1
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Parente E, Ricciardi A. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 2024; 13:1689. [PMID: 38890917 PMCID: PMC11171936 DOI: 10.3390/foods13111689] [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: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.
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Affiliation(s)
- Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy;
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2
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Imai K, Niwa R, Fujioka M, Ito K. Understanding the quality and safety of food production through the lens of The Microbiome of The Built Environment. Biosci Biotechnol Biochem 2024; 88:254-259. [PMID: 37994666 DOI: 10.1093/bbb/zbad164] [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: 10/02/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023]
Abstract
The Microbiome of the Built Environment (MoBE) is profoundly implicated in various sectors, including food science. The balance between beneficial and pathogenic microbes in these facilities directly influences product quality and public health. Maintaining a careful check on MoBE and external microbes is vital to the food industry to ensure quality control. There is also a risk of contamination in the meat processing facility as well. However, over-sanitization can increase drug-resistant microbes, highlighting the importance of balanced microbial management. Additionally, facility design, influenced by understanding MoBE, can optimize the growth of beneficial microbes and inhibit pathogenic microbes. Microbial mapping, an emerging practice, offers insights into microbial hotspots within facilities, resulting in targeted interventions. As the food industry evolves, the intricate understanding and management of MoBE will be pivotal to ensuring optimal food quality, safety, and innovation.
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Affiliation(s)
- Kota Imai
- BIOTA Inc., Tokyo, Japan
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Ryo Niwa
- BIOTA Inc., Tokyo, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Fujioka
- BIOTA Inc., Tokyo, Japan
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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3
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Lake FB, Chen J, van Overbeek LS, Baars JJP, Abee T, den Besten HMW. Biofilm formation and desiccation survival of Listeria monocytogenes with microbiota on mushroom processing surfaces and the effect of cleaning and disinfection. Int J Food Microbiol 2024; 411:110509. [PMID: 38101188 DOI: 10.1016/j.ijfoodmicro.2023.110509] [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: 05/09/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
Abstract
Microbial multispecies communities consisting of background microbiota and Listeria monocytogenes could be established on materials used in food processing environments. The presence, abundance and diversity of the strains within these microbial multispecies communities may be affected by mutual interactions and differences in resistance towards regular cleaning and disinfection (C&D) procedures. Therefore, this study aimed to characterize the growth and diversity of a L. monocytogenes strain cocktail (n = 6) during biofilm formation on polyvinyl chloride (PVC) and stainless steel (SS) without and with the presence of a diverse set of background microbiota (n = 18). L. monocytogenes and background microbiota strains were isolated from mushroom processing environments and experiments were conducted in simulated mushroom processing environmental conditions using mushroom extract as growth medium and ambient temperature (20 °C) as culturing temperature. The L. monocytogenes strains applied during monospecies biofilm incubation formed biofilms on both PVC and SS coupons, and four cycles of C&D treatment were applied with a chlorinated alkaline cleaning agent and a disinfection agent based on peracetic acid and hydrogen peroxide. After each C&D treatment, the coupons were re-incubated for two days during an incubation period for 8 days in total, and C&D resulted in effective removal of biofilms from SS (reduction of 4.5 log CFU/cm2 or less, resulting in counts below detection limit of 1.5 log CFU/cm2 after every C&D treatment), while C&D treatments on biofilms formed on PVC resulted in limited reductions (reductions between 1.2 and 2.4 log CFU/cm2, which equals a reduction of 93.7 % and 99.6 %, respectively). Incubation of the L. monocytogenes strains with the microbiota during multispecies biofilm incubation led to the establishment of L. monocytogenes in the biofilm after 48 h incubation with corresponding high L. monocytogenes strain diversity in the multispecies biofilm on SS and PVC. C&D treatments removed L. monocytogenes from multispecies biofilm communities on SS (reduction of 3.5 log CFU/cm2 or less, resulting in counts below detection limit of 1.5 log CFU/cm2 after every C&D treatment), with varying dominance of microbiota species during different C&D cycles. However, C&D treatments of multispecies biofilm on PVC resulted in lower reductions of L. monocytogenes (between 0.2 and 2.4 log CFU/cm2) compared to single species biofilm, and subsequent regrowth of L. monocytogenes and stable dominance of Enterobacteriaceae and Pseudomonas. In addition, planktonic cultures of L. monocytogenes were deposited and desiccated on dry surfaces without and with the presence of planktonic background microbiota cultures. The observed decline of desiccated cell counts over time was faster on SS compared to PVC. However, the application of C&D resulted in counts below the detection limit of 1.7 log CFU/coupon on both surfaces (reduction of 5.9 log CFU/coupon or less). This study shows that L. monocytogenes is able to form single and multispecies biofilms on PVC with high strain diversity following C&D treatments. This highlights the need to apply more stringent C&D regime treatments for especially PVC and similar surfaces to efficiently remove biofilm cells from food processing surfaces.
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Affiliation(s)
- Frank B Lake
- Food Microbiology, Wageningen University and Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands
| | - Jingjie Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Center for Life Sciences, Yunnan University, Kunming 650091, China
| | - Leo S van Overbeek
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708, PB, Wageningen, the Netherlands
| | - Johan J P Baars
- Plant Breeding, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708, PB, Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands
| | - Heidy M W den Besten
- Food Microbiology, Wageningen University and Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands.
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4
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Abstract
For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.
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Affiliation(s)
- Nicolas L Louw
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Kasturi Lele
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Collin B Edwards
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
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5
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Ajibola OO, Thomas R, Bakare BF. Selected fermented indigenous vegetables and fruits from Malaysia as potential sources of natural probiotics for improving gut health. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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6
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An F, Wu J, Feng Y, Pan G, Ma Y, Jiang J, Yang X, Xue R, Wu R, Zhao M. A systematic review on the flavor of soy-based fermented foods: Core fermentation microbiome, multisensory flavor substances, key enzymes, and metabolic pathways. Compr Rev Food Sci Food Saf 2023; 22:2773-2801. [PMID: 37082778 DOI: 10.1111/1541-4337.13162] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023]
Abstract
The characteristic flavor of fermented foods has an important impact on the purchasing decisions of consumers, and its production mechanisms are a concern for scientists worldwide. The perception of food flavor is a complex process involving olfaction, taste, vision, and oral touch, with various senses contributing to specific properties of the flavor. Soy-based fermented products are popular because of their unique flavors, especially in Asian countries, where they occupy an important place in the dietary structure. Microorganisms, known as the souls of fermented foods, can influence the sensory properties of soy-based fermented foods through various metabolic pathways, and are closely related to the formation of multisensory properties. Therefore, this review systematically summarizes the core microbiome and its interactions that play an active role in representative soy-based fermented foods, such as fermented soymilk, soy sauce, soybean paste, sufu, and douchi. The mechanism of action of the core microbial community on multisensory flavor quality is revealed here. Revealing the fermentation core microbiome and related enzymes provides important guidance for the development of flavor-enhancement strategies and related genetically engineered bacteria.
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Affiliation(s)
- Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, China
- Liaoning Provincial Engineering Research Center of Food Fermentation Technology, Shenyang, China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China
- Liaoning Provincial Engineering Research Center of Food Fermentation Technology, Shenyang, China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, China
| | - Yunzi Feng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Guoyang Pan
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Yuanyuan Ma
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Jinhui Jiang
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Xuemeng Yang
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Ruixia Xue
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China
- Liaoning Provincial Engineering Research Center of Food Fermentation Technology, Shenyang, China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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7
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Chen L, Wang G, Teng M, Wang L, Yang F, Jin G, Du H, Xu Y. Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration. Compr Rev Food Sci Food Saf 2023; 22:1902-1932. [PMID: 36880579 DOI: 10.1111/1541-4337.13135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 03/08/2023]
Abstract
Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.
