1
|
Zhang Y, Yang J, Peng L, Liao E, Wang H. Behavior of Spoilage Bacterial Communities in Different Cuts of Enshi Black Pork under Refrigerated Storage (4 °C). Foods 2024; 13:2081. [PMID: 38998587 PMCID: PMC11241765 DOI: 10.3390/foods13132081] [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: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
The Enshi black pig is a Chinese native breed known for its rich nutrition content and high quality, which has notable traction in the consumer market. In this study, the potential impact of the main commercial cuts from Enshi black pork carcasses (ham, loin, and belly) on the bacteria community of spoiled meat under refrigerated storage (4 °C) was assessed by using a high-throughput sequencing method. Moreover, the spoilage potential of isolated strains from spoiled pork was investigated. The results demonstrated significant differences (p < 0.05) in bacterial community diversity and composition among spoiled ham, loin, and belly samples. Linear discriminant analysis effect size (LEfSe) analysis revealed a total of 20 significantly different potential bacterial biomarkers, with the dominant genera of Pseudomonas, Psychrobacter, Shewanella and Carnobacterium. Additionally, C. divergens THT1-5, isolated from spoiled ham samples, displayed cold adaptation and higher spoilage potential in Enshi black pork. These findings are helpful for identifying key factors contributing to spoilage in Enshi black pork and developing strategies to inhibit bacterial growth during preservation.
Collapse
Affiliation(s)
- Ying Zhang
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jiang Yang
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Lijuan Peng
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| | - E Liao
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| | - Haibin Wang
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan Polytechnic University, Wuhan 430023, China
| |
Collapse
|
2
|
Hu YY, Lo IH, Hsiao JT, Sheu F. Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38925544 DOI: 10.1002/jsfa.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. RESULTS QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. CONCLUSION The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- You-Yun Hu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Jhih-Ting Hsiao
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fuu Sheu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
3
|
Liu Z, Zhuang J, Zheng K, Luo C. Differential response of the soil nutrients, soil bacterial community structure and metabolic functions to different risk areas in Lead-Zine tailings. Front Microbiol 2023; 14:1131770. [PMID: 37779699 PMCID: PMC10536257 DOI: 10.3389/fmicb.2023.1131770] [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: 12/26/2022] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
Rapid growth in the mining industry has brought about a large formation of tailings, which result in serious destruction of the ecological environment and severe soil pollution problems. This study assesses soil nutrients, soil bacterial community and soil microbes' metabolic function in heavily polluted areas (W1), moderately polluted areas (W2), lightly polluted areas (W3) and clean areas (CK) using 16S Illumina sequencing. The results of this study showed that compared with CK, a severe loss of soil nutrients and richness of OTUs (Chao1 and ACE indices) were observed with the aggravated pollution of tailings. The Chao1 and ACE indices in the W1 group decreased significantly by 15.53 and 16.03%, respectively, (p < 0.01). Besides, the relative abundance of Actinobacteria and Proteobacteria was high whereas and relative abundance of Chloroflexi in the polluted areas. Among them, W1 groups increased significantly the relative abundance of Actinobacteria and decreased significantly the relative abundance of Chloroflexi, these can be used as indicator phyla for changes in soil community structures under polluted stress. Tax4 Fun analysis showed that W1 groups affected the soil bacterial community and altered the primary types of biological metabolism in polluted areas. Tailings have adverse impacts on soil bacterial community and metabolic functions, and the deterioration in soil quality is dependent on the levels of tailings pollution. Cumulatively, this study provides valuable information on the bacterial community structure and metabolic functions in the tailing polluted soil.
Collapse
Affiliation(s)
| | - Jiayao Zhuang
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing, China
| | | | | |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Sun XH, Qi X, Han YD, Guo ZJ, Cui CB, Lin CQ. Characteristics of changes in volatile organic compounds and microbial communities during the storage of pickles. Food Chem 2023; 409:135285. [PMID: 36586248 DOI: 10.1016/j.foodchem.2022.135285] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 10/27/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
The variations of volatile organic compounds (VOCs) and microbial communities of three pickles during storage at 4°C for one week were analyzed by headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), high-throughput sequencing, and Spearman correlation analysis. A total of 50 VOCs were identified from three pickles. During storage, most alcohols, aldehydes, ketones, and esters decreased, while acids increased, and sulfides, alkenes, and phenols were relatively equal. Firmicutes, Cyanobacteria, and Proteobacteria were the predominant bacterial phyla, and Weissella, Streptophyta, Leuconostoc, Bacillariophyta, and Lactobacillus were the predominant bacterial genera in three pickles. The bacterial diversity level significantly decreased during storage (P < 0.05). Spearman correlation coefficient indicated that Leuconostoc, Lactobacillus, and Weissella were highly correlated with the flavor of pickles, while Bacillariophyta and Streptophyta were highly correlated with the flavor formation of pickles during storage. These results could contribute to a better understanding of the impact of bacteria in flavor formation during pickle storage.
