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Microorganisms
Special Issues
Biotechnological Applications of Bacteriophages and Enteric Viruses
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Biotechnological Applications of Bacteriophages and Enteric Viruses

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

Deadline for manuscript submissions: 15 May 2024 | Viewed by 8656

Special Issue Editors

Prof. Dr. Gislaine Fongaro

E-Mail Website
Guest Editor
Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina (UFSC), Florianópolis 88034-000, SC, Brazil
Interests: biotechnological applications of bacteriophages and enteric viruses – environmental; one health; virology
Prof. Dr. David Rodríguez-Lázaro

E-Mail Website
Guest Editor
1. Microbiology Division, Faculty of Sciences, University of Burgos, Burgos, Spain
2. Centre for Emerging Pathogens and Global Health, University of Burgos, Burgos, Spain
Interests: food safety; food microbiology; one health; veterinary microbiology; antimicrobial resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Studies of enteric viruses and bacteriophages have attracted interest worldwide for tge purposes of sanitary control and biotechnological uses in the face of global challenges in One Health.

This Special Issue is focused on publishing reviews and research articles on the bioprospecting of bacteriophages and enteric viruses as health biomarkers, food and environmental contaminants (water, soil, sewage, and air), and viral monitoring and microbial control based on scientifically observed phages in the topic of virology applied to One Health.

Prof. Dr. Gislaine Fongaro
Prof. Dr. David Rodríguez-Lázaro
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 (5 papers)

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Research

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17 pages, 2299 KiB  
Article
Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models
by Oluwaseun A. Ishola, Susanne Kublik, Abilash Chakravarthy Durai Raj, Caspar Ohnmacht, Stefanie Schulz, Bärbel U. Foesel and Michael Schloter
Microorganisms 2024, 12(2), 255; https://doi.org/10.3390/microorganisms12020255 - 25 Jan 2024
Viewed by 988
Abstract
Gnotobiotic murine models are important to understand microbiota–host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and [...] Read more.
Gnotobiotic murine models are important to understand microbiota–host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host’s environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome “dark matter” and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome. Full article
(This article belongs to the Special Issue Biotechnological Applications of Bacteriophages and Enteric Viruses)
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17 pages, 2802 KiB  
Article
Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host
by Jimena Barrero-Canosa, Luyao Wang, Angelah Oyugi, Simon Klaes, Pascal Fischer, Lorenz Adrian, Ulrich Szewzyk and Myriel Cooper
Microorganisms 2023, 11(11), 2688; https://doi.org/10.3390/microorganisms11112688 - 02 Nov 2023
Cited by 1 | Viewed by 2366
Abstract
Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class [...] Read more.
Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class Caudoviricetes. It has an icosahedral capsid with a long non-contractile tail and a dsDNA genome with an approximate size of 44 kb and a 54.6% GC content. Phage vB_EcoS-EE09 infected 12 out of the 17 E. coli strains tested. We identified 16 structural phage proteins, including the major capsid protein, in cell-free lysates by protein mass spectrometry. Comparative proteomics of protein extracts of infected E. coli cells revealed that proteins involved in amino acid and protein metabolism were more abundant in infected compared to non-infected cells. Among the proteins involved in the stress response, 74% were less abundant in the infected cultures compared to the non-infected controls, with six proteins showing significant less abundance. Repressing the expression of these proteins may be a phage strategy to evade host defense mechanisms. Our results contribute to diversifying phage collections, identifying structural proteins to enable better reliability in annotating taxonomically related phage genomes, and understanding phage–host interactions at the protein level. Full article
(This article belongs to the Special Issue Biotechnological Applications of Bacteriophages and Enteric Viruses)
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13 pages, 2068 KiB  
Article
Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil
by Danitza Xiomara Romero-Calle, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tomé, Vagner Fonseca, Raquel Guimarães Benevides, Leila Thaise Santana de Oliveira Santos, Tulio de Oliveira, Mateus Matiuzzi da Costa, Luiz Carlos Junior Alcantara, Vasco Ariston de Carvalho Azevedo, Bertram Brenig, Thiago M. Venancio, Craig Billington and Aristóteles Góes-Neto
Microorganisms 2023, 11(7), 1837; https://doi.org/10.3390/microorganisms11071837 - 19 Jul 2023
Cited by 1 | Viewed by 1420
Abstract
Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. [...] Read more.
Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara, was isolated from environmental water samples at the Subaé River Basin, Salvador de Bahia, Brazil. The basin has environmental impacts in its main watercourses arising from the dumping of domestic and industrial effluents and agricultural and anthropological activities. The phage genome sequence was determined by Oxford Nanopore Technologies (ONT) MinION and Illumina HiSeq sequencing, and assembly was carried out by Racon (MinION) and Unicycler (Illumina, Illumina + MinION). The genome was annotated and compared to other Salmonella phages using various bioinformatics approaches. MinION DNA sequencing combined with Racon assembly gave the best complete genome sequence. Phylogenetic analysis revealed that Wara is a member of the Tequintavirus genus. A lack of lysogeny genes, antimicrobial resistance, and virulence genes indicated that Wara has therapeutic and biocontrol potential against Salmonella species in healthcare and agriculture. Full article
(This article belongs to the Special Issue Biotechnological Applications of Bacteriophages and Enteric Viruses)
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18 pages, 9305 KiB  
Article
Isolation and Characterization of Jumbo Coliphage vB_EcoM_Lh1B as a Promising Therapeutic Agent against Chicken Colibacillosis
by Pavel Alexyuk, Andrey Bogoyavlenskiy, Madina Alexyuk, Kuralay Akanova, Yergali Moldakhanov and Vladimir Berezin
Microorganisms 2023, 11(6), 1524; https://doi.org/10.3390/microorganisms11061524 - 08 Jun 2023
Cited by 3 | Viewed by 1713
Abstract
Colibacillosis in chickens can cause the death of young stock, decrease weight gain and lead to significant economic losses. Currently, antibiotic therapy is the main method of treatment of infected animals, but unchecked use of antibiotics has led to widespread antibiotic resistance among [...] Read more.
Colibacillosis in chickens can cause the death of young stock, decrease weight gain and lead to significant economic losses. Currently, antibiotic therapy is the main method of treatment of infected animals, but unchecked use of antibiotics has led to widespread antibiotic resistance among microorganisms. Therefore, it is necessary to develop alternative methods of treating bacterial infections that are fully consistent with the One Health concept and introduce them into practice. Phage therapy meets the specified requirements perfectly. This study describes the isolation and characterization of the lytic jumbo phage vB_EcoM_Lh1B and evaluates its potential use in controlling antibiotic-resistant E. coli infection in poultry. The complete phage genome is 240,200 bp long. Open reading frame (ORF) prediction shows that the phage genome does not contain genes encoding antibiotic resistance and lysogeny factors. Based on phylogenetic and electron microscopic analysis, vB_EcoM_Lh1B belongs to the group of myoviruses of the Seoulvirus genus of the Caudoviricetes class. The bacteriophage has good resistance to a wide range of pH and temperatures and has the ability to suppress 19 out of 30 studied pathogenic E. coli strains. The biological and lytic properties of the isolated vB_EcoM_Lh1B phage make it a promising target of further study as a therapeutic agent against E. coli infections in poultry. Full article
(This article belongs to the Special Issue Biotechnological Applications of Bacteriophages and Enteric Viruses)
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Review

