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Lemée P, Bridier A. Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics. Methods Mol Biol 2025; 2852:289-309. [PMID: 39235751 DOI: 10.1007/978-1-0716-4100-2_19] [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] [Indexed: 09/06/2024]
Abstract
Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.
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Affiliation(s)
- Pierre Lemée
- Antibiotics, Biocides, Residues and Resistance (AB2R) Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance (AB2R) Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France.
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Yang X, Narvaez-Bravo C, Zhang P. Driving forces shaping the microbial ecology in meat packing plants. Front Microbiol 2024; 14:1333696. [PMID: 38322759 PMCID: PMC10844536 DOI: 10.3389/fmicb.2023.1333696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/22/2023] [Indexed: 02/08/2024] Open
Abstract
Meat production is a complex system, continually receiving animals, water, air, and workers, all of which serve as carriers of bacteria. Selective pressures involved in different meat processing stages such as antimicrobial interventions and low temperatures, may promote the accumulation of certain residential microbiota in meat cutting facilities. Bacteria including human pathogens from all these sources can contaminate meat surfaces. While significant advancements have been made in enhancing hygienic standards and pathogen control measures in meat plants, resulting in a notable reduction in STEC recalls and clinical cases, STEC still stands as a predominant contributor to foodborne illnesses associated with beef and occasionally with pork. The second-and third-generation sequencing technology has become popular in microbiota related studies and provided a better image of the microbial community in the meat processing environments. In this article, we reviewed the potential factors influencing the microbial ecology in commercial meat processing facilities and conducted a meta-analysis on the microbiota data published in the last 10 years. In addition, the mechanisms by which bacteria persist in meat production environments have been discussed with a focus on the significant human pathogen E. coli O157:H7 and generic E. coli, an indicator often used for the hygienic condition in food production.
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Affiliation(s)
- Xianqin Yang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | | | - Peipei Zhang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
- Department of Animal Sciences, Center for Meat Safety and Quality, Colorado State University, Fort Collins, CO, United States
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Prabhukhot GS, Eggleton CD, Patel J. Multispecies Bacterial Biofilms and Their Evaluation Using Bioreactors. Foods 2023; 12:4495. [PMID: 38137299 PMCID: PMC10742677 DOI: 10.3390/foods12244495] [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: 09/26/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Pathogenic biofilm formation within food processing industries raises a serious public health and safety concern, and places burdens on the economy. Biofilm formation on equipment surfaces is a rather complex phenomenon, wherein multiple steps are involved in bacterial biofilm formation. In this review we discuss the stages of biofilm formation, the existing literature on the impact of surface properties and shear stress on biofilms, types of bioreactors, and antimicrobial coatings. The review underscores the significance of prioritizing biofilm prevention strategies as a first line of defense, followed by control measures. Utilizing specific biofilm eradication strategies as opposed to a uniform approach is crucial because biofilms exhibit different behavioral outcomes even amongst the same species when the environmental conditions change. This review is geared towards biofilm researchers and food safety experts, and seeks to derive insights into the scope of biofilm formation, prevention, and control. The use of suitable bioreactors is paramount to understanding the mechanisms of biofilm formation. The findings provide useful information to researchers involved in bioreactor selection for biofilm investigation, and food processors in surfaces with novel antimicrobial coatings, which provide minimal bacterial attachment.
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Affiliation(s)
- Grishma S. Prabhukhot
- Department of Mechanical Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, USA; (G.S.P.); (C.D.E.)
| | - Charles D. Eggleton
- Department of Mechanical Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, USA; (G.S.P.); (C.D.E.)
| | - Jitendra Patel
- US Department of Agriculture, Agricultural Research Service, Environmental and Microbial Food Safety Laboratory, Beltsville, MD 20705, USA
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Sadiq FA, De Reu K, Steenackers H, Van de Walle A, Burmølle M, Heyndrickx M. Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms - an example from dairy isolates. ISME COMMUNICATIONS 2023; 3:118. [PMID: 37968339 PMCID: PMC10651889 DOI: 10.1038/s43705-023-00328-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.
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Affiliation(s)
- Faizan Ahmed Sadiq
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium.
| | - Koen De Reu
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Hans Steenackers
- Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Ann Van de Walle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium.
- Ghent University, Department of Pathobiology, Pharmacology and Zoological Medicine, Salisburylaan 133, B-9820, Merelbeke, Belgium.
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Xu ZS, Ju T, Yang X, Gänzle M. A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities. Microorganisms 2023; 11:1575. [PMID: 37375077 DOI: 10.3390/microorganisms11061575] [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: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.
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Affiliation(s)
- Zhaohui S Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tingting Ju
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Xianqin Yang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada
| | - Michael Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Sadiq FA, De Reu K, Burmølle M, Maes S, Heyndrickx M. Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries. Front Microbiol 2023; 14:1159434. [PMID: 37125177 PMCID: PMC10133454 DOI: 10.3389/fmicb.2023.1159434] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Most biofilms within the food industry are formed by multiple bacterial species which co-exist on surfaces as a result of interspecies interactions. These ecological interactions often make these communities tolerant against antimicrobials. Our previous work led to the identification of a large number (327) of highly diverse bacterial species on food contact surfaces of the dairy, meat, and egg industries after routine cleaning and disinfection (C&D) regimes. In the current study, biofilm-forming ability of 92 bacterial strains belonging to 26 genera and 42 species was assessed and synergistic interactions in biofilm formation were investigated by coculturing species in all possible four-species combinations. Out of the total 455 four-species biofilm combinations, greater biofilm mass production, compared to the sum of biofilm masses of individual species in monoculture, was observed in 34 combinations. Around half of the combinations showed synergy in biofilm mass > 1.5-fold and most of the combinations belonged to dairy strains. The highest synergy (3.13-fold) was shown by a combination of dairy strains comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus. The observed synergy in mixed biofilms turned out to be strain-specific rather than species-dependent. All biofilm combinations showing remarkable synergy appeared to have certain common species in all combinations which shows there are keystone industry-specific bacterial species which stimulate synergy or antagonism and this may have implication for biofilm control in the concerned food industries.
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Affiliation(s)
- Faizan Ahmed Sadiq
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Faizan Ahmed Sadiq,
| | - Koen De Reu
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sharon Maes
- The Department of Ecotechnology and Sustainable Building Engineering, Mid Sweden University, Östersund, Sweden
| | - Marc Heyndrickx
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- *Correspondence: Marc Heyndrickx,
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