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Affiliation(s)
- Liangqiang Chen
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | | | | | - Li Wang
- Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Fan Yang
- Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Guangyuan Jin
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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8
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Sangkaew O, Prombutara P, Roytrakul S, Yompakdee C. Metatranscriptomics Reveals Sequential Expression of Genes Involved in the Production of Melanogenesis Inhibitors by the Defined Microbial Species in Fermented Unpolished Black Rice. Microbiol Spectr 2023; 11:e0313922. [PMID: 36861996 PMCID: PMC10100879 DOI: 10.1128/spectrum.03139-22] [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: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Fermented products require metabolic enzymes from the microbial community for desired final products. Using a metatranscriptomic approach, the role of microorganisms in fermented products on producing compounds with a melanogenesis inhibition activity has not yet been reported. Previously, unpolished black rice (UBR) fermented with the E11 starter containing Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Rhizopus oryzae, and Pediococcus pentosaceus (FUBR) showed potent melanogenesis inhibition activity. This study aimed to investigate the function of these defined microbial species in producing melanogenesis inhibitors in the FUBR using a metatranscriptomic approach. The melanogenesis inhibition activity increased in a fermentation time-dependent manner. Genes related to melanogenesis inhibitors synthesis such as carbohydrate metabolism, amino acids synthesis, fatty acids/unsaturated fatty acids synthesis, and carbohydrate transporters were analyzed. Most genes from R. oryzae and P. pentosaceus were upregulated in the early stage of the fermentation process, while those of S. cerevisiae and S. fibuligera were upregulated in the late stage. FUBR production using different combinations of the four microbial species shows that all species were required to produce the highest activity. The FUBR containing at least R. oryzae and/or P. pentosaceus exhibited a certain level of activity. These findings were in agreement with the metatranscriptomic results. Overall, the results suggested that all four species sequentially and/or coordinately synthesized metabolites during the fermentation that led to a FUBR with maximum melanogenesis inhibition activity. This study not only sheds light on crucial functions of certain microbial community on producing the melanogenesis inhibitors, but also paves the way to initiate quality improvement of melanogenesis inhibition activity in the FUBR. IMPORTANCE Fermentation of food is a metabolic process through the action of enzymes from certain microorganisms. Although roles of the microbial community in the fermented food were investigated using metatranscriptomic approach in terms of flavors, but no study has been reported so far on the function of the microorganisms on producing compounds with a melanogenesis inhibition activity. Therefore, this study explained the roles of the defined microorganisms from the selected starter in the fermented unpolished black rice (FUBR) that can produce melanogenesis inhibitor(s) using metatranscriptomic analysis. Genes from different species were upregulated at different fermentation time. All four microbial species in the FUBR sequentially and/or coordinately synthesized metabolites during fermentation that led to a FUBR with maximal melanogenesis inhibition activity. This finding contributes to a deeper understanding of the roles of certain microbial community during fermentation and led to the knowledge-based improvement for the fermented rice with potent melanogenesis inhibition activity.
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Affiliation(s)
- Orrarat Sangkaew
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Pinidphon Prombutara
- Omics Science & Bioinformatics Center, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani, Thailand
| | - Chulee Yompakdee
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
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9
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Wolfe BE. Are fermented foods an overlooked reservoir and vector of antimicrobial resistance? Curr Opin Food Sci 2023. [DOI: 10.1016/j.cofs.2023.101018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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10
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Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation. Foods 2023; 12:foods12030673. [PMID: 36766201 PMCID: PMC9914028 DOI: 10.3390/foods12030673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.
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11
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Emamjomeh M, Mohd Hashim A, Abdul-Mutalib NA, Khairil Mokhtar NF, Mustapha NA, Maeda T, Amin-Nordin S. Profiling bacterial communities and foodborne pathogens on food-associated surface following contact with raw beef, chicken and pork using 16S amplicon metagenomics. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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12
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Shi H, An F, Lin H, Li M, Wu J, Wu R. Advances in fermented foods revealed by multi-omics: A new direction toward precisely clarifying the roles of microorganisms. Front Microbiol 2022; 13:1044820. [PMID: 36590428 PMCID: PMC9794733 DOI: 10.3389/fmicb.2022.1044820] [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: 09/15/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
Fermented foods generally comprise a complex micro-ecosystem with beneficial microbiota, functional products, and special flavors and qualities that are welcomed globally. Single-omics analysis allows for a comprehensive characterization of the main microbial factors influencing the function, flavor, and quality of fermented foods. However, the species, relative abundance, viability, growth patterns, and metabolic processes of microorganisms vary with changes in processing and environmental conditions during fermentation. Furthermore, the mechanisms underlying the complex interaction among microorganisms are still difficult to completely understand and analyze. Recently, multi-omics analysis and the integration of multiple types of omics data allowed researchers to more comprehensively explore microbial communities and understand the precise relationship between fermented foods and their functions, flavors, and qualities. Multi-omics approaches might help clarify the mechanisms underpinning the fermentation processes, metabolites, and functional components of these communities. This review clarified the recent advances in the roles of microorganisms in fermented foods based on multi-omics data. Current research achievements may allow for the precise control of the whole industrial processing technology of fermented foods, meeting consumers' expectations of healthy products.
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Affiliation(s)
- Haisu Shi
- College of Food Science, Shenyang Agricultural University, Shenyang, China,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, China,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, China
| | - Feiyu An
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Hao Lin
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Mo Li
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, China,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, China,Junrui Wu,
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, China,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, China,*Correspondence: Rina Wu,
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13
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Kang J, Xue Y, Chen X, Han BZ. Integrated multi-omics approaches to understand microbiome assembly in Jiuqu, a mixed-culture starter. Compr Rev Food Sci Food Saf 2022; 21:4076-4107. [PMID: 36038529 DOI: 10.1111/1541-4337.13025] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 01/28/2023]
Abstract
The use of Jiuqu as a saccharifying and fermenting starter in the production of fermented foods is a very old biotechnological process that can be traced back to ancient times. Jiuqu harbors a hub of microbial communities, in which prokaryotes and eukaryotes cohabit, interact, and communicate. However, the spontaneous fermentation based on empirical processing hardly guarantees the stable assembly of the microbiome and a standardized quality of Jiuqu. This review describes the state of the art, limitations, and challenges towards the application of traditional and omics-based technology to study the Jiuqu microbiome and highlights the need for integrating meta-omics data. In addition, we review the varieties of Jiuqu and their production processes, with particular attention to factors shaping the microbiota of Jiuqu. Then, the potentials of integrated omics approaches used in Jiuqu research are examined in order to understand the assembly of the microbiome and improve the quality of the products. A variety of different approaches, including molecular and mass spectrometry-based techniques, have led to scientific advances in the analysis of the complex ecosystem of Jiuqu. To date, the extensive research on Jiuqu has mainly focused on the microbial community diversity, flavor profiles, and biochemical characteristics. An integrative approach to large-scale omics datasets and cultivated microbiota has great potential for understanding the interrelation of the Jiuqu microbiome. Further research on the Jiuqu microbiome may explain the inherent property of compositional stability and stable performance of a complex microbiota coping with environmental perturbations and provide important insights to reconstruct synthetic microbiota and develop modern intelligent manufacturing procedures for Jiuqu.
