Distribution of Prophages in the Oenococcus oeni Species.

Amel Chaïb,Claire Le Marrec,Cécile Philippe,Fety Jaomanjaka,Patrick M Lucas,Yasma Barchi,Olivier Claisse

doi:10.3390/microorganisms9040856

Abstract

Oenococcus oeni is the most exploited lactic acid bacterium in the wine industry and drives the malolactic fermentation of wines. Although prophage-like sequences have been identified in the species, many are not characterized, and a global view of their integration and distribution amongst strains is currently lacking. In this work, we analyzed the complete genomes of 231 strains for the occurrence of prophages, and analyzed their size and positions of insertion. Our data show the limited variation in the number of prophages in O. oeni genomes, and that six sites of insertion within the bacterial genome are being used for site-specific recombination. Prophage diversity patterns varied significantly for different host lineages, and environmental niches. Overall, the findings highlight the pervasive presence of prophages in the O. oeni species, their role as a major source of within-species bacterial diversity and drivers of horizontal gene transfer. Our data also have implications for enhanced understanding of the prophage recombination events which occurred during evolution of O. oeni, as well as the potential of prophages in influencing the fitness of these bacteria in their distinct niches.

Highlights

The wine-making process starts with the selection of the fruit and the fermentation of sugars into alcohol by yeasts
Wine conditions become progressively harsher for most bacteria, except for O. oeni, which becomes the sole detectable lactic acid bacterium (LAB) species isolated from wine when malolactic fermentation (MLF) typically occurs, and is the best adapted species to the combined inhibitory effects of low pH, low oxygen, high alcohol, polyphenolic compounds and sulfur dioxide contents [2]
We explored whether quantitative and qualitative differences in patterns of prophages differ across lineages and niches occupied by strains of O. oeni (Table 1)

Summary

Introduction

The wine-making process starts with the selection of the fruit and the fermentation of sugars into alcohol by yeasts. This bacterium is rarely detected in the natural environment, including the surface of grape berries [2], and its population only increases after crushing At this step, O. oeni is part of a complex microbiota that still comprises different LAB. Intra-species diversity is reported in the O. oeni species and large phenotypic differences among indigenous strains corresponding to variable capacities to withstand stringent wine compositions and impact aromas have been repeatedly observed. This has become the focus of more detailed studies, with the aim to explain microbial phenotypes on a genomic scale. Such a specialization to life in wine is visible in the small (1.6 to 2.2 Mbp) genome of O. oeni because the species has lost many metabolic abilities due to its adaptation to an environment rich

Methods

Results

Conclusion