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Bacteriophage—Molecular Studies 3.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 51117

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Prof. Dr. Alicja Wegrzyn

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Phage Therapy Center, University Center for Applied and Interdisciplinary Research, University of Gdansk, Gdansk, Poland
Interests: biology of bacteriophages; biodiversity of bacteriophages; regulation of bacteriophage development; regulation of phage gene expression; control of phage DNA replication; phage therapy; phages bearing genes of toxins; bacteriophage genomics
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Dear Colleagues,

Bacteriophages, the viruses infecting bacterial cells, were first described 100 years ago, in 1915, by Frederick Twort. The scientist who introduced the name “bacteriophage” was Felix d’Herelle, who investigated these viruses for many years, leading to new fields of research, including bacteriophage therapy. In the following years, bacteriophages became important model organisms in molecular biology and genetics. Many basic discoveries were made during studies of these viruses, with such spectacular examples as demonstrating that DNA is a genetic material, viruses can encode enzymes, gene expression proceeds through mRNA molecules, the genetic code is based on nucleotide triplets, gene expression can be regulated by transcription antitermination, specific genes encode heat shock proteins, and that specific mechanisms regulate DNA replication initiation based on the formation and rearrangements of protein–DNA complexes. The regulatory processes occurring in bacteriophage-infected cells have been considered paradigms of the control of developmental pathways. On the other hand, the history of research on bacteriophages also passed through dark times when, at the end of 20th century, there was the collective impression that we knew almost everything there was to know about these simple viruses, and that it was time to investigate more complex organisms instead. Nevertheless, subsequent discoveries have indicated that such an assumption was unequivocally false, and studies on the molecular biology and biotechnology of bacteriophages have once again become extensive. The interest in these viruses has increased dramatically, and it appears that we are far from understanding the biology of the vast majority of bacteriophages.

This Special Issue of the International Journal of Molecular Sciences is devoted to publishing papers on studies of bacteriophages at the molecular level. Papers on phage biodiversity, regulation of processes occurring during phage development, as well as the practical use of bacteriophages—including biotechnology and phage therapy—are welcome, providing the studies deal with the molecular level and utilize molecular biology methods. I am hopeful of building a great collection of articles devoted to recent discoveries in the field of bacteriophage molecular biology. Therefore, I invite you to submit manuscripts to this Special Issue as an excellent forum to share your discoveries in this fascinating research field.

Dr. Alicja Wegrzyn
Guest Editor

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Keywords

bacteriophage biodiversity
regulation of bacteriophage development
molecular processes in bacteriophages
bacteriophage-based biotechnology
phage therapy

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Related Special Issues

Bacteriophage—Molecular Studies 4.0 in International Journal of Molecular Sciences (12 articles)
Bacteriophage—Molecular Studies 5.0 in International Journal of Molecular Sciences (12 articles)
Bacteriophage—Molecular Studies 6.0 in International Journal of Molecular Sciences (1 article)

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20 pages, 5509 KiB

Open AccessArticle

Functional Dissection of P1 Bacteriophage Holin-like Proteins Reveals the Biological Sense of P1 Lytic System Complexity

by Agnieszka Bednarek, Agata Cena, Wioleta Izak, Joanna Bigos and Małgorzata Łobocka

Int. J. Mol. Sci. 2022, 23(8), 4231; https://doi.org/10.3390/ijms23084231 - 11 Apr 2022

Cited by 2 | Viewed by 2984

Abstract

P1 is a model temperate myovirus. It infects different Enterobacteriaceae and can develop lytically or form lysogens. Only some P1 adaptation strategies to propagate in different hosts are known. An atypical feature of P1 is the number and organization of cell lysis-associated genes. In addition to SAR-endolysin Lyz, holin LydA, and antiholin LydB, P1 encodes other predicted holins, LydC and LydD. LydD is encoded by the same operon as Lyz, LydA and LydB are encoded by an unlinked operon, and LydC is encoded by an operon preceding the lydA gene. By analyzing the phenotypes of P1 mutants in known or predicted holin genes, we show that all the products of these genes cooperate with the P1 SAR-endolysin in cell lysis and that LydD is a pinholin. The contributions of holins/pinholins to cell lysis by P1 appear to vary depending on the host of P1 and the bacterial growth conditions. The pattern of morphological transitions characteristic of SAR-endolysin–pinholin action dominates during lysis by wild-type P1, but in the case of lydC lydD mutant it changes to that characteristic of classical endolysin-pinholin action. We postulate that the complex lytic system facilitates P1 adaptation to various hosts and their growth conditions. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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14 pages, 2022 KiB

