Strain-level multiomics analysis reveals significant variation in cheeses from different regions

Yang, Chengcong; You, Lijun; Kwok, Lai‐Yu; Jin, Hao; Peng, Jiangying; Zhao, Zhixin; Sun, Zhihong

doi:10.1016/j.lwt.2021.112043

Cited by 24 publications

(10 citation statements)

References 42 publications

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“…Substantial evidence indicates the existence of distinguishable microbial patterns in ripened cheeses originating from different areas and produced using different manufacturing conditions [ 1 , 4 , 40 , 41 ]. Apart from the cheese manufacturing environment, factors including the origin of the milk, the addition of starter cultures or natural whey, herbs, salt, and other ingredients, and the processing conditions, such as milk heating or pasteurization, influence the shaping of unique microbial consortia in each type of cheese [ 1 ].…”

Section: Discussionmentioning

confidence: 99%

Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses

Kamilari

Tsaltas

Stanton

et al. 2022

Foods

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The distinct sensorial characteristics of local cheeses influence consumer preferences, and make an essential contribution to the local economy. Microbial diversity in cheese is among the fundamental contributors to sensorial and qualitative characteristics. However, knowledge regarding the existence of microbial patterns associated with regional production practices in ripened cheeses remains limited. The present research was conducted to test the hypothesis that the background metagenome of cheeses could be used as a marker of their origin. We compared Irish versus Eastern Mediterranean cheeses—namely Greek and Cypriot—using High Throughput Sequencing (HTS). The study identified a significantly distinct separation among cheeses originating from the three different countries, in terms of the total microbial community composition. The use of machine learning and biomarkers discovery algorithms defined key microbes that differentiate each geographic region. Finally, the development of interaction networks revealed that the key species developed mostly negative interactions with the other members of the communities, highlighting their dominance in the community. The findings of the present research demonstrate that metagenome could indeed be used as a biological marker of the origin of mature cheeses, and could provide further insight into the dynamics of microbial community composition in ripened cheeses.

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Section: Discussionmentioning

confidence: 99%

Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses

Kamilari

Tsaltas

Stanton

et al. 2022

Foods

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“…In the current study, a metagenomic approach was carried out to observe prophage signatures in bacterial metagenomes throughout the cider fermentation process. A total of 1174 putative prophage contigs were identified in silico in the bacterial metagenomes using VIBRANT software, such as has been done in cheese [44] and kefir [45]. Among them, two complete prophages were found, NODE_55 and NODE_129, matching with phages isolated from human gut metagenomic data.…”

Section: Discussionmentioning

confidence: 99%

“…The main barrier for these types of approaches in cider, and probably in other fermented beverages, is the problematic extraction of phage DNA, due to their very low occurrence, and also to the particular physicochemical conditions encountered in these fermented beverages. Positive and negative correlations could be made in future experiments between lytic phages, prophages and bacterial proportions in cider throughout the fermentation process by combining the analyses of metabolites and food properties, as it has been described in cheese, for example [44]. For a better view of these dynamics in cider, and especially with LAB, it would be interesting to extend the timespan of the study looking at longer fermentation processes, such as cider intended to be used for the making of spirits and vinegars [53].…”

Section: Discussionmentioning

confidence: 99%

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

et al. 2022

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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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“…Yang et al . (2021a) examined the microbiomes and metabolomes of four Chinese and four European cheeses by using deep metagenome sequencing and LC–MS, respectively. The findings showed that amino acids and a few volatile compounds were the key metabolites that differed between Chinese and European cheeses.…”

Section: Metabolomics For Dairy Traceability and Authenticitymentioning

confidence: 99%

Review of the applications of metabolomics approaches in dairy science: From factory to human

Zhang¹,

Zheng²,

Liu³

et al. 2023

Int J of Dairy Tech

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Dairy products are nutritious and are increasingly consumed as an important dietary component in China. Exploring the factors that affect the nutritional quality of dairy products and ensuring their safety have become the main focus of dairy research. The composition of metabolites in dairy products is large and complex. The levels and types of metabolites vary according to various factors in the process from factory to human dining table. Therefore, metabolites might be used to assess the nutritional value, traceability and authenticity, and physiological function of dairy products. This review's main goal is to introduce the most recent developments and applications of metabolomics as an efficient tool for comprehensively characterising the composition and dynamic changes of metabolites in the area of food science and nutrition research in the process of getting dairy products from factory to human. The examples are taken from the most relevant metabolomics work published from 2018 to 2022, focusing on potential marker metabolites and metabolic mechanisms related to dairy product quality, authenticity/traceability and dairy intake monitoring. The future direction of metabolomics in the field of dairy science was also discussed. This information will provide a reference for the further application of metabolomics technology to Chinese dairy products to develop their quality, safety and nutritional value.

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Strain-level multiomics analysis reveals significant variation in cheeses from different regions

Cited by 24 publications

References 42 publications

Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses

Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

Review of the applications of metabolomics approaches in dairy science: From factory to human

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