[PRECELLYS] Transcriptomic analysis of cheese-ripening microbial communities with Dual RNA-Seq

Ripening cultures containing fungi and bacteria have a crucial role in the production of smear-ripened cheeses. Unfortunately, little is known about the biotic interactions within these microbial communities at the cheese surface, except for the positive impact of the pH increase initiated by fungi on the growth of several acid-sensitive bacteria such as Brevibacterium aurantiacum, and Hafnia alvei. In this work, the biotic interactions of a cheese-ripening community composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei, are explored thanks to a lab- scale mini-cheese model which aims to reproduce cheese-ripening conditions. The development of next generation sequencing techniques (NGS) over the past decade now allows researchers to analyze the transcriptome of multiple species present in the same sample simultaneously. Here, a relatively novel technique, dual RNA-seq, was used to capture the transcriptome of D. hansenii, B. aurantiacum, and H. alvei and analyze the metabolic interactions between these species at the cheese surface.