ArticleApplied and environmental microbiology2011
Metagenomic analysis of the viral communities in fermented foods.
Article in Applied and environmental microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- Genetic Diversity and Genomic Characteristics of the Respiratory Virome in Patients With Severe Fungal Infections.Journal of medical virology · 2026Article
- Microbial ecology of fermented foods.FEMS yeast research · 2026Review
- What a pickle-a metagenomic perspective on the cucumber fermentation.Frontiers in microbiology · 2026Article
- Isolation, Characterization, and Preliminary Application of Staphylococcal Bacteriophages in SichuanMicroorganisms · 2025Article
- Investigation of Microbial Community of Korean Soy Sauce (Microorganisms · 2024Article
- Synoptic Variation Drives Genetic Diversity and Transmission Mode of Airborne DNA Viruses in Urban Space.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce.Frontiers in microbiology · 2023Article
- Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.Microorganisms · 2022Review
- Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage.Microorganisms · 2022Article
- Characterization of Prophages inJournal of microbiology and biotechnology · 2022Article
- Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges,Microorganisms · 2022Article
- Insights into the global freshwater virome.Frontiers in microbiology · 2022Article
- Contribution of omics to biopreservation: Toward food microbiome engineering.Frontiers in microbiology · 2022Review
- Exploring the diversity of bacteriophage specific to Oenococcus oeni and Lactobacillus spp and their role in wine production.Applied microbiology and biotechnology · 2021Review
- Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods.International journal of environmental research and public health · 2021Article
- Viruses in fermented foods: are they good or bad? Two sides of the same coin.Food microbiology · 2021Review
- NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water.Foods (Basel, Switzerland) · 2021Article
- Kimchi bacteriophages of lactic acid bacteria: population, characteristics, and their role in watery kimchi.Food science and biotechnology · 2021Article
- Differences in microbiome and virome between cattle and horses in the same farm.Asian-Australasian journal of animal sciences · 2020Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganism-infecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral order Caudovirales (i.e., Myoviridae, Podoviridae, and Siphoviridae). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.
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