The Experts below are selected from a list of 99 Experts worldwide ranked by ideXlab platform
Francoise Irlinger - One of the best experts on this subject based on the ideXlab platform.
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Preservation of Preservation of a smear Surface-Ripened Cheese ecosystem by freezing and freeze-drying: a proof of concepta smear Surface-Ripened Cheese ecosystem by freezing and freeze-drying: a proof of concept
2017Co-Authors: Wenfan Cao, Francoise Irlinger, Thomas Cattenoz, Marie Noelle Leclercq-perlat, Stéphanie Passot, Fernanda FonsecaAbstract:Preservation of Preservation of a smear Surface-Ripened Cheese ecosystem by freezing and freeze-drying: a proof of concepta smear Surface-Ripened Cheese ecosystem by freezing and freeze-drying: a proof of concept. 7. Congress of European Microbiologists FEMS 2017
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Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis
Frontiers in microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated approximately 75 million reads per sample. Except for Brevibacterium aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to day 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
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Investigation of the activity of the microorganisms in a reblochon-style Cheese by metatranscriptomic analysis
Frontiers in Microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated ~75 million reads per sample. Except for B. aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids, and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
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Overview of a Surface-Ripened Cheese community functioning by meta-omics analyses
PLoS ONE, 2015Co-Authors: Eric Dugat-bony, Francoise Irlinger, Marie Noelle Leclercq-perlat, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, Christophe Monnet, Sophie Landaud-liautaud, Pascal BentoAbstract:Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-Ripened Cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on Surface-Ripened Cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental Surface-Ripened Cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the Cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the Cheese-making process.
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Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics
2015Co-Authors: Eric Dugat-bony, Francoise Irlinger, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, Christophe Monnet, Pascal Bento, Sophie Landaud, Jean-françois GibratAbstract:Abstract Cheeseripeningisacomplexbiochemicalprocessdrivenbymicrobialcommunitiescom-posedofbotheukaryotesandprokaryotes.Surface-RipenedCheesesarewidelyconsumedallovertheworldandareappreciatedfortheircharacteristicflavor.MicrobialcommunitycompositionhasbeenstudiedforalongtimeonSurface-RipenedCheeses,butonlylimitedknowledgehasbeenacquiredaboutitsinsitumetabolicactivities.Weappliedmetagenomic,metatranscriptomicandbiochemicalanalysestoanexperimentalSurface-RipenedCheesecomposedofninemicrobialspeciesduringfourweeksofripening.Bycombiningallofthedata,wewereabletoobtainanoverviewoftheCheesematurationprocessandtobetterun-derstandthemetabolicactivitiesofthedifferentcommunitymembersandtheirpossibleinter-actions.Furthermore,differentialexpressionanalysiswasusedtoselectasetofbiomarkergenes,providingavaluabletoolthatcanbeusedtomonitortheCheese-makingprocess. Introduction Microbial communities are of major importance inthe fermentation offood products.Fer-mentation remains a widespread means for food processing and preservation,and fermentedfoods (including Cheese)are widely consumed worldwide. Thecomposition and behavior ofthe microbial communities in a Cheese are important for its characteristicorganolepticprop-erties, shelflifeandsafety[1]. These communities are involved in the generationofa wide
Pascal Bonnarme - One of the best experts on this subject based on the ideXlab platform.
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Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis
Frontiers in microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated approximately 75 million reads per sample. Except for Brevibacterium aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to day 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
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The effect of reduced sodium chloride content on the microbiological and biochemical properties of a soft Surface-Ripened Cheese
Journal of Dairy Science, 2016Co-Authors: Eric Dugat-bony, Annesophie Sarthou, Marie-claire Perello, Pascal Bonnarme, Gilles De Revel, Sandra HelinckAbstract:Many health authorities have targeted salt reduction in food products as a means to reduce dietary sodium intake due to the harmful effects associated with its excessive consumption. In the present work, we evaluated the effect of reducing sodium chloride (NaCl) content on the microbiological and biochemical characteristics of an experimental Surface-Ripened Cheese. A control Cheese (1.8% NaCl) and a Cheese with a reduced NaCl content (1.3% NaCl) were sampled weekly over a period of 27 d. Reducing NaCl content induced microbial perturbations such as the lesser development of the yeast Debaryomyces hansenii and the greater development of the gram-negative bacterium Hafnia alvei. This was accompanied by changes in proteolytic kinetics and in profiles of volatile aroma compounds and biogenic amine production. Finally, the development of the spoilage microorganism Pseudomonas fragi was significantly higher in the Cheese with a reduced salt content.
