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Infection, Genetics and Evolution :... Aug 2021Mycoplasma anserisalpingitidis is a bacterial waterfowl pathogen. In these days of growing antibiotic resistance, it is necessary to search for alternative methods of...
Mycoplasma anserisalpingitidis is a bacterial waterfowl pathogen. In these days of growing antibiotic resistance, it is necessary to search for alternative methods of defense against Mycoplasma impacts in flocks. In order to identify prophage-like sequences, three established bioinformatics tools (PHASTER, PhiSpy, Prophage Hunter) were used in this study for the in silico screening of 