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

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

doi:10.1016/j.ijfoodmicro.2018.05.017

Ilhan Cem Duru, Pia Laine + Show 6 more

Open Access

https://doi.org/10.1016/j.ijfoodmicro.2018.05.017

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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.

Highlights

The microbiota of cheese is one of the most important factors in cheese ripening and flavor forming
In addition to lactobacilli and S. thermophilus, Propionibacterium freudenreichii is a key species for the Swiss-type cheese production, since its growth is associated with propionate and CO2 production during fermentation of lactate produced by the starter cultures (Ojala et al, 2017)
Mesophilic Propionibacterium freudenreichii subsp. shermanii JS and Lactobacillus rhamnosus, as well as thermophilic Lactobacillus helveticus were used as adjunct cultures

Summary

Introduction

The microbiota of cheese is one of the most important factors in cheese ripening and flavor forming. Swiss-type cheeses are ripened for 30 to 60 days in a warm room (20–24 °C) and transferred to a cold room (4–11 °C) for another 30 to 60 days (Guggisberg et al, 2015). The eye formation requires sufficient time in a warm room, and after enough holes are formed, cheese needs to be transferred to a cold room to avoid excessive gas production (Daly et al, 2010; Guggisberg et al, 2015). In addition to lactobacilli and S. thermophilus, Propionibacterium freudenreichii is a key species for the Swiss-type cheese production, since its growth is associated with propionate (typical flavor) and CO2 production (eye formation) during fermentation of lactate produced by the starter cultures (Ojala et al, 2017). Adjunct mesophilic Lactobacillus can be added to Swiss-type cheeses, since

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