Open AccessArticle

Transcriptional Organization of the Salmonella Typhimurium Phage P22 pid ORFan Locus

by Sanne Wolput, Angela Makumi, Laura Wicke, Leonard E. Bäcker, William Cenens, Yves Briers, Nicolas A. Wenner, Siân V. Owen, Jay C. D. Hinton, Rob Lavigne and Abram Aertsen

Int. J. Mol. Sci. 2022, 23(3), 1253; https://doi.org/10.3390/ijms23031253 - 23 Jan 2022

Cited by 2 | Viewed by 2725

Abstract

Many phage genes lack sequence similarity to any other open reading frame (ORF) in current databases. These enigmatic ORFan genes can have a tremendous impact on phage propagation and host interactions but often remain experimentally unexplored. We previously revealed a novel interaction between phage P22 and its Salmonella Typhimurium host, instigated by the ORFan gene pid (for phage P22 encoded instigator of dgo expression) and resulting in derepression of the host dgoRKAT operon. The pid gene is highly expressed in phage carrier cells that harbor a polarly located P22 episome that segregates asymmetrically among daughter cells. Here, we discovered that the pid locus is fitted with a weak promoter, has an exceptionally long 5′ untranslated region that is instructive for a secondary pid mRNA species, and has a 3′ Rho-independent termination loop that is responsible for stability of the pid transcript. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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19 pages, 3770 KiB

Open AccessArticle

Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil’s Disease

by Eric Olo Ndela, François Enault and Ariane Toussaint

Int. J. Mol. Sci. 2021, 22(24), 13434; https://doi.org/10.3390/ijms222413434 - 14 Dec 2021

Cited by 4 | Viewed by 2848

Abstract

The virome associated with the corkscrew shaped bacterium Leptospira, responsible for Weil’s disease, is scarcely known, and genetic tools available for these bacteria remain limited. To reduce these two issues, potential transposable prophages were searched in Leptospiraceae genomes. The 236 predicted transposable prophages were particularly abundant in the most pathogenic leptospiral clade, being potentially involved in the acquisition of virulent traits. According to genomic similarities and phylogenies, these prophages are distantly related to known transposable phages and are organized into six groups, one of them encompassing prophages with unusual TA-TA ends. Interestingly, structural and transposition proteins reconstruct different relationships between groups, suggesting ancestral recombinations. Based on the baseplate phylogeny, two large clades emerge, with specific gene-contents and high sequence divergence reflecting their ancient origin. Despite their high divergence, the size and overall genomic organization of all prophages are very conserved, a testimony to the highly constrained nature of their genomes. Finally, similarities between these prophages and the three known non-transposable phages infecting L. biflexa, suggest gene transfer between different Caudovirales inside their leptospiral host, and the possibility to use some of the transposable prophages in that model strain. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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14 pages, 4636 KiB

Open AccessArticle

Properties of Two Broad Host Range Phages of Yersinia enterocolitica Isolated from Wild Animals

by Jens A. Hammerl, Andrea Barac, Philipp Erben, Julius Fuhrmann, Ashish Gadicherla, Franziska Kumsteller, Anne Lauckner, Felix Müller and Stefan Hertwig

Int. J. Mol. Sci. 2021, 22(21), 11381; https://doi.org/10.3390/ijms222111381 - 21 Oct 2021

