Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process

Vermote, Louise; Verce, Marko; Vuyst, Luc De; Weckx, Stefan

doi:10.1016/j.idairyj.2018.07.010

Cited by 45 publications

(41 citation statements)

References 57 publications

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“…To enable culture-independent microbial species diversity analysis, total DNA extracts were prepared from the cell pellets obtained from the original samples, following a method combining enzymatic, chemical, and mechanical treatments for cell lysis and phenol/chloroform/isoamyl alcohol treatment and column purification to extract and purify the DNA, as described before ( Vermote et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species

2018

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The present study combined high-throughput culture-dependent plating and culture-independent amplicon sequencing with a metabolite target analysis to systematically dissect the identity, evolution, and role of the microorganisms, substrates, and metabolites during the four-phase fermentation and maturation process of lambic beer production. This led to the following new insights. The changing physicochemical parameters and substrate and metabolite compositions of the fermenting wort and maturing lambic beer provoked several transitions between microbial species and explained the four-step production process. Manual wort acidification with lactic acid shortened the enterobacterial phase and thus kept biogenic amine formation by enterobacteria present during the early stages of fermentation at a minimum. Growth advantages during the alcoholic fermentation phase caused a transition from the prevalence by Hanseniaspora uvarum and Kazachstania species to that by Saccharomyces cerevisiae and later on Saccharomyces kudriavzevii, due to changing environmental parameters. During the acidification phase, Pediococcus damnosus was prevalent and performed a malolactic fermentation. Acetobacter pasteurianus produced acetic acid and acetoin. Upon maturation, Dekkera species appeared, together with P. damnosus and Pichia membranifaciens, thereby contributing to acetic acid production, depending on the oxygen availability. Moreover, the Dekkera species consumed the acetoin produced by the acetic acid bacteria for redox balancing. The breakdown of maltooligosaccharides seemed to be independent of the occurrence of Dekkera species and started already early in the fermentation process.

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Section: Methodsmentioning

confidence: 99%

Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species

2018

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“…Brine is a major source for salt‐tolerant yeasts. Yeast counts were found to reach 3.5–9 log cfu·ml −1 in a brine solution, with Debaryomyces being the most prevalent genus (Bockelmann, ; Bokulich & Mills, ; Garnier, Valence, & Mounier, ; Mounier et al, ; Vermote, Verce, De Vuyst, & Weckx, ; Viljoen, Knox, De Jager, & Lourens‐Hattingh, ). Recent studies have enabled the detection of further highly salt‐tolerant species, such as Yamadazyma triangularis and Sterigmatomyces halophilus (Kragelund Haastrup et al, ; Stellato et al, ).…”

Section: Sources Of Yeastsmentioning

confidence: 99%

Cheese yeasts

Fröhlich-Wyder

Arias-Roth

Jakob

2019

Yeast

106

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Numerous traditionally aged cheeses are surface ripened and develop a biofilm, known as the cheese rind, on their surfaces. The rind of such cheeses comprises a complex community of bacterial and fungal species that are jointly responsible for the typical characteristics of the various cheese varieties. Surface ripening starts directly after brining with the rapid colonization of the cheese surface by yeasts. The initially dominant yeasts are acid and salt‐tolerant and are capable of metabolizing the lactate produced by the starter lactic acid bacteria and of producing NH3 from amino acids. Both processes cause the pH of the cheese surface to rise dramatically. This so‐called deacidification process enables the establishment of a salt‐tolerant, Gram‐positive bacterial community that is less acid‐tolerant. Over the past decade, knowledge of yeast diversity in cheeses has increased considerably. The yeast species with the highest prevalence on surface‐ripened cheeses are Debaryomyces hansenii and Geotrichum candidum, but up to 30 species can be found. In the cheese core, only lactose‐fermenting yeasts, such as Kluyveromyces marxianus, are expected to grow. Yeasts are recognized as having an indispensable impact on the development of cheese flavour and texture because of their deacidifying, proteolytic, and/or lipolytic activity. Yeasts are used not only in the production of surface‐ripened cheeses but also as adjunct cultures in the vat milk in order to modify ripening behaviour and flavour of the cheese. However, yeasts may also be responsible for spoilage of cheese, causing early blowing, off‐flavour, brown discolouration, and other visible alterations of cheese.

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“…It does not depend on PCR amplification and used to examine the functional potential and microbial composition of the community. It is the only way to study the microbial community with no markers like viruses (Quince et al, 2017;Vermote et al, 2018). It allows strain-level remodeling in the taxonomic analysis and pathway predictions for the functional annotation of the microbiome under study (Han et al, 2020).…”

Section: Shotgun Sequencingmentioning

confidence: 99%

“…Figure 5 shows a schematic illustration signifying the standard metagenomic workflow. It has been used to new and existing microbial community, analyze new viruses (Yozwiak et al, 2012;Quince et al, 2017;Vermote et al, 2018), uncultured bacteria (Wrighton et al, 2012), unique proteins (Godzik, 2011), and metabolic pathways (Morgan et al, 2012).…”

Section: Shotgun Sequencingmentioning

confidence: 99%

Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches

Chandran

Meena

Sharma

2020

Front. Environ. Chem.

123

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Industrialization, population burst, and changing lifestyles have resulted in the genesis of non-degradable pollutants languishing the environment and human health. Biological approaches using microorganisms are gaining importance as an eco-friendly and cost-effective substitute to mitigate the pollution load. Microorganisms can survive in a divergent environment and produce metabolites that can degrade and transform pollutants making it possible to revive contaminated sites naturally. Modern omics technologies like metagenomics, transcriptomics, proteomics, etc. have been used nowadays design strategies to study ecology and diversity of microorganisms and their application in environmental monitoring and bioremediation. The present article will focus on the omics techniques reportedly used in environmental monitoring to tackle the pollution load.

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Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process

Cited by 45 publications

References 57 publications

Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species

Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species

Cheese yeasts

Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches

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