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Salamandane A, Leech J, Almeida R, Silva C, Crispie F, Cotter PD, Malfeito-Ferreira M, Brito L. Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach. Food Res Int 2024; 189:114556. [PMID: 38876593 DOI: 10.1016/j.foodres.2024.114556] [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: 03/14/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/microorganisms. Eight samples of raw ewe's milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese.
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Affiliation(s)
- Acácio Salamandane
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; Faculdade de Ciências de Saúde, Universidade Lúrio, Campus Universitário de Marrere, Nampula 4250, Mozambique
| | - John Leech
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
| | - Rita Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Carolina Silva
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; VistaMilk, Ireland
| | - Manuel Malfeito-Ferreira
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Luísa Brito
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal.
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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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Lee S, Portlock T, Le Chatelier E, Garcia-Guevara F, Clasen F, Oñate FP, Pons N, Begum N, Harzandi A, Proffitt C, Rosario D, Vaga S, Park J, von Feilitzen K, Johansson F, Zhang C, Edwards LA, Lombard V, Gauthier F, Steves CJ, Gomez-Cabrero D, Henrissat B, Lee D, Engstrand L, Shawcross DL, Proctor G, Almeida M, Nielsen J, Mardinoglu A, Moyes DL, Ehrlich SD, Uhlen M, Shoaie S. Global compositional and functional states of the human gut microbiome in health and disease. Genome Res 2024; 34:967-978. [PMID: 39038849 PMCID: PMC11293553 DOI: 10.1101/gr.278637.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 06/05/2024] [Indexed: 07/24/2024]
Abstract
The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.
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Affiliation(s)
- Sunjae Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), 61005, Gwangju, Republic of Korea
| | - Theo Portlock
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | | | - Fernando Garcia-Guevara
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Frederick Clasen
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | | | - Nicolas Pons
- University Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France
| | - Neelu Begum
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | - Azadeh Harzandi
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | - Ceri Proffitt
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | - Dorines Rosario
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | - Stefania Vaga
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | - Junseok Park
- Department of Bio and Brain Engineering, KAIST, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Lindsey A Edwards
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
- Institute of Liver Studies, Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London SE5 9NU, United Kingdom
| | - Vincent Lombard
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13288, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille 13288, France
| | - Franck Gauthier
- University Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London WC2R 2LS, United Kingdom
| | - David Gomez-Cabrero
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
- Translational Bioinformatics Unit, Navarrabiomed, Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Doheon Lee
- Department of Bio and Brain Engineering, KAIST, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Debbie L Shawcross
- Institute of Liver Studies, Department of Inflammation Biology, School of Immunology and Microbial Sciences, King's College London, London SE5 9NU, United Kingdom
| | - Gordon Proctor
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | - Mathieu Almeida
- University Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- BioInnovation Institute, DK-2200 Copenhagen N, Denmark
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - David L Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom
| | - Stanislav Dusko Ehrlich
- University Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France
- Department of Clinical and Movement Neurosciences, University College London, London NW3 2PF, United Kingdom
| | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden;
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, United Kingdom;
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, SE-171 21, Sweden
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4
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Elizabeth George S, Wan Y. Microbial functionalities and immobilization of environmental lead: Biogeochemical and molecular mechanisms and implications for bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131738. [PMID: 37285788 PMCID: PMC11249206 DOI: 10.1016/j.jhazmat.2023.131738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/09/2023]
Abstract
The increasing environmental and human health concerns about lead in the environment have stimulated scientists to search for microbial processes as innovative bioremediation strategies for a suite of different contaminated media. In this paper, we provide a compressive synthesis of existing research on microbial mediated biogeochemical processes that transform lead into recalcitrant precipitates of phosphate, sulfide, and carbonate, in a genetic, metabolic, and systematics context as they relate to application in both laboratory and field immobilization of environmental lead. Specifically, we focus on microbial functionalities of phosphate solubilization, sulfate reduction, and carbonate synthesis related to their respective mechanisms that immobilize lead through biomineralization and biosorption. The contributions of specific microbes, both single isolates or consortia, to actual or potential applications in environmental remediation are discussed. While many of the approaches are successful under carefully controlled laboratory conditions, field application requires optimization for a host of variables, including microbial competitiveness, soil physical and chemical parameters, metal concentrations, and co-contaminants. This review challenges the reader to consider bioremediation approaches that maximize microbial competitiveness, metabolism, and the associated molecular mechanisms for future engineering applications. Ultimately, we outline important research directions to bridge future scientific research activities with practical applications for bioremediation of lead and other toxic metals in environmental systems.
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Affiliation(s)
- S Elizabeth George
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA
| | - Yongshan Wan
- US EPA Office of Research and Development, Center for Environmental Measurement and Modeling, Gulf Ecosystem Measurement and Modeling Division, One Sabine Island Drive, Gulf Breeze, FL 32561, USA.
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5
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Viacava K, Qiao J, Janowczyk A, Poudel S, Jacquemin N, Meibom KL, Shrestha HK, Reid MC, Hettich RL, Bernier-Latmani R. Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium. THE ISME JOURNAL 2022; 16:1740-1749. [PMID: 35338334 PMCID: PMC9213503 DOI: 10.1038/s41396-022-01220-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
Soil microbiomes harbour unparalleled functional and phylogenetic diversity. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. As methylation was proposed to be catalysed by sulfate-reducing bacteria. However, to date, there are no available anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harbouring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.
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Affiliation(s)
- Karen Viacava
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Environmental Microbiology Laboratory, CH-1015, Lausanne, Switzerland.,Soil Science Group, Institute of Geography, University of Bern, Bern, Switzerland
| | - Jiangtao Qiao
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Environmental Microbiology Laboratory, CH-1015, Lausanne, Switzerland
| | - Andrew Janowczyk
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Suresh Poudel
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Nicolas Jacquemin
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Environmental Microbiology Laboratory, CH-1015, Lausanne, Switzerland.,Translational Bioinformatics and Statistics, Department of Oncology, Université de Lausanne, Lausanne, Switzerland
| | - Karin Lederballe Meibom
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Environmental Microbiology Laboratory, CH-1015, Lausanne, Switzerland
| | - Him K Shrestha
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology Graduate School, University of Tennessee, Knoxville, TN, USA
| | - Matthew C Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Robert L Hettich
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rizlan Bernier-Latmani
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Environmental Microbiology Laboratory, CH-1015, Lausanne, Switzerland.
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6
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Altafini RDM, Martins TM, Bruni AT, Reginatto V. Upgraded medium composition highlights the relevance of iron sulfate for 1,3-propanediol production by a Clostridium beijerinckii strain. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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McHugh AJ, Yap M, Crispie F, Feehily C, Hill C, Cotter PD. Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples. NPJ Sci Food 2021; 5:4. [PMID: 33589631 PMCID: PMC7884712 DOI: 10.1038/s41538-021-00087-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/13/2021] [Indexed: 01/01/2023] Open
Abstract
Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.
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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
| | - Min Yap
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Conor Feehily
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland.,APC Microbiome Ireland, 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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8
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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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9
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Ethnic seafood products sold on the Italian market: labelling assessment and biological, chemical and physical risk characterization. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.05.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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