Cited by 10 | Viewed by 2221

Abstract

Yersinia (Y.) enterocolitica and Y. pseudotuberculosis are important zoonotic agents which can infect both humans and animals. To combat these pathogens, the application of strictly lytic phages may be a promising tool. Since only few Yersinia phages have been described yet, some of which demonstrated a high specificity for certain serotypes, we isolated two phages from game animals and characterized them in terms of their morphology, host specificity, lytic activity on two bio-/serotypes and genome composition. The T7-related podovirus vB_YenP_Rambo and the myovirus vB_YenM_P281, which is very similar to a previously described phage PY100, showed a broad host range. Together, they lysed all the 62 tested pathogenic Y. enterocolitica strains belonging to the most important bio-/serotypes in Europe. A cocktail containing these two phages strongly reduced cultures of a bio-/serotype B4/O:3 and a B2/O:9 strain, even at very low MOIs (multiplicity of infection) and different temperatures, though, lysis of bio-/serotype B2/O:9 by vB_YenM_P281 and also by the related phage PY100 only occurred at 37 °C. Both phages were additionally able to lyse various Y. pseudotuberculosis strains at 28 °C and 37 °C, but only when the growth medium was supplemented with calcium and magnesium cations. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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28 pages, 6597 KiB

Open AccessArticle

Unraveling Protein Interactions between the Temperate Virus Bam35 and Its Bacillus Host Using an Integrative Yeast Two Hybrid–High Throughput Sequencing Approach

by Ana Lechuga, Cédric Lood, Mónica Berjón-Otero, Alicia del Prado, Jeroen Wagemans, Vera van Noort, Rob Lavigne, Margarita Salas and Modesto Redrejo-Rodríguez

Int. J. Mol. Sci. 2021, 22(20), 11105; https://doi.org/10.3390/ijms222011105 - 14 Oct 2021

Viewed by 3000

Abstract

Bacillus virus Bam35 is the model Betatectivirus and member of the family Tectiviridae, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. Interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, which are known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein–protein interactions (PPIs) network for a tectivirus–host system by studying the Bam35–Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and high-throughput sequencing (Y2H-HTS). We generated and thoroughly analyzed a genomic library of Bam35′s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait–prey couples. Initial analysis of the raw data enabled the identification of over 4000 candidate interactions, which were sequentially filtered to produce 182 high-confidence interactions that were defined as part of the core virus–host interactome. Overall, host metabolism proteins and peptidases were particularly enriched within the detected interactions, distinguishing this host–phage system from the other reported host–phage PPIs. Our approach also suggested biological roles for several Bam35 proteins of unknown function, including the membrane structural protein P25, which may be a viral hub with a role in host membrane modification during viral particle morphogenesis. This work resulted in a better understanding of the Bam35–B. thuringiensis interaction at the molecular level and holds great potential for the generalization of the Y2H-HTS approach for other virus–host models. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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26 pages, 5881 KiB

Open AccessArticle

Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of Shewanella sp. M16 Provides Insights into the Genetic Diversity of the Shewanella Virome

by Katarzyna Bujak, Przemyslaw Decewicz, Joanna M. Rosinska and Monika Radlinska

Int. J. Mol. Sci. 2021, 22(20), 11070; https://doi.org/10.3390/ijms222011070 - 14 Oct 2021

Cited by 3 | Viewed by 4076

Abstract

Shewanella is a ubiquitous bacterial genus of aquatic ecosystems, and its bacteriophages are also isolated from aquatic environments (oceans, lakes, ice, and wastewater). In this study, the isolation and characterization of a novel virulent Shewanella phage vB_SspS_KASIA and the identification of three prophages of its host, Shewanella sp. M16, including a mitomycin-inducible Mu-like siphovirus, vB_SspS_MuM16-1, became the starting point for comparative analyses of phages infecting Shewanella spp. and the determination of their position among the known bacterial viruses. A similarity networking analysis revealed the high diversity of Shewanella phages in general, with vB_SspS_KASIA clustering exclusively with Colwellia phage 9A, with which it forms a single viral cluster composed of two separate viral subclusters. Furthermore, vB_SspS_MuM16-1 presented itself as being significantly different from the phages deposited in public databases, expanding the diversity of the known Mu-like phages and giving potential molecular markers for the identification of Mu-like prophages in bacterial genomes. Moreover, the functional analysis performed for vB_SspS_KASIA suggested that, despite the KASIA host, the M16 strain grows better in a rich medium and at 30 °C the phage replication cycle seems to be optimal in restrictive culture conditions mimicking their natural environment, the Zloty Stok gold and arsenic mine. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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11 pages, 2111 KiB

