Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses

Dugat-Bony, Éric; Straub, Cécile; Teissandier, Aurélie; Onésime, Djamila; Loux, Valentin; Monnet, Christophe; Irlinger, Françoise; Landaud, Sophie; Leclercq-Perlat, M.-N.; Bento, Pascal; Fraud, Sébastien; Gibrat, Jean‐François; Aubert, Julie; Fer, Frédéric; Guédon, Éric; Pons, Nicolas; Kennedy, Sean; Beckerich, Jean-Marie; Swennen, Dominique; Bonnarme, Pascal

doi:10.1371/journal.pone.0124360

Cited by 113 publications

(75 citation statements)

References 75 publications

(83 reference statements)

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“…Analysis of the genomic diversity in biofilms could further allow identifying at a global scale phase-variation mechanisms, a key but overlooked aspect of epigenetic regulation in bacteria (Henderson et al, 1999), which play an essential role in sessile development (Chauhan et al, 2013). At a larger scale, especially to investigate complex multi-species biofilms, the development of meta-omics is the promise of major breakthrough ahead in our understanding of bacterial interaction and physiology within highly diverse microbial communities (Dugat-Bony et al, 2015).…”

Section: Analyzing the -Omics Datamentioning

confidence: 99%

Critical review on biofilm methods

Azeredo

Azevedo

Briandet

et al. 2016

Critical Reviews in Microbiology

721

604

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Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms. ARTICLE HISTORY

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Section: Analyzing the -Omics Datamentioning

confidence: 99%

Critical review on biofilm methods

Azeredo

Azevedo

Briandet

et al. 2016

Critical Reviews in Microbiology

721

604

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“…Insights about microbial activities involved in cheese ripening process were provided. Monitoring of microbial gene expression during ripening of a Camembert‐type (Lessard et al ., 2014) and a surface‐ripened cheese (Dugat‐Bony et al ., 2015) by metatranscriptomics revealed the presence of microbial genes involved in flavour production from amino acids and highlighted that these activities were enhanced in the first phase of ripening. Moreover, Monnet et al .…”

Section: Exploring Microbial Functions Directly In Foodmentioning

confidence: 99%

Metagenomics insights into food fermentations

Filippis

Parente

2016

Microbial Biotechnology

186

102

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SummaryThis review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.

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“…However, more information is needed regarding the function and the activity of the microbiota during the process. Few studies based on metatranscriptomic analysis are applied on cheese matrix aiming at exploring the function of the cheese-associated microbiota (14)(15)(16).…”

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confidence: 99%

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

Alessandria

Ferrocino

Filippis

et al. 2016

Appl Environ Microbiol

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The microbial ecology of cheese involves a rich and complex interaction between starter lactic acid bacteria and nonstarter lactic acid bacteria (NSLAB), mainly originating from raw milk and/or from the environment, that can contribute to the final characteristics of cheese. The aim of the present research was the exploration of the active microbiota by RNA-based approaches during the manufacturing and ripening of a Grana-like cheese. Reverse transcriptase PCR (RT-PCR)-denaturing gradient gel electrophoresis (DGGE) and RNA-based high-throughput sequencing were applied to profile microbial populations, while the enumeration of active bacteria was carried out by using quantitative PCR (qPCR). Three different cheese productions (named D, E, and F) collected in the same month from the same dairy plant were analyzed. The application of the qPCR protocol revealed the presence of 7 log CFU/ml of bacterial load in raw milk, while, during ripening, active bacterial populations ranged from <4 to 8 log CFU/ml. The natural whey starters used in the three productions showed the same microbiota composition, characterized by the presence of Lactobacillus helveticus and Lactobacillus delbrueckii. Nevertheless, beta-diversity analysis of the 16S rRNA sequencing data and RT-PCR-DGGE showed a clear clustering of the samples according to the three productions, probably driven by the different milks used. Milk samples were found to be characterized by the presence of several contaminants, such as Propionibacterium acnes, Acidovorax, Acinetobacter, Pseudomonas, and NSLAB. The core genera of the starter tended to limit the development of the spoilage bacteria only in two of the three batches. This study underlines the influence of different factors that can affect the final microbiota composition of the artisanal cheese. IMPORTANCEThis study highlights the importance of the quality of the raw milk in the production of a hard cheese. Independent from the use of a starter culture, raw milk with low microbiological quality can negatively affect the populations of lactic acid bacteria and, as a consequence, impact the quality of the final product due to metabolic processes associated with spoilage bacteria. G rana-like hard cheese is a typical raw cow's milk cheese produced in the Piedmont region in northwest Italy. Curd fermentation is carried out by natural thermophilic whey cultures obtained from the manufacturing of the previous day, after heating at 53 to 55°C, and the ripening is commonly carried out for 12 months.Natural whey starters (NWS) are used for several protected designation of origin (PDO) cheeses. They are usually dominated by thermophilic lactic acid bacteria (LAB), but subdominant species, including mesophilic LAB, may also occur. NWS have a complex microbial association of various species as well as a large number of biotypes (1).Temperature is the main factor associated with the variability of the microbiota composition of the NWS. Cooking treatment and whey cooling lead to the selection of a characteristic mi...

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Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses

Cited by 113 publications

References 75 publications

Critical review on biofilm methods

Critical review on biofilm methods

Metagenomics insights into food fermentations

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

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