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Kim J, Kim BS. Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster. J Microbiol Biotechnol 2023; 33:1162-1169. [PMID: 37415086 PMCID: PMC10580894 DOI: 10.4014/jmb.2302.02007] [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: 02/04/2023] [Revised: 05/06/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.
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Affiliation(s)
- Jaeeun Kim
- Department of Food Science and Biotechnology, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
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2
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Planý M, Sitarčík J, Pavlović J, Budiš J, Koreňová J, Kuchta T, Pangallo D. Evaluation of bacterial consortia associated with dairy fermentation by ribosomal RNA (rrn) operon metabarcoding strategy using MinION device. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2022.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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3
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Lin WF, Guo HQ, Zhu LJ, Yang K, Li HZ, Cui L. Temporal variation of antibiotic resistome and pathogens in food waste during short-term storage. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129261. [PMID: 35739780 DOI: 10.1016/j.jhazmat.2022.129261] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
The massive food wastes pose a growing health concern for spreading of antibiotic resistance and pathogens due to food spoilage. However, little is known about these microbial hazards during collection, classification, and transportation before eventual treatment. Here, we profiled the temporal variations of antibiotic resistance genes (ARGs), pathogens, bacterial and fungal communities across four typical food wastes (vegetable, fish, meat, and rice) during storage at room temperature in summer (maximum 28-29 °C) of typical southeast city in China. A total of 171 ARGs and 32 mobile genetic elements were detected, and the absolute abundance of ARGs significantly increased by up to 126-fold with the storage time. Additionally, five bacterial pathogens containing virulence factor genes were detected, and Klebsiella pneumoniae was persistently detected throughout the storage time in all food types except rice. Moreover, fungal pathogens (e.g., Aspergillus, Penicillium, and Fusarium) were also frequently detected. Notably, animal food wastes were demonstrated to harbor higher abundance of ARGs and more types of pathogens, indicating a higher level of hazard. Mobile genetic elements and food types were demonstrated to mainly impact ARG profiles and pathogens, respectively. This work provides a comprehensive understanding of the microbial hazards associated with food waste recycling, and will contribute to optimize the food waste management to ensure biosecurity and benefit human health.
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Affiliation(s)
- Wen-Fang Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong-Qin Guo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long-Ji Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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4
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Xu JG, Huang XN, Meng J, Chen JY, Han BZ. Characterization and comparison of the bacterial community on environmental surfaces through a fresh-cut vegetables processing line in China. Food Res Int 2022; 155:111075. [DOI: 10.1016/j.foodres.2022.111075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/20/2022]
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5
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Kort R, Schlösser J, Vazquez AR, Atukunda P, Muhoozi GKM, Wacoo AP, Sybesma WFH, Westerberg AC, Iversen PO, Schoen ED. Model Selection Reveals the Butyrate-Producing Gut Bacterium Coprococcus eutactus as Predictor for Language Development in 3-Year-Old Rural Ugandan Children. Front Microbiol 2021; 12:681485. [PMID: 34149673 PMCID: PMC8206532 DOI: 10.3389/fmicb.2021.681485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023] Open
Abstract
Introduction The metabolic activity of the gut microbiota plays a pivotal role in the gut-brain axis through the effects of bacterial metabolites on brain function and development. In this study we investigated the association of gut microbiota composition with language development of 3-year-old rural Ugandan children. Methods We studied the language ability in 139 children of 36 months in our controlled maternal education intervention trial to stimulate children’s growth and development. The dataset includes 1170 potential predictors, including anthropometric and cognitive parameters at 24 months, 542 composition parameters of the children’s gut microbiota at 24 months and 621 of these parameters at 36 months. We applied a novel computationally efficient version of the all-subsets regression methodology and identified predictors of language ability of 36-months-old children scored according to the Bayley Scales of Infant and Toddler Development (BSID-III). Results The best three-term model, selected from more than 266 million models, includes the predictors Coprococcus eutactus at 24 months of age, Bifidobacterium at 36 months of age, and language development at 24 months. The top 20 four-term models, selected from more than 77 billion models, consistently include C. eutactus abundance at 24 months, while 14 of these models include the other two predictors as well. Mann–Whitney U tests suggest that the abundance of gut bacteria in language non-impaired children (n = 78) differs from that in language impaired children (n = 61). While anaerobic butyrate-producers, including C. eutactus, Faecalibacterium prausnitzii, Holdemanella biformis, Roseburia hominis are less abundant, facultative anaerobic bacteria, including Granulicatella elegans, Escherichia/Shigella and Campylobacter coli, are more abundant in language impaired children. The overall predominance of oxygen tolerant species in the gut microbiota was slightly higher in the language impaired group than in the non-impaired group (P = 0.09). Conclusion Application of the all-subsets regression methodology to microbiota data established a correlation between the relative abundance of the anaerobic butyrate-producing gut bacterium C. eutactus and language development in Ugandan children. We propose that the gut redox potential and the overall bacterial butyrate-producing capacity in the gut are important factors for language development.
