Siphophages Infecting Food Processing Bacteria

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (30 December 2021) | Viewed by 15768

Special Issue Editors

1. Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille CEDEX 09, France
2. School of Microbiology, University College Cork, Cork T12, Ireland
Interests: structural biology; bacteriophage–host interactions; bacteriophage structure
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Special Issue Information

Dear Colleagues,

More than 25% of food is destroyed or spoiled globally, with considerable economic and environmental impacts. Sustainable food production systems require that foods be of the highest microbiological standards in order to reduce the risk associated with spoilage and/or pathogenic organisms.

Bacteriophage (or phage) infection of starter and adjunct cultures in fermented foods can impose a considerable threat to the quality and microbiological stability of these foods, and are thus considered a nuisance. Conversely, the presence of phages that may target spoilage or pathogenic bacteria can greatly enhance the safety and stability of foods. Therefore, this Special Issue aims to explore the diversity and functionality of phages that infect dairy starter cultures in food fermentations including Lactococcus lactis, Streptococcus thermophilus, Lactobacillus spp. etc., and those involved in and associated with fermented beverages, including Oenococcus and Pediococcus. Furthermore, this Special Issue will explore the potential role of phages and associated enzymes in controlling spoilage and pathogenic bacteria to enhance the microbial stability of foods and thereby reduce food waste.

A wide range of approaches are welcomed, such as phage biology, new phage reports, host–phage interactions, enzymology, structural biology, etc.

Prof. Christian CAMBILLAU
Dr. Jennifer Mahony
Guest Editors

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Keywords

  • food fermentation
  • bacteriophage–host interactions
  • lactic acid bacteria
  • bacteriophage structure

Published Papers (5 papers)