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Investigation of the activity of the microorganisms in a reblochon-style Cheese by metatranscriptomic analysis
Frontiers in Microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated ~75 million reads per sample. Except for B. aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids, and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
Eric Dugat-bony - One of the best experts on this subject based on the ideXlab platform.
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Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis
Frontiers in microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated approximately 75 million reads per sample. Except for Brevibacterium aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to day 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
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The effect of reduced sodium chloride content on the microbiological and biochemical properties of a soft Surface-Ripened Cheese
Journal of Dairy Science, 2016Co-Authors: Eric Dugat-bony, Annesophie Sarthou, Marie-claire Perello, Pascal Bonnarme, Gilles De Revel, Sandra HelinckAbstract:Many health authorities have targeted salt reduction in food products as a means to reduce dietary sodium intake due to the harmful effects associated with its excessive consumption. In the present work, we evaluated the effect of reducing sodium chloride (NaCl) content on the microbiological and biochemical characteristics of an experimental Surface-Ripened Cheese. A control Cheese (1.8% NaCl) and a Cheese with a reduced NaCl content (1.3% NaCl) were sampled weekly over a period of 27 d. Reducing NaCl content induced microbial perturbations such as the lesser development of the yeast Debaryomyces hansenii and the greater development of the gram-negative bacterium Hafnia alvei. This was accompanied by changes in proteolytic kinetics and in profiles of volatile aroma compounds and biogenic amine production. Finally, the development of the spoilage microorganism Pseudomonas fragi was significantly higher in the Cheese with a reduced salt content.
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Investigation of the activity of the microorganisms in a reblochon-style Cheese by metatranscriptomic analysis
Frontiers in Microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated ~75 million reads per sample. Except for B. aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids, and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
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Overview of a Surface-Ripened Cheese community functioning by meta-omics analyses
PLoS ONE, 2015Co-Authors: Eric Dugat-bony, Francoise Irlinger, Marie Noelle Leclercq-perlat, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, Christophe Monnet, Sophie Landaud-liautaud, Pascal BentoAbstract:Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-Ripened Cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on Surface-Ripened Cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental Surface-Ripened Cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the Cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the Cheese-making process.
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Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics
2015Co-Authors: Eric Dugat-bony, Francoise Irlinger, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, Christophe Monnet, Pascal Bento, Sophie Landaud, Jean-françois GibratAbstract:Abstract Cheeseripeningisacomplexbiochemicalprocessdrivenbymicrobialcommunitiescom-posedofbotheukaryotesandprokaryotes.Surface-RipenedCheesesarewidelyconsumedallovertheworldandareappreciatedfortheircharacteristicflavor.MicrobialcommunitycompositionhasbeenstudiedforalongtimeonSurface-RipenedCheeses,butonlylimitedknowledgehasbeenacquiredaboutitsinsitumetabolicactivities.Weappliedmetagenomic,metatranscriptomicandbiochemicalanalysestoanexperimentalSurface-RipenedCheesecomposedofninemicrobialspeciesduringfourweeksofripening.Bycombiningallofthedata,wewereabletoobtainanoverviewoftheCheesematurationprocessandtobetterun-derstandthemetabolicactivitiesofthedifferentcommunitymembersandtheirpossibleinter-actions.Furthermore,differentialexpressionanalysiswasusedtoselectasetofbiomarkergenes,providingavaluabletoolthatcanbeusedtomonitortheCheese-makingprocess. Introduction Microbial communities are of major importance inthe fermentation offood products.Fer-mentation remains a widespread means for food processing and preservation,and fermentedfoods (including Cheese)are widely consumed worldwide. Thecomposition and behavior ofthe microbial communities in a Cheese are important for its characteristicorganolepticprop-erties, shelflifeandsafety[1]. These communities are involved in the generationofa wide
Christophe Monnet - One of the best experts on this subject based on the ideXlab platform.