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Affiliation(s)
- Jiamu Kang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yansong Xue
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xiaoxue Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Bei-Zhong Han
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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14
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Zhang X, Zhang X, Yan Y, Liu Y, Zhao X, Xu H, He L, Huang Y. Relationship between flavor compounds and changes of microbial community in the solid fermented vinegar. Biosci Biotechnol Biochem 2022; 86:1581-1589. [PMID: 35998319 DOI: 10.1093/bbb/zbac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/19/2022] [Indexed: 11/14/2022]
Abstract
The relationship between volatile compounds of vinegar and microorganisms is not clear, especially pyrazine, a trace component. In order to reveal their potential relationship, high throughput sequencing, solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) and Spearman's correlation analysis were used. Results showed that Acetobacter and Lactobacillus with opposite abundance trends were the predominant bacteria, and the total abundance of them exceeds 98%, while the predominant fungal genera were Aspergillus and Malassezia, their highest abundances are 75.4% and 81.5% respectively. In the whole process of microbial community succession, six pyrazines were detected including trimethylpyrazine and tetramethylpyrazine, etc, and Spearman's correlation analysis showed that they were positively correlated with the presence of Vibrionimonas, Paraburkholderia, Paucibacter, Komagataeibacter, Acinetobacter and Slinibacter. In general, this study further revealed more species related to pyrazines, it will be helpful to understand the formation of pyrazines and promote the improvement of vinegar quality.
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Affiliation(s)
- Xuelin Zhang
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
| | - Xingrong Zhang
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
| | - Yongheng Yan
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
| | - Yang Liu
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
| | - Xiangying Zhao
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
| | - Hui Xu
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
| | - Lianzhi He
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
| | - Yanhong Huang
- Shandong Food Ferment Industry Research and Design Institute, Qilu University of Technology, Jinan, Shandong, China
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15
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Stevens EL, Carleton HA, Beal J, Tillman GE, Lindsey RL, Lauer AC, Pightling A, Jarvis KG, Ottesen A, Ramachandran P, Hintz L, Katz LS, Folster JP, Whichard JM, Trees E, Timme RE, McDERMOTT P, Wolpert B, Bazaco M, Zhao S, Lindley S, Bruce BB, Griffin PM, Brown E, Allard M, Tallent S, Irvin K, Hoffmann M, Wise M, Tauxe R, Gerner-Smidt P, Simmons M, Kissler B, Defibaugh-Chavez S, Klimke W, Agarwala R, Lindsay J, Cook K, Austerman SR, Goldman D, McGARRY S, Hale KR, Dessai U, Musser SM, Braden C. Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States. J Food Prot 2022; 85:755-772. [PMID: 35259246 DOI: 10.4315/jfp-21-437] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety. HIGHLIGHTS
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Affiliation(s)
- Eric L Stevens
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Heather A Carleton
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jennifer Beal
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Glenn E Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Rebecca L Lindsey
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - A C Lauer
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Arthur Pightling
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Karen G Jarvis
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Andrea Ottesen
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Padmini Ramachandran
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Leslie Hintz
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Lee S Katz
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jason P Folster
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Jean M Whichard
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eija Trees
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Ruth E Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Patrick McDERMOTT
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Beverly Wolpert
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Michael Bazaco
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, Maryland 20708
| | - Sabina Lindley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Beau B Bruce
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Patricia M Griffin
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Eric Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Sandra Tallent
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Kari Irvin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Maria Hoffmann
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Matt Wise
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Robert Tauxe
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Mustafa Simmons
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Bonnie Kissler
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | | | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Richa Agarwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - James Lindsay
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Kimberly Cook
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
| | - Suelee Robbe Austerman
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, Iowa 50010, USA
| | - David Goldman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Sherri McGARRY
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
| | - Kis Robertson Hale
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250
| | - Steven M Musser
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, Maryland 20740
| | - Chris Braden
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, Georgia 30329
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16
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Jiang N, Wu R, Wu C, Wang R, Wu J, Shi H. Multi-omics approaches to elucidate the role of interactions between microbial communities in cheese flavor and quality. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2070199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Nan Jiang
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P. R. China
| | - Chen Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Ruhong Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P. R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P. R. China
| | - Haisu Shi
- College of Food Science, Shenyang Agricultural University, Shenyang, P. R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, P. R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, P. R. China
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17
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Zhou C, Xia Q, Du L, He J, Sun Y, Dang Y, Geng F, Pan D, Cao J, Zhou G. Recent developments in off-odor formation mechanism and the potential regulation by starter cultures in dry-cured ham. Crit Rev Food Sci Nutr 2022; 63:8781-8795. [PMID: 35373656 DOI: 10.1080/10408398.2022.2057418] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Foul-smelling odors are main quality defects of dry-cured ham, which are connected with the excessive degradation of the structural proteins and excessive oxidation of lipids caused by the abnormal growth of spoilage microorganisms, threatening the development of dry-cured ham industry. Characterizing the key microorganisms and metabolites resulted in the spoilage of dry-cured ham, and discussing the relationship between spoilage microorganisms and metabolites are the key aspects to deeply understand the formation mechanism of off-odor in dry-cured ham. Until now, there is no detailed discussion or critical review on the role of spoilage microorganisms in developing the off-odor of dry-cured ham, and the regulation of off-odor and spoilage microorganisms by starter cultures has been not discussed. This review shows the recent achievement in the off-odor formation mechanism of dry-cured ham, and outlines the potential regulation of off-odor defects in dry-cured ham by starter cultures. Results from current research show that the abnormal growth of Lactic acid bacteria, Micrococcaceae, Enterobacteriaceae, Yeasts and Molds plays a key role in developing the off-odor defects of dry-cured ham, while the key spoilage microorganisms of different type hams are discrepant. High profile of aldehydes, acids, sulfur compounds and biogenic amines are responsible for off-odor development in spoiled dry-cured ham. Several starter cultures derived from these species of Staphylococcus, Penicillium, Debaryomyces, Pediococcus and Lactobacillus show a great potential to prevent microbiological hazards and improve flavor quality of dry-cured ham, whereas, the ecology, function and compatibility of these starter cultures with the processing parameters of dry-cured ham need to be further evaluated in the future.
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Affiliation(s)
- Changyu Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province; College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Qiang Xia
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province; College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Lihui Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province; College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Jun He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province; College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Yangying Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province; College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Yali Dang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province; College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province; College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Jinxuan Cao
- School of Food and Health, Beijing Technology and Business University, Beijing, P.R. China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
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18
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Gu G, Kroft B, Lichtenwald M, Luo Y, Millner P, Patel J, Nou X. Dynamics of Listeria monocytogenes and the microbiome on fresh-cut cantaloupe and romaine lettuce during storage at refrigerated and abusive temperatures. Int J Food Microbiol 2022; 364:109531. [PMID: 35033975 DOI: 10.1016/j.ijfoodmicro.2022.109531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/09/2021] [Accepted: 01/03/2022] [Indexed: 12/25/2022]
Abstract
Listeria monocytogenes (Lm) outbreaks and recalls associated with fresh produce in recent years have heightened concerns and demands from industry and consumers to more effectively mitigate the contamination risk of this foodborne pathogen on fresh produce. In this study, the growth of Lm and indigenous bacteria on fresh-cut cantaloupe and romaine lettuce held at refrigerated (4 °C) and abusive (10-24 °C) temperatures was determined by both culture dependent and independent methods. Composition and dynamics of bacterial communities on Lm inoculated and non-inoculated samples were analyzed by 16S rRNA high-throughput sequencing. Fresh-cut cantaloupe provided favorable growth conditions for Lm proliferation (1.7 and >6 log increase at refrigerated and abusive temperatures, respectively) to overtake indigenous bacteria. The Lm population also increased on fresh-cut lettuce, but the growth rate was lower than that of the total mesophilic bacteria, resulting in 0.4 and >2 log increase at refrigerated and abusive temperatures. Microbial diversity of fresh-cut cantaloupe was significantly lower than that of fresh-cut romaine lettuce. The Shannon index of microbial communities on cantaloupe declined after storage, but it was not significantly changed on lettuce samples. Shifts in the bacterial microbiome on cantaloupe were mainly affected by Lm inoculation, while both inoculation and storage temperature played significant roles on lettuce bacterial communities. Multiple indigenous bacteria, including Leuconostoc and Weissella spp., were negatively correlated to Lm abundance on romaine lettuce, and were determined by bioassay as potential anti-listerial species. Data derived from this study contribute to better understanding of the relationship between Lm and indigenous microbiota on fresh-cut produce during storage.