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Affiliation(s)
- Remco Kort
- Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Yoba for Life Foundation, Amsterdam, Netherlands.,ARTIS-Micropia, Amsterdam, Netherlands
| | - Job Schlösser
- Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Alan R Vazquez
- Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Prudence Atukunda
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Grace K M Muhoozi
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Human Nutrition and Home Economics, Kyambogo University, Kampala, Uganda
| | - Alex Paul Wacoo
- Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Yoba for Life Foundation, Amsterdam, Netherlands.,Department of Medical Biochemistry, Makerere University, Kampala, Uganda
| | | | - Ane C Westerberg
- Institute of Health Sciences, Kristiania University College, Oslo, Norway
| | - Per Ole Iversen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Eric D Schoen
- Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
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6
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Lewis E, Hudson JA, Cook N, Barnes JD, Haynes E. Next-generation sequencing as a screening tool for foodborne pathogens in fresh produce. J Microbiol Methods 2020; 171:105840. [PMID: 31945388 DOI: 10.1016/j.mimet.2020.105840] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 01/10/2023]
Abstract
Next generation sequencing (NGS) approaches are increasingly applied to tracing microbial contaminants entering the food chain due to NGS' untargeted nature and ability to investigate non-culturable (and/or difficult to culture) organisms while yielding genomic information about the microbiota. So far, a plethora of microbes has been shown to be associated with fresh produce, but few studies have utilised NGS to identify contamination with human pathogens. This study aims to establish the limit of detection (LoD) for Salmonella and phage MS2 (a Norovirus surrogate) contamination of fresh produce employing NGS approaches on the Illumina MiSeq: 16S amplicon-sequencing, and RNA-seq, using ScriptSeq (Illumina) and NEBNext (New England BioLabs) kits. ScriptSeq proved the most sensitive approach; delivering an LoD of 104 CFU reaction-1 (Colony Forming Units) for Salmonella and 105 PFU reaction-1 (Plaque Forming Units) for phage MS2. Use of the NEBNext kit resulted in detection of Salmonella at 106 CFU reaction-1 and phage MS2 at 107 PFU reaction-1. 16S amplicon-sequencing yielded a similar LoD of 105 CFU reaction-1 for Salmonella but could not detect MS2. The tested NGS methodologies, in combination with bioinformatics approaches applied, proved less sensitive than conventional microbial detection approaches.
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Affiliation(s)
- E Lewis
- IAFRI, Newcastle University, Newcastle upon Tyne, UK; Fera, National Agrifood Innovation Campus, Sand Hutton, York, UK.
| | | | - N Cook
- Jorvik Food Safety Services, York, UK
| | - J D Barnes
- IAFRI, Newcastle University, Newcastle upon Tyne, UK
| | - E Haynes
- Fera, National Agrifood Innovation Campus, Sand Hutton, York, UK
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7
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Jagadeesan B, Gerner-Smidt P, Allard MW, Leuillet S, Winkler A, Xiao Y, Chaffron S, Van Der Vossen J, Tang S, Katase M, McClure P, Kimura B, Ching Chai L, Chapman J, Grant K. The use of next generation sequencing for improving food safety: Translation into practice. Food Microbiol 2019; 79:96-115. [PMID: 30621881 PMCID: PMC6492263 DOI: 10.1016/j.fm.2018.11.005] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 01/06/2023]
Abstract
Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.
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Affiliation(s)
- Balamurugan Jagadeesan
- Nestlé Research, Nestec Ltd, Route du Jorat 57, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland.
