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Ma J, Qian C, Hu Q, Zhang J, Gu G, Liang X, Zhang L. The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation. Food Res Int 2024; 184:114244. [PMID: 38609223 DOI: 10.1016/j.foodres.2024.114244] [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: 10/17/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.
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Affiliation(s)
- Jiawen Ma
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Chenggong Qian
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China
| | - Qijie Hu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Jianping Zhang
- Haining Yufeng Brewing Co., Ltd, Haining, Zhejiang Province 314408, China
| | - Guizhang Gu
- Huzhou Institute of Food and Drug Control, Huzhou, Zhejiang Province 313002, China
| | - Xinle Liang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
| | - Lei Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province 310018, China.
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Mun SY, Lee W, Lee SY, Chang JY, Chang HC. Pediococcus inopinatus with a well-developed CRISPR-Cas system dominates in long-term fermented kimchi, Mukeunji. Food Microbiol 2024; 117:104385. [PMID: 37919000 DOI: 10.1016/j.fm.2023.104385] [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: 06/26/2023] [Revised: 08/16/2023] [Accepted: 09/12/2023] [Indexed: 11/04/2023]
Abstract
Kimchi is produced through a low-temperature fermentation without pre-sterilization, resulting in a heterogeneous microbial community. As fermentation progresses, dominant lactic acid bacteria (LAB) species emerge and undergo a transition process. In this study, LAB were isolated from Mukeunji, a long-term fermented kimchi that is in the final stage of kimchi fermentation process. It was confirmed, through culture-dependent and independent analysis, as well as metagenome analysis, that Pediococcus inopinatus are generally dominant in long-term fermented kimchi. Comparative analysis of the de novo assembled whole genome of P. inopinatus with other kimchi LAB revealed that this species has a well-developed clustered regularly interspaced short palindromic repeats (CRISPR) system. The CRISPR system of P. inopinatus has an additional copy of the csa3 gene, a transcription factor for cas genes. Indeed, this species not only highly expresses cas1 and cas2, which induce spacer acquisition, but also has many diverse spacers that are actively expressed. These findings indicate that the well-developed CRISPR-Cas system is enabling P. inopinatus to dominate in long-fermented kimchi. Overall, this study revealed that LAB with a robust defense system dominate in the final stage of kimchi fermentation and presented a model for the succession mechanism of kimchi LAB.
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Affiliation(s)
- So Yeong Mun
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea; Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea
| | - Wooje Lee
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea
| | - Soo-Young Lee
- Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea
| | - Ji Yoon Chang
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea
| | - Hae Choon Chang
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea; Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea.
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3
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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [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: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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4
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White K, Eraclio G, Lugli GA, Ventura M, Mahony J, Bello FD, van Sinderen D. A Metagenomics Approach to Enumerate Bacteriophages in a Food Niche. Methods Mol Biol 2024; 2738:185-199. [PMID: 37966600 DOI: 10.1007/978-1-0716-3549-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Dairy fermentation relies on the activity of starter cultures composed primarily of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus strains to produce consistent, high-quality products. Bacteriophages are a constant threat to the industry, often causing slowed or failed fermentation resulting in significant economic losses. To ensure the continuation of reliable fermentation practices, it is important to detect and monitor the phage populations impacting different starter cultures. This has traditionally been done primarily through culture-dependent methods but has since expanded into viral metagenomics. Here we outline a protocol for a targeted virome extraction from a dairy whey sample, followed by subsequent sequencing and phageome analysis of the sample.
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Affiliation(s)
- Kelsey White
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | | | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland.
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5
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Tan G, Qi S, Wang Y, Li X, Li X, Li M, Li L, Zhao L, Hu M. Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce. Front Microbiol 2023; 14:1328158. [PMID: 38188564 PMCID: PMC10766790 DOI: 10.3389/fmicb.2023.1328158] [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: 10/26/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Although the composition and succession of microbial communities in soy sauce fermentation have been well-characterized, the understanding of phage communities in soy sauce remains limited. Methods This study determined the diversity, taxonomic composition, and predicted function of phage communities and the phage-host interactions in two types of raw soy sauce (Cantonese-type fermentation, NJ; Japanese-type fermentation, PJ) using shotgun metagenomics. Results and discussion These two raw soy sauces showed differences in phage composition (121 viral operational taxonomic units (vOTUs) in NJ and 387 vOTUs in PJ), with a higher abundance of the family Siphoviridae (58.50%) in the NJ phage community and a higher abundance of Myoviridae (33.01%) in PJ. Auxiliary metabolic functional annotation analyses showed that phages in the raw soy sauces mostly encoded genes with unknown functions (accounting for 66.33% of COG profiles), but the NJ sample contained genes mostly annotated to conventional functions related to carbohydrate metabolism (0.74%) and lipid metabolism (0.84%), while the PJ sample presented a higher level of amino acid metabolism functions (0.12%). Thirty auxiliary metabolism genes (AMGs) were identified in phage genomes, which were associated with carbohydrate utilization, cysteine and methionine metabolism, and aspartic acid biosynthesis for the host. To identify phage-host interactions, 30 host genomes (affiliated with 22 genera) were also recruited from the metagenomic dataset. The phage-host interaction analysis revealed a wide range of phage hosts, for which a total of 57 phage contigs were associated with 17 host genomes, with Shewanella fodinae and Weissella cibaria infected by the most phages. This study provides a comprehensive understanding of the phage community composition, auxiliary metabolic functions, and interactions with hosts in two different types of raw soy sauce.
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Affiliation(s)
- Guiliang Tan
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Shaohan Qi
- College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yi Wang
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Xueyan Li
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Xiangli Li
- School of Health Industry, Zhongshan Torch Polytechnic, Zhongshan, China
| | - Mei Li
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Lin Li
- School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China
| | - Lichao Zhao
- College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Min Hu
- School of Environmental Science and Engineering, Changzhou University, Changzhou, China
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Tomar S, Mitra D, Kumar G, Kashyap P, Sharma M, Kumar S, Sridhar K, Pant K. Microbial Diversity and Functional Potential of Keem: A Traditional Starter Culture for Alcoholic Beverage-Application of Next-Generation Amplicon and Shotgun Metagenome Sequences. Mol Biotechnol 2023:10.1007/s12033-023-00839-3. [PMID: 37566190 DOI: 10.1007/s12033-023-00839-3] [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: 02/22/2023] [Accepted: 07/13/2023] [Indexed: 08/12/2023]
Abstract
"Pakhoi" is an ethnic drink of the Tons valley, Uttarakhand, India produced by fermenting jaggery and barley with the help of a starter culture called "keem". In the present study, we investigated the microbial diversity and associated functional potential of "keem" using shotgun metagenome sequencing and amplicon sequencing. We also compared the taxonomic data obtained using these two sequencing techniques. The results showed that shotgun sequencing revealed a higher resolution of taxonomic profiling as compared to the amplicon sequencing. Furthermore, it was found that the genera detected by shotgun sequencing were valuable for facilitating the fermentation process. Additionally, to understand the functional profiling of the genera, different databases were used for annotation, resulting in a total of 13 metabolic pathways. The five most abundant KEGG functions were genetic information processing, metabolism, translation, cofactor and vitamin metabolism and xenobiotic degradation. In contrast, the top five COG were in order of highest frequency sequences belonging to transcription, followed by general function prediction, carbohydrate transport metabolism, amino acid transport and metabolism and translation and biogenesis. Gene ontology revealed many pathways, biochemical processes and molecular functions associated with the organisms forming the starter culture. Overall, the present study can help to understand the microbial diversity and its role in fermentation of traditional alcoholic beverages using "Keem".