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Affiliation(s)
- Ganyu Gu
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, USA
| | - Brenda Kroft
- Centre for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Marina Lichtenwald
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, USA
| | - Yaguang Luo
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, USA
| | - Patricia Millner
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, USA
| | - Jitendra Patel
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, USA
| | - Xiangwu Nou
- Environmental Microbial and Food Safety Laboratory, USDA ARS, Beltsville, MD 20705, USA.
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19
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Lacorte GA, Cruvinel LA, de Paula Ávila M, Dias MF, de Abreu Pereira A, Nascimento AMA, de Melo Franco BDG. Investigating the influence of Food Safety Management Systems (FSMS) on microbial diversity of Canastra cheeses and their processing environments. Food Microbiol 2022; 105:104023. [DOI: 10.1016/j.fm.2022.104023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
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20
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Irlinger F, Monnet C. Temporal differences in microbial composition of Époisses cheese rinds during ripening and storage. J Dairy Sci 2021; 104:7500-7508. [PMID: 33838885 DOI: 10.3168/jds.2021-20123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/24/2021] [Indexed: 12/30/2022]
Abstract
Époisses is a protected designation of origin smear-ripened cheese from the Burgundy region in France. It has an orange color and a strong flavor, both of which are generated by surface microorganisms. The objective of the present study was to investigate the microbial dynamics at the surface of Époisses cheese during ripening and postmanufacturing storage at low temperatures. Rind samples were analyzed by enumeration on agar plates and by 16S rRNA gene and internal transcribed spacer amplicon sequencing. During most of the ripening process, the counts of yeasts, which corresponded to the species Debaryomyces hansenii and Geotrichum candidum, were higher than those of the aerobic acid-sensitive bacteria. Debaryomyces hansenii reached a level of about 3 × 108 cfu/cm2, and its viability strongly decreased in the late stage of ripening and during storage at 4°C. Two of the inoculated bacterial species, Brevibacterium aurantiacum and Staphylococcus xylosus, did not establish themselves at the cheese surface. At the end of ripening, among the 18 most abundant bacterial species detected by amplicon sequencing, 14 were gram-negative, mainly from genera Psychrobacter, Vibrio, Halomonas, and Mesonia. It was hypothesized that the high moisture level of the Époisses rinds, due the humid atmosphere of the ripening rooms and to the frequent washings of the curds, favored growth of these gram-negative species. These species may be of interest for the development of efficient ripening cultures. In addition, because the orange color of Époisses cheeses could not be attributed to the growth of Brevibacterium, it would be interesting to investigate the type and origin of the pigments that confer color to this cheese.
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Affiliation(s)
- F Irlinger
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - C Monnet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France.
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21
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Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, Reid G, Wolfe BE, Hutkins R. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol 2021; 18:196-208. [PMID: 33398112 PMCID: PMC7925329 DOI: 10.1038/s41575-020-00390-5] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2020] [Indexed: 02/07/2023]
Abstract
An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.
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Affiliation(s)
- Maria L Marco
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
| | - Michael Gänzle
- University of Alberta, Department of Agricultural, Food and Nutritional Science, Edmonton, Canada
| | - Marie Claire Arrieta
- Department of Physiology and Pharmacology, International Microbiome Center, University of Calgary, Calgary, Canada
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Wilhelm Holzapfel
- Advanced Green Energy and Environment Institute, Handong Global University, Pohang, Gyeongbuk, South Korea
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Dan Merenstein
- Department of Family Medicine, Georgetown University, Washington, DC, USA
| | - Gregor Reid
- Lawson Health Research Institute, and Departments of Microbiology & Immunology and Surgery, University of Western Ontario, London, Ontario, Canada
| | | | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA.
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22
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Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage. Foods 2021; 10:foods10020362. [PMID: 33562402 PMCID: PMC7914861 DOI: 10.3390/foods10020362] [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: 11/27/2020] [Revised: 01/23/2021] [Accepted: 02/02/2021] [Indexed: 02/03/2023] Open
Abstract
Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3—V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia,Pantoea, γ-Proteobacteria Psychrobacter, Shewanella and Pseudomonas. Specific operational taxonomic units were identified during the 28-day storage study period. Operational taxonomic units specific to the processing environment were also identified. Although the 45 cold-smoked salmon products shared a core microbiota, a processing plant signature was found. This suggest that the bacterial communities of cold-smoked salmon products are impacted by the processing environment, and this environment could have a negative effect on product quality. The use of a polyphasic approach for seafood products and food processing environments could provide better insights into residential bacteria dynamics and their impact on food safety and quality.
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23
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The spatial variation of soil bacterial community assembly processes affects the accuracy of source tracking in ten major Chinese cities. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1546-1559. [PMID: 33439456 DOI: 10.1007/s11427-020-1843-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
Abstract
Urban soils harbor billions of bacterial cells and millions of species. However, the distribution patterns and assembly processes of bacterial communities remain largely uncharacterized in urban soils. It is also unknown if we can use the bacteria to track soil sources to certain cities and districts. Here, Illumina MiSeq sequencing was used to survey soil bacterial communities from 529 random plots spanning 61 districts and 10 major cities in China. Over a 3,000 km range, community similarity declined with increasing geographic distance (Mantel r=0.62), and community composition was clustered by city (R2=0.50). Within cities (<100 km), the aforementioned biogeographic patterns were weakened. Process analysis showed that homogenizing dispersal and dispersal limitation dominated soil bacterial assembly at small and large spatial scales, respectively. Accordingly, the probabilities of accurately tracking random soil sources to certain cities and districts were 90.0% and 66.7%, respectively. When the tested samples originated from cities that were more than 1,265 km apart, the soil sources could be identified with nearly 100% accuracy. Overall, this study demonstrates the strong distance-decay relationship and the clear geographic zoning of urban soil bacterial communities among cities. The varied importance of different community assembly processes at multiple spatial scales strongly affects the accuracy of microbial source tracking.
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Frigerio J, Agostinetto G, Galimberti A, De Mattia F, Labra M, Bruno A. Tasting the differences: Microbiota analysis of different insect-based novel food. Food Res Int 2020; 137:109426. [DOI: 10.1016/j.foodres.2020.109426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/18/2020] [Accepted: 06/05/2020] [Indexed: 01/04/2023]
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25
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Li S, Yang Z, Hu D, Cao L, He Q. Understanding building-occupant-microbiome interactions toward healthy built environments: A review. FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING 2020; 15:65. [PMID: 33145119 PMCID: PMC7596174 DOI: 10.1007/s11783-020-1357-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/30/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Built environments, occupants, and microbiomes constitute a system of ecosystems with extensive interactions that impact one another. Understanding the interactions between these systems is essential to develop strategies for effective management of the built environment and its inhabitants to enhance public health and well-being. Numerous studies have been conducted to characterize the microbiomes of the built environment. This review summarizes current progress in understanding the interactions between attributes of built environments and occupant behaviors that shape the structure and dynamics of indoor microbial communities. In addition, this review also discusses the challenges and future research needs in the field of microbiomes of the built environment that necessitate research beyond the basic characterization of microbiomes in order to gain an understanding of the causal mechanisms between the built environment, occupants, and microbiomes, which will provide a knowledge base for the development of transformative intervention strategies toward healthy built environments. The pressing need to control the transmission of SARS-CoV-2 in indoor environments highlights the urgency and significance of understanding the complex interactions between the built environment, occupants, and microbiomes, which is the focus of this review.