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, MS-CO-3, 1600 Clifton Road, 30329-4027, Atlanta, USA
| | - Marc W Allard
- US Food and Drug Administration, 5001 Campus Drive, College Park, MD, 02740, USA
| | - Sébastien Leuillet
- Institut Mérieux, Mérieux NutriSciences, 3 route de la Chatterie, 44800, Saint Herblain, France
| | - Anett Winkler
- Cargill Deutschland GmbH, Cerestarstr. 2, 47809, Krefeld, Germany
| | - Yinghua Xiao
- Arla Innovation Center, Agro Food Park 19, 8200, Aarhus, Denmark
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, 2 rue de la Houssinière, 44322, Nantes, France
| | - Jos Van Der Vossen
- The Netherlands Organisation for Applied Scientific Research, TNO, Utrechtseweg 48, 3704 HE, Zeist, NL, the Netherlands
| | - Silin Tang
- Mars Global Food Safety Center, Yanqi Economic Development Zone, 101407, Beijing, China
| | - Mitsuru Katase
- Fuji Oil Co., Ltd., Sumiyoshi-cho 1, Izumisano Osaka, 598-8540, Japan
| | - Peter McClure
- Mondelēz International, Linden 3, Bournville Lane, B30 2LU, Birmingham, United Kingdom
| | - Bon Kimura
- Tokyo University of Marine Science & Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Lay Ching Chai
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - John Chapman
- Unilever Research & Development, Postbus, 114, 3130 AC, Vlaardingen, the Netherlands
| | - Kathie Grant
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, United Kingdom.
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8
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Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1918:229-245. [PMID: 30580413 DOI: 10.1007/978-1-4939-9000-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.
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Characterization of four Paenibacillus species isolated from pasteurized, chilled ready-to-eat meals. Int J Food Microbiol 2017; 252:35-41. [DOI: 10.1016/j.ijfoodmicro.2017.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/30/2017] [Accepted: 04/18/2017] [Indexed: 12/11/2022]
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10
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Ferrario C, Lugli GA, Ossiprandi MC, Turroni F, Milani C, Duranti S, Mancabelli L, Mangifesta M, Alessandri G, van Sinderen D, Ventura M. Next generation sequencing-based multigene panel for high throughput detection of food-borne pathogens. Int J Food Microbiol 2017; 256:20-29. [PMID: 28578266 DOI: 10.1016/j.ijfoodmicro.2017.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 01/20/2023]
Abstract
Contamination of food by chemicals or pathogenic bacteria may cause particular illnesses that are linked to food consumption, commonly referred to as foodborne diseases. Bacteria are present in/on various foods products, such as fruits, vegetables and ready-to-eat products. Bacteria that cause foodborne diseases are known as foodborne pathogens (FBPs). Accurate detection methods that are able to reveal the presence of FBPs in food matrices are in constant demand, in order to ensure safe foods with a minimal risk of causing foodborne diseases. Here, a multiplex PCR-based Illumina sequencing method for FBP detection in food matrices was developed. Starting from 25 bacterial targets and 49 selected PCR primer pairs, a primer collection called foodborne pathogen - panel (FPP) consisting of 12 oligonucleotide pairs was developed. The FPP allows a more rapid and reliable identification of FBPs compared to classical cultivation methods. Furthermore, FPP permits sensitive and specific FBP detection in about two days from food sample acquisition to bioinformatics-based identification. The FPP is able to simultaneously identify eight different bacterial pathogens, i.e. Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Salmonella enterica subsp. enterica serovar enteritidis, Escherichia coli, Shigella sonnei, Staphylococcus aureus and Yersinia enterocolitica, in a given food matrix at a threshold contamination level of 101cell/g. Moreover, this novel detection method may represent an alternative and/or a complementary approach to PCR-based techniques, which are routinely used for FBP detection, and could be implemented in (parts of) the food chain as a quality check.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute, School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
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Piotrowska-Cyplik A, Myszka K, Czarny J, Ratajczak K, Kowalski R, Biegańska-Marecik R, Staninska-Pięta J, Nowak J, Cyplik P. Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:659-668. [PMID: 27144959 DOI: 10.1002/jsfa.7785] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/07/2016] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Knowledge regarding microaerophilic and anaerobic specific spoilage organisms (SSOs) is crucial for an appropriate evaluation of vacuum-packed ham. The objective of this study was to characterize the SSO community in vacuum-packed ham by a culture-dependent technique and MiSeq next-generation sequencing (NGS) platform. The relation between changes among the SSO group in the ham and changes in sensory characteristics of the product was also assessed. RESULTS In the study, conventional microbiological analyses were employed in order to establish the participation of several groups of microorganisms in the deterioration of vacuum-packed ham. The diversity of the SSO group in the product was further assessed with the use of MiSeq NGS technology. The bacteria identified in sliced cooked ham belonged mostly to four phyla, namely Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. A temperature of 4 °C favoured the development of mesophilic and psychrophilic/psychrotrophic flora, mainly Lactobacillaceae, Enterobacteriaceae and Micrococcaceae families. A high ratio of Brochothrix thermosphacta species and new, cold-tolerant Clostridium spp. was also observed. The growth of these microorganisms facilitated changes in the pH value and organoleptic characteristics of the product. CONCLUSION This study confirms that the combination of culturing and MiSeq NGS technology improves the microbial evaluation of food. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Agnieszka Piotrowska-Cyplik
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Kamila Myszka
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland
| | - Jakub Czarny
- Institute of Forensic Genetics, Al. Mickiewicza 3/4, PL-85-071, Bydgoszcz, Poland
| | - Katarzyna Ratajczak
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Ryszard Kowalski
- Institute of Meat Technology, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Róża Biegańska-Marecik
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Justyna Staninska-Pięta
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland
| | - Jacek Nowak
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland
| | - Paweł Cyplik
- Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland
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12
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Thompson GR, Tuscano JM, Dennis M, Singapuri A, Libertini S, Gaudino R, Torres A, Delisle JMP, Gillece JD, Schupp JM, Engelthaler DM. A microbiome assessment of medical marijuana. Clin Microbiol Infect 2016; 23:269-270. [PMID: 27956269 DOI: 10.1016/j.cmi.2016.12.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 11/28/2016] [Accepted: 12/03/2016] [Indexed: 11/25/2022]
Affiliation(s)
- G R Thompson
- Department of Medical Microbiology and Immunology, University of California - Davis, Davis, CA, USA; Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA.
| | - J M Tuscano
- Department of Internal Medicine, Division of Hematology/Oncology, University of California Davis Medical Center, Sacramento, CA, USA
| | - M Dennis
- Department of Medical Microbiology and Immunology, University of California - Davis, Davis, CA, USA
| | - A Singapuri
- Department of Medical Microbiology and Immunology, University of California - Davis, Davis, CA, USA
| | - S Libertini
- Department of Medical Microbiology and Immunology, University of California - Davis, Davis, CA, USA
| | - R Gaudino
- Steep Hill Laboratories Inc, Oakland, CA, USA
| | - A Torres
- Steep Hill Laboratories Inc, Oakland, CA, USA
| | - J M P Delisle
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - J D Gillece
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - J M Schupp
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - D M Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, USA
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13
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Prospects for improved control of dairy-relevant sporeformers using -omics technologies. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Anvarian AHP, Cao Y, Srikumar S, Fanning S, Jordan K. Flow Cytometric and 16S Sequencing Methodologies for Monitoring the Physiological Status of the Microbiome in Powdered Infant Formula Production. Front Microbiol 2016; 7:968. [PMID: 27446009 PMCID: PMC4916166 DOI: 10.3389/fmicb.2016.00968] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
The aim of this study was to develop appropriate protocols for flow cytometric (FCM) and 16S rDNA sequencing investigation of the microbiome in a powdered infant formula (PIF) production facility. Twenty swabs were collected from each of the three care zones of a PIF production facility and used for preparing composite samples. For FCM studies, the swabs were washed in 200 mL phosphate buffer saline (PBS). The cells were harvested by three-step centrifugation followed by a single stage filtration. Cells were dispersed in fresh PBS and analyzed with a flow cytometer for membrane integrity, metabolic activity, respiratory activity and Gram characteristics of the microbiome using various fluorophores. The samples were also plated on agar plates to determine the number of culturable cells. For 16S rDNA sequencing studies, the cells were harvested by centrifugation only. Genomic DNA was extracted using a chloroform-based method and used for 16S rDNA sequencing studies. Compared to the dry low and high care zones, the wet medium care zone contained a greater number of viable, culturable, and metabolically active cells. Viable but non-culturable cells were also detected in dry-care zones. In total, 243 genera were detected in the facility of which 42 were found in all three care zones. The greatest diversity in the microbiome was observed in low care. The genera present in low, medium and high care were mostly associated with soil, water, and humans, respectively. The most prevalent genera in low, medium and high care were Pseudomonas, Acinetobacter, and Streptococcus, respectively. The integration of FCM and metagenomic data provided further information on the density of different species in the facility.
