Mobilome of Brevibacterium aurantiacum Sheds Light on Its Genetic Diversity and Its Adaptation to Smear-Ripened Cheeses

Abstract

Brevibacterium aurantiacum is an actinobacterium that confers key organoleptic properties to washed-rind cheeses during the ripening process. Although this industrially relevant species has been gaining an increasing attention in the past years, its genome plasticity is still understudied due to the unavailability of complete genomic sequences. To add insights on the mobilome of this group, we sequenced the complete genomes of five dairy Brevibacterium strains and one non-dairy strain using PacBio RSII. We performed phylogenetic and pan-genome analyses, including comparisons with other publicly available Brevibacterium genomic sequences. Our phylogenetic analysis revealed that these five dairy strains, previously identified as Brevibacterium linens , belong instead to the B. aurantiacum species. A high number of transposases and integrases were observed in the Brevibacterium spp. strains. In addition, we identified 14 and 12 new insertion sequences (IS) in B. aurantiacum and B. linens genomes, respectively. Several stretches of homologous DNA sequences were also found between B. aurantiacum and other cheese rind actinobacteria, suggesting horizontal gene transfer (HGT). A HGT region from an iRon Uptake/Siderophore Transport Island (RUSTI) and an iron uptake composite transposon were found in five B. aurantiacum genomes. These findings suggest that low iron availability in milk is a driving force in the adaptation of this bacterial species to this niche. Moreover, the exchange of iron uptake systems suggests cooperative evolution between cheese rind actinobacteria. We also demonstrated that the integrative and conjugative element BreLI ( Brevibacterium Lanthipeptide Island) can excise from B. aurantiacum SMQ-1417 chromosome. Our comparative genomic analysis suggests that mobile genetic elements played an important role into the adaptation of B. aurantiacum to cheese ecosystems.

DNAtandem repeats contribute to the genetic diversity of Brevibacterium aurantiacum phages

“…We recently reported the genomic characterization of B. aurantiacum strain SMQ‐1335, formerly identified as B. linens (de Melo et al ., 2016; Levesque et al ., 2019). This strain has been extensively used as a ripening culture for the production of washed‐rind cheeses at three manufacturing sites and was used here as a phage‐sensitive host.…”

“…On the other hand, this was expected considering that its host SMQ‐1335 takes approximately 3 h to duplicate in laboratory conditions (data not shown). Five other distinct B. aurantiacum strains (SMQ‐1417 to SMQ‐1421) (Levesque et al ., 2019) were tested for phage sensitivity and were fully resistant to these phages.…”

“…The presence of genes that possibly encode for a truncated integrase (ORF31) as well as putative immunity repressor (ORF33), and excisionase (ORF34) suggests that these virulent phages are likely derived from a prophage that lost the ability to integrate into the host genome. The host strain (SMQ‐1335) does not contain a functional prophage as previously described (de Melo et al ., 2016; Levesque et al ., 2019).…”

“…5). Recent comparative and phylogenetic analyses of Brevibacterium strains identified VCM10 as a strain of B. linens (Pham et al ., 2017; Levesque et al ., 2019).…”

“…The microbial system of washed rind cheeses is also very complex, and its balance is a key to develop the specific cheese flavour and colour. Brevibacterium aurantiacum is among the most important bacterial species used as a surface ripening culture for such cheeses (Cogan et al ., 2014; Bonham et al ., 2017; Pham et al ., 2017; Anast et al ., 2019; Levesque et al ., 2019). This bacterial species is part of the taxonomic group of orange pigment‐producing Brevibacterium genus (Gavrish et al ., 2004), in which Brevibacterium linens is the type species (Gavrish et al ., 2004; Forquin et al ., 2009).…”