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Affiliation(s)
- Shikha Tomar
- Department of Life Sciences, Graphic Era (Deemed to Be University), Dehradun, 248002, India
| | - Debasis Mitra
- Department of Microbiology, Raiganj University, Raiganj, West Bengal, 733134, India
| | - Gaurav Kumar
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Piyush Kashyap
- Department of Food Technology and Nutrition, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Minaxi Sharma
- Department of Applied Biology, University of Science and Technology, Baridua, Meghalaya, 793101, India
| | - Shiv Kumar
- MMICT&BM (HM), Maharishi Markandeshwar (Deemed to Be University), Mullana, Haryana, 133207, India.
| | - Kandi Sridhar
- Department of Food Technology, Karpagam Academy of Higher Education (Deemed to Be University), Coimbatore, 641021, India.
| | - Kumud Pant
- Department of Biotechnology, Graphic Era (Deemed to Be University), Dehradun, Uttarakhand, 248002, India.
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7
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He Y, Lei JN, Zhu S, Liu YF, Xu YJ. Monomethyl branched-chain fatty acids-a pearl dropped in the ocean. Crit Rev Food Sci Nutr 2023:1-13. [PMID: 37140184 DOI: 10.1080/10408398.2023.2207655] [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: 05/05/2023]
Abstract
As an emerging group of bioactive fatty acids, monomethyl branched-chain fatty acids (mmBCFAs) have sparked the interest of many researchers both domestically and internationally. In addition to documenting the importance of mmBCFAs for growth and development, there is increasing evidence that mmBCFAs are highly correlated with obesity and insulin resistance. According to previous pharmacological investigations, mmBCFAs also exhibit anti-inflammatory effects and anticancer properties. This review summarized the distribution of mmBCFAs, which are widely found in dairy products, ruminants, fish, and fermented foods. Besides, we discuss the biosynthesis pathway in different species and detection methods of mmBCFAs. With the hope to unveil their mechanisms of action, we recapitulated detailed the nutrition and health benefits of mmBCFAs. Furthermore, this study provides a thorough, critical overview of the current state of the art, upcoming difficulties, and trends in mmBCFAs.
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Affiliation(s)
- Yuan He
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Jing-Nan Lei
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Shuang Zhu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Yuan-Fa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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8
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Composition and function of viruses in sauce-flavor baijiu fermentation. Int J Food Microbiol 2023; 387:110055. [PMID: 36527793 DOI: 10.1016/j.ijfoodmicro.2022.110055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/21/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Viruses are highly abundant in nature, associated with quality and safety of traditional fermented foods. However, the overall viral diversity and function are still poorly understood in food microbiome. Traditional baijiu fermentation is an ideal model system to examine the diversity and function of viruses owing to easy access, stable operation, and domesticated microbial community. Equipped with cutting-edge viral metagenomics, we investigated the viral community in the fermented grain and fermentation environment, as well as their contribution to baijiu fermentation. Viral communities in the fermented grains and fermentation environment are highly similar. The dominant viruses were bacteriophages, mainly including the order Caudovirales and the family Inoviridae. Furtherly, association network analysis showed that viruses and bacteria were significantly negatively correlated (P < 0.01). Viral diversity could significantly influence bacterial and fungal succession (P < 0.05). Moreover, we proved that starter phages could significantly inhibit the growth of Bacillus licheniformis in the logarithmic growth stage (P < 0.05) under culture condition. Based on the functional annotations, viruses and bacteria both showed high distribution of genes related to amino acid and carbohydrate metabolism. In addition, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were also identified in viruses, indicating that viruses were involved in the decomposition of complex polysaccharides during fermentation. Our results revealed that viruses could crucially affect microbial community and metabolism during traditional fermentation.
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9
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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10
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Elbehery AHA, Deng L. Insights into the global freshwater virome. Front Microbiol 2022; 13:953500. [PMID: 36246212 PMCID: PMC9554406 DOI: 10.3389/fmicb.2022.953500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.
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Affiliation(s)
- Ali H. A. Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
- *Correspondence: Ali H. A. Elbehery,
| | - Li Deng
- Helmholtz Centre Munich – German Research Centre for Environmental Health, Institute of Virology, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
- Li Deng,
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11
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Borges F, Briandet R, Callon C, Champomier-Vergès MC, Christieans S, Chuzeville S, Denis C, Desmasures N, Desmonts MH, Feurer C, Leroi F, Leroy S, Mounier J, Passerini D, Pilet MF, Schlusselhuber M, Stahl V, Strub C, Talon R, Zagorec M. Contribution of omics to biopreservation: Toward food microbiome engineering. Front Microbiol 2022; 13:951182. [PMID: 35983334 PMCID: PMC9379315 DOI: 10.3389/fmicb.2022.951182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/14/2022] [Indexed: 01/12/2023] Open
Abstract
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
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Affiliation(s)
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage, Aurillac, France
| | | | | | - Sarah Chuzeville
- ACTALIA, Pôle d’Expertise Analytique, Unité Microbiologie Laitière, La Roche sur Foron, France
| | | | | | | | - Carole Feurer
- IFIP, Institut de la Filière Porcine, Le Rheu, France
| | | | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | | | | | | | - Caroline Strub
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Régine Talon
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
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12
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Kang J, Chen X, Han BZ, Xue Y. Insights into the bacterial, fungal, and phage communities and volatile profiles in different types of Daqu. Food Res Int 2022; 158:111488. [DOI: 10.1016/j.foodres.2022.111488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 11/25/2022]
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13
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Jung MJ, Kim J, Lee SH, Whon TW, Sung H, Bae JW, Choi YE, Roh SW. Role of combinated lactic acid bacteria in bacterial, viral, and metabolite dynamics during fermentation of vegetable food, kimchi. Food Res Int 2022; 157:111261. [DOI: 10.1016/j.foodres.2022.111261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 12/20/2022]
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Ledormand P, Desmasures N, Midoux C, Rué O, Dalmasso M. Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage. Microorganisms 2022; 10:1203. [PMID: 35744720 PMCID: PMC9230842 DOI: 10.3390/microorganisms10061203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Phageomes are known to play a key role in the functioning of their associated microbial communities. The phageomes of fermented foods have not been studied thoroughly in fermented foods yet, and even less in fermented beverages. Two approaches were employed to investigate the presence of phages in cider, a fermented beverage made from apple, during a fermentation process of two cider tanks, one from an industrial producer and one from a hand-crafted producer. The phageome (free lytic phages) was explored in cider samples with several methodological developments for total phage DNA extraction, along with single phage isolation. Concentration methods, such as tangential flow filtration, flocculation and classical phage concentration methods, were employed and tested to extract free phage particles from cider. This part of the work revealed a very low occurrence of free lytic phage particles in cider. In parallel, a prophage investigation during the fermentation process was also performed using a metagenomic approach on the total bacterial genomic DNA. Prophages in bacterial metagenomes in the two cider tanks seemed also to occur in low abundance, as a total of 1174 putative prophages were identified in the two tanks overtime, and only two complete prophages were revealed. Prophage occurrence was greater at the industrial producer than at the hand-crafted producer, and different dynamics of prophage trends were also observed during fermentation. This is the first report dealing with the investigation of the phageome and of prophages throughout a fermentation process of a fermented beverage.
