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Mather AE, Gilmour MW, Reid SWJ, French NP. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nat Rev Microbiol 2024; 22:543-555. [PMID: 38789668 DOI: 10.1038/s41579-024-01051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2024] [Indexed: 05/26/2024]
Abstract
Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system.
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Affiliation(s)
- Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.
- University of East Anglia, Norwich, UK.
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Nigel P French
- Tāuwharau Ora, School of Veterinary Science, Te Kunenga Ki Pūrehuroa, Massey University, Papaioea, Palmerston North, Aotearoa New Zealand
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2
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Corradini MG, Homez-Jara AK, Chen C. Virtualization and digital twins of the food supply chain for enhanced food safety. ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 111:71-91. [PMID: 39103218 DOI: 10.1016/bs.afnr.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Meeting food safety requirements without jeopardizing quality attributes or sustainability involves adopting a holistic perspective of food products, their manufacturing processes and their storage and distribution practices. The virtualization of the food supply chain offers opportunities to evaluate, simulate, and predict challenges and mishaps potentially contributing to present and future food safety risks. Food systems virtualization poses several requirements: (1) a comprehensive framework composed of instrumental, digital, and computational methods to evaluate internal and external factors that impact food safety; (2) nondestructive and real-time sensing methods, such as spectroscopic-based techniques, to facilitate mapping and tracking food safety and quality indicators; (3) a dynamic platform supported by the Internet of Things (IoT) interconnectivity to integrate information, perform online data analysis and exchange information on product history, outbreaks, exposure to risky situations, etc.; and (4) comprehensive and complementary mathematical modeling techniques (including but not limited to chemical reactions and microbial inactivation and growth kinetics) based on extensive data sets to make realistic simulations and predictions possible. Despite current limitations in data integration and technical skills for virtualization to reach its full potential, its increasing adoption as an interactive and dynamic tool for food systems evaluation can improve resource utilization and rational design of products, processes and logistics for enhanced food safety. Virtualization offers affordable and reliable options to assist stakeholders in decision-making and personnel training. This chapter focuses on definitions and requirements for developing and applying virtual food systems, including digital twins, and their role and future trends in enhancing food safety.
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Affiliation(s)
- Maria G Corradini
- Department of Food Science & Arrell Food Institute, University of Guelph, Guelph, ON, Canada.
| | | | - Chang Chen
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY, United States
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3
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Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
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Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
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4
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Mohan B, Singh G, Chauhan A, Pombeiro AJL, Ren P. Metal-organic frameworks (MOFs) based luminescent and electrochemical sensors for food contaminant detection. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131324. [PMID: 37080033 DOI: 10.1016/j.jhazmat.2023.131324] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/10/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
With the increasing population, food toxicity has become a prevalent concern due to the growing contaminants of food products. Therefore, the need for new materials for toxicant detection and food quality monitoring will always be in demand. Metal-organic frameworks (MOFs) based on luminescence and electrochemical sensors with tunable porosity and active surface area are promising materials for food contaminants monitoring. This review summarizes and studies the most recent progress on MOF sensors for detecting food contaminants such as pesticides, antibiotics, toxins, biomolecules, and ionic species. First, with the introduction of MOFs, food contaminants and materials for toxicants detection are discussed. Then the insights into the MOFs as emerging materials for sensing applications with luminescent and electrochemical properties, signal changes, and sensing mechanisms are discussed. Next, recent advances in luminescent and electrochemical MOFs food sensors and their sensitivity, selectivity, and capacities for common food toxicants are summarized. Further, the challenges and outlooks are discussed for providing a new pathway for MOF food contaminant detection tools. Overall, a timely source of information on advanced MOF materials provides materials for next-generation food sensors.
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Affiliation(s)
- Brij Mohan
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Gurjaspreet Singh
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Archana Chauhan
- Department of Chemistry, Kurukshetra University, Kurukshetra, Haryana 136119, India
| | - Armando J L Pombeiro
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Peng Ren
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China.
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Hu Y, Wu W. Application of Membrane Filtration to Cold Sterilization of Drinks and Establishment of Aseptic Workshop. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:89-106. [PMID: 36933166 PMCID: PMC10024305 DOI: 10.1007/s12560-023-09551-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/27/2023] [Indexed: 06/01/2023]
Abstract
Aseptic packaging of high quality beverage is necessary and its cold-pasteurization or sterilization is vital. Studies on application of ultrafiltration or microfiltration membrane to cold- pasteurization or sterilization for the aseptic packaging of beverages have been reviewed. Designing and manufacturing ultrafiltration or microfiltration membrane systems for cold-pasteurization or sterilization of beverage are based on the understanding of size of microorganisms and theoretical achievement of filtration. It is concluded that adaptability of membrane filtration, especially its combination with other safe cold method, to cold- pasteurization and sterilization for the aseptic packaging of beverages should be assured without a shadow of doubt in future.
