AUTHOR=Monnet Christophe , Dugat-Bony Eric , Swennen Dominique , Beckerich Jean-Marie , Irlinger Françoise , Fraud Sébastien , Bonnarme Pascal 

TITLE=Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis

JOURNAL=Frontiers in Microbiology

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2016.00536

DOI=10.3389/fmicb.2016.00536

ISSN=1664-302X

ABSTRACT=<p>The microbial communities in cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. <italic>In situ</italic> 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 (<italic>Streptococcus thermophilus</italic> and <italic>Lactobacillus delbrueckii</italic> ssp. <italic>bulgaricus</italic>), one ripening bacterium (<italic>Brevibacterium aurantiacum</italic>), and two yeasts (<italic>Debaryomyces hansenii</italic> and <italic>Geotrichum candidum</italic>). 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 <italic>B. aurantiacum</italic>, 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, <italic>G. candidum</italic> 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 <italic>G. candidum</italic> from day 14 to day 35, whereas in <italic>D. hansenii</italic>, 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.</p>