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Affiliation(s)
- Pierre Ledormand
- Normandie Univ., UNICAEN, UNIROUEN, ABTE, 14000 Caen, France; (P.L.); (N.D.)
| | - Nathalie Desmasures
- Normandie Univ., UNICAEN, UNIROUEN, ABTE, 14000 Caen, France; (P.L.); (N.D.)
| | - Cédric Midoux
- INRAE, MaIAGE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- INRAE, PROSE, Université Paris-Saclay, 92761 Antony, France
| | - Olivier Rué
- INRAE, MaIAGE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marion Dalmasso
- Normandie Univ., UNICAEN, UNIROUEN, ABTE, 14000 Caen, France; (P.L.); (N.D.)
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15
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Kim SH, Park JH. Characterization of Prophages in Leuconostoc Derived from Kimchi and Genomic Analysis of the Induced Prophage in Leuconostoc lactis. J Microbiol Biotechnol 2022; 32:333-340. [PMID: 34949750 PMCID: PMC9628853 DOI: 10.4014/jmb.2110.10046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
Leuconostoc has been used as a principal starter in natural kimchi fermentation, but limited research has been conducted on its phages. In this study, prophage distribution and characterization in kimchi-derived Leuconostoc strains were investigated, and phage induction was performed. Except for one strain, 16 Leuconostoc strains had at least one prophage region with questionable and incomplete regions, which comprised 0.5-6.0% of the bacterial genome. Based on major capsid protein analysis, ten intact prophages and an induced incomplete prophage of Leu. lactis CBA3626 belonged to the Siphoviridae family and were similar to Lc-Nu-like, sha1-like, phiMH1-like, and TPA_asm groups. Bacterial immunology genes, such as superinfection exclusion proteins and methylase, were found on several prophages. One prophage of Leu. lactis CBA3626 was induced using mitomycin C and was confirmed as belonging to the Siphoviridae family. Homology of the induced prophage with 21 reported prophages was not high (< 4%), and 47% identity was confirmed only with TPA_asm from Siphoviridae sp. isolate ct3pk4. Therefore, it is suggested that Leuconostoc from kimchi had diverse prophages with less than 6% genome proportion and some immunological genes. Interestingly, the induced prophage was very different from the reported prophages of other Leuconostoc species.
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Affiliation(s)
- Song-Hee Kim
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea,Corresponding author J.H. Park Phone: +82-31-750-5523 Fax: +82-31-750-5283 E-mail:
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16
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Butina TV, Petrushin IS, Khanaev IV, Bukin YS. Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera. Microorganisms 2022; 10:microorganisms10020480. [PMID: 35208935 PMCID: PMC8876492 DOI: 10.3390/microorganisms10020480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/10/2022] Open
Abstract
Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.
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17
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Tamang JP, Das S, Kharnaior P, Pariyar P, Thapa N, Jo SW, Yim EJ, Shin DH. Shotgun metagenomics of Cheonggukjang, a fermented soybean food of Korea: Community structure, predictive functionalities and amino acids profile. Food Res Int 2022; 151:110904. [PMID: 34980421 DOI: 10.1016/j.foodres.2021.110904] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 09/10/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022]
Abstract
Cheonggukjang is a naturally fermented soybean food of Korea. The present study was aimed to reveal the whole microbial community structure of naturally fermented cheonggukjang along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. Metataxonomic profile of cheonggukjang samples showed different domains viz. bacteria (95.83%), virus (2.26%), unclassified (1.84%), eukaryotes (0.05%) and archaea (0.005%). Overall, 44 phyla, 286 families, 722 genera and 1437 species were identified. Firmicutes was the most abundant phylum (98.04%) followed by Proteobacteria (1.49%), Deinococcus-Thermus (0.14%). Bacillus thermoamylovorans was the most abundant species in cheonggukjang followed by Bacillus licheniformis, Bacillus glycinifermentans, Bacillus subtilis, Bacillus paralicheniformis, Bacillus amyloliquifaciens, Brevibacillus borstelensis, Brevibacillus sonorensis Brevibacillus, Acinetobacter, Carnobacterium, Paenibacillus, Cronobacter Enterococcus, Enterobacter, Terriglobus, Psychrobacter and Virgibacillus. A colossal diversity of the genus Bacillus was detected with 150 species. Functional analysis of cheonggukjang metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including, various essential amino acids, conjugated amino acids, different vitamins, flavonoids, and enzymes. Amino acid profiles obtained from KEGG annotation in cheonggukjang were validated with experimental result of amino acid profiles.