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Affiliation(s)
- Yunhao Hu
- College of Food Science, Southwest University, No.2 Tian Shengqiao, Beibei, Chongqing, People's Republic of China
| | - Wenbiao Wu
- College of Food Science, Southwest University, No.2 Tian Shengqiao, Beibei, Chongqing, People's Republic of China.
- Research Center of Grains, Oils and Foods Engineering Design, Industrial Research Institute, Southwest University, No.2 Tian Shengqiao, Beibei, Chongqing, People's Republic of China.
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:2140. [PMID: 37297385 PMCID: PMC10252221 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea;
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea;
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Sengupta P, Sivabalan SKM, Mahesh A, Palanikumar I, Kuppa Baskaran DK, Raman K. Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes. J Indian Inst Sci 2023; 103:1-17. [PMID: 37362854 PMCID: PMC10073628 DOI: 10.1007/s41745-023-00370-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/05/2023] [Indexed: 06/28/2023]
Abstract
Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.
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Affiliation(s)
- Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | | | - Amrita Mahesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Indumathi Palanikumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Dinesh Kumar Kuppa Baskaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu 600036 India
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Mohamad-Fauzi N, Shaw C, Foutouhi SH, Hess M, Kong N, Kol A, Storey DB, Desai PT, Shah J, Borjesson D, Murray JD, Weimer BC. Salmonella enhances osteogenic differentiation in adipose-derived mesenchymal stem cells. Front Cell Dev Biol 2023; 11:1077350. [PMID: 37009487 PMCID: PMC10055666 DOI: 10.3389/fcell.2023.1077350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/17/2023] [Indexed: 03/17/2023] Open
Abstract
The potential of mesenchymal stem cells (MSCs) for tissue repair and regeneration has garnered great attention. While MSCs are likely to interact with microbes at sites of tissue damage and inflammation, like in the gastrointestinal system, the consequences of pathogenic association on MSC activities have yet to be elucidated. This study investigated the effects of pathogenic interaction on MSC trilineage differentiation paths and mechanisms using model intracellular pathogen Salmonella enterica ssp enterica serotype Typhimurium. The examination of key markers of differentiation, apoptosis, and immunomodulation demonstrated that Salmonella altered osteogenic and chondrogenic differentiation pathways in human and goat adipose-derived MSCs. Anti-apoptotic and pro-proliferative responses were also significantly upregulated (p < 0.05) in MSCs during Salmonella challenge. These results together indicate that Salmonella, and potentially other pathogenic bacteria, can induce pathways that influence both apoptotic response and functional differentiation trajectories in MSCs, highlighting that microbes have a potentially significant role as influencers of MSC physiology and immune activity.
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Affiliation(s)
- Nuradilla Mohamad-Fauzi
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Claire Shaw
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Soraya H. Foutouhi
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Matthias Hess
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Nguyet Kong
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Amir Kol
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, CA, United States
| | - Dylan Bobby Storey
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Prerak T. Desai
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Jigna Shah
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
| | - Dori Borjesson
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, CA, United States
| | - James D. Murray
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
- *Correspondence: James D. Murray, ; Bart C. Weimer,
| | - Bart C. Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, Davis, CA, United States
- *Correspondence: James D. Murray, ; Bart C. Weimer,
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Pinho RM, Garas LC, Huang BC, Weimer BC, Maga EA. Malnourishment affects gene expression along the length of the small intestine. Front Nutr 2022; 9:894640. [PMID: 36118759 PMCID: PMC9478944 DOI: 10.3389/fnut.2022.894640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Malnourishment is a risk factor for childhood mortality, jeopardizing the health of children by aggravating pneumonia/acute respiratory infections and diarrheal diseases. Malnourishment causes morphophysiological changes resulting in stunting and wasting that have long-lasting consequences such as cognitive deficit and metabolic dysfunction. Using a pig model of malnutrition, the interplay between the phenotypic data displayed by the malnourished animals, the gene expression pattern along the intestinal tract, microbiota composition of the intestinal contents, and hepatic metabolite concentrations from the same animals were correlated using a multi-omics approach. Samples from the duodenum, jejunum, and ileum of malnourished (protein and calorie-restricted diet) and full-fed (no dietary restrictions) piglets were subjected to RNA-seq. Gene co-expression analysis and phenotypic correlations were made with WGCNA, while the integration of transcriptome with microbiota composition and the hepatic metabolite profile was done using mixOmics. Malnourishment caused changes in tissue gene expression that influenced energetic balance, cell proliferation, nutrient absorption, and response to stress. Repression of antioxidant genes, including glutathione peroxidase, in coordination with induction of metal ion transporters corresponded to the hepatic metabolite changes. These data indicate oxidative stress in the intestine of malnourished animals. Furthermore, several of the phenotypes displayed by these animals could be explained by changes in gene expression.