Open AccessArticle

High Resolution Structure of the Mature Capsid of Ralstonia solanacearum Bacteriophage ϕRSA1 by Cryo-Electron Microscopy

by Grégory Effantin, Akiko Fujiwara, Takeru Kawasaki, Takashi Yamada and Guy Schoehn

Int. J. Mol. Sci. 2021, 22(20), 11053; https://doi.org/10.3390/ijms222011053 - 13 Oct 2021

Cited by 3 | Viewed by 2651

Abstract

The ϕRSA1 bacteriophage has been isolated from Ralstonia solanacearum, a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature capsid to 3.9 Å resolution by cryo-electron microscopy. The capsid shell, that contains the 39 kbp of dsDNA genome, has an icosahedral symmetry characterized by an unusual triangulation number of T = 7, dextro. The ϕRSA1 capsid is composed solely of the polymerization of the major capsid protein, gp8, which exhibits the typical “Johnson” fold first characterized in E. coli bacteriophage HK97. As opposed to the latter, the ϕRSA1 mature capsid is not stabilized by covalent crosslinking between its subunits, nor by the addition of a decoration protein. We further describe the molecular interactions occurring between the subunits of the ϕRSA1 capsid and their relationships with the other known bacteriophages. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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33 pages, 18917 KiB

Open AccessArticle

Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages

by Peter Evseev, Anna Lukianova, Nina Sykilinda, Anna Gorshkova, Alexander Bondar, Mikhail Shneider, Marsel Kabilov, Valentin Drucker and Konstantin Miroshnikov

Int. J. Mol. Sci. 2021, 22(19), 10350; https://doi.org/10.3390/ijms221910350 - 26 Sep 2021

Cited by 11 | Viewed by 3367

Abstract

Pseudomonas phage MD8 is a temperate phage isolated from the freshwater lake Baikal. The organisation of the MD8 genome resembles the genomes of lambdoid bacteriophages. However, MD8 gene and protein sequences have little in common with classified representatives of lambda-like phages. Analysis of phage genomes revealed a group of other Pseudomonas phages related to phage MD8 and the genomic layout of MD8-like phages indicated extensive gene exchange involving even the most conservative proteins and leading to a high degree of genomic mosaicism. Multiple horizontal transfers and mosaicism of the genome of MD8, related phages and other λ-like phages raise questions about the principles of taxonomic classification of the representatives of this voluminous phage group. Comparison and analysis of various bioinformatic approaches applied to λ-like phage genomes demonstrated different efficiency and contradictory results in the estimation of genomic similarity and relatedness. However, we were able to make suggestions for the possible origin of the MD8 genome and the basic principles for the taxonomic classification of lambdoid phages. The group comprising 26 MD8-related phages was proposed to classify as two close genera belonging to a big family of λ-like phages. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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21 pages, 48519 KiB

Open AccessArticle

Novel Lytic Enzyme of Prophage Origin from Clostridium botulinum E3 Strain Alaska E43 with Bactericidal Activity against Clostridial Cells

by Agnieszka Morzywolek, Magdalena Plotka, Anna-Karina Kaczorowska, Monika Szadkowska, Lukasz P. Kozlowski, Dariusz Wyrzykowski, Joanna Makowska, Jerel J. Waters, Steven M. Swift, David M. Donovan and Tadeusz Kaczorowski

Int. J. Mol. Sci. 2021, 22(17), 9536; https://doi.org/10.3390/ijms22179536 - 2 Sep 2021