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Affiliation(s)
- Jyoti Prakash Tamang
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India.
| | - Souvik Das
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Pynhunlang Kharnaior
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Priyambada Pariyar
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Namrata Thapa
- Biotech Hub, Department of Zoology, Nar Bahadur Bhandari Degree College, Sikkim University, Tadong 737102, Sikkim, India.
| | - Seung-Wha Jo
- Microbial Institute for Fermentation Industry (MIFI), Sunchang 56048, Republic of Korea
| | - Eun-Jung Yim
- Microbial Institute for Fermentation Industry (MIFI), Sunchang 56048, Republic of Korea
| | - Dong-Hwa Shin
- Shindonghwa Food Research Institute, Seoul 06192, Republic of Korea
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Distribution and characterization of prophages in Lactobacillus plantarum derived from kimchi. Food Microbiol 2021; 102:103913. [PMID: 34809939 DOI: 10.1016/j.fm.2021.103913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/28/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022]
Abstract
Prophage distribution and phage characteristics based on the genome of Lactobacillus plantarum derived from kimchi were investigated. Prophage genomes retrieved from a database were analyzed in silico with prophage inducibility. Twenty-one kimchi-derived L. plantarum had at least one intact prophage, including a putative cryptic state on the chromosome. They were all confirmed to belong to the Siphoviridae family. Intact prophages can be classified into three different groups: PM411-like, Sha1-like, and unclassified phage groups. Some prophage regions were encoded with superinfection exclusion proteins and orphan methylases, suggesting that the phages co-evolved with their hosts. Interestingly, prophage inducibility showed that only DNA damage could induce prophages and that pH stresses by organic acids could not. Therefore, the prophage of L. plantarum did not affect the host unless DNA was damaged, and it would hardly affect the viability of the host through phage induction during kimchi fermentation. Our results might provide insights into the distribution and non-inducibility of prophages, existence of phage-immunity genes, and role of plant-derived L. plantarum prophages in host survival during late acidic kimchi fermentation.
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19
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Exploring the diversity of bacteriophage specific to Oenococcus oeni and Lactobacillus spp and their role in wine production. Appl Microbiol Biotechnol 2021; 105:8575-8592. [PMID: 34694447 DOI: 10.1007/s00253-021-11509-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022]
Abstract
The widespread existence of bacteriophage has been of great interest to the biological research community and ongoing investigations continue to explore their diversity and role. They have also attracted attention and in-depth research in connection to fermented food processing, in particular from the dairy and wine industries. Bacteriophage, mostly oenophage, may in fact be a 'double edged sword' for winemakers: whilst they have been implicated as a causal agent of difficulties with malolactic fermentation (although not proven), they are also beginning to be considered as alternatives to using sulphur dioxide to prevent wine spoilage. Investigation and characterisation of oenophage of Oenococcus oeni, the main species used in winemaking, are still limited compared to lactococcal bacteriophage of Lactococcus lactis and Lactiplantibacillus plantarum (formally Lactobacillus plantarum), the drivers of most fermented dairy products. Interestingly, these strains are also being used or considered for use in winemaking. In this review, the genetic diversity and life cycle of phage, together with the debate on the consequent impact of phage predation in wine, and potential control strategies are discussed. KEY POINTS: • Bacteriophage detected in wine are diverse. • Many lysogenic bacteriophage are found in wine bacteria. • Phage impact on winemaking can depend on the stage of the winemaking process. • Bacteriophage as potential antimicrobial agents against spoilage organisms.
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20
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Alekseeva AY, Groenenboom AE, Smid EJ, Schoustra SE. Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph181910093. [PMID: 34639397 PMCID: PMC8508538 DOI: 10.3390/ijerph181910093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.
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Affiliation(s)
- Anna Y. Alekseeva
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Correspondence:
| | - Anneloes E. Groenenboom
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Laboratory of Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, The Netherlands;
| | - Eddy J. Smid
- Laboratory of Food Microbiology, Wageningen University and Research, 6700 HB Wageningen, The Netherlands;
| | - Sijmen E. Schoustra
- Laboratory of Genetics, Wageningen University and Research, 6700 HB Wageningen, The Netherlands; (A.E.G.); (S.E.S.)
- Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka 10101, Zambia
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21
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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22
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23
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Mahony J, van Sinderen D. Virome studies of food production systems: time for 'farm to fork' analyses. Curr Opin Biotechnol 2021; 73:22-27. [PMID: 34252795 DOI: 10.1016/j.copbio.2021.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022]
Abstract
The food industry is under increasing pressure to produce high quality, traceable and minimally processed foods that are produced using sustainable approaches and ingredients. In line with the latter, there is an increased pressure for plant-based products to replace animal-derived products. Until recently, research efforts have mainly focused on dairy and meat products owing to their economic importance. The shift towards plant-based diets and food production requires a corresponding shift in research efforts to define the microbial requirements for and composition of (novel) plant-based foods, the (micro)organisms that are beneficial to such production systems, and the abundance and role of (bacterio)phages in shaping the microbial landscape of these foods. In this review, we explore current efforts in the area of virome analysis of foods and food production environments and highlight the need for more unified approaches to understand the contribution of phages in food safety and quality, and to develop novel tools to enhance the traceability of foods.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
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Park WJ, Kong SJ, Park JH. Kimchi bacteriophages of lactic acid bacteria: population, characteristics, and their role in watery kimchi. Food Sci Biotechnol 2021; 30:949-957. [PMID: 34395026 PMCID: PMC8302715 DOI: 10.1007/s10068-021-00930-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/18/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022] Open
Abstract
The bacteriophages (phages) in the watery kimchis (Baek-kimchi and Dongchimi) were characterized to determine the phage ecology of lactic acid bacteria (LAB). Kimchi obtained from the Seoul markets had an average of 2.1 log phage particles/mL, corresponding to 28% of the bacterial counts on a log scale. High counts of 5.5-6.5 log particles/mL of phages were noted in the early phase of fermentation (reaching pH 4), and 2.1-3.0 log phage particles/mL were found in the later phase, with some fluctuation in numbers. The LAB hosts changed from Weissella and Leuconostoc to Lactobacillus during Dongchimi fermentation. Fifteen phages, except for those of Lactobacillus, were isolated from diverse strains in the early phase. Five Weissella phages were Podoviridae, and all 10 Leuconostoc phages were Myoviridae. Phages had narrow and different host infection spectra to strains of the same species and high acidic stability. Therefore, the mortality and diversity of LAB during natural kimchi fermentation may be related to the specific phages of the hosts. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10068-021-00930-y.
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Affiliation(s)
- Won-Jeong Park
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam, 13120 Republic of Korea
| | - Se-Jin Kong
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam, 13120 Republic of Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, College of Bionano Technology, Gachon University, Seongnam, 13120 Republic of Korea
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Maske BL, de Melo Pereira GV, da Silva Vale A, Marques Souza DS, De Dea Lindner J, Soccol CR. Viruses in fermented foods: are they good or bad? Two sides of the same coin. Food Microbiol 2021; 98:103794. [PMID: 33875222 PMCID: PMC7992106 DOI: 10.1016/j.fm.2021.103794] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/21/2021] [Indexed: 12/23/2022]
Abstract
The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.