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Affiliation(s)
- Shuai Li
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Zhiyao Yang
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Da Hu
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Liu Cao
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Institute for a Secure & Sustainable Environment, University of Tennessee, Knoxville, TN 37996 USA
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High-throughput sequencing approach to reveal the bacterial diversity of traditional yak jerky from the Tibetan regions. Meat Sci 2020; 172:108348. [PMID: 33120176 DOI: 10.1016/j.meatsci.2020.108348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 07/09/2020] [Accepted: 10/13/2020] [Indexed: 11/23/2022]
Abstract
A high-throughput sequencing approach was used to investigate the bacterial community diversity of traditional Tibetan yak jerky, which was collected from three different regions in Tibet and with different natural drying times. Tibetan yak jerky from different regions had different bacterial communities, which was mainly reflected in the relative abundance levels of unclassified Cyanobacteria, Psychrobacter and Acinetobacter. The unclassified Cyanobacteria was the dominant genus of Qamdo yak jerky, Acinetobacter was the dominant genus of Shigatse yak jerky, and Psychrobacteria was the dominant genus of Nyingchi yak jerky. With increasing natural drying time, the diversity of bacterial communities in yak jerky decreased, and unclassified Cyanobacteria become the dominant genus. Spearman's correlation analysis and canonical correspondence analysis revealed that physicochemical factors (moisture content, water activity, shear force and pH) were significantly correlated with bacterial community. Our results will be beneficial to improve and standardize the safety and quality of traditional Tibetan yak jerky.
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Hamilton A, Harper SJ, Critzer F. Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces. Microorganisms 2020; 8:microorganisms8101480. [PMID: 32993184 PMCID: PMC7601045 DOI: 10.3390/microorganisms8101480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022] Open
Abstract
Apples are the most consumed fruit in the United States and have recently been shown to exhibit some vulnerability to contamination across the supply chain. It is unclear what role a fruit microbiome analysis may serve in future food safety programs interested in understanding changes in the product and the processing environment. Ultimately, sample integrity is key if any of these approaches are to be employed; low microbial loads on apple surfaces, the inability to sample the entire surface, and inefficiency of removal may act as barriers to achieving high-quality DNA. As such, the objective of this study was to identify a reproducible method to concentrate and quantify bacterial and fungal DNA from fresh apple surfaces. Five methods were evaluated: two variations of wash solutions for bath sonication, wash filtration, epidermis excision, and surface swabbing. Epidermis excision returned the highest mean DNA quantities, followed by the sonicated washes and wash filtration. Surface swabbing was consistently below the limit of detection. Based on the quantity of host DNA contamination in surface excision, the sonicated wash solution containing a surfactant presents the greatest opportunity for consistent, high-yielding DNA recovery from the entire apple surface.
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Affiliation(s)
- Alexis Hamilton
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
- Correspondence: ; Tel.:+1-509-786-9209
| | - Scott J. Harper
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA;
| | - Faith Critzer
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
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The sources and transmission routes of microbial populations throughout a meat processing facility. NPJ Biofilms Microbiomes 2020; 6:26. [PMID: 32651393 PMCID: PMC7351959 DOI: 10.1038/s41522-020-0136-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/11/2020] [Indexed: 02/02/2023] Open
Abstract
Microbial food spoilage is responsible for a considerable amount of waste and can cause food-borne diseases in humans, particularly in immunocompromised individuals and children. Therefore, preventing microbial food spoilage is a major concern for health authorities, regulators, consumers, and the food industry. However, the contamination of food products is difficult to control because there are several potential sources during production, processing, storage, distribution, and consumption, where microorganisms come in contact with the product. Here, we use high-throughput full-length 16S rRNA gene sequencing to provide insights into bacterial community structure throughout a pork-processing plant. Specifically, we investigated what proportion of bacteria on meat are presumptively not animal-associated and are therefore transferred during cutting via personnel, equipment, machines, or the slaughter environment. We then created a facility-specific transmission map of bacterial flow, which predicted previously unknown sources of bacterial contamination. This allowed us to pinpoint specific taxa to particular environmental sources and provide the facility with essential information for targeted disinfection. For example, Moraxella spp., a prominent meat spoilage organism, which was one of the most abundant amplicon sequence variants (ASVs) detected on the meat, was most likely transferred from the gloves of employees, a railing at the classification step, and the polishing tunnel whips. Our results suggest that high-throughput full-length 16S rRNA gene sequencing has great potential in food monitoring applications.
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29
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De Filippis F, Pasolli E, Ercolini D. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 2020; 44:454-489. [PMID: 32556166 PMCID: PMC7391071 DOI: 10.1093/femsre/fuaa015] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Lactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università, 100, 80055, Portici (NA)Italy
- Task Force on Microbiome Studies, Corso Umberto I, 40, 80100, Napoli, Italy
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Woods DF, Kozak IM, O'Gara F. Microbiome and Functional Analysis of a Traditional Food Process: Isolation of a Novel Species ( Vibrio hibernica) With Industrial Potential. Front Microbiol 2020; 11:647. [PMID: 32373093 PMCID: PMC7179675 DOI: 10.3389/fmicb.2020.00647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 03/20/2020] [Indexed: 11/29/2022] Open
Abstract
Traditional food preservation processes are vital for the food industry. They not only preserve a high-quality protein and nutrient source but can also provide important value-added organoleptic properties. The Wiltshire process is a traditional food curing method applied to meat, and special recognition is given to the maintenance of a live rich microflora within the curing brine. We have previously analyzed a curing brine from this traditional meat process and characterized a unique microbial core signature. The characteristic microbial community is actively maintained and includes the genera, Marinilactibacillus, Carnobacterium, Leuconostoc, and Vibrio. The bacteria present are vital for Wiltshire curing compliance. However, the exact function of this microflora is largely unknown. A microbiome profiling of three curing brines was conducted and investigated for functional traits by the robust bioinformatic tool, Tax4Fun. The key objective was to uncover putative metabolic functions associated with the live brine and to identify changes over time. The functional bioinformatic analysis revealed metabolic enrichments over time, with many of the pathways identified as being involved in organoleptic development. The core bacteria present in the brine are Lactic Acid Bacteria (LAB), with the exception of the Vibrio genus. LAB are known for their positive contribution to food processing, however, little work has been conducted on the use of Vibrio species for beneficial processes. The Vibrio genome was sequenced by Illumina MiSeq technologies and annotated in RAST. A phylogenetic reconstruction was completed using both the 16S rRNA gene and housekeeping genes, gapA, ftsZ, mreB, topA, gyrB, pyrH, recA, and rpoA. The isolated Vibrio species was defined as a unique novel species, named Vibrio hibernica strain B1.19. Metabolic profiling revealed that the bacterium has a unique substrate scope in comparison to other closely related Vibrio species tested. The possible function and industrial potential of the strain was investigated using carbohydrate metabolizing profiling under food processing relevant conditions. Vibrio hibernica is capable of metabolizing a unique carbohydrate profile at low temperatures. This characteristic provides new application options for use in the industrial food sector, as well as highlighting the key role of this bacterium in the Wiltshire curing process.
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Affiliation(s)
- David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Iwona M Kozak
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,Human Microbiome Programme, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Telethon Kids Institute, Perth Children's Hospital, Perth, WA, Australia
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31
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Khachatryan L, de Leeuw RH, Kraakman MEM, Pappas N, Te Raa M, Mei H, de Knijff P, Laros JFJ. Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples. Forensic Sci Int Genet 2020; 46:102257. [PMID: 32058299 DOI: 10.1016/j.fsigen.2020.102257] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 12/30/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022]
Abstract
The assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed using different state of the art techniques and reference databases, can produce widely different results. In light of the fact that most forensic metagenomic analysis are still performed using 16S data, our results are especially important.