Cited by 5 | Viewed by 3741

Abstract

Clostridium botulinum is a Gram-positive, anaerobic, spore-forming bacterium capable of producing botulinum toxin and responsible for botulism of humans and animals. Phage-encoded enzymes called endolysins, which can lyse bacteria when exposed externally, have potential as agents to combat bacteria of the genus Clostridium. Bioinformatics analysis revealed in the genomes of several Clostridium species genes encoding putative N-acetylmuramoyl-l-alanine amidases with anti-clostridial potential. One such enzyme, designated as LysB (224-aa), from the prophage of C. botulinum E3 strain Alaska E43 was chosen for further analysis. The recombinant 27,726 Da protein was expressed and purified from E. coli Tuner(DE3) with a yield of 37.5 mg per 1 L of cell culture. Size-exclusion chromatography and analytical ultracentrifugation experiments showed that the protein is dimeric in solution. Bioinformatics analysis and results of site-directed mutagenesis studies imply that five residues, namely H25, Y54, H126, S132, and C134, form the catalytic center of the enzyme. Twelve other residues, namely M13, H43, N47, G48, W49, A50, L73, A75, H76, Q78, N81, and Y182, were predicted to be involved in anchoring the protein to the lipoteichoic acid, a significant component of the Gram-positive bacterial cell wall. The LysB enzyme demonstrated lytic activity against bacteria belonging to the genera Clostridium, Bacillus, Staphylococcus, and Deinococcus, but did not lyse Gram-negative bacteria. Optimal lytic activity of LysB occurred between pH 4.0 and 7.5 in the absence of NaCl. This work presents the first characterization of an endolysin derived from a C. botulinum Group II prophage, which can potentially be used to control this important pathogen. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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21 pages, 6907 KiB

Open AccessArticle

Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA

by Monika Šimoliūnienė, Emilija Žukauskienė, Lidija Truncaitė, Liang Cui, Geoffrey Hutinet, Darius Kazlauskas, Algirdas Kaupinis, Martynas Skapas, Valérie de Crécy-Lagard, Peter C. Dedon, Mindaugas Valius, Rolandas Meškys and Eugenijus Šimoliūnas

Int. J. Mol. Sci. 2021, 22(14), 7333; https://doi.org/10.3390/ijms22147333 - 8 Jul 2021

Cited by 2 | Viewed by 3432

Abstract

A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage–host interactions, and DNA metabolism. In addition, a gene encoding a preQ₀ DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC–MS/MS analysis indicates 2′-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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18 pages, 1551 KiB

Open AccessArticle

Intra-Population Competition during Adaptation to Increased Temperature in an RNA Bacteriophage

by María Arribas and Ester Lázaro

Int. J. Mol. Sci. 2021, 22(13), 6815; https://doi.org/10.3390/ijms22136815 - 24 Jun 2021

Cited by 6 | Viewed by 2649

Abstract

Evolution of RNA bacteriophages of the family Leviviridae is governed by the high error rates of their RNA-dependent RNA polymerases. This fact, together with their large population sizes, leads to the generation of highly heterogeneous populations that adapt rapidly to most changes in the environment. Throughout adaptation, the different mutants that make up a viral population compete with each other in a non-trivial process in which their selective values change over time due to the generation of new mutations. In this work we have characterised the intra-population dynamics of a well-studied levivirus, Qβ, when it is propagated at a higher-than-optimal temperature. Our results show that adapting populations experienced rapid changes that involved the ascent of particular genotypes and the loss of some beneficial mutations of early generation. Artificially reconstructed populations, containing a fraction of the diversity present in actual populations, fixed mutations more rapidly, illustrating how population bottlenecks may guide the adaptive pathways. The conclusion is that, when the availability of beneficial mutations under a particular selective condition is elevated, the final outcome of adaptation depends more on the occasional occurrence of population bottlenecks and how mutations combine in genomes than on the selective value of particular mutations. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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14 pages, 3818 KiB

Open AccessArticle

Characterization of an Endolysin Targeting Clostridioides difficile That Affects Spore Outgrowth

by Shakhinur Islam Mondal, Arzuba Akter, Lorraine A. Draper, R. Paul Ross and Colin Hill

Int. J. Mol. Sci. 2021, 22(11), 5690; https://doi.org/10.3390/ijms22115690 - 26 May 2021