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Affiliation(s)
- Bruna Leal Maske
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | | | - Alexander da Silva Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Doris Sobral Marques Souza
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil; Applied Virology Laboratory, UFSC, Florianópolis, SC, Brazil
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches. Appl Microbiol Biotechnol 2020; 104:7731-7744. [PMID: 32749526 DOI: 10.1007/s00253-020-10804-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 12/31/2022]
Abstract
Kimchi is a traditional Korean fermented food prepared via spontaneous fermentation by various microorganisms originating from vegetables such as kimchi cabbage, radishes, and garlic. Recent advances in meta-omics approaches that integrate metataxonomics, metagenomics, metatranscriptomics, and metabolomics have contributed to explaining and understanding food fermentation processes. Kimchi microbial communities are composed of majorly lactic acid bacteria such as Leuconostoc, Lactobacillus, and Weissella and fewer eukaryotic microorganisms and kimchi fermentation are accomplished by complex microbial metabolisms to produce diverse metabolites such as lactate, acetate, CO2, ethanol, mannitol, amino acids, formate, malate, diacetyl, acetoin, and 2, 3-butanediol, which determine taste, quality, health benefit, and safety of fermented kimchi products. Therefore, in the future, kimchi researches should be systematically performed using the meta-omics approaches to understand complex microbial metabolisms during kimchi fermentation. KEY POINTS: • Spontaneous fermentation by raw material microbes gives kimchi its unique flavor. • The kimchi microbiome is altered by environmental factors and raw materials. • Through the multi-omics approaches, it is possible to accurately analyze the diversity and metabolic characteristics of kimchi microbiome and discover potential functionalities.
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Ledormand P, Desmasures N, Dalmasso M. Phage community involvement in fermented beverages: an open door to technological advances? Crit Rev Food Sci Nutr 2020; 61:2911-2920. [PMID: 32649837 DOI: 10.1080/10408398.2020.1790497] [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] [Indexed: 12/26/2022]
Abstract
Bacteriophages (phages) are considered the most abundant biological entities on Earth. An increasing interest in understanding phage communities, also called viromes or phageomes, has arisen over the past decade especially thanks to the development and the accessibility of Next Generation Sequencing techniques. Despite the increasing amount of available metagenomic data on microbial communities in various habitats, viromes remain poorly described in the scientific literature particularly when it comes to fermented food and beverages such as wine and cider. In this review, a particular attention is paid to the current knowledge on phage communities, with a special focus on fermented food viromes and the methodological tools available to undertake their study. There is a striking lack of available data on the fermented foods and beverages viromes. As far as we know, and although a number of phages have been isolated from wine, no general study has to date been carried out to assess the diversity of viromes in fermented beverages and their possible interactions with microbiota throughout the fermentation process. With the aim of establishing connections between the currently used technologies to carry out the analysis of viromes, possible applications of current knowledge to fermented beverages are examined.
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28
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Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles. Food Microbiol 2020; 85:103278. [DOI: 10.1016/j.fm.2019.103278] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 01/12/2023]
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29
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Next-generation sequencing reveals predominant bacterial communities during fermentation of Thai fish sauce in large manufacturing plants. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108375] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Park J, Kim EB. Differences in microbiome and virome between cattle and horses in the same farm. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:1042-1055. [PMID: 32054207 PMCID: PMC7206377 DOI: 10.5713/ajas.19.0267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Abstract
Objective The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal’s health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated. Methods Here, we collected feces and dust samples (4 groups: cattle feces, C_F; horse feces, H_F; cattle dust, C_D; and horse dust, H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing. Results Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% to max 42.8%), Firmicutes (19.1% to 24.9%), Bacteroidetes (10.6% to 22.1%), and Actinobacteria (6.1% to 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected. Conclusion Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.
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Affiliation(s)
- Jongbin Park
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea
| | - Eun Bae Kim
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea.,Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea
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31
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Jeong SG, Lee JY, Yoon SR, Moon EW, Ha JH. A quantitative PCR based method using propidium monoazide for specific and sensitive detection of Pectobacterium carotovorum ssp. carotovorum in kimchi cabbage (Brassica rapa L. subsp. pekinensis). Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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32
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May A, Narayanan S, Alcock J, Varsani A, Maley C, Aktipis A. Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem. PeerJ 2019; 7:e7565. [PMID: 31534844 PMCID: PMC6730531 DOI: 10.7717/peerj.7565] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/29/2019] [Indexed: 01/02/2023] Open
Abstract
Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science.
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Affiliation(s)
- Alexander May
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Psychology, Arizona State University, Tempe, AZ, USA
| | - Shrinath Narayanan
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Joe Alcock
- University of New Mexico, Albuquerque, NM, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Carlo Maley
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
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33
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Kumar J, Sharma N, Kaushal G, Samurailatpam S, Sahoo D, Rai AK, Singh SP. Metagenomic Insights Into the Taxonomic and Functional Features of Kinema, a Traditional Fermented Soybean Product of Sikkim Himalaya. Front Microbiol 2019; 10:1744. [PMID: 31428064 PMCID: PMC6688588 DOI: 10.3389/fmicb.2019.01744] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
Kinema is an ethnic, naturally fermented soybean product consumed in the Sikkim Himalayan region of India. In the present study, the whole metagenome sequencing approach was adopted to examine the microbial diversity and related functional potential of Kinema, consumed in different seasons. Firmicutes was the abundant phylum in Kinema, ranging from 82.31 to 93.99% in different seasons, followed by Actinobacteria and Proteobacteria. At the species level, the prevalent microorganisms were Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis, Corynebacterium glutamicum, Bacillus pumilus, and Lactococcus lactis. The abundance of microbial species varied significantly in different seasons. Further, the genomic presence of some undesirable microbes like Bacillus cereus, Proteus mirabilis, Staphylococcus aureus, Proteus penneri, Enterococcus faecalis, and Staphylococcus saprophyticus, were also detected in the specific season. The metagenomic analysis also revealed the existence of bacteriophages belonging to the family Siphoviridae, Myoviridae, and Podoviridae. Examination of the metabolic potential of the Kinema metagenome depicted information about the biocatalysts, presumably involved in the transformation of protein and carbohydrate polymers into bioactive molecules of health-beneficial effects. The genomic resource of several desirable enzymes was identified, such as β-galactosidase, β-glucosidase, β-xylosidase, and glutamate decarboxylase, etc. The catalytic function of a novel glutamate decarboxylase gene was validated for the biosynthesis of γ-aminobutyric acid (GABA). The results of the present study highlight the microbial and genomic resources associated with Kinema, and its importance in functional food industry.
