Phage-host interactions as a driver of population dynamics during wine fermentation: Betting on underdogs

Chaïb, Amel; Philippe, Cécile; Jaomanjaka, Féty; Barchi, Yasma; Oviedo-Hernandez, Florencia; Claisse, Olivier; Marrec, Claire Le

doi:10.1016/j.ijfoodmicro.2022.109936

Cited by 7 publications

(4 citation statements)

References 62 publications

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“…The phylogeny of temperate, ex-temperate and strictly virulent phages showed (i) the presence of similar prophages in distinct strains, (ii) the extensive modularity of phage genomes and (iii) the segregation of phages into distinct and well-supported clusters [ 19 , 24 ]. Taking as input the set of 189 available prophage genomes, as well as the four newly sequenced oenophages OE33PA and Vinitor 162, 27 and 28 [ 21 , 22 ], we identified diverse genetic loci, whose presence or absence could rapidly group the so far uncharacterized oenophages isolated during previous surveys.…”

Section: Methodsmentioning

confidence: 99%

“…All oenophages described so far have a tailed morphology with a dsDNA genome and belong to the Caudovirales order [ 23 ]. More than 95% of the known oenophages are temperate phages [ 24 ] and carry out site-specific recombination (SSR). The two major constituents of the SSR unit, corresponding to the phage integrases and attachment sites, have been studied in detail and this resulted in the clustering of prophages into six major groups (Int A to Int F ), which are related to the integration site in the host chromosome [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Strains of O. oeni can defend themselves against viral infections with diverse antiphage mechanisms, such as restriction-modification and superinfection exclusion systems, which have been identified by whole genome sequencing [ 24 ]. Yet, CRISPR-Cas adaptive defence mechanisms [ 25 ] are lacking conserved homologs in the sequenced strains of O. oeni [ 24 , 26 ]. CRISPR-Cas systems are unevenly distributed across taxa and environments, and recent analyses have shown that less than half of mesophilic bacteria have CRISPR arrays [ 27 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

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Phage Encounters Recorded in CRISPR Arrays in the Genus Oenococcus

Barchi¹,

Philippe²,

Chaïb³

et al. 2022

Viruses

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The Oenococcus genus comprises four recognized species, and members have been found in different types of beverages, including wine, kefir, cider and kombucha. In this work, we implemented two complementary strategies to assess whether oenococcal hosts of different species and habitats were connected through their bacteriophages. First, we investigated the diversity of CRISPR-Cas systems using a genome-mining approach, and CRISPR-endowed strains were identified in three species. A census of the spacers from the four identified CRISPR-Cas loci showed that each spacer space was mostly dominated by species-specific sequences. Yet, we characterized a limited records of potentially recent and also ancient infections between O. kitaharae and O. sicerae and phages of O. oeni, suggesting that some related phages have interacted in diverse ways with their Oenococcus hosts over evolutionary time. Second, phage-host interaction analyses were performed experimentally with a diversified panel of phages and strains. None of the tested phages could infect strains across the species barrier. Yet, some infections occurred between phages and hosts from distinct beverages in the O. oeni species.

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