Isolates obtained from incubation or storage conditions were identified using molecular techniques (16S or rpoB sequencing). Based on the identification of the isolates and their relatedness, strains found in raw, pasteurized, and concentrated milk were determined to be similar. Paenibacillus spp. were associated with both raw and concentrated milk. Due to their known ability to cause spoilage under refrigeration, this shows the potential risk associated with the transferring of these problematic organisms into other dairy products. Other Bacillus species found in concentrated milk included Bacillus clausii, Bacillus subtilis, Lysinibacillus sp., Bacillus safensis, Bacillus licheniformis, Bacillus sonorensis, and Brevibacillus sp., with the last 3 organisms being capable of growing at thermophilic temperatures. These strains can also be translocated to other dairy products, such as milk powder, representing a quality problem. The results of this research highlight the importance of understanding spore-formers associated with the processing of condensed milk, which then may allow for specific interventions to be applied to control these microorganisms in this processing chain. To our knowledge, this is the first study evaluating spore-formers associated with concentrated milk in the United States.
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Affiliation(s)
- Bismarck A Martinez
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588
| | - Jayne Stratton
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588; The Food Processing Center, University of Nebraska-Lincoln, Lincoln 68588
| | - Andreia Bianchini
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588; The Food Processing Center, University of Nebraska-Lincoln, Lincoln 68588.
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Berendsen EM, Koning RA, Boekhorst J, de Jong A, Kuipers OP, Wells-Bennik MHJ. High-Level Heat Resistance of Spores of Bacillus amyloliquefaciens and Bacillus licheniformis Results from the Presence of a spoVA Operon in a Tn 1546 Transposon. Front Microbiol 2016; 7:1912. [PMID: 27994575 PMCID: PMC5133452 DOI: 10.3389/fmicb.2016.01912] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/15/2016] [Indexed: 11/19/2022] Open
Abstract
Bacterial endospore formers can produce spores that are resistant to many food processing conditions, including heat. Some spores may survive heating processes aimed at production of commercially sterile foods. Recently, it was shown that a spoVA operon, designated spoVA2mob, present on a Tn1546 transposon in Bacillus subtilis, leads to profoundly increased wet heat resistance of B. subtilis spores. Such Tn1546 transposon elements including the spoVA2mob operon were also found in several strains of Bacillus amyloliquefaciens and Bacillus licheniformis, and these strains were shown to produce spores with significantly higher resistances to wet heat than their counterparts lacking this transposon. In this study, the locations and compositions of Tn1546 transposons encompassing the spoVA2mob operons in B. amyloliquefaciens and B. licheniformis were analyzed. Introduction of these spoVA2mob operons into B. subtilis 168 (producing spores that are not highly heat resistant) rendered mutant 168 strains that produced high-level heat resistant spores, demonstrating that these elements in B. amyloliquefaciens and B. licheniformis are responsible for high level heat resistance of spores. Assessment of growth of the nine strains of each species between 5.2°C and 57.7°C showed some differences between strains, especially at lower temperatures, but all strains were able to grow at 57.7°C. Strains of B. amyloliquefaciens and B. licheniformis that contain the Tn1546 elements (and produce high-level heat resistant spores) grew at temperatures similar to those of their Tn1546-negative counterparts that produce low-level heat resistant spores. The findings presented in this study allow for detection of B. amyloliquefaciens and B. licheniformis strains that produce highly heat resistant spores in the food chain.
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Affiliation(s)
- Erwin M Berendsen
- Top Institute Food and NutritionWageningen, Netherlands; Laboratory of Molecular Genetics, University of GroningenGroningen, Netherlands; NIZO Food ResearchEde, Netherlands
| | - Rosella A Koning
- Top Institute Food and NutritionWageningen, Netherlands; NIZO Food ResearchEde, Netherlands
| | - Jos Boekhorst
- Top Institute Food and NutritionWageningen, Netherlands; NIZO Food ResearchEde, Netherlands
| | - Anne de Jong
- Top Institute Food and NutritionWageningen, Netherlands; Laboratory of Molecular Genetics, University of GroningenGroningen, Netherlands
| | - Oscar P Kuipers
- Top Institute Food and NutritionWageningen, Netherlands; Laboratory of Molecular Genetics, University of GroningenGroningen, Netherlands
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Miller RA, Beno SM, Kent DJ, Carroll LM, Martin NH, Boor KJ, Kovac J. Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments. Int J Syst Evol Microbiol 2016; 66:4744-4753. [PMID: 27520992 DOI: 10.1099/ijsem.0.001421] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA-DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T).
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Affiliation(s)
- Rachel A Miller
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sarah M Beno
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Kathryn J Boor
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Kovac J, Miller RA, Carroll LM, Kent DJ, Jian J, Beno SM, Wiedmann M. Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade. BMC Genomics 2016; 17:581. [PMID: 27507015 PMCID: PMC4979109 DOI: 10.1186/s12864-016-2883-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 07/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacillus cereus group isolates that produce diarrheal or emetic toxins are frequently isolated from raw milk and, in spore form, can survive pasteurization. Several species within the B. cereus group are closely related and cannot be reliably differentiated by established taxonomical criteria. While B. cereus is traditionally recognized as the principal causative agent of foodborne disease in this group, there is a need to better understand the distribution and expression of different toxin and virulence genes among B. cereus group food isolates to facilitate reliable characterization that allows for assessment of the likelihood of a given isolate to cause a foodborne disease. RESULTS We performed whole genome sequencing of 22 B. cereus group dairy isolates, which represented considerable genetic diversity not covered by other isolates characterized to date. Maximum likelihood analysis of these genomes along with 47 reference genomes representing eight validly published species revealed nine phylogenetic clades. Three of these clades were represented by a single species (B. toyonensis -clade V, B. weihenstephanensis - clade VI, B. cytotoxicus - VII), one by two dairy-associated isolates (clade II; representing a putative new species), one by two species (B. mycoides, B. pseudomycoides - clade I) and four by three species (B. cereus, B. thuringiensis, B. anthracis - clades III-a, b, c and IV). Homologues of genes encoding a principal diarrheal enterotoxin (hemolysin BL) were distributed across all, except the B. cytotoxicus clade. Using a lateral flow immunoassay, hemolysin BL was detected in 13 out of 18 isolates that carried hblACD genes. Isolates from clade III-c (which included B. cereus and B. thuringiensis) consistently did not carry hblACD and did not produce hemolysin BL. Isolates from clade IV (B. cereus, B. thuringiensis) consistently carried hblACD and produced hemolysin BL. Compared to others, clade IV was significantly (p = 0.0001) more likely to produce this toxin. Isolates from clade VI (B. weihenstephanensis) carried hblACD homologues, but did not produce hemolysin BL, possibly due to amino acid substitutions in different toxin-encoding genes. CONCLUSIONS Our results demonstrate that production of diarrheal enterotoxin hemolysin BL is neither inclusive nor exclusive to B. cereus sensu stricto, and that phylogenetic classification of isolates may be better than taxonomic identification for assessment of B. cereus group isolates risk for causing a diarrheal foodborne disease.
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Affiliation(s)
- Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Rachel A Miller
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jiahui Jian
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah M Beno
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
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Prospects for improved control of dairy-relevant sporeformers using -omics technologies. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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