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Affiliation(s)
- Jitesh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Mohali, India
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing, Mohali, India
| | | | - Dinabandhu Sahoo
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong, India.,Institute of Bioresources and Sustainable Development, Imphal, India
| | - Amit K Rai
- Institute of Bioresources and Sustainable Development, Sikkim Centre, Tadong, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Mohali, India
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Santiago-Rodriguez TM, Hollister EB. Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut. Viruses 2019; 11:v11070656. [PMID: 31323792 PMCID: PMC6669467 DOI: 10.3390/v11070656] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023] Open
Abstract
The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.
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Affiliation(s)
| | - Emily B Hollister
- Diversigen Inc., 2450 Holcombe Blvd, Suite BCMA, 77021 Houston, TX, USA.
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35
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Agyirifo DS, Wamalwa M, Otwe EP, Galyuon I, Runo S, Takrama J, Ngeranwa J. Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities. Heliyon 2019; 5:e02170. [PMID: 31388591 PMCID: PMC6667825 DOI: 10.1016/j.heliyon.2019.e02170] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/05/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Fermentation of Theobroma cacao L. beans is the most critical stage in the production of cocoa products such as chocolates and its derivatives. There is a limited understanding of the complex response of microbial diversity during cocoa bean fermentation. The aim of the present study was to investigate microbial communities in the cocoa bean fermentation heap using a culture-independent approach to elucidate microbial diversity, structure, functional annotation and mapping unto metabolic pathways. Genomic DNA was extracted and purified from a sample of cocoa beans fermentation heap and was followed by library preparations. Sequence data was generated on Illumina Hiseq 2000 paired-end technology (Macrogen Inc). Taxonomic analysis based on genes predicted from the metagenome identified a high percentage of Bacteria (90.0%), Yeast (9%), and bacteriophages (1%) from the cocoa microbiome. Lactobacillus (20%), Gluconacetobacter (9%), Acetobacter (7%) and Gluconobacter (6%) dominated this study. The mean species diversity, measured by Shannon alpha-diversity index, was estimated at 142.81. Assignment of metagenomic sequences to SEED database categories at 97% sequence similarity identified a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates and aromatic amino acids. Metabolism of aromatic compounds, amino acids and their derivatives and carbohydrates occupied 0.6%, 8% and 13% respectively. Overall, these results provide insights into the cocoa microbiome, identifying fermentation processes carried out broadly by complex microbial communities and metabolic pathways encoding aromatic compounds such as phenylacetaldehyde, butanediol, acetoin, and theobromine that are required for flavour and aroma production. The results obtained will help develop targeted inoculations to produce desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compounds formation.
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Affiliation(s)
- Daniel S. Agyirifo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Mark Wamalwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
- International Livestock Research Institute-Bioscience East and Central Africa, Kenya
| | - Emmanuel Plas Otwe
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Isaac Galyuon
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - Steven Runo
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
| | - Jemmy Takrama
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
- Cocoa Research Institute of Ghana, Ghana
| | - Joseph Ngeranwa
- Biochemistry and Biotechnology Department, Kenyatta University, Kenya
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Chopyk J, Kulkarni P, Nasko DJ, Bradshaw R, Kniel KE, Chiu P, Sharma M, Sapkota AR. Zero-valent iron sand filtration reduces concentrations of virus-like particles and modifies virome community composition in reclaimed water used for agricultural irrigation. BMC Res Notes 2019; 12:223. [PMID: 30975220 PMCID: PMC6458639 DOI: 10.1186/s13104-019-4251-y] [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: 09/19/2018] [Accepted: 04/03/2019] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE Zero-valent iron sand filtration can remove multiple contaminants, including some types of pathogenic bacteria, from contaminated water. However, its efficacy at removing complex viral populations, such as those found in reclaimed water used for agricultural irrigation, has not been fully evaluated. Therefore, this study utilized metagenomic sequencing and epifluorescent microscopy to enumerate and characterize viral populations found in reclaimed water and zero-valent iron-sand filtered reclaimed water sampled three times during a larger greenhouse study. RESULTS Zero-valent iron-sand filtered reclaimed water samples had significantly less virus-like particles than reclaimed water samples at all collection dates, with the reclaimed water averaging between 108 and 109 and the zero-valent iron-sand filtered reclaimed water averaging between 106 and 107 virus-like particles per mL. In addition, for both sample types, viral metagenomes (viromes) were dominated by bacteriophages of the order Caudovirales, largely Siphoviridae, and genes related to DNA metabolism. However, the proportion of sequences homologous to bacteria, as well as the abundance of genes possibly originating from a bacterial host, was higher in the viromes of zero-valent iron-sand filtered reclaimed water samples. Overall, zero-valent iron-sand filtered reclaimed water had a lower total concentration of virus-like particles and a different virome community composition compared to unfiltered reclaimed water.
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Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA
| | - Prachi Kulkarni
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA
| | - Daniel J Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Rhodel Bradshaw
- United States Department of Agriculture, Agricultural Research Service, Environmental and Microbial Food Safety Laboratory, Beltsville, MD, 20705, USA
| | - Kalmia E Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Pei Chiu
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Manan Sharma
- United States Department of Agriculture, Agricultural Research Service, Environmental and Microbial Food Safety Laboratory, Beltsville, MD, 20705, USA
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA.
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37
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Jayasundara D, Herath D, Senanayake D, Saeed I, Yang CY, Sun Y, Chang BC, Tang SL, Halgamuge SK. ENVirT: inference of ecological characteristics of viruses from metagenomic data. BMC Bioinformatics 2019; 19:377. [PMID: 30717665 PMCID: PMC7394321 DOI: 10.1186/s12859-018-2398-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/25/2018] [Indexed: 12/23/2022] Open
Abstract
Background Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases. Results In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses. Conclusions These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations. Electronic supplementary material The online version of this article (10.1186/s12859-018-2398-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Duleepa Jayasundara
- School of Public Health and Community Medicine, University of New South Wales, Randwick, NSW 2052, Australia.
| | - Damayanthi Herath
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Australia.,Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - Damith Senanayake
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Isaam Saeed
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan
| | - Yuan Sun
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Bill C Chang
- Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.