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Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis
Frontiers in microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated approximately 75 million reads per sample. Except for Brevibacterium aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to day 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
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Investigation of the activity of the microorganisms in a reblochon-style Cheese by metatranscriptomic analysis
Frontiers in Microbiology, 2016Co-Authors: Christophe Monnet, Eric Dugat-bony, Francoise Irlinger, Dominique Swennen, Jean-marie Beckerich, Sébastien Fraud, Pascal BonnarmeAbstract:The microbial communities in Cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during Cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a Surface-Ripened Cheese by means of metatranscriptomic analysis. The Cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the Cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated ~75 million reads per sample. Except for B. aurantiacum, which failed to grow in the Cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids, and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the Cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of Cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of Cheese microorganisms.
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Overview of a Surface-Ripened Cheese community functioning by meta-omics analyses
PLoS ONE, 2015Co-Authors: Eric Dugat-bony, Francoise Irlinger, Marie Noelle Leclercq-perlat, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, Christophe Monnet, Sophie Landaud-liautaud, Pascal BentoAbstract:Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-Ripened Cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on Surface-Ripened Cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental Surface-Ripened Cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the Cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the Cheese-making process.
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Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics
2015Co-Authors: Eric Dugat-bony, Francoise Irlinger, Cecile Straub, Aurélie Teissandier, Djamila Onesime, Valentin Loux, Christophe Monnet, Pascal Bento, Sophie Landaud, Jean-françois GibratAbstract:Abstract Cheeseripeningisacomplexbiochemicalprocessdrivenbymicrobialcommunitiescom-posedofbotheukaryotesandprokaryotes.Surface-RipenedCheesesarewidelyconsumedallovertheworldandareappreciatedfortheircharacteristicflavor.MicrobialcommunitycompositionhasbeenstudiedforalongtimeonSurface-RipenedCheeses,butonlylimitedknowledgehasbeenacquiredaboutitsinsitumetabolicactivities.Weappliedmetagenomic,metatranscriptomicandbiochemicalanalysestoanexperimentalSurface-RipenedCheesecomposedofninemicrobialspeciesduringfourweeksofripening.Bycombiningallofthedata,wewereabletoobtainanoverviewoftheCheesematurationprocessandtobetterun-derstandthemetabolicactivitiesofthedifferentcommunitymembersandtheirpossibleinter-actions.Furthermore,differentialexpressionanalysiswasusedtoselectasetofbiomarkergenes,providingavaluabletoolthatcanbeusedtomonitortheCheese-makingprocess. Introduction Microbial communities are of major importance inthe fermentation offood products.Fer-mentation remains a widespread means for food processing and preservation,and fermentedfoods (including Cheese)are widely consumed worldwide. Thecomposition and behavior ofthe microbial communities in a Cheese are important for its characteristicorganolepticprop-erties, shelflifeandsafety[1]. These communities are involved in the generationofa wide
Mary C. Rea - One of the best experts on this subject based on the ideXlab platform.
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detection of volatile compounds of Cheese and their contribution to the flavor profile of surface ripened Cheese
Comprehensive Reviews in Food Science and Food Safety, 2018Co-Authors: Andrea S. Bertuzzi, Paul L.h. Mcsweeney, Mary C. Rea, Kieran N. KilcawleyAbstract:The volatiles responsible for the typical aroma of Cheese are produced mainly by lipolytic and proteolytic pathways and by the metabolism of lactose, lactate, and citrate. The volatile profile of Cheese is determined by gas chromatography (GC), which includes the extraction, separation, and detection of volatiles. A wide range of extraction techniques is available, and technological improvements have been developed in GC separation and detection that enhance our understanding of the role of individual key volatiles to Cheese flavor. To date, for Surface-Ripened Cheese, the main volatiles detected that contribute to flavor include acids, ketones, alcohols, and sulfur compounds. However, based on the limited number of studies undertaken and the approaches used, it appears that a significant degree of bias possibly exists that may have over- or underestimated the impact of specific chemical classes involved in the flavor of these types of Cheese.
