bacterial viruses
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2021 ◽  
Author(s):  
Dominik Merges ◽  
Alexandra Schmidt ◽  
Imke Schmitt ◽  
Eike Lena Neuschulz ◽  
Francesco Dal Grande ◽  
...  

Soil microbial diversity affects ecosystem functioning and global biogeochemical cycles. Soil bacterial communities catalyze a diversity of biogeochemical reactions and have thus sparked considerable scientific interest. One driver of bacterial community dynamics in natural ecosystems has so far been largely neglected: the predator-prey interactions between bacterial viruses (bacteriophages) and bacteria. To generate ground level knowledge on environmental drivers of these particular predator-prey dynamics we propose an activity-based ecological framework to simultaneous capture community dynamics of bacteria and bacteriophages in soils. An ecological framework and specifically the analyses of community dynamics across latitudinal and altitudinal gradients have been widely used in ecology to understand community-wide responses of innumerable taxa to environmental change, in particular to climate. Here, we tested the hypothesis that the activity of bacteria and bacteriophages co-decline across an elevational gradient. We used metatranscriptomics to investigate bacterial and bacteriophage activity patterns at 5 sites across 400 elevational meters in the Swiss Alps in 2015 and 2017. We found that metabolic activity (transcription levels) of bacteria declined significantly with increasing elevation, but activity of bacteriophages did not. We showed that bacteriophages are consistently active in soil along the entire gradient. Bacteriophage activity pattern, however, is divergent from that of their putative bacterial prey. Future efforts will be necessary to link the environment-activity relationship to predator-prey dynamics, to understand the magnitude of viral contributions to mobilize bacterial cell carbon when infection causes bacterial cell death, a process that may represent an overlooked component of soil biogeochemical cycles.


2021 ◽  
Author(s):  
Igor Vinícius Pimentel Rodrigues ◽  
Katia Regina Assunção Borges ◽  
Maria do Desterro Soares Brandão Nascimento ◽  
Geusa Felipa de Barros Bezerra

Bacteriophages or phages are bacterial viruses that are known to invade bacterial cells and, in the case of the lytic phages, impair bacterial metabolism, causing them to lyse. Since the discovery of these microorganisms by Felix d’Herelle, a French-Canadian microbiologist who worked at Institut Pasteur in Paris, Bacteriophages begin to be used in the treatment of human diseases, like dysentery and staphylococcal skin disease. However, due to the controversial efficacy of phage preparations, and with the advent of antibiotics, commercial production of therapeutic phage preparations ceased in most of the Western world. Nevertheless, phages continued to be used as therapeutic agents (together with or instead of antibiotics) in Eastern Europe and in the former Soviet Union. Therefore, there is a sufficient body of data that incite the accomplishment of further studies in the field of phage therapy.


EcoSal Plus ◽  
2021 ◽  
Author(s):  
Geoffrey Hutinet ◽  
Yan-Jiun Lee ◽  
Valérie de Crécy-Lagard ◽  
Peter R. Weigele

The DNA in bacterial viruses collectively contains a rich, yet relatively underexplored, chemical diversity of nucleobases beyond the canonical adenine, guanine, cytosine, and thymine. Herein, we review what is known about the genetic and biochemical basis for the biosynthesis of complex DNA modifications, also called DNA hypermodifications, in the DNA of tailed bacteriophages infecting Escherichia coli and Salmonella enterica .


2021 ◽  
Author(s):  
Nitzan Aframian ◽  
Shira Omer Bendori ◽  
Stav Hen ◽  
Polina Guler ◽  
Avigail Stokar-Avihail ◽  
...  

Temperate bacterial viruses (phages) can transition between lysis - replicating and killing the host, and lysogeny - existing as dormant prophages while keeping the host viable. It was recently shown that upon invading a naïve cell, some phages communicate using a peptide signal, termed arbitrium, to control the decision of entering lysogeny. Whether communication can also serve to regulate exit from lysogeny (known as phage induction) remains unclear. Here we show that arbitrium-coding prophages continue to communicate from the lysogenic state by secreting and sensing the arbitrium signal. Signaling represses DNA-damage dependent phage induction, enabling prophages to reduce induction rate when surrounded by other lysogens. We show that the mechanism by which DNA damage and communication are integrated differs between distantly related arbitrium-coding phages. Additionally, signaling by prophages tilts the decision of nearby infecting phages towards lysogeny. Altogether, we find that phages use small molecule communication throughout their entire life-cycle to measure the abundance of lysogens in the population, thus avoiding wasteful attempts at secondary infections when they are unlikely to succeed.


2021 ◽  
Vol 9 (9) ◽  
pp. 1819
Author(s):  
Konstantin A. Miroshnikov ◽  
Peter V. Evseev ◽  
Anna A. Lukianova ◽  
Alexander N. Ignatov

The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.