| | - Saman K Halgamuge
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Australia.,Research School of Engineering, College of Engineering and Computer Science, The Australian National University, Canberra, ACT 2601, Australia
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Jung MJ, Kim MS, Yun JH, Lee JY, Kim PS, Lee HW, Ha JH, Roh SW, Bae JW. Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community. Food Microbiol 2018; 76:319-327. [DOI: 10.1016/j.fm.2018.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
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Xu Y, Yu Y, Tian Y, Su Y, Li X, Zhang Z, Zhu H, Han J, Zhang H, Liu L, Zhang L. Analysis of Beijing Douzhir Microbiota by High-Throughput Sequencing and Isolation of Acidogenic, Starch-Flocculating Strains. Front Microbiol 2018; 9:1142. [PMID: 29896188 PMCID: PMC5987674 DOI: 10.3389/fmicb.2018.01142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
Beijing Douzhir is a traditional Chinese fermented drink produced by the natural fermentation of mung beans as the raw material. Ma tofu is an edible by-product of Douzhir processing. Douzhir microbiota, particularly bacteria involved in the natural fermentation process, has not been clearly established, resulting in limited industrial Douzhir production. Here, three uncooked Douzhir samples (D group) and three uncooked Ma tofu samples (M group) (two replicates per sample) were collected from three manufacturers in different locations in Beijing. The composition and diversity of the bacterial communities in each sample were analyzed by high-throughput sequencing. In total, 637 operational taxonomic units (OTUs) were revealed in the D group through database alignment, and 656 OTUs were found in the M group. The Chao, ACE, and Shannon indices were not significantly different in Douzhir samples from different manufacturers (p > 0.05). Representatives of six phyla were found in all 12 samples. Dominant bacteria were isolated and identified using mung bean juice as the growth medium. In both Douzhir and Ma tofu samples, dominant bacteria belonging to Firmicutes and Proteobacteria comprised > 94% of the total microbiota. The dominant bacteria included members of the Lactococcus, Acetobacter, Streptococcus, and Lactobacillus genera. Considering the dominant-microbiota information, we employed a plate-separation technique and isolated two strains of acid-producing bacteria from the Douzhir and Ma tofu samples with starch-flocculating activity: Acetobacter indonesiensis and Lactococcus lactis subsp. lactis. Such strains can serve as a foundation for the standardized industrial production of Douzhir.
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Affiliation(s)
- Yunhe Xu
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
| | - Yang Yu
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
| | - Yumin Tian
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
| | - Yuhong Su
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
| | - Xiaona Li
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Zhen Zhang
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
| | - Hongyan Zhu
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
| | - Jie Han
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Huajiang Zhang
- School of Food Science, Northeast Agricultural University, Harbin, China
| | - Liying Liu
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
| | - Lili Zhang
- Department of Food Science and Engineering, Jinzhou Medical University, Jinzhou, China
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Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
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Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
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Bokulich NA, Bamforth CW, Mills DA. A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2012-0709-01] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nicholas A. Bokulich
- Department of Viticulture and Enology and Department of Food Science and Technology
| | | | - David A. Mills
- Department of Viticulture and Enology and Department of Food Science and Technology, University of California, Davis 95616
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Fernandez-Cassi X, Timoneda N, Gonzales-Gustavson E, Abril JF, Bofill-Mas S, Girones R. A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water. Int J Food Microbiol 2017. [PMID: 28646670 DOI: 10.1016/j.ijfoodmicro.2017.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food. To advance this promising field, parsley was planted and grown under controlled conditions and irrigated using contaminated river water. Viruses polluting the irrigation water and the parsley leaves were studied by using metagenomics. To address possible contamination due to sample manipulation, library preparation, and other sources, parsley plants irrigated with nutritive solution were used as a negative control. In parallel, viruses present in the river water used for plant irrigation were analyzed using the same methodology. It was possible to assign viral taxons from 2.4 to 74.88% of the total reads sequenced depending on the sample. Most of the viral reads detected in the river water were related to the plant viral families Tymoviridae (66.13%) and Virgaviridae (14.45%) and the phage viral families Myoviridae (5.70%), Siphoviridae (5.06%), and Microviridae (2.89%). Less than 1% of the viral reads were related to viral families that infect humans, including members of the Adenoviridae, Reoviridae, Picornaviridae and Astroviridae families. On the surface of the parsley plants, most of the viral reads that were detected were assigned to the Dicistroviridae family (41.52%). Sequences related to important viral pathogens, such as the hepatitis E virus, several picornaviruses from species A and B as well as human sapoviruses and GIV noroviruses were detected. The high diversity of viral sequences found in the parsley plants suggests that irrigation on fecally-tainted food may have a role in the transmission of a wide diversity of viral families. This finding reinforces the idea that the best way to avoid food-borne viral diseases is to introduce good field irrigation and production practices. New strains have been identified that are related to the Picornaviridae and distantly related to the Hepeviridae family. However, the detection of a viral genome alone does not necessarily indicate there is a risk of infection or disease development. Thus, further investigation is crucial for correlating the detection of viral metagenomes in samples with the risk of infection. There is also an urgent need to develop new methods to improve the sensitivity of current Next Generation Sequencing (NGS) techniques in the food safety area.
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Affiliation(s)
- X Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - N Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - E Gonzales-Gustavson
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - S Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
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Mahmoud H, Jose L. Phage and Nucleocytoplasmic Large Viral Sequences Dominate Coral Viromes from the Arabian Gulf. Front Microbiol 2017; 8:2063. [PMID: 29114244 PMCID: PMC5660727 DOI: 10.3389/fmicb.2017.02063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 10/09/2017] [Indexed: 11/25/2022] Open
Abstract
Corals that naturally thrive under extreme conditions are gaining increasing attention due to their importance as living models to understand the impact of global warming on world corals. Here, we present the first metagenomic study of viral communities in corals thriving in a thermally variable water body in which the temperature fluctuates between 11 and 39°C in different seasons. The viral assemblages of two of the most abundant massive (Porites harrisoni) and branching (Acropora downingi) corals in offshore and inshore reef systems in the northern Arabian Gulf were investigated. Samples were collected from five reef systems during summer, autumn and winter of 2011/2012. The two coral viromes contain 12 viral families, including 10 dsDNA viral families [Siphoviridae, Podoviridae, Myoviridae, Phycodnaviridae, Baculoviridae, Herpesviridae, Adenoviridae, Alloherpesviridae, Mimiviridae and one unclassified family], one-ssDNA viral family (Microviridae) and one RNA viral family (Retroviridae). Overall, sequences significantly similar to Podoviridae were the most abundant in the P. harrisoni and A. downingi viromes. Various morphological types of virus-like particles (VLPs) were confirmed in the healthy coral tissue by transmission electron microscopy, including large tailless VLPs and electron-dense core VLPs. Tailed bacteriophages were isolated from coral tissue using a plaque assay. Higher functional gene diversity was recorded in A. downingi than in P. harrisoni, and comparative metagenomics revealed that the Gulf viral assemblages are functionally distinct from Pacific Ocean coral viral communities.
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Affiliation(s)
- Huda Mahmoud
- Faculty of Science, Department of Biological Sciences, Kuwait University, Safat, Kuwait
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Cao Y, Fanning S, Proos S, Jordan K, Srikumar S. A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies. Front Microbiol 2017; 8:1829. [PMID: 29033905 PMCID: PMC5627019 DOI: 10.3389/fmicb.2017.01829] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.