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Research

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20 pages, 2498 KiB  
Article
Novel Salmonella Phage, vB_Sen_STGO-35-1, Characterization and Evaluation in Chicken Meat
by Dácil Rivera, Andrea I. Moreno-Switt, Thomas G. Denes, Lauren K. Hudson, Tracey L. Peters, Reham Samir, Ramy K. Aziz, Jean-Paul Noben, Jeroen Wagemans and Fernando Dueñas
Microorganisms 2022, 10(3), 606; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030606 - 12 Mar 2022
Cited by 8 | Viewed by 3855
Abstract
Salmonellosis is one of the most frequently reported zoonotic foodborne diseases worldwide, and poultry is the most important reservoir of Salmonella enterica serovar Enteritidis. The use of lytic bacteriophages (phages) to reduce foodborne pathogens has emerged as a promising biocontrol intervention for Salmonella [...] Read more.
Salmonellosis is one of the most frequently reported zoonotic foodborne diseases worldwide, and poultry is the most important reservoir of Salmonella enterica serovar Enteritidis. The use of lytic bacteriophages (phages) to reduce foodborne pathogens has emerged as a promising biocontrol intervention for Salmonella spp. Here, we describe and evaluate the newly isolated Salmonella phage STGO-35-1, including: (i) genomic and phenotypic characterization, (ii) an analysis of the reduction of Salmonella in chicken meat, and (iii) genome plasticity testing. Phage STGO-35-1 represents an unclassified siphovirus, with a length of 47,483 bp, a G + C content of 46.5%, a headful strategy of packaging, and a virulent lifestyle. Phage STGO-35-1 reduced S. Enteritidis counts in chicken meat by 2.5 orders of magnitude at 4 °C. We identified two receptor-binding proteins with affinity to LPS, and their encoding genes showed plasticity during an exposure assay. Phenotypic, proteomic, and genomic characteristics of STGO-35-1, as well as the Salmonella reduction in chicken meat, support the potential use of STGO-35-1 as a targeted biocontrol agent against S. Enteritidis in chicken meat. Additionally, computational analysis and a short exposure time assay allowed us to predict the plasticity of genes encoding putative receptor-binding proteins. Full article
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
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13 pages, 27008 KiB  
Article
Structure and Topology Prediction of Phage Adhesion Devices Using AlphaFold2: The Case of Two Oenococcus oeni Phages
by Adeline Goulet and Christian Cambillau
Microorganisms 2021, 9(10), 2151; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9102151 - 14 Oct 2021
Cited by 18 | Viewed by 2686
Abstract
Lactic acid bacteria (LAB) are important microorganisms in food fermentation. In the food industry, bacteriophages (phages or bacterial viruses) may cause the disruption of LAB-dependent processes with product inconsistencies and economic losses. LAB phages use diverse adhesion devices to infect their host, yet [...] Read more.
Lactic acid bacteria (LAB) are important microorganisms in food fermentation. In the food industry, bacteriophages (phages or bacterial viruses) may cause the disruption of LAB-dependent processes with product inconsistencies and economic losses. LAB phages use diverse adhesion devices to infect their host, yet the overall picture of host-binding mechanisms remains incomplete. Here, we aimed to determine the structure and topology of the adhesion devices of two lytic siphophages, OE33PA and Vinitor162, infecting the wine bacteria Oenococcus oeni. These phages possess adhesion devices with a distinct composition and morphology and likely use different infection mechanisms. We primarily used AlphaFold2, an algorithm that can predict protein structure with unprecedented accuracy, to obtain a 3D model of the adhesion devices’ components. Using our prior knowledge of the architecture of the LAB phage host-binding machineries, we also reconstituted the topology of OE33PA and Vinitor162 adhesion devices. While OE33PA exhibits original structures in the assembly of its bulky adhesion device, Vinitor162 harbors several carbohydrate-binding modules throughout its long and extended adhesion device. Overall, these results highlight the ability of AlphaFold2 to predict protein structures and illustrate its great potential in the study of phage structures and host-binding mechanisms. Full article
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
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19 pages, 3534 KiB  
Article
Distribution of Prophages in the Oenococcus oeni Species
by Olivier Claisse, Amel Chaïb, Fety Jaomanjaka, Cécile Philippe, Yasma Barchi, Patrick M. Lucas and Claire Le Marrec
Microorganisms 2021, 9(4), 856; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040856 - 16 Apr 2021
Cited by 11 | Viewed by 2537
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
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10 pages, 13872 KiB  
Communication
Ectopic Spacer Acquisition in Streptococcus thermophilus CRISPR3 Array
by Rodrigo Achigar, Martina Scarrone, Geneviève M. Rousseau, Cécile Philippe, Felipe Machado, Valentina Duvós, María Pía Campot, Moïra B. Dion, Yuyu Shao, María Julia Pianzzola and Sylvain Moineau
Microorganisms 2021, 9(3), 512; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9030512 - 01 Mar 2021
Cited by 6 | Viewed by 2675
Abstract
Streptococcus thermophilus relies heavily on two type II-A CRISPR-Cas systems, CRISPR1 and CRISPR3, to resist siphophage infections. One hallmark of these systems is the integration of a new spacer at the 5′ end of the CRISPR arrays following phage infection. However, we have [...] Read more.
Streptococcus thermophilus relies heavily on two type II-A CRISPR-Cas systems, CRISPR1 and CRISPR3, to resist siphophage infections. One hallmark of these systems is the integration of a new spacer at the 5′ end of the CRISPR arrays following phage infection. However, we have previously shown that ectopic acquisition of spacers can occur within the CRISPR1 array. Here, we present evidence of the acquisition of new spacers within the array of CRISPR3 of S. thermophilus. The analysis of randomly selected bacteriophage-insensitive mutants of the strain Uy01 obtained after phage infection, as well as the comparison with other S. thermophilus strains with similar CRISPR3 content, showed that a specific spacer within the array could be responsible for misguiding the adaptation complex. These results also indicate that while the vast majority of new spacers are added at the 5′ end of the CRISPR array, ectopic spacer acquisition is a common feature of both CRISPR1 and CRISPR3 systems in S. thermophilus, and it can still provide phage resistance. Ectopic spacer acquisition also appears to have occurred naturally in some strains of Streptococcus pyogenes, suggesting that it is a general phenomenon, at least in type II-A systems. Full article
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
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Review

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13 pages, 3598 KiB  
Review
Biodiversity of Phages Infecting the Dairy Bacterium Streptococcus thermophilus
by Laurens Hanemaaijer, Philip Kelleher, Horst Neve, Charles M. A. P. Franz, Paul P. de Waal, Noël N. M. E. van Peij, Douwe van Sinderen and Jennifer Mahony
Microorganisms 2021, 9(9), 1822; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091822 - 27 Aug 2021
Cited by 6 | Viewed by 3059
Abstract
Streptococcus thermophilus-infecting phages represent a major problem in the dairy fermentation industry, particularly in relation to thermophilic production systems. Consequently, numerous studies have been performed relating to the biodiversity of such phages in global dairy operations. In the current review, we provide [...] Read more.
Streptococcus thermophilus-infecting phages represent a major problem in the dairy fermentation industry, particularly in relation to thermophilic production systems. Consequently, numerous studies have been performed relating to the biodiversity of such phages in global dairy operations. In the current review, we provide an overview of the genetic and morphological diversity of these phages and highlight the source and extent of genetic mosaicism among phages infecting this species through comparative proteome analysis of the replication and morphogenesis modules of representative phages. The phylogeny of selected phage-encoded receptor binding proteins (RBPs) was assessed, indicating that in certain cases RBP-encoding genes have been acquired separately to the morphogenesis modules, thus highlighting the adaptability of these phages. This review further highlights the significant advances that have been made in defining emergent genetically diverse groups of these phages, while it additionally summarizes remaining knowledge gaps in this research area. Full article
(This article belongs to the Special Issue Siphophages Infecting Food Processing Bacteria)
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