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Affiliation(s)
- Lusine Khachatryan
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Rick H de Leeuw
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Margriet E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Nikos Pappas
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Marije Te Raa
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
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32
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Luo Y, Kong L, Xue R, Wang W, Xia X. Bitterness in alcoholic beverages: The profiles of perception, constituents, and contributors. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.12.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Lu Y, Yang L, Yang G, Chi Y, Sun Q, He Q. Insight into the Fermentation of Chinese Horse Bean-chili-paste. FOOD REVIEWS INTERNATIONAL 2020. [DOI: 10.1080/87559129.2020.1717525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yunhao Lu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, P. R. China
| | - Linzi Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, P. R. China
| | - Guohua Yang
- Sichuan Dandan Pixian-douban Co.; Ltd., Chengdu, P. R. China
| | - Yuanlong Chi
- College of Biomass Science and Engineering, Sichuan University, Chengdu, P. R. China
| | - Qun Sun
- College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Qiang He
- College of Biomass Science and Engineering, Sichuan University, Chengdu, P. R. China
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34
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Ansari AF, Acharya NIS, Kumaran S, Ravindra K, Reddy YBS, Dixit NM, Raut J. 110th Anniversary: High-Order Interactions Can Eclipse Pairwise Interactions in Shaping the Structure of Microbial Communities. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aamir Faisal Ansari
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | | | | | | | | | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Janhavi Raut
- Unilever R&D India Pvt, Ltd., Bangalore 560066, India
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35
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Fungal Diversity of Deteriorated Sparkling Wine and Cork Stoppers in Catalonia, Spain. Microorganisms 2019; 8:microorganisms8010012. [PMID: 31861653 PMCID: PMC7023407 DOI: 10.3390/microorganisms8010012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/28/2023] Open
Abstract
Filamentous fungi are rarely reported as responsible for spoiling wine. Cork taint was detected in sparkling wine; therefore, we investigated fungal contamination as a possible cause of organoleptic alteration. Spoiled wine was filtered and membranes were plated onto potato dextrose agar (PDA). The cork stoppers used for sealing bottles were cut and also plated onto PDA. Fungal strains were phenotypically characterized and molecularly identified by sequencing of a fragment of the 28S nrRNA gene (LSU) and (occasionally) by other additional molecular markers. Twenty-seven strains were isolated and sixteen species were identified, all of them belonging to the phylum Ascomycota. The fungi isolated from wine were three species of Aspergillus section Nidulantes, a species of Penicillium section Exicaulis and Beauveria bassiana. Candida patagonica was isolated from both sort of samples, and the fungi isolated from cork stoppers were Altenaria alternata and Cladosporium cladosporioides. Surprisingly, most of the taxa recovered from the cork stoppers and/or wine were new to the science: a new genus (Dactylodendron) and seven new species belonging to the genera Cladophialophora, Dactylodendron, Kirschsteiniothelia, Rasamsonia, and Talaromyces. Future studies could let us know if these fungi would be able to produce compounds responsible for cork taint.
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36
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Falardeau J, Keeney K, Trmčić A, Kitts D, Wang S. Farm-to-fork profiling of bacterial communities associated with an artisan cheese production facility. Food Microbiol 2019; 83:48-58. [DOI: 10.1016/j.fm.2019.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/31/2019] [Accepted: 04/05/2019] [Indexed: 11/26/2022]
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37
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Tan X, Chung T, Chen Y, Macarisin D, LaBorde L, Kovac J. The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities. MICROBIOME 2019; 7:115. [PMID: 31431193 PMCID: PMC6702733 DOI: 10.1186/s40168-019-0726-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/29/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Multistate foodborne disease outbreaks and recalls of apples and apple products contaminated with Listeria monocytogenes demonstrate the need for improved pathogen control in the apple supply chain. Apple processing facilities have been identified in the past as potential sources of persisting L. monocytogenes contamination. In this study, we sought to understand the composition of microbiota in built apple and other tree fruit processing environments and its association with the occurrence of the foodborne pathogen L. monocytogenes. RESULTS Analysis of 117 samples collected from three apple and other tree fruit packing facilities (F1, F2, and F3) showed that facility F2 had a significantly higher L. monocytogenes occurrence compared to F1 and F3 (p < 0.01). The microbiota in facility F2 was distinct compared to facilities F1 and F3 as supported by the mean Shannon index for bacterial and fungal alpha diversities that was significantly lower in F2, compared to F1 and F3 (p < 0.01). Microbiota in F2 was uniquely predominated by bacterial family Pseudomonadaceae and fungal family Dipodascaceae. CONCLUSIONS The composition and diversity of microbiota and mycobiota present in the investigated built food processing environments may be indicative of persistent contamination with L. monocytogenes. These findings support the need for further investigation of the role of the microbial communities in the persistence of L. monocytogenes to support the optimization of L. monocytogenes control strategies in the apple supply chain.
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Affiliation(s)
- Xiaoqing Tan
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Taejung Chung
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Dumitru Macarisin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Luke LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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38
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He J, Chen C, He Q, Li J, Ying F, Chen G. The central bacterial community in Pericarpium Citri Reticulatae 'Chachiensis'. Food Res Int 2019; 125:108624. [PMID: 31554059 DOI: 10.1016/j.foodres.2019.108624] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022]
Abstract
The dried and aged pericarps of Citri Reticulatae are condiments and medicinal products in southeast and eastern Asia for hundreds of years, among which Pericarpium Citri Reticulatae 'Chachiensis' (PCR-C) is the premium one with obvious health benefits. In order to explore the microbiota in PCR-C and their relationship with the chemical components during aging, culture-independent methods were applied to investigate PCR-C microbiota for the first time. Here in different PCR-C samples, 16S rRNA gene amplicon sequencing revealed common central bacterial community, which were absent or only accounted for small proportion in fresh pericarps or jute bag controls. Bacillus and Lactococcus were the top two dominant genera in PCR-C with acidic pH (4.06-4.51) and low moisture (11.48%-19.13%). Several OTUs were found to closely relate with specific compositions in essential oils and phenolics, such as d-limonene and nobiletin, which contributed to PCR-C flavor and quality. As the first study to reveal the central bacterial communities in PCR-C, it provides new insights to improve the quality and aging process of traditional Pericarpium Citri Reticulatae, and lays foundation for functional characterization of the microbes within.
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Affiliation(s)
- Jing He
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China
| | - Congcong Chen
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China
| | - Qianxian He
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China
| | - Jingyu Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China
| | - Fan Ying
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China
| | - Gu Chen
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, 510641 Guangzhou, China.
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39
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Jaba A, Dagher F, Hamidi Oskouei AM, Guertin C, Constant P. Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds. Can J Microbiol 2019; 65:668-680. [PMID: 31158321 DOI: 10.1139/cjm-2019-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia (Salvia hispanica L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.
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Affiliation(s)
- Asma Jaba
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Fadi Dagher
- Agri-Neo Inc., 435 Horner Avenue, Unit 1, Toronto, ON M8W 4W3, Canada
| | | | - Claude Guertin
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
| | - Philippe Constant
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC H7V 1B7, Canada
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40
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Han HW, Ko LN, Yang CS, Hsu SH. Potential of Engineered Bacteriorhodopsins as Photoactivated Biomaterials in Modulating Neural Stem Cell Behavior. ACS Biomater Sci Eng 2019; 5:3068-3078. [PMID: 33405539 DOI: 10.1021/acsbiomaterials.9b00367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacteriorhodopsin (BR), a light-sensitive bacterial proton pump, has been demonstrated the capacity for regulating the neural activity in mammalian cells. Because of the difficulty in production and purification in large quantities, the BR proteins have neither been directly employed to biomedical applications nor verified the functionality by protein administration. Previously, we have invented a highly expressible bacteriorhodopsin (HEBR) and established the massive production protocol. In the current study, we mass-produced the two types of HEBR proteins that have normal or abnormal activity on the proton pumping, and then we treated murine neural stem cells (NSCs) with these HEBR proteins. We discovered that the cell behaviors including growth, metabolism, mitochondrial inner membrane potential, and differentiation were obviously affected in NSCs after the treatment of HEBR proteins. Particularly, these effects induced by HEBR proteins were correlated to their proton pump activity and could be altered by cell culture substrate materials. Current findings suggest that the engineered light-sensitive HEBR protein can serve as a biological material to directly influence the multiple behaviors of mammalian cells, which is further modified by the cell culture substrate material, revealing the versatile potential of HEBR protein in biomaterial applications.