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Affiliation(s)
- Yu Cao
- UCD-Centre for Food Safety, Science Centre South, University College DublinDublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College DublinDublin, Ireland
| | - Sinéad Proos
- Food for Health Ireland, Science Centre South, University College DublinDublin, Ireland
| | | | - Shabarinath Srikumar
- UCD-Centre for Food Safety, Science Centre South, University College DublinDublin, Ireland
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Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures. Appl Environ Microbiol 2017; 83:AEM.00888-17. [PMID: 28754704 DOI: 10.1128/aem.00888-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023] Open
Abstract
Despite being potentially highly useful for characterizing the biodiversity of phages, metagenomic studies are currently not available for dairy bacteriophages, partly due to the lack of a standard procedure for phage extraction. We optimized an extraction method that allows the removal of the bulk protein from whey and milk samples with losses of less than 50% of spiked phages. The protocol was applied to extract phages from whey in order to test the notion that members of Lactococcus lactis 936 (now Sk1virus), P335, c2 (now C2virus) and Leuconostoc phage groups are the most frequently encountered in the dairy environment. The relative abundance and diversity of phages in eight and four whey mixtures from dairies using undefined mesophilic mixed-strain cultures containing Lactococcus lactis subsp. lactis biovar diacetylactis and Leuconostoc species (i.e., DL starter cultures) and defined cultures, respectively, were assessed. Results obtained from transmission electron microscopy and high-throughput sequence analyses revealed the dominance of Lc. lactis 936 phages (order Caudovirales, family Siphoviridae) in dairies using undefined DL starter cultures and Lc. lactis c2 phages (order Caudovirales, family Siphoviridae) in dairies using defined cultures. The 936 and Leuconostoc phages demonstrated limited diversity. Possible coinduction of temperate P335 prophages and satellite phages in one of the whey mixtures was also observed.IMPORTANCE The method optimized in this study could provide an important basis for understanding the dynamics of the phage community (abundance, development, diversity, evolution, etc.) in dairies with different sizes, locations, and production strategies. It may also enable the discovery of previously unknown phages, which is crucial for the development of rapid molecular biology-based methods for phage burden surveillance systems. The dominance of only a few phage groups in the dairy environment signifies the depth of knowledge gained over the past decades, which served as the basis for designing current phage control strategies. The presence of a correlation between phages and the type of starter cultures being used in dairies might help to improve the selection and/or design of suitable, custom, and cost-efficient phage control strategies.
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46
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He GQ, Liu TJ, Sadiq FA, Gu JS, Zhang GH. Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches. J Zhejiang Univ Sci B 2017; 18:289-302. [PMID: 28378567 DOI: 10.1631/jzus.b1600148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.
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Affiliation(s)
- Guo-Qing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Tong-Jie Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Faizan A Sadiq
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Jing-Si Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Hua Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
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47
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Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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48
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Chen G, Chen C, Lei Z. Meta-omics insights in the microbial community profiling and functional characterization of fermented foods. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.05.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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49
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Orosco FL, Lluisma AO. Variation in virome diversity in wild populations of Penaeus monodon (Fabricius 1798) with emphasis on pathogenic viruses. Virusdisease 2017; 28:262-271. [PMID: 29291212 DOI: 10.1007/s13337-017-0389-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/20/2017] [Indexed: 11/28/2022] Open
Abstract
Marine animals typically harbor a community of viruses, a number of which are known to cause diseases. In shrimp aquaculture, viral pathogens are the principal causes of major economic losses. However, the composition of the viral load of shrimps in wild population is poorly known. In this study, we explored the viral diversity in the microbiome of wild Penaeus monodon collected from six sites in the Philippines, with a view to detecting pathogenic forms. We employed a metagenomic approach via particle-associated nucleic acid isolation, sequence-independent single primer amplification, and pyrosequencing. Virome analysis of shrimp samples from different sites revealed distinct virome profiles, and hence significant differences in diversity, among the various sites based on number of OTUs, Shannon-Weaver Index, and Inverse Simpson Index. Sequences of key shrimp pathogens were detected such as the white spot syndrome virus (WSSV), and Penaeus stylirostris densovirus (PstDV). However, the patterns of distribution of the pathogenic viruses varied; whereas WSSV was found only in three out of six sites and PstDV were found in all but one site. The results also revealed shrimp-associated viruses that have not yet been observed in P. monodon such as avian virus-like, insect virus-like, plankton virus-like and bacteriophage-like sequences. Despite the diverse array of viruses detected in the study, a large proportion remains unidentified (i.e., similarity to sequences in the database was lower than the threshold required for definitive identification), and therefore could represent unexplored virus sequences and viral genomes in the environment.
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Affiliation(s)
- Fredmoore L Orosco
- Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines - Diliman, 1101 Quezon City, Philippines.,Institute of Biology, University of the Philippines - Diliman, 1101 Quezon City, Philippines
| | - Arturo O Lluisma
- Marine Genomics and Molecular Genetics Laboratory, Marine Science Institute, University of the Philippines - Diliman, 1101 Quezon City, Philippines
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50
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Aw TG, Wengert S, Rose JB. Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses. Int J Food Microbiol 2016; 223:50-6. [PMID: 26894328 DOI: 10.1016/j.ijfoodmicro.2016.02.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/04/2016] [Accepted: 02/08/2016] [Indexed: 01/20/2023]
Abstract
The emergence of culture- and sequence-independent metagenomic methods has not only provided great insight into the microbial community structure in a wide range of clinical and environmental samples but has also proven to be powerful tools for pathogen detection. Recent studies of the food microbiome have revealed the vast genetic diversity of bacteria associated with fresh produce. However, no work has been done to apply metagenomic methods to tackle viruses associated with fresh produce for addressing food safety. Thus, there is a little knowledge about the presence and diversity of viruses associated with fresh produce from farm-to-fork. To address this knowledge gap, we assessed viruses on commercial romaine and iceberg lettuces in fields and a produce distribution center using a shotgun metagenomic sequencing targeting both RNA and DNA viruses. Commercial lettuce harbors an immense assemblage of viruses that infect a wide range of hosts. As expected, plant pathogenic viruses dominated these communities. Sequences of rotaviruses and picobirnaviruses were also identified in both field-harvest and retail lettuce samples, suggesting an emerging foodborne transmission threat that has yet to be fully recognized. The identification of human and animal viruses in lettuce samples in the field emphasizes the importance of preventing viral contamination on leafy greens starting at the field. Although there are still some inherent experimental and bioinformatics challenges in applying viral metagenomic approaches for food safety testing, this work will facilitate further application of this unprecedented deep sequencing method to food samples.
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Affiliation(s)
- Tiong Gim Aw
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, United States.
| | - Samantha Wengert
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, United States
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, United States
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