Metagenomic insights into the dynamics of microbial communities in food

Kergourlay, Gilles; Taminiau, Bernard; Daube, Georges; Vergès, Marie‐Christine Champomier

doi:10.1016/j.ijfoodmicro.2015.09.010

Cited by 124 publications

(70 citation statements)

References 88 publications

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“…Metagenomic analyses of various fermented foods like sourdough , kefir (Marsh et al, 2013;Nalbantoglu et al, 2014), fermented mung beans , Mexican Cotija cheese (Escobar-Zepeda et al, 2016), and kimchi (Park et al, 2011) have been performed. A recently published review provides detailed information on the application of high-throughput 16S rRNA sequencing to a variety of fermented foods to elucidate microbiota (Kergourlay et al, 2015).…”

Section: Profiling the Microbial Diversity Of Fermented Foodsmentioning

confidence: 99%

“…In the field of food fermentation, HTS has been widely employed in profiling microbial ecosystems throughout the world (Bokulich and Mills, 2012;Kergourlay et al, 2015). Considering the extensive and promising applications of HTS, this review will focus on the use of HTS methods and their roles in unraveling the complex microbial ecosystems of Chinese traditional fermented foods.…”

Section: Introductionmentioning

confidence: 99%

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Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

Liu

Sadiq

et al. 2017

J. Zhejiang Univ. Sci. B

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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 culturedependent 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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Section: Profiling the Microbial Diversity Of Fermented Foodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

Liu

Sadiq

et al. 2017

J. Zhejiang Univ. Sci. B

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“…Fortunately, molecular technologies can elucidate the microbial communities, including the identification and quantification of culturable and non-culturable organisms, and can do so at a much higher resolution than was previously possible with culture-based methods (Kergourlay et al, 2015;Elizaquível et al, 2015). Many bacterial species putatively responsible for food spoilage have been reported, thanks to the development of high throughput sequencing methods, that allow for a more detailed and deeper description of bacterial species present in food (Benson et al, 2014;Chaillou et al, 2014;Delcenserie et al, 2014;Galimberti et al, 2015;Riquelme et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: the example of white pudding

Cauchie

Gand

Kergourlay

et al. 2017

International Journal of Food Microbiology

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In order to control food losses and wastage, monitoring the microbial diversity of food products, during processing and storage is important, as studies have highlighted the metabolic activities of some microorganisms which can lead to spoilage. Knowledge of this diversity can be greatly improved by using a metagenetic approach based on high throughput 16S rRNA gene sequencing, which enables a much higher resolution than culture-based methods. Moreover, the Jameson effect, a phenomenon described by Jameson in 1962, is often used to classify bacterial strains within an ecosystem. According to this, we have studied the bacterial microbiota of Belgian white pudding during storage at different temperatures using culture-dependent and independent methods. The product was inoculated with a mix of dominant strains previously isolated from this foodstuff at the end of its shelf life (Carnobacterium maltaromaticum, Lactobacillus fuchuensis, Lactobacillus graminis, Lactobacillus oligofermentans, Lactococcus lactis, Leuconostoc mesenteroides, Raoultella terrigena and Serratia sp.). Daily during 16 days, the absolute abundance of inoculated strain was monitored by combining total count on plate agar and metagenetic analysis. The results were confirmed by qPCR analysis. The growth of each species was modelled for each temperature conditions, representative of good or bad storage practices. These data allowed the bacterial strains subdivision into three classes based on criteria of growth parameters for the studied temperature: the "dominant", the "subdominant" and the "inhibited" bacterial species, according to their maximal concentration (Nmax, log CFU/g), growth rate (μmax, 1/h) and time to reach the stationary phase (TRSP, days). Thereby, depending on the storage conditions, these data have permitted to follow intrinsically the evolution of each strain on the bacterial ecosystem of Belgian white pudding. Interestingly, it has shown that the reliability of the Jameson effect can be discussed. For example, at 4°C when Lactococcus lactis and Serratia sp. stopped growth at day 12, at the same time Carnobacterium maltaromaticum reached its maximal concentration and entered its stationary phase. In opposition to this, it can be noticed that in the same condition, the "sub-dominant" organisms continued their growth independently of the "dominant" species behaviour. In this case, the Jameson effect was not illustrated. This pattern is described for all storage conditions with the same strain classifications. These results highlighted the importance of combining metagenetic analysis and classical methods, with modelling, to offer a new tool for studying the evolution of microorganisms present in perishable food within different environmental conditions.

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“…Investigating the stable DNA of a microbial community can reveal the microbial diversity and ecology, conducing to the fermentation process accordingly (Cocolin, Dolci, & Rantsiou, ). Recently, metagenomics has been utilized to research food microbial ecosystems, which can serve as a promising tool in describing food transformation, safety and storage (Kergourlay, Taminiau, Daube, & Champomier Vergès, ). Many researches have studied the microbial community of fermented meat products.…”

Section: Introductionmentioning

confidence: 99%

Diversity study of microbial community in bacon using metagenomic analysis

et al. 2016

Journal of Food Safety

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This study is aimed to explore the diversity and dynamics of microorganisms in bacon. The microbes in 36 bacon samples collected from different plots (BC, BL, and BY) and process stages (stage I, II, III, and IV) were investigated by 16S rDNA sequencing. Quality control and operational taxonomic units clustering was performed by Quantitative Insights Into Microbial Ecology software. Total 1,460 representative sequences were identified. The relative abundance of Firmicutes in BC samples was significantly lower than BY samples (p value = .0304). The relative abundance of Proteobacteria in BC samples was significantly higher than BL (p value = .0072) and BY (p value = .0258) samples. The relative abundance of Proteobacteria in stage I was higher than stage IV (p value = .0148). Similarity clustering tree showed that Staphylococcus, Sphingomonas, Pseudomonas, Enterobacteriaceae, and Leuconostoc had higher abundances. These dominant categories might be used for controlling the transformation process and improving flavor and safety of bacon. Practical applications Bacon is a well‐known fermented meat product that contains many microbes. Using 16S rDNA sequencing, the microbial community in 36 bacon samples collected from different plots and different process stages were investigated. After quality control and OUT clustering, the representative sequences of operational taxonomic units were annotated by Recombination Detection Program‐classifier method. Alpha diversity analysis, species composition analysis and abundance difference analysis separately were performed using Mothur software, Quantitative Insights Into Microbial Ecology software and the metastats command in Mothur. Staphylococcus was abundant in BY samples, which could result in infection. Sphingomonas, which was a major bacteria in BC samples, might affect the flavor of bacon in the stage I of processing. Additionally, Pseudomonas, Enterobacteriaceae, and Leuconostoc might have correlation with spoilage of bacon. These findings might be valuable for finding the bacterial species that can be used for controlling the transformation process of raw materials and improving flavor and safety of bacon.

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Metagenomic insights into the dynamics of microbial communities in food

Cited by 124 publications

References 88 publications

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: the example of white pudding

Diversity study of microbial community in bacon using metagenomic analysis

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