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Affiliation(s)
| | - Yu Cao
- UCD Centre for Food Safety, Science Centre South, University College DublinDublin, Ireland
| | - Shabarinath Srikumar
- UCD Centre for Food Safety, Science Centre South, University College DublinDublin, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, Science Centre South, University College DublinDublin, Ireland
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15
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Brandwein M, Al-Quntar A, Goldberg H, Mosheyev G, Goffer M, Marin-Iniesta F, López-Gómez A, Steinberg D. Mitigation of Biofilm Formation on Corrugated Cardboard Fresh Produce Packaging Surfaces Using a Novel Thiazolidinedione Derivative Integrated in Acrylic Emulsion Polymers. Front Microbiol 2016; 7:159. [PMID: 26909074 PMCID: PMC4754437 DOI: 10.3389/fmicb.2016.00159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/29/2016] [Indexed: 11/29/2022] Open
Abstract
Various surfaces associated with the storage and packing of food are known to harbor distinct bacterial pathogens. Conspicuously absent among the plethora of studies implicating food packaging materials and machinery is the study of corrugated cardboard packaging, the worldwide medium for transporting fresh produce. In this study, we observed the microbial communities of three different store-bought fruits and vegetables, along with their analog cardboard packaging using high throughput sequencing technology. We further developed an anti-biofilm polymer meant to coat corrugated cardboard surfaces and mediate bacterial biofilm growth on said surfaces. Integration of a novel thiazolidinedione derivative into the acrylic emulsion polymers was assessed using Energy Dispersive X-ray Spectrometry (EDS) analysis and surface topography was visualized and quantified on corrugated cardboard surfaces. Biofilm growth was measured using q-PCR targeting the gene encoding 16s rRNA. Additionally, architectural structure of the biofilm was observed using SEM. The uniform integration of the thiazolidinedione derivative TZD-6 was confirmed, and it was determined via q-PCR to reduce biofilm growth by ~80% on tested surfaces. A novel and effective method for reducing microbial load and preventing contamination on food packaging is thereby proposed.
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Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of JerusalemJerusalem, Israel
| | - Abed Al-Quntar
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of JerusalemJerusalem, Israel
- Institute for Drug Science, School of Pharmacy, The Hebrew University of JerusalemJerusalem, Israel
| | | | | | | | - Fulgencio Marin-Iniesta
- Food Technology, Nutrition and Bromatology Department, Facultad de Veterinaria, Universidad de MurciaMurcia, Spain
| | - Antonio López-Gómez
- Department of Food Engineering and Agricultural Equipment, Technical University of CartagenaCartagena, Spain
| | - Doron Steinberg
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of JerusalemJerusalem, Israel
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16
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A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing. BMC Genomics 2016; 17:108. [PMID: 26868371 PMCID: PMC4751728 DOI: 10.1186/s12864-016-2388-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/08/2016] [Indexed: 11/10/2022] Open
Abstract
Background The high error rate of next generation sequencing (NGS) restricts some of its applications, such as monitoring virus mutations and detecting rare mutations in tumors. There are two commonly employed sequencing library preparation strategies to improve sequencing accuracy by correcting sequencing errors: read-pairing method and tag-clustering method (i.e. primer ID or UID). Here, we constructed a homogeneous library from a single clone, and compared the variant calling accuracy of these error-correction methods. Result We comprehensively described the strengths and pitfalls of these methods. We found that both read-pairing and tag-clustering methods significantly decreased sequencing error rate. While the read-pairing method was more effective than the tag-clustering method at correcting insertion and deletion errors, it was not as effective as the tag-clustering method at correcting substitution errors. In addition, we observed that when the read quality was poor, the tag-clustering method led to huge coverage loss. We also tested the effect of applying quality score filtering to the error-correction methods and demonstrated that quality score filtering was able to impose a minor, yet statistically significant improvement to the error-correction methods tested in this study. Conclusion Our study provides a benchmark for researchers to select suitable error-correction methods based on the goal of the experiment by balancing the trade-off between sequencing cost (i.e. sequencing coverage requirement) and detection sensitivity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2388-9) contains supplementary material, which is available to authorized users.
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