Collapse
Affiliation(s)
- Xi-Han Sun
- Agricultural College, Yanbian University, Yanji, Jilin 133000, China
| | - Xin Qi
- Pharma College, Yanbian University, Yanji, Jilin 133000, China
| | - Yu-di Han
- Convergence College, Yanbian University, Yanji, Jilin 133000, China
| | - Zhi-Jun Guo
- Agricultural College, Yanbian University, Yanji, Jilin 133000, China
| | - Cheng-Bi Cui
- Agricultural College, Yanbian University, Yanji, Jilin 133000, China; Pharma College, Yanbian University, Yanji, Jilin 133000, China; Convergence College, Yanbian University, Yanji, Jilin 133000, China; Key Laboratory of Natural Medicine Research of Changbai Mountain, Ministry of Education, Yanbian University, Yanji, Jilin 133000, China.
| | - Chang-Qing Lin
- Medical College, Yanbian University, Yanji, Jilin 133000, China.
| |
Collapse
|
6
|
Kajla M, Roy A, Singh IK, Singh A. Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1126567. [PMID: 36938003 PMCID: PMC10017880 DOI: 10.3389/fpls.2023.1126567] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.
Collapse
Affiliation(s)
- Mohini Kajla
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Jagdish Chandra Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
| |
Collapse
|
7
|
Zhong H, Wei S, Kang M, Sun Q, Xia Q, Wang Z, Han Z, Liu Y, Liu M, Liu S. Effects of different storage conditions on microbial community and quality changes of greater amberjack (Seriola dumerili) fillets. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
|
8
|
Saelens G, Houf K. Systematic review and critical reflection on the isolation and identification methods for spoilage associated bacteria in fresh marine fish. J Microbiol Methods 2022; 203:106599. [PMID: 36243229 DOI: 10.1016/j.mimet.2022.106599] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.
Collapse
Affiliation(s)
- Ganna Saelens
- Laboratory of Foodborne Parasites, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium; Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
| |
Collapse
|
9
|
Hammond SW, Lodolo L, Hu SK, Pasulka AL. Methodological 'lenses' influence the characterization of phytoplankton dynamics in a coastal upwelling ecosystem. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:897-906. [PMID: 36071313 DOI: 10.1111/1758-2229.13116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
New technologies enable the opportunity to improve our monitoring and understanding of marine phytoplankton communities. However, careful consideration for how different methodological approaches, or 'lenses', influence our interpretation of phytoplankton ecology is important, particularly when drawing conclusions about change over time or space. Using both high-throughput 18S rRNA gene sequencing and microscopy, we explored how phytoplankton community structure varied over the course of a year within a nearshore semi-enclosed coastal embayment along the Central Coast of California. The seasonal shift in the relative community dominance (i.e., diatom vs. dinoflagellate dominance) was captured in the microscopy results but not effectively captured in the molecular-based findings. However, the molecular approach explained more of the variability in composition across seasons relative to the microscopy approach. Temporal dynamics of specific bloom-forming taxa also differed between the molecular and microscopy results. Overall, the observed differences between the molecular- and microscopy-derived characterization of phytoplankton dynamics suggest that the approaches are best suited to answer different research questions. Moreover, the approaches complement each other for a more comprehensive perspective of a coastal phytoplankton ecosystem. Therefore, identifying the biases of each approach within natural communities is necessary to effectively and accurately characterize phytoplankton communities.
