Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community

Jung, Myeong Ho; Kim, Min‐Soo; Yun, Ji-Hyun; Lee, June-Young; Kim, Pil Soo; Lee, Hae-Won; Ha, Ji‐Hyoung; Roh, Seong Woon; Bae, Jin-Woo

doi:10.1016/j.fm.2018.06.010

Cited by 30 publications

(9 citation statements)

References 47 publications

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“…Through analysis of metagenome data sets which capture entire microbial ecosystems, some phage-associated reads have been identified, though the extraction protocol had to be optimised in order to obtain a more complete image of phage prevalence, abundance and diversity [115] . Consequently, more targeted extraction methods for viral nucleic acid have been developed [116] . Viral metagenomics (or phageomics) has clearly increased our understanding of the prevalence, abundance, dynamics, and role of phages in a number of food fermentation processes.…”

Section: Phageomes Of Fermented Foodsmentioning

confidence: 99%

Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods

White¹,

Yu²,

Eraclio³

et al. 2022

MRR

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Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.

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Section: Phageomes Of Fermented Foodsmentioning

confidence: 99%

Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods

White¹,

Yu²,

Eraclio³

et al. 2022

MRR

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“…In addition, bacterial viruses, bacteriophages, have recently been recognised as crucial members of food microbial communities and taken more into account as also playing a key role in community performance [64]. New phage-filtration and isolation protocols in combination with sequencing and bioinformatic analysis allow us to estimate the role of bacteriophages in food production and food microbiology, e.g., clarify the geographical origin of a product, predict the community composition after several cycles of batch fermentation [65,66]. The extended knowledge of metabolite production and growth profiles of these microorganisms in fermented foods can help to understand the observed evolutionary pathways.…”

Section: Traditional Fermented Foods With Complex Microbial Communitiesmentioning

confidence: 99%

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Alekseeva

Groenenboom

Smid

et al. 2021

IJERPH

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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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“…The viral community from ten samples representative of Korean and Chinese kimchi was also investigated [47]. Viral concentrates were obtained through filtration and Polyethylene Glycol (PEG) concentration, and DNA was sequenced providing several thousands of contigs >500 bp per sample, and revealing a very high diversity.…”

Section: New Contributions Of Whole Metagenome Sequencing and Viral Metagenomicsmentioning

confidence: 99%

Bacteriophage ecology of fermented foods: anything new under the sun?

Paillet

Dugat-Bony

2021

Current Opinion in Food Science

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Bacteriophage ecology has raised an increasing attention over the last few years, thanks to the improvement and contributions of microscopy, comparative genomics and viral metagenomics methods. Fermented foods host dense and diverse microbial communities and, therefore, represent an ideal biotope for bacteriophages. If their occurrence in such environments has been demonstrated decades ago, data highlighting their impact on mixed communities and their ecological roles are scarce when compared to other microbial ecosystems. This review summarizes most recent knowledge into the bacteriophage diversity of fermented foods and stress evidences suggesting the impact of these entities on the dynamics of food microbial communities. The main ecological roles played by bacteriophages in microbial ecosystems are also addressed. Understanding the impact of bacteriophages in fermented foods will further help in designing adapted microbial consortia and thus providing a better control of the food fermentations.

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Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community

Cited by 30 publications

References 47 publications

Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods

Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Bacteriophage ecology of fermented foods: anything new under the sun?

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