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Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese
mSystems, 2018Co-Authors: Andrea S. Bertuzzi, Aaron M. Walsh, Jeremiah J. Sheehan, Paul D. Cotter, Fiona Crispie, Paul L.h. Mcsweeney, Kieran N. Kilcawley, Mary C. ReaAbstract:ABSTRACT In this study, a young Cheddar curd was used to produce two types of Surface-Ripened Cheese, using two commercial smear-culture mixes of yeasts and bacteria. Whole-metagenome shotgun sequencing was used to screen the microbial population within the smear-culture mixes and on the Cheese surface, with comparisons of microorganisms at both the species and the strain level. The use of two smear mixes resulted in the development of distinct microbiotas on the surfaces of the two test Cheeses. In one case, most of the species inoculated on the Cheese established themselves successfully on the surface during ripening, while in the other, some of the species inoculated were not detected during ripening and the most dominant bacterial species, Glutamicibacter arilaitensis , was not a constituent of the culture mix. Generally, yeast species, such as Debaryomyces hansenii and Geotrichum candidum , were dominant during the first stage of ripening but were overtaken by bacterial species, such as Brevibacterium linens and G. arilaitensis , in the later stages. Using correlation analysis, it was possible to associate individual microorganisms with volatile compounds detected by gas chromatography-mass spectrometry in the Cheese surface. Specifically, D. hansenii correlated with the production of alcohols and carboxylic acids, G. arilaitensis with alcohols, carboxylic acids and ketones, and B. linens and G. candidum with sulfur compounds. In addition, metagenomic sequencing was used to analyze the metabolic potential of the microbial populations on the surfaces of the test Cheeses, revealing a high relative abundance of metagenomic clusters associated with the modification of color, variation of pH, and flavor development. IMPORTANCE Fermented foods, in particular, Surface-Ripened Cheese, represent a model to explain the metabolic interactions which regulate microbial succession in complex environments. This study explains the role of individual species in a heterogeneous microbial environment, i.e., the exterior of Surface-Ripened Cheese. Through whole-metagenome shotgun sequencing, it was possible to investigate the metabolic potential of the resident microorganisms and show how variations in the microbial populations influence important aspects of Cheese ripening, especially flavor development. Overall, in addition to providing fundamental insights, this research has considerable industrial relevance relating to the production of fermented food with specific qualities.
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Growth characteristics of Brevibacterium, Corynebacterium, Microbacterium, and Staphylococcus spp. isolated from Surface-Ripened Cheese
Applied and Environmental Microbiology, 2007Co-Authors: Jerome Mounier, Mary C. Rea, Gerald F Fitzgerald, Paula M. O'connor, Timothy M CoganAbstract:The growth characteristics of five bacteria, Brevibacterium aurantiacum 1-16-58, Corynebacterium casei DPC 5298T, Corynebacterium variabile DPC 5310, Microbacterium gubbeenense DPC 5286T, and Staphylococcus saprophyticus 4E61, all of which were isolated from the surface of smear Cheese, were studied in complex and chemically defined media. All of the coryneforms, except M. gubbeenense, grew in 12% salt, while B. aurantiacum and S. saprophyticus grew in 15% salt. All five bacteria assimilated lactate in a semisynthetic medium, and none of the coryneform bacteria assimilated lactose. Glucose assimilation was poor, except by S. saprophyticus and C. casei. Five to seven amino acids were assimilated by the coryneforms and 12 by S. saprophyticus. Glutamate, phenylalanine, and proline were utilized by all five bacteria, whereas utilization of serine, threonine, aspartate, histidine, alanine, arginine, leucine, isoleucine, and glycine depended on the organism. Growth of C. casei restarted after addition of glutamate, proline, serine, and lactate at the end of the exponential phase, indicating that these amino acids and lactate can be used as energy sources. Pantothenic acid was essential for the growth of C. casei and M. gubbeenense. Omission of biotin reduced the growth of B. aurantiacum, C. casei, and M. gubbeenense. All of the bacteria contained lactate dehydrogenase activity (with both pyruvate and lactate as substrates) and glutamate pyruvate transaminase activity but not urease activity.