Collapse
Affiliation(s)
- S William Hammond
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Laura Lodolo
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| | - Sarah K Hu
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Alexis L Pasulka
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, USA
| |
Collapse
|
10
|
Ma S, Qiao L, Liu X, Zhang S, Zhang L, Qiu Z, Yu C. Microbial community succession in soils under long-term heavy metal stress from community diversity-structure to KEGG function pathways. ENVIRONMENTAL RESEARCH 2022; 214:113822. [PMID: 35803340 DOI: 10.1016/j.envres.2022.113822] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/04/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Currently, understanding the structure and function of the microbial community is the key step in artificially constructing microbial communities to control soil heavy metal pollution. Abundant/rare microbial communities play different roles in different levels of concentrations. However, the correlation between heavy metals and rare/abundant subgroups is poorly understood. In this study, we used a metagenomics approach to comprehensively investigate the evolutionary changes in microbial diversity, structure, and function under different heavy metal concentration stress in soils surrounding gold tailings. The results show that the main pollutants were Pb, As, and Zn. Indigenous microorganisms have different responses to heavy metal concentrations. Bacteria are the main components of indigenous microorganisms, mainly including Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. With the increase of heavy metal pollution, the relative abundance of Proteobacteria increased, and that of Actinobacteria decreased. Archaea was significantly inhibited by heavy metal stress and was more sensitive to heavy metal concentration. The response of fungi to heavy metal concentration was not obvious. The results of KEGG pathways showed that carbon fixation was inhibited with increasing heavy metal concentrations, while nitrogen metabolism was in contrast. Abundant subcommunity had a greater correlation mainly with metal resistance mechanisms, and rare subcommunity plays a key role for soil nutrient cycling such as N, S cycling in soils contaminated. Overall, this study provides a comprehensive analysis of the effects of heavy metal stress at different concentrations on microorganisms in farmland around gold tailings and reveals the relationship between heavy metals on KEGG pathways.
Collapse
Affiliation(s)
- Suya Ma
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Longkai Qiao
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Xiaoxia Liu
- Beijing Station of Agro-Environmental Monitoring, Test and Supervision Center of Agro-Environmental Quality, MOA, 100032 Beijing, China
| | - Shuo Zhang
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Luying Zhang
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Ziliang Qiu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Caihong Yu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China.
| |
Collapse
|
11
|
Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
Collapse
Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
| |
Collapse
|
12
|
Flint A, Laidlaw A, Li L, Raitt C, Rao M, Cooper A, Weedmark K, Carrillo C, Tamber S. Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast. BMC Microbiol 2022; 22:230. [PMID: 36180850 PMCID: PMC9524001 DOI: 10.1186/s12866-022-02650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequence-based methods for the detection of bacteria such as 16S rRNA amplicon sequencing and metagenomics can provide a comprehensive view of the bacterial microbiome of food. These methods rely on the detection of gene sequences to indicate the presence of viable bacteria. This indirect form of detection can be prone to experimental artefacts. Sample handling and processing are key sources of variation that require standard approaches. Extracting sufficient quantities of high quality DNA from food matrices is challenging because target bacterial species are usually minor components of the microbiota and foods contain an array of compounds that are inhibitory to downstream DNA applications. Here, three DNA extraction methods are compared for their ability to extract high quality bacterial DNA from retail chicken breast rinses, with or without enrichment. Method performance was assessed by comparing ease of use, DNA yield, DNA quality, PCR amplicon yield, and the detection of bacterial taxa by 16S rRNA amplicon sequencing. RESULTS All three DNA extraction methods yielded DNA of sufficient quantity and quality to perform quantitative PCR and 16S rRNA amplicon sequencing. The extraction methods differed in ease of use, with the two commercial kits (PowerFood, PowerSoil) offering considerable time and cost savings over a hybrid method that used laboratory reagents for lysis and commercial column based kits for further purification. Bacterial richness as determined by 16S rRNA amplicon sequencing was similar across the three DNA extraction methods. However, differences were noted in the relative abundance of bacterial taxa, with significantly higher abundance of Gram-positive genera detected in the DNA samples prepared using the PowerFood DNA extraction kit. CONCLUSION The choice of DNA extraction method can affect the detection of bacterial taxa by 16S rRNA amplicon sequencing in chicken meat rinses. Investigators should be aware of this procedural bias and select methods that are fit for the purposes of their investigation.
