Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening

Ilhan Cem Duru, Pia Kati Sofia Laine, Margarita Andreevskaya, Lars Göran Paulin, Soila Kananen, Soile Tynkkynen, Petri Olli Viljami Auvinen, Olli-Pekka Aukusti Smolander

Research output: Contribution to journalArticleScientificpeer-review

Abstract

In Swiss-type cheeses, characteristic nut-like and sweet flavor develops during the cheese ripening due to the metabolic activities of cheese microbiota. Temperature changes during warm and cold room ripening, and duration of ripening can significantly change the gene expression of the cheese microbiota, which can affect the flavor formation. In this study, a metagenomic and metatranscriptomic analysis of Swiss-type Maasdam cheese was performed on samples obtained during ripening in the warm and cold rooms. We reconstructed four different bacterial genomes (Lactococcus lactis, Lactobacillus rhamnosus, Lactobacillus helveticus, and Propionibacterium freudenreichii subsp. shermanii strain JS) from the Maasdam cheese to near completeness. Based on the DNA and RNA mean coverage, Lc. lactis strongly dominated (~80–90%) within the cheese microbial community. Genome annotation showed the potential for the presence of several flavor forming pathways in these species, such as production of methanethiol, free fatty acids, acetoin, diacetyl, acetate, ethanol, and propionate. Using the metatranscriptomic data, we showed that, with the exception of Lc. lactis, the central metabolism of the microbiota was downregulated during cold room ripening suggesting that fewer flavor compounds such as acetoin and propionate were produced. In contrast, Lc. lactis genes related to the central metabolism, including the vitamin biosynthesis and homolactic fermentation, were upregulated during cold room ripening.
Original languageEnglish
JournalInternational Journal of Food Microbiology
Volume281
Pages (from-to)10-22
Number of pages12
ISSN0168-1605
DOIs
Publication statusPublished - 19 May 2018
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 1184 Genetics, developmental biology, physiology
  • Metagenomics
  • metatranscriptomics
  • Bioinformatics
  • 416 Food Science
  • Food Microbiology
  • Cheese microbiota
  • Cheese ripening

Cite this

@article{6318675e5fa343c48fc9428b885416a7,
title = "Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening",
abstract = "In Swiss-type cheeses, characteristic nut-like and sweet flavor develops during the cheese ripening due to the metabolic activities of cheese microbiota. Temperature changes during warm and cold room ripening, and duration of ripening can significantly change the gene expression of the cheese microbiota, which can affect the flavor formation. In this study, a metagenomic and metatranscriptomic analysis of Swiss-type Maasdam cheese was performed on samples obtained during ripening in the warm and cold rooms. We reconstructed four different bacterial genomes (Lactococcus lactis, Lactobacillus rhamnosus, Lactobacillus helveticus, and Propionibacterium freudenreichii subsp. shermanii strain JS) from the Maasdam cheese to near completeness. Based on the DNA and RNA mean coverage, Lc. lactis strongly dominated (~80–90{\%}) within the cheese microbial community. Genome annotation showed the potential for the presence of several flavor forming pathways in these species, such as production of methanethiol, free fatty acids, acetoin, diacetyl, acetate, ethanol, and propionate. Using the metatranscriptomic data, we showed that, with the exception of Lc. lactis, the central metabolism of the microbiota was downregulated during cold room ripening suggesting that fewer flavor compounds such as acetoin and propionate were produced. In contrast, Lc. lactis genes related to the central metabolism, including the vitamin biosynthesis and homolactic fermentation, were upregulated during cold room ripening.",
keywords = "1184 Genetics, developmental biology, physiology, Metagenomics, metatranscriptomics, Bioinformatics, 416 Food Science, Food Microbiology, Cheese microbiota, Cheese ripening",
author = "Duru, {Ilhan Cem} and Laine, {Pia Kati Sofia} and Margarita Andreevskaya and Paulin, {Lars G{\"o}ran} and Soila Kananen and Soile Tynkkynen and Auvinen, {Petri Olli Viljami} and Smolander, {Olli-Pekka Aukusti}",
year = "2018",
month = "5",
day = "19",
doi = "10.1016/j.ijfoodmicro.2018.05.017",
language = "English",
volume = "281",
pages = "10--22",
journal = "International Journal of Food Microbiology",
issn = "0168-1605",
publisher = "Elsevier Scientific Publ. Co",

}

Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening. / Duru, Ilhan Cem; Laine, Pia Kati Sofia; Andreevskaya, Margarita; Paulin, Lars Göran; Kananen, Soila; Tynkkynen, Soile; Auvinen, Petri Olli Viljami; Smolander, Olli-Pekka Aukusti.