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12 pages, 2018 KiB  
Review
Bacteriophages as Potential Clinical Immune Modulators
by Estêvão Brasiliense de Souza, Aguinaldo Roberto Pinto and Gislaine Fongaro
Microorganisms 2023, 11(9), 2222; https://doi.org/10.3390/microorganisms11092222 - 01 Sep 2023
Viewed by 1520
Abstract
Bacteriophages (phages for short) are bacteria-specific viruses that have been drawing attention when it comes to countering the ever-growing antibiotic bacterial resistance, and are being seen as one of the most promising technologies against multi-antibiotic-resistant bacteria. Although bacteriophages are commonly regarded only as [...] Read more.
Bacteriophages (phages for short) are bacteria-specific viruses that have been drawing attention when it comes to countering the ever-growing antibiotic bacterial resistance, and are being seen as one of the most promising technologies against multi-antibiotic-resistant bacteria. Although bacteriophages are commonly regarded only as anti-bacterial objects unable to directly interact with eukaryotic cell metabolism, an increasing quantity of evidence has indicated that bacteriophages can directly affect cells bacteria in both in vitro and in vivo applications, influencing the behavior of tissues and immune systems. In sight of this new range of applications, several authors have expressed enthusiasm in phage therapy as direct modulators of eukaryotic cells for clinical usage, highlighting the need for further investigations covering the pharmacology of these new “eukaryotic-viruses”, as even harmful interactions with eukaryotic cells were detected after phage therapy. The present review aims to cover and highlight mechanisms through which bacteriophages may interact with immune cells, analyzing potential clinical applications and obstacles presented in the use of bacteriophages as anti-inflammatory tools. Full article
(This article belongs to the Special Issue Biotechnological Applications of Bacteriophages and Enteric Viruses)
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