Collapse
Affiliation(s)
- Annika Flint
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Anna Laidlaw
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Leo Li
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Courtney Raitt
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Mary Rao
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Ashley Cooper
- Canadian Food Inspection Agency, 960 Carling Road, Ottawa, ON, K1A 0Z2, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada
| | - Catherine Carrillo
- Canadian Food Inspection Agency, 960 Carling Road, Ottawa, ON, K1A 0Z2, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards Health Canada, 251 Sir Frederick Banting Driveway, A.L. 2204E, Ottawa, ON, K1A 0K9, Canada.
| |
Collapse
|
13
|
Microbiota Succession of Whole and Filleted European Sea Bass ( Dicentrarchus labrax) during Storage under Aerobic and MAP Conditions via 16S rRNA Gene High-Throughput Sequencing Approach. Microorganisms 2022; 10:microorganisms10091870. [PMID: 36144472 PMCID: PMC9505548 DOI: 10.3390/microorganisms10091870] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
In the present work, the profiles of bacterial communities of whole and filleted European sea bass (Dicentrarchus labrax), during several storage temperatures (0, 4, 8 and 12 °C) under aerobic and Modified Atmosphere Packaging (MAP) conditions, were examined via the 16S rRNA High-Throughput Sequencing (HTS) approach. Sensorial attributes were also assessed to determine products’ shelf-life. Results indicated that shelf-life was strongly dependent on handling, as well as on temperature and atmosphere conditions. HTS revealed the undisputed dominance of Pseudomonas from the very beginning and throughout storage period in the majority of treatments. However, a slightly different microbiota profile was recorded in MAP-stored fillets at the middle stages of storage, which mainly referred to the sporadic appearance of some bacteria (e.g., Carnobacterium, Shewanella, etc.) that followed the dominance of Pseudomonas. It is noticeable that a major difference was observed at the end of shelf-life of MAP-stored fillets at 12 °C, where the dominant microbiota was constituted by the genus Serratia, while the relative abundance of Pseudomonas and Brochothrix was more limited. Furthermore, at the same temperature under aerobic storage of both whole and filleted fish, Pseudomonas almost co-existed with Acinetobacter, while the presence of both Erwinia and Serratia in whole fish was noteworthy. Overall, the present study provides useful information regarding the storage fate and spoilage status of whole and filleted European sea bass, suggesting that different handling and storage conditions influence the shelf-life of sea bass by favoring or delaying the dominance of Specific Spoilage Organisms (SSOs), affecting in parallel to some extent the formation of their consortium that is responsible for products’ sensorial deterioration. Such findings enrich the current knowledge and should be used as a benchmark to develop specific strategies aiming to delay spoilage and thus increase the products’ added value.
Collapse
|
14
|
Sequino G, Valentino V, Villani F, De Filippis F. Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality. Food Res Int 2022; 157:111242. [DOI: 10.1016/j.foodres.2022.111242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022]
|
15
|
Characterization of metabolite, genome and volatile organic compound changes provides insights into the spoilage and cold adaptive markers of Acinetobacter johnsonii XY27. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
Ekonomou S, Parlapani F, Kyritsi M, Hadjichristodoulou C, Boziaris I. Preservation status and microbial communities of vacuum-packed hot smoked rainbow trout fillets. Food Microbiol 2022; 103:103959. [DOI: 10.1016/j.fm.2021.103959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/05/2021] [Accepted: 11/29/2021] [Indexed: 01/22/2023]
|
17
|
Yuan Y, Xu W, Ma M, Zhang S, Wang D, Xu Y. Effect of fish sperm deoxyribonucleic acid encapsulation on stability, bioaccessibility, redispersibility, and solubilization of curcumin. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101746] [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]
|
18
|
Billington C, Kingsbury JM, Rivas L. Metagenomics Approaches for Improving Food Safety: A Review. J Food Prot 2022; 85:448-464. [PMID: 34706052 DOI: 10.4315/jfp-21-301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/21/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology. HIGHLIGHTS
Collapse
Affiliation(s)
- Craig Billington
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Joanne M Kingsbury
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Lucia Rivas
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| |
Collapse
|
19
|
Volatile Organic Compounds and 16S Metabarcoding in Ice-Stored Red Seabream Pagrus major. Foods 2022; 11:foods11050666. [PMID: 35267299 PMCID: PMC8909714 DOI: 10.3390/foods11050666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 01/09/2023] Open
Abstract