In: International Journal of Food Microbiology, Vol. 281, 19.05.2018, p. 10-22.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening

AU - Duru, Ilhan Cem

AU - Laine, Pia Kati Sofia

AU - Andreevskaya, Margarita

AU - Paulin, Lars Göran

AU - Kananen, Soila

AU - Tynkkynen, Soile

AU - Auvinen, Petri Olli Viljami

AU - Smolander, Olli-Pekka Aukusti

PY - 2018/5/19

Y1 - 2018/5/19

N2 - In Swiss-type cheeses, characteristic nut-like and sweet flavor develops during the cheese ripening due to the metabolic activities of cheese microbiota. Temperature changes during warm and cold room ripening, and duration of ripening can significantly change the gene expression of the cheese microbiota, which can affect the flavor formation. In this study, a metagenomic and metatranscriptomic analysis of Swiss-type Maasdam cheese was performed on samples obtained during ripening in the warm and cold rooms. We reconstructed four different bacterial genomes (Lactococcus lactis, Lactobacillus rhamnosus, Lactobacillus helveticus, and Propionibacterium freudenreichii subsp. shermanii strain JS) from the Maasdam cheese to near completeness. Based on the DNA and RNA mean coverage, Lc. lactis strongly dominated (~80–90%) within the cheese microbial community. Genome annotation showed the potential for the presence of several flavor forming pathways in these species, such as production of methanethiol, free fatty acids, acetoin, diacetyl, acetate, ethanol, and propionate. Using the metatranscriptomic data, we showed that, with the exception of Lc. lactis, the central metabolism of the microbiota was downregulated during cold room ripening suggesting that fewer flavor compounds such as acetoin and propionate were produced. In contrast, Lc. lactis genes related to the central metabolism, including the vitamin biosynthesis and homolactic fermentation, were upregulated during cold room ripening.

AB - In Swiss-type cheeses, characteristic nut-like and sweet flavor develops during the cheese ripening due to the metabolic activities of cheese microbiota. Temperature changes during warm and cold room ripening, and duration of ripening can significantly change the gene expression of the cheese microbiota, which can affect the flavor formation. In this study, a metagenomic and metatranscriptomic analysis of Swiss-type Maasdam cheese was performed on samples obtained during ripening in the warm and cold rooms. We reconstructed four different bacterial genomes (Lactococcus lactis, Lactobacillus rhamnosus, Lactobacillus helveticus, and Propionibacterium freudenreichii subsp. shermanii strain JS) from the Maasdam cheese to near completeness. Based on the DNA and RNA mean coverage, Lc. lactis strongly dominated (~80–90%) within the cheese microbial community. Genome annotation showed the potential for the presence of several flavor forming pathways in these species, such as production of methanethiol, free fatty acids, acetoin, diacetyl, acetate, ethanol, and propionate. Using the metatranscriptomic data, we showed that, with the exception of Lc. lactis, the central metabolism of the microbiota was downregulated during cold room ripening suggesting that fewer flavor compounds such as acetoin and propionate were produced. In contrast, Lc. lactis genes related to the central metabolism, including the vitamin biosynthesis and homolactic fermentation, were upregulated during cold room ripening.

KW - 1184 Genetics, developmental biology, physiology

KW - Metagenomics

KW - metatranscriptomics

KW - Bioinformatics

KW - 416 Food Science

KW - Food Microbiology

KW - Cheese microbiota

KW - Cheese ripening

U2 - 10.1016/j.ijfoodmicro.2018.05.017

DO - 10.1016/j.ijfoodmicro.2018.05.017

M3 - Article

VL - 281

SP - 10

EP - 22

JO - International Journal of Food Microbiology

JF - International Journal of Food Microbiology

SN - 0168-1605

ER -