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Affiliation(s)
| | | | | | - Shan-Hui Hsu
- Institute of Cellular and System Medicine, National Health Research Institutes, No. 35 Keyan Road, Zhunan, Miaoli County, Taiwan 35053, R.O.C
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41
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Christoff AP, Sereia AFR, Hernandes C, de Oliveira LFV. Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions. Exp Biol Med (Maywood) 2019; 244:534-542. [PMID: 30616384 PMCID: PMC6547007 DOI: 10.1177/1535370218821857] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
IMPACT STATEMENT Research concerning the microbiome of indoor environments like hospitals, houses or buildings could have several implications for human health. Today, there is an ongoing shift in the paradigm of microbial analysis, from single isolated bacterial samples to entire microbiome profiles using high-throughput DNA sequencing methods. The use of sequencing methods in several studies has revealed an unprecedented microbial diversity in indoor environments, leading to a larger comprehension of the entire microbiome context. Here, we present a review of these microbiome studies using high-throughput DNA sequencing, including some new approaches and ideas that can be broadly applied in microbial tracking and epidemiological surveillance of indoor environments.
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Affiliation(s)
- Ana P Christoff
- Neoprospecta Microbiome Technologies, CEP 88057-260, SC –
Brasil
| | - Aline FR Sereia
- Neoprospecta Microbiome Technologies, CEP 88057-260, SC –
Brasil
| | - Camila Hernandes
- Hospital Israelita Albert Einstein, São Paulo, CEP 05651-901, SP
– Brasil
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42
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Gu G, Ottesen A, Bolten S, Wang L, Luo Y, Rideout S, Lyu S, Nou X. Impact of routine sanitation on the microbiomes in a fresh produce processing facility. Int J Food Microbiol 2019; 294:31-41. [DOI: 10.1016/j.ijfoodmicro.2019.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 12/18/2022]
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43
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Yi Z, Jin Y, Xiao Y, Chen L, Tan L, Du A, He K, Liu D, Luo H, Fang Y, Zhao H. Unraveling the Contribution of High Temperature Stage to Jiang-Flavor Daqu, a Liquor Starter for Production of Chinese Jiang-Flavor Baijiu, With Special Reference to Metatranscriptomics. Front Microbiol 2019; 10:472. [PMID: 30930875 PMCID: PMC6423406 DOI: 10.3389/fmicb.2019.00472] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/22/2019] [Indexed: 12/27/2022] Open
Abstract
Jiang-flavor (JF) daqu is a liquor starter used for production of JF baijiu, a well-known distilled liquor in China. Although a high temperature stage (70°C) is necessary for qualifying JF daqu, little is known regarding its active microbial community and functional enzymes, along with its role in generating flavor precursors for JF baijiu aroma. In this investigation, based on metatranscriptomics, fungi, such as Aspergillus and Penicillium, were identified as the most active microbial members and 230 carbohydrate-active enzymes were identified as potential saccharifying enzymes at 70°C of JF daqu. Notably, most of enzymes in identified carbohydrate and energy pathways showed lower expression levels at 70°C of JF daqu than those at the high temperature stage (62°C) of Nong-flavor (NF) daqu, indicating lowering capacities of saccharification and fermentation by high temperature stage. Moreover, many enzymes, especially those related to the degradation of aromatic compounds, were only detected with low expression levels at 70°C of JF daqu albeit not at 62°C of NF daqu, indicating enhancing capacities of generating special trace aroma compounds in JF daqu by high temperature stage. Additionally, most of enzymes related to those capacities were highly expressed at 70°C by fungal genus of Aspergillus, Coccidioides, Paracoccidioides, Penicillium, and Rasamsonia. Therefore, this study not only sheds light on the crucial functions of high temperature stage but also paves the way to improve the quality of JF baijiu and provide active community and functional enzymes for other fermentation industries.
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Affiliation(s)
- Zhuolin Yi
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Yao Xiao
- Analytical and Testing Center, Sichuan University of Science and Engineering, Zigong, China
| | - Lanchai Chen
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Li Tan
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Anping Du
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Kaize He
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Dayu Liu
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Huibo Luo
- Bioengineering College, Sichuan University of Science and Engineering, Zigong, China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
| | - Hai Zhao
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu, China
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44
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Hartmann AL, Behrendt RA, Frøst MB. Fermentation as a driver for food innovation. FEMS Microbiol Lett 2019; 366:5382037. [PMID: 30877768 DOI: 10.1093/femsle/fnz058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022] Open
Abstract
The following paper is reviewing the current trends in research connected to fermentation, highlighting the work carried out in the various research kitchens that have gained a new understanding of fermentation in the recent years. The reflection on the developments made both on microbiological as well on the technological level aims to create pathways within the research fields in order to foster new innovations within the food production system.
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Affiliation(s)
- Anna Loraine Hartmann
- Department of Food Science, Design and Consumer Behaviour, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
| | - Rikke Adelsten Behrendt
- Department of Food Science, Design and Consumer Behaviour, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
| | - Michael Bom Frøst
- Department of Food Science, Design and Consumer Behaviour, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
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45
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Thaler DS, Head MG, Horsley A. Precision public health to inhibit the contagion of disease and move toward a future in which microbes spread health. BMC Infect Dis 2019; 19:120. [PMID: 30727964 PMCID: PMC6364421 DOI: 10.1186/s12879-019-3715-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance continues to outpace the development of new chemotherapeutics. Novel pathogens continue to evolve and emerge. Public health innovation has the potential to open a new front in the war of "our wits against their genes" (Joshua Lederberg). Dense sampling coupled to next generation sequencing can increase the spatial and temporal resolution of microbial characterization while sensor technologies precisely map physical parameters relevant to microbial survival and spread. Microbial, physical, and epidemiological big data could be combined to improve prospective risk identification. However, applied in the wrong way, these approaches may not realize their maximum potential benefits and could even do harm. Minimizing microbial-human interactions would be a mistake. There is evidence that microbes previously thought of at best "benign" may actually enhance human health. Benign and health-promoting microbiomes may, or may not, spread via mechanisms similar to pathogens. Infectious vaccines are approaching readiness to make enhanced contributions to herd immunity. The rigorously defined nature of infectious vaccines contrasts with indigenous "benign or health-promoting microbiomes" but they may converge. A "microbial Neolithic revolution" is a possible future in which human microbial-associations are understood and managed analogously to the macro-agriculture of plants and animals. Tradeoffs need to be framed in order to understand health-promoting potentials of benign, and/or health-promoting microbiomes and infectious vaccines while also discouraging pathogens. Super-spreaders are currently defined as individuals who play an outsized role in the contagion of infectious disease. A key unanswered question is whether the super-spreader concept may apply similarly to health-promoting microbes. The complex interactions of individual rights, community health, pathogen contagion, the spread of benign, and of health-promoting microbiomes including infectious vaccines require study. Advancing the detailed understanding of heterogeneity in microbial spread is very likely to yield important insights relevant to public health.
