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Microorganisms
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Phages from the Fermented Products
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Phages from the Fermented Products

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

Deadline for manuscript submissions: closed (1 December 2022) | Viewed by 4809

Special Issue Editors

Dr. Nathalie Desmasures

E-Mail Website
Guest Editor
Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France
Interests: food microbiology
Dr. Marion Dalmasso

E-Mail Website
Guest Editor
Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France
Interests: diversity of food microbial ecosystems; lactic acid bacteria; food safety; bacteriophages; phageoma; metagenomics; transcriptomics; proteomics

Special Issue Information

Dear Colleagues,

Fermented foods and beverages are consumed worldwide, currently accounting for approximately one third of the human diet globally. Understanding the microbial communities of fermented foods has become a hot topic for the production of sustainable foods for tomorrow, for limiting food wastage, and ensuring the economical durability of agribusinesses. A neglected aspect of food microbial communities is the phageome (phage community). The role of phages and phageomes in influencing the temporal development, equilibria and functionalities of food bacterial communities is still under investigation.

For this Special Issue, we invite authors to submit original and unpublished research papers, reviews, or short communications covering different research topics related to the diversity, roles or applications of phages and phageomes in food products, and especially in fermented foods. This may include phageome ecology, phage–host interactions and interaction modelling, the phage-based biocontrol of spoilage bacteria or food-borne pathogens in fermented foods and beverages and related products or fields.

Dr. Nathalie Desmasures
Dr. Marion Dalmasso
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (2 papers)

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Research

14 pages, 18829 KiB  
Article
Exploring Structural Diversity among Adhesion Devices Encoded by Lactococcal P335 Phages with AlphaFold2
by Adeline Goulet, Jennifer Mahony, Christian Cambillau and Douwe van Sinderen
Microorganisms 2022, 10(11), 2278; https://doi.org/10.3390/microorganisms10112278 - 16 Nov 2022
Cited by 2 | Viewed by 1764
Abstract
Bacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and [...] Read more.
Bacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and adhesion to, a suitable host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limit their structural analyses by experimental approaches. The protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of adhesion devices from siphophages belonging to the P335 group infecting Lactococcus spp., one of the most extensively applied lactic acid bacteria in dairy fermentations. The predictions of representative adhesion devices from types I-IV P335 phages illustrate their very diverse topology. Adhesion devices from types III and IV phages share a common topology with that of Skunavirus p2, with a receptor binding protein anchored to the virion by a distal tail protein loop. This suggests that they exhibit an activation mechanism similar to that of phage p2 prior to host binding. Full article
(This article belongs to the Special Issue Phages from the Fermented Products)
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13 pages, 1186 KiB  
Article
Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage
by Pierre Ledormand, Nathalie Desmasures, Cédric Midoux, Olivier Rué and Marion Dalmasso
Microorganisms 2022, 10(6), 1203; https://doi.org/10.3390/microorganisms10061203 - 12 Jun 2022
Cited by 5 | Viewed by 2310
Abstract
Phageomes are known to play a key role in the functioning of their associated microbial communities. The phageomes of fermented foods have not been studied thoroughly in fermented foods yet, and even less in fermented beverages. Two approaches were employed to investigate the [...] Read more.
Phageomes are known to play a key role in the functioning of their associated microbial communities. The phageomes of fermented foods have not been studied thoroughly in fermented foods yet, and even less in fermented beverages. Two approaches were employed to investigate the presence of phages in cider, a fermented beverage made from apple, during a fermentation process of two cider tanks, one from an industrial producer and one from a hand-crafted producer. The phageome (free lytic phages) was explored in cider samples with several methodological developments for total phage DNA extraction, along with single phage isolation. Concentration methods, such as tangential flow filtration, flocculation and classical phage concentration methods, were employed and tested to extract free phage particles from cider. This part of the work revealed a very low occurrence of free lytic phage particles in cider. In parallel, a prophage investigation during the fermentation process was also performed using a metagenomic approach on the total bacterial genomic DNA. Prophages in bacterial metagenomes in the two cider tanks seemed also to occur in low abundance, as a total of 1174 putative prophages were identified in the two tanks overtime, and only two complete prophages were revealed. Prophage occurrence was greater at the industrial producer than at the hand-crafted producer, and different dynamics of prophage trends were also observed during fermentation. This is the first report dealing with the investigation of the phageome and of prophages throughout a fermentation process of a fermented beverage. Full article
(This article belongs to the Special Issue Phages from the Fermented Products)
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