Cited by 16 | Viewed by 5147

Abstract

Clostridioides difficile is a spore-forming enteric pathogen causing life-threatening diarrhoea and colitis. Microbial disruption caused by antibiotics has been linked with susceptibility to, and transmission and relapse of, C. difficile infection. Therefore, there is an urgent need for novel therapeutics that are effective in preventing C. difficile growth, spore germination, and outgrowth. In recent years bacteriophage-derived endolysins and their derivatives show promise as a novel class of antibacterial agents. In this study, we recombinantly expressed and characterized a cell wall hydrolase (CWH) lysin from C. difficile phage, phiMMP01. The full-length CWH displayed lytic activity against selected C. difficile strains. However, removing the N-terminal cell wall binding domain, creating CWH_351—656, resulted in increased and/or an expanded lytic spectrum of activity. C. difficile specificity was retained versus commensal clostridia and other bacterial species. As expected, the putative cell wall binding domain, CWH_1—350, was completely inactive. We also observe the effect of CWH_351—656 on preventing C. difficile spore outgrowth. Our results suggest that CWH_351—656 has therapeutic potential as an antimicrobial agent against C. difficile infection. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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13 pages, 1617 KiB

Open AccessArticle

High-Throughput Sequencing of Phage Display Libraries Reveals Parasitic Enrichment of Indel Mutants Caused by Amplification Bias

by Sander Plessers, Vincent Van Deuren, Rob Lavigne and Johan Robben

Int. J. Mol. Sci. 2021, 22(11), 5513; https://doi.org/10.3390/ijms22115513 - 24 May 2021

Cited by 4 | Viewed by 3613

Abstract

The combination of phage display technology with high-throughput sequencing enables in-depth analysis of library diversity and selection-driven dynamics. We applied short-read sequencing of the mutagenized region on focused display libraries of two homologous nucleic acid modification eraser proteins—AlkB and FTO—biopanned against methylated DNA. This revealed enriched genotypes with small indels and concomitant doubtful amino acid motifs within the FTO library. Nanopore sequencing of the entire display vector showed additional enrichment of large deletions overlooked by region-specific sequencing, and further impacted the interpretation of the obtained amino acid motifs. We could attribute enrichment of these corrupted clones to amplification bias due to arduous FTO display slowing down host cell growth as well as phage production. This amplification bias appeared to be stronger than affinity-based target selection. Recommendations are provided for proper sequence analysis of phage display data, which can improve motive discovery in libraries of proteins that are difficult to display. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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21 pages, 1540 KiB

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Phage Therapy as a Focused Management Strategy in Aquaculture

by José Ramos-Vivas, Joshua Superio, Jorge Galindo-Villegas and Félix Acosta

Int. J. Mol. Sci. 2021, 22(19), 10436; https://doi.org/10.3390/ijms221910436 - 28 Sep 2021

Cited by 26 | Viewed by 6373

Abstract

Therapeutic bacteriophages, commonly called as phages, are a promising potential alternative to antibiotics in the management of bacterial infections of a wide range of organisms including cultured fish. Their natural immunogenicity often induces the modulation of a variated collection of immune responses within several types of immunocytes while promoting specific mechanisms of bacterial clearance. However, to achieve standardized treatments at the practical level and avoid possible side effects in cultivated fish, several improvements in the understanding of their biology and the associated genomes are required. Interestingly, a particular feature with therapeutic potential among all phages is the production of lytic enzymes. The use of such enzymes against human and livestock pathogens has already provided in vitro and in vivo promissory results. So far, the best-understood phages utilized to fight against either Gram-negative or Gram-positive bacterial species in fish culture are mainly restricted to the Myoviridae and Podoviridae, and the Siphoviridae, respectively. However, the current functional use of phages against bacterial pathogens of cultured fish is still in its infancy. Based on the available data, in this review, we summarize the current knowledge about phage, identify gaps, and provide insights into the possible bacterial control strategies they might represent for managing aquaculture-related bacterial diseases. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 3.0)

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