The profiles of bacterial communities and volatile organic compounds (VOCs) of farmed red seabream (Pagrus major) from two batches during ice storage were studied using 16S metabarcoding (culture independent approach) and headspace Solid Phase Micro-Extraction—Gas Chromatography/Mass Spectrometry (SPME-GC/MS) analysis, respectively. Sensory attributes and microbiological parameters were also evaluated. At Day 12 (shelf-life for both batches based on sensory evaluation), using classical microbiological analysis, Total Viable Counts (TVC) were found at the levels of 7–8 log cfu/g, and Pseudomonas and/or H2S producing bacteria dominated. On the other hand, the culture independent 16S metabarcoding analysis showed that Psychrobacter were the most abundant bacteria in fish tissue from batch 1, while Pseudomonas and Psychrobacter (at lower abundance) were the most abundant in fish from batch 2. Differences were also observed in VOC profiles between the two batches. However, combining the VOC results of the two batches, 15 compounds were found to present a similar trend during fish storage. Of them, 2-methylbutanal, 3-methylbutanal, 3-methyl-1-butanol, ethanol, 2,4 octadiene (2 isomers), ethyl lactate, acetaldehyde and (E)-2-penten-1-ol could be used as potential spoilage markers of red seabream because they increased during storage, mainly due to Psychrobacter and/or Pseudomonas activity and/or chemical activity (e.g., oxidation). Additionally, VOCs such as propanoic acid, nonanoic acid, decanoic acid, 1-propanol, 3,4-hexanediol and hexane decreased gradually with time, so they could be proposed as freshness markers of red seabream. Such information will be used to develop intelligent approaches for the rapid evaluation of spoilage course in red seabream during ice storage.
Collapse
|
20
|
Anagnostopoulos DA, Parlapani FF, Boziaris IS. The evolution of knowledge on seafood spoilage microbiota from the 20th to the 21st century: Have we finished or just begun? Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
21
|
Yu Q, Pan H, Qian C, Shao H, Han J, Li Y, Lou Y. Determination of the optimal electron beam irradiation dose for treating shrimp (Solenocera melantho) by means of physical and chemical properties and bacterial communities. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
22
|
De Oliveira Mota J, Boué G, Prévost H, Maillet A, Jaffres E, Maignien T, Arnich N, Sanaa M, Federighi M. Environmental monitoring program to support food microbiological safety and quality in food industries: A scoping review of the research and guidelines. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
23
|
Malacrinò A. Host species identity shapes the diversity and structure of insect microbiota. Mol Ecol 2021; 31:723-735. [PMID: 34837439 DOI: 10.1111/mec.16285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/04/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022]
Abstract
As for most of the life that inhabits our planet, microorganisms play an essential role in insect nutrition, reproduction, defence, and support their host in many other functions. More recently, we assisted to an exponential growth of studies describing the taxonomical composition of bacterial communities across insects' phylogeny. However, there is still an outstanding question that needs to be answered: Which factors contribute most to shape insects' microbiomes? This study tries to find an answer to this question by taking advantage of publicly available sequencing data and reanalysing over 4000 samples of insect-associated bacterial communities under a common framework. Results suggest that insect taxonomy has a wider impact on the structure and diversity of their associated microbial communities than the other factors considered (diet, sex, life stage, sample origin and treatment). However, when specifically testing for signatures of codiversification of insect species and their microbiota, analyses found weak support for this, suggesting that while insect species strongly drive the structure and diversity of insect microbiota, the diversification of those microbial communities did not follow their host's phylogeny. Furthermore, a parallel survey of the literature highlights several methodological limitations that need to be considered in the future research endeavours.
Collapse
Affiliation(s)
- Antonino Malacrinò
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität Münster, Münster, Germany
| |
Collapse
|
24
|
Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food. Processes (Basel) 2021. [DOI: 10.3390/pr9091669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Suansun, made from fresh bamboo shoots fermented without salt, is a traditional food in China’s southern region and is popular for its nutritious and unique flavor. To comprehensively understand the microbial species and characteristics of suansun, Illumina HiSeq metagenomic sequencing technology was used to sequence suansun’s fermentation broth obtained from six traditional producing areas in southern China, and the microbial community structure, diversity, and functional genes were analyzed. A total of 8 phyla, 16 classes, 30 orders, 63 families, 92 genera, and 156 species of microorganisms were identified in the suansun samples, with Lactiplantibacillus predominating, accounting for up to 81% of the species, among which 12 species, including Lactiplantibacillus plantarum, were the main species. A total of 12,751 unigenes were annotated to 385 metabolic pathway classes, of which 2927 unigenes were involved in carbohydrate metabolism. Lactiplantibacillus fermentum, Lactiplantibacillus plantarum, and Lactiplantibacillus brucei were involved in the metabolism of most nutrients and flavor substances in suansun. Overall, these results provide insights into the suansun microbiota and shed light on the fermentation processes carried out by complex microbial communities.