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Affiliation(s)
- Raquel M. Pinho
- Department of Animal Science, University of California, Davis, Davis, CA, United States
- *Correspondence: Raquel M. Pinho
| | - Lydia C. Garas
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - B. Carol Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Elizabeth A. Maga
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems. NPJ Sci Food 2022; 6:35. [PMID: 35974024 PMCID: PMC9381742 DOI: 10.1038/s41538-022-00150-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.
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11
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Investigating the microbial terroir of fermented foods produced in a professional kitchen. Int J Gastron Food Sci 2022. [DOI: 10.1016/j.ijgfs.2022.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Joshi A, Bhardwaj D, Kaushik A, Juneja VK, Taneja P, Thakur S, Kumra Taneja N. Advances in multi-omics based quantitative microbial risk assessment in the dairy sector: A semi-systematic review. Food Res Int 2022; 156:111323. [PMID: 35651076 DOI: 10.1016/j.foodres.2022.111323] [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: 11/09/2021] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
With the increasing consumption of packaged and ready-to-eat food products, the risk of foodborne illness has drastically increased and so has the dire need for proper management. The conventional Microbial Risk Assessment (MRA) investigations require prior knowledge of process flow, exposure, and hazard assessment throughout the supply chain. These data are often generated using conventional microbiological approaches based either on shelf-life studies or specific spoilage organisms (SSOs), frequently overlooking crucial information such as antimicrobial resistance (AMR), biofilm formation, virulence factors and other physiological variations coupled with bio-chemical characteristics of food matrix. Additionally, the microbial risks in food are diverse and heterogenous, that might be an outcome of growth and activity of multiple microbial populations rather than a single species contamination. The uncertainty on the microbial source, time as well as point of entry into the food supply chain poses a constraint to the efficiency of preventive approaches and conventional MRA. In the last few decades, significant breakthroughs in molecular methods and continuously progressing bioinformatics tools have opened up a new horizon for risk analysis-based approaches in food safety. Real time polymerase chain reaction (qPCR) and kit-based assays provide better accuracy and precision with shorter processing time. Despite these improvements, the effect of complex food matrix on growth environment and recovery of pathogen is a persistent problem for risk assessors. The dairy industry is highly impacted by spoilage and pathogenic microorganisms. Therefore, this review discusses the evolution and recent advances in MRAmethodologies equipped with predictive interventions and "multi-omics" approach for robust MRA specifically targeting dairy products. It also highlights the limiting gap area and the opportunity for improvement in this field to ensure precision food safety.
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Affiliation(s)
- Akanksha Joshi
- Dept. of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, Haryana 131028, India
| | - Dinesh Bhardwaj
- Dept. of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, Haryana 131028, India
| | - Abhishek Kaushik
- Dept. of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, Haryana 131028, India
| | | | - Pankaj Taneja
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Sheetal Thakur
- Department of Food Science and Technology, MMICT & BM (HM), MMDU, Mullana, Ambala, Haryana, India
| | - Neetu Kumra Taneja
- Dept. of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, Haryana 131028, India; Center for Advance Translational Research in Food Nanobiotechnology (CATR-FNB), National Institute of Food Technology Entrepreneurship and Management, Haryana 131028, India.
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Wassermann B, Abdelfattah A, Müller H, Korsten L, Berg G. The microbiome and resistome of apple fruits alter in the post-harvest period. ENVIRONMENTAL MICROBIOME 2022; 17:10. [PMID: 35256002 PMCID: PMC8900306 DOI: 10.1186/s40793-022-00402-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/06/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing. RESULTS All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing. CONCLUSION Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, Republic of South Africa
- DSI-NRF Centre of Excellence in Food Security, Pretoria, Republic of South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, 14476 Potsdam OT Golm, Germany
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14
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Chelliah R, Banan-MwineDaliri E, Khan I, Wei S, Elahi F, Yeon SJ, Selvakumar V, Ofosu FK, Rubab M, Ju HH, Rallabandi HR, Madar IH, Sultan G, Oh DH. A review on the application of bioinformatics tools in food microbiome studies. Brief Bioinform 2022; 23:6533500. [PMID: 35189636 DOI: 10.1093/bib/bbac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.