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Affiliation(s)
- David S. Thaler
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Michael G. Head
- Clinical Informatics Research Unit, Faculty of Medicine, University of Southampton, University Hospital Southampton, Coxford Road, Southampton, SO16 6YD UK
| | - Andrew Horsley
- Research School of Physics and Engineering, The Australian National University, Mills Rd., Canberra, ACT 2601 Australia
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46
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Woods DF, Kozak IM, Flynn S, O’Gara F. The Microbiome of an Active Meat Curing Brine. Front Microbiol 2019; 9:3346. [PMID: 30687300 PMCID: PMC6336708 DOI: 10.3389/fmicb.2018.03346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/28/2018] [Indexed: 11/13/2022] Open
Abstract
Traditional food products are important to our culture and heritage, and to the continued success of the food industry. Many of the production processes associated with these products have not been subjected to an in-depth microbial compositional analysis. The traditional process of curing meat, both preserves a natural protein source, as well as increasing its organoleptic qualities. One of the most important salting processes is known as Wiltshire curing. The Wiltshire process involves injecting pork with a curing solution and immersing the meat into microbial-rich brine which promotes the development of the distinct organoleptic characteristics. The important microbial component of Wiltshire brine has not been extensively characterized. We analyzed the key microbial component of Wiltshire brine by performing microbiome analysis using Next Generation Sequencing (NGS) technologies. This analysis identified the genera, Marinilactibacillus, Carnobacterium, Leuconostoc, and Vibrio as the core microflora present in Wiltshire curing brine. The important food industrial applications of these bacteria were also assessed. The bacterial diversity of the brine was investigated, and the community composition of the brine was demonstrated to change over time. New knowledge on the characterization of key microbiota associated with a productive Wiltshire brine is an important development linked to promoting enhanced quality and safety of meat processing in the food industry.
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Affiliation(s)
- David F. Woods
- Biomerit Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Iwona M. Kozak
- Biomerit Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Stephanie Flynn
- Biomerit Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O’Gara
- Biomerit Research Centre, School of Microbiology, University College Cork, Cork, Ireland
- Telethon Kids Institute, Subiaco, WA, Australia
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
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47
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Xu X, Luo D, Bao Y, Liao X, Wu J. Characterization of Diversity and Probiotic Efficiency of the Autochthonous Lactic Acid Bacteria in the Fermentation of Selected Raw Fruit and Vegetable Juices. Front Microbiol 2018; 9:2539. [PMID: 30405588 PMCID: PMC6205992 DOI: 10.3389/fmicb.2018.02539] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
The diversity of indigenous lactic acid bacteria (LAB) in fermented broccoli, cherry, ginger, white radish, and white-fleshed pitaya juices was analyzed using culture-independent and -dependent approaches. The major properties of selected probiotic strains, including dynamic variations in pH, viable cell counts, antibiotic resistance, bacterial adhesion to hydrophobic compounds, and survivability during simulated gastrointestinal transit, were investigated using broccoli as the fermentation substrate. In broccoli and ginger juices, the genus Lactobacillus occupied the dominant position (abundances of 79.0 and 30.3%, respectively); in cherry and radish juices, Weissella occupied the dominant position (abundances of 78.3 and 83.2%, respectively); and in pitaya juice, Streptococcus and Lactococcus occupied the dominant positions (52.2 and 37.0%, respectively). Leuconostoc mesenteroides, Weissella cibaria/soli/confusa, Enterococcus gallinarum/durans/hirae, Pediococcus pentosaceus, Bacillus coagulans, and Lactococcus garvieae/lactis subspecies were identified by partial 16S rRNA gene sequencing. In general, the selected autochthonous LAB isolates displayed no significant differences in comparison with commercial strains with regard to growth rates or acidification in fermented broccoli juice. Among all the isolates, L. mesenteroides B4-25 exhibited the highest antibiotic resistance profile (equal to that of L. plantarum CICC20265), and suitable adhesion properties (adhesion of 13.4 ± 5.2% ∼ 36.4 ± 3.2% and 21.6 ± 1.4% ∼ 69.6 ± 2.3% to ethyl acetate and xylene, respectively). Furthermore, P. pentosaceus Ca-4 and L. mesenteroides B-25 featured the highest survival rates (22.4 ± 2.6 and 21.2 ± 1.4%, respectively), after simulated gastrointestinal transit. These results indicated a high level of diversity among the autochthonous bacterial community in fermented fruit and vegetable juices, and demonstrated the potential of these candidate probiotics for applications in fermentation.
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Affiliation(s)
- Xinxing Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Dongsheng Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Yejun Bao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Xiaojun Liao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Jihong Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
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Rivera D, Toledo V, Reyes-Jara A, Navarrete P, Tamplin M, Kimura B, Wiedmann M, Silva P, Moreno Switt AI. Approaches to empower the implementation of new tools to detect and prevent foodborne pathogens in food processing. Food Microbiol 2018; 75:126-132. [DOI: 10.1016/j.fm.2017.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/13/2017] [Indexed: 11/15/2022]
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49
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Ssepuuya G, Wynants E, Verreth C, Crauwels S, Lievens B, Claes J, Nakimbugwe D, Van Campenhout L. Microbial characterisation of the edible grasshopper Ruspolia differens in raw condition after wild-harvesting in Uganda. Food Microbiol 2018; 77:106-117. [PMID: 30297041 DOI: 10.1016/j.fm.2018.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 01/01/2023]
Abstract
This research aimed at establishing the chemical intrinsic properties and the microbial quality of an edible grasshopper Ruspolia differens and the effect of its source (geographical area) in Uganda, trading point, swarming season and plucking on these parameters. The intrinsic properties of the grasshopper can support the growth of a wide variety of microorganisms. High counts of total aerobic microbes, Enterobacteriaceae, lactic acid bacteria, total aerobic spores, and yeasts and moulds were obtained. Metagenetic analyses yielded 1793 Operational Taxonomic Units (OTUs) belonging to 24 phyla. Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were the most abundant phyla, while members of the genera Acinetobacter, Buttiauxella, Lactococcus, Staphylococcus and Undibacterium were the most abundant OTUs. A number of genera harbouring potential pathogens (Acinetobacter, Bacillus, Buttiauxella, Campylobacter, Clostridium, Staphylococcus, Pseudomonas and Neisseria) were identified. The geographical area, trading point, swarming season and plucking significantly influenced microbial counts and bacterial diversity. The high microbial counts predispose R. differens to fast microbial spoilage, while the presence of Clostridium and Campylobacter makes this grasshopper a potential source of food borne diseases. Further research should identify the specific spoilage microorganisms of R. differens and assess the characteristics of this grasshopper that support growth of food pathogens.
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Affiliation(s)
- Geoffrey Ssepuuya
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; Makerere University, Department of Food Technology and Nutrition, CAES, P. O. Box, 7062, Kampala, Uganda
| | - Enya Wynants
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium
| | - Christel Verreth
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium
| | - Sam Crauwels
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium
| | - Bart Lievens
- KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium; KU Leuven, Department of Microbial and Molecular Systems (M2S), Laboratory for Process Microbial Ecology and Bioinspirational Management (PME & BIM), Campus De Nayer, B-2860, Sint-Katelijne-Waver, Belgium
| | - Johan Claes
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium
| | - Dorothy Nakimbugwe
- Makerere University, Department of Food Technology and Nutrition, CAES, P. O. Box, 7062, Kampala, Uganda
| | - Leen Van Campenhout
- KU Leuven, Department of Microbial and Molecular Systems (M2S), Lab4Food, Technology Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium; KU Leuven, Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium.
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50
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Holle MJ, Ibarra-Sánchez LA, Liu X, Stasiewicz MJ, Miller MJ. Microbial analysis of commercially available US Queso Fresco. J Dairy Sci 2018; 101:7736-7745. [DOI: 10.3168/jds.2017-14037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/28/2018] [Indexed: 11/19/2022]
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