Author(s):  
Mart Krupovic ◽  
Dann Turner ◽  
Vera Morozova ◽  
Mike Dyall-Smith ◽  
Hanna M. Oksanen ◽  
...  

AbstractIn this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).


2021 ◽  
Vol 6 (1) ◽  
pp. 113-119
Author(s):  
A. F. Aishat ◽  
◽  
S. B. Manga ◽  
I. O. Obaroh ◽  
R. J. Bioku ◽  
...  

The practice of phage therapy, which uses bacterial viruses (phages) to treat bacterial infections, has been around for almost a century. The universal decline in the effectiveness of antibiotics has generated renewed interest in revisiting this practice. Conventionally, phage therapy relies on the use of naturally-occurring phages to infect and lyse bacteria at the site of infection. Biotechnological advances have further expanded the repertoire of potential phage therapeutics to include novel strategies using bioengineered phages and purified phage lytic proteins. Current research on the use of phages and their lytic proteins, specifically against multidrug resistant bacterial infections, suggests phage therapy has the potential to be used as either an alternative or a supplement to antibiotic treatments. Antibacterial therapies, whether phage- or antibioticbased, have relative advantages and disadvantages accordingly. Many considerations must be taken into account when designing novel therapeutic approaches for preventing and treating bacterial infections. Although much is still unknown about the interactions between phage, bacteria, and human host, the time to take phage therapy seriously seems to be rapidly approaching Keywords: Antibiotic resistance; Antimicrobial; Bacteriophage; Biofilms; Multidrug resistance; Phage; Phage safety; Therapy.


Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1095
Author(s):  
Eugenia N. Bugaeva ◽  
Maya V. Voronina ◽  
Dmitry M. Vasiliev ◽  
Anna A. Lukianova ◽  
Nikolay N. Landyshev ◽  
...  

Using bacteriophages (bacterial viruses) to control pathogenic bacteria is a promising approach in horticulture. However, the application of this strategy in real conditions requires compliance with particular technological and environmental restraints. The presented paper concerns the process of phage selection to create a cocktail that is efficient against the circulating causal agents of potato soft rot. The resulting phage cocktail causes a complete lysis of a mixture of circulating pectobacterial strains in vitro. In the context of being used to treat ware potatoes during off-season storage, the protocol of phage application via the humidity maintenance system was designed. The phage cocktail was shown to reduce the population of Pectobacterium spp. 10–12-fold, achieving a population that was below a symptomatic threshold.


2021 ◽  
Author(s):  
Helena Leinweber ◽  
Raphael Sieber ◽  
Jesper Larsen ◽  
Marc Stegger ◽  
Hanne Ingmer

AbstractIn recent years there has been an increase in human infections with methicillin-resistant Staphylococcus aureus (MRSA) originating from livestock and strains carrying bacterial viruses of the Sa3int-family have disseminated into the community. Sa3int phages express immune evasion factors and are common in human staphylococcal strains. As the bacterial attachment site (attB) for Sa3int phages is mutated in livestock-associated strains, the integration frequency is low and a key question is how the phages are established. Here we show that Sa3int phages adapt to alternative bacterial integration sites by mutating the phage attachment sequence, attP, leading to enhanced integration at these sites. Using a model strain carrying the mutated attBLA of livestock-associated strains we find that once established, the Sa3int phage, Φ13 is inducible with release of heterogenous phage populations carrying mutations in attP that in part increase homology to alternative integration sites or attBLA. Compared to the original phage, the adaptive mutations increase phage integration in new rounds of infection. Also, Sa3int phages induced from livestock-associated outbreak strains reveal mutated attP sequences. We suspect that promiscuity of the phage-encoded recombinase allows this adaptation and propose it may explain how phages mediate “host jumps” that are regularly observed for staphylococcal lineages.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Emma G. Piligrimova ◽  
Olesya A. Kazantseva ◽  
Andrey N. Kazantsev ◽  
Nikita A. Nikulin ◽  
Anna V. Skorynina ◽  
...  

AbstractBacteriophages are bacterial viruses and the most abundant biological entities on Earth. Temperate bacteriophages can form prophages stably maintained in the host population: they either integrate into the host genome or replicate as plasmids in the host cytoplasm. As shown, tailed temperate bacteriophages may form circular plasmid prophages in many bacterial species of the taxa Firmicutes, Gammaproteobacteria and Spirochaetes. The actual number of such prophages is thought to be underestimated for two main reasons: first, in bacterial whole genome-sequencing assemblies, they are difficult to distinguish from actual plasmids; second, there is an absence of experimental studies which are vital to confirm their existence. In Firmicutes, such prophages appear to be especially numerous. In the present study, we identified 23 genomes from species of the Bacillus cereus group that were deposited in GenBank as plasmids and may belong to plasmid prophages with little or no homology to known viruses. We consider these putative prophages worth experimental assays since it will broaden our knowledge of phage diversity and suggest that more attention be paid to such molecules in all bacterial sequencing projects as this will help in identifying previously unknown phages.


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