Collapse
|
25
|
Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing. Microorganisms 2021; 9:microorganisms9081574. [PMID: 34442653 PMCID: PMC8401261 DOI: 10.3390/microorganisms9081574] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023] Open
Abstract
Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination.
Collapse
|
26
|
Antibacterial Effect of Dihydromyricetin on Specific Spoilage Organisms of Hybrid Grouper. J FOOD QUALITY 2021. [DOI: 10.1155/2021/5569298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
This study aimed to investigate the mechanism of antibacterial activity level inhibition of dihydromyricetin (DMY) against specific spoilage bacteria of grouper. Firstly, the specific spoilage bacteria of grouper in the cold storage process are Pseudomonas antarctica (P. antarctica), which are selected by calculating the spoilage metabolite yield factor. It was determined that the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of DMY against grouper spoilage bacteria were 2.0 mg/mL and 6.4 mg/mL, respectively. DMY was added to the matrix of chitosan and sodium alginate, and DMY emulsions of different concentrations (0 MIC, 1 MIC, 2 MIC, 4 MIC) were prepared and characterized by differential calorimetry methods. Through analyzing cell permeability, enzyme activity, and images of the confocal laser scanning microscope (CLSM), we further studied the antibacterial mechanism of DMY emulsion on specific spoilage bacteria. The results showed that, with the increase of DMY concentration in the treatment group, the leakage of nucleic acid and protein increased significantly, the activity of ATPase and three critical enzymes in the Embden-Meyerhof-Parnas (EMP) pathway decreased significantly, and the activity of AKPase did not decrease significantly, . The metabolic activity and viability are reduced considerably. Analysis of the above results shows that DMY inhibits the growth and reproduction of P. antarctica by interfering with the metabolic activity of bacteria and destroying the function of bacterial cell membranes but has no inhibitory effect on the activity of AKPase. This study proves that DMY could be an effective and natural antibacterial agent against specific spoilage bacteria in aquatic products.
Collapse
|
27
|
Lim ES, Kim JJ, Sul WJ, Kim JS, Kim B, Kim H, Koo OK. Metagenomic Analysis of Microbial Composition Revealed Cross-Contamination Pathway of Bacteria at a Foodservice Facility. Front Microbiol 2021; 12:636329. [PMID: 33912146 PMCID: PMC8071874 DOI: 10.3389/fmicb.2021.636329] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/18/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial contamination of food-contact surfaces can be a potential risk factor for food quality and safety. To evaluate the spatial and temporal variations of the potential cross-contamination routes, we conducted a biogeographical assessment of bacteria in a foodservice facility based on the diversity of microflora on each surface. To this end, we performed high-throughput amplicon sequencing of 13 food-contact and non-food contact surfaces in a foodservice facility throughout a year. The results showed that Bacillus, Acinetobacter, Streptophyta, Enterobacter, Pseudomonas, Serratia, Enhydrobacter, Staphylococcus, Paracoccus, and Lysinibacillus were the dominant genera found on the kitchen surfaces of the foodservice facility. Depending on the season, changes in Firmicute/Proteobacteria ratios were observed, and the fan becomes the main source of outdoor air contamination. The microbial flow associated with spoilage was also observed throughout food preparation. Taken together, our results would be a powerful reference to hygiene managers for improvement of food processes.
Collapse
Affiliation(s)
- Eun Seob Lim
- Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, South Korea.,Food Safety Research Team, Korea Food Research Institute, Wanju-gun, South Korea
| | - Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Joo-Sung Kim
- Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, South Korea.,Food Safety Research Team, Korea Food Research Institute, Wanju-gun, South Korea
| | - Bomin Kim
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea.,Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Hun Kim
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea.,Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Ok Kyung Koo
- Department of Food and Nutrition, Gyeongsang National University, Jinju, South Korea.,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
| |
Collapse
|