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Affiliation(s)
- Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Eric Banan-MwineDaliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Imran Khan
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Department of Biotechnology, University of Malakand, Khyber Pakhtunkhwa Pakistan
| | - Shuai Wei
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fazle Elahi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Su-Jung Yeon
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Vijayalakshmi Selvakumar
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Momna Rubab
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Hum Hun Ju
- Department of Biological Environment, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Harikrishna Reddy Rallabandi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Inamul Hasan Madar
- Department of Biochemistry, School of Life Science, Bharathidasan, University, Thiruchirappalli, Tamilnadu, India
| | - Ghazala Sultan
- Department of Computer Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Deog Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
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15
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Jang HB, Chittick L, Li YF, Zablocki O, Sanderson CM, Carrillo A, van den Engh G, Sullivan MB. Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs. ISME COMMUNICATIONS 2022; 2:12. [PMID: 37938680 PMCID: PMC9723727 DOI: 10.1038/s43705-022-00093-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 04/27/2023]
Abstract
Viral metagenomics (viromics) has reshaped our understanding of DNA viral diversity, ecology, and evolution across Earth's ecosystems. However, viromics now needs approaches to link newly discovered viruses to their host cells and characterize them at scale. This study adapts one such method, sequencing-enabled viral tagging (VT), to establish "Viral Tag and Grow" (VT + Grow) to rapidly capture and characterize viruses that infect a cultivated target bacterium, Pseudoalteromonas. First, baseline cytometric and microscopy data improved understanding of how infection conditions and host physiology impact populations in VT flow cytograms. Next, we extensively evaluated "and grow" capability to assess where VT signals reflect adsorption alone or wholly successful infections that lead to lysis. Third, we applied VT + Grow to a clonal virus stock, which, coupled to traditional plaque assays, revealed significant variability in burst size-findings that hint at a viral "individuality" parallel to the microbial phenotypic heterogeneity literature. Finally, we established a live protocol for public comment and improvement via protocols.io to maximally empower the research community. Together these efforts provide a robust foundation for VT researchers, and establish VT + Grow as a promising scalable technology to capture and characterize viruses from mixed community source samples that infect cultivable bacteria.
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Affiliation(s)
- Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Lauren Chittick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Alfonso Carrillo
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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16
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Zarzecka U, Zadernowska A, Chajęcka-Wierzchowska W. Effects of osmotic and high pressure stress on expression of virulence factors among Enterococcus spp. isolated from food of animal origin. Food Microbiol 2021; 102:103900. [PMID: 34809932 DOI: 10.1016/j.fm.2021.103900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/22/2021] [Accepted: 09/09/2021] [Indexed: 01/01/2023]
Abstract
The aim of study was to determine the occurrence of virulence factors and virulence-related genes among enterococci isolated from food of animal origin and effects of osmotic and high pressure stress on expression of virulence-related genes. The number of 78 isolates were analyzed. None of them showed a strong ability to form biofilm, 38.5% (n = 30) had the slime production ability, 41% (n = 32) had gelatinase activity, γ -type hemolysis was observed in 55% of isolates, and α-type hemolysis in 45%. All of the isolates carried 1-13 virulence-related genes. The most common genes were gelE (85.9%), sprE (78.2%) and asa1 (75.6%). There were also observed changes in the expression of the gelE, esp, asa1 and cylL genes in response to various NaCl concentration and high pressure processing. Results obtained in this study indicate that enterococci isolated from food may act as reservoirs of virulence genes. The presence of virulence factors among enterococci, especially the ability to biofilm formation is important for food safety and the protection of public health. The results presented in our work demonstrate that stress that can occur during food preservation and food processing can induce the changes in the virulence-related genes expression.
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Affiliation(s)
- Urszula Zarzecka
- Chair of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury, Plac Cieszyński 1, 10-726, Olsztyn, Poland.
| | - Anna Zadernowska
- Chair of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury, Plac Cieszyński 1, 10-726, Olsztyn, Poland
| | - Wioleta Chajęcka-Wierzchowska
- Chair of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury, Plac Cieszyński 1, 10-726, Olsztyn, Poland
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17
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Fanelli V, Mascio I, Miazzi MM, Savoia MA, De Giovanni C, Montemurro C. Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review. Foods 2021; 10:1644. [PMID: 34359514 PMCID: PMC8306823 DOI: 10.3390/foods10071644] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
In the last decades, the demand for molecular tools for authenticating and tracing agri-food products has significantly increased. Food safety and quality have gained an increased interest for consumers, producers, and retailers, therefore, the availability of analytical methods for the determination of food authenticity and the detection of major adulterations takes on a fundamental role. Among the different molecular approaches, some techniques such as the molecular markers-based methods are well established, while some innovative approaches such as isothermal amplification-based methods and DNA metabarcoding have only recently found application in the agri-food sector. In this review, we provide an overview of the most widely used molecular techniques for fresh and processed agri-food authentication and traceability, showing their recent advances and applications and discussing their main advantages and limitations. The application of these techniques to agri-food traceability and authentication can contribute a great deal to the reassurance of consumers in terms of transparency and food safety and may allow producers and retailers to adequately promote their products.
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Affiliation(s)
- Valentina Fanelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Michele Antonio Savoia
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Claudio De Giovanni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute for Sustainable Plant Protection–Support Unit Bari, National Research Council of Italy (CNR), Via Amendola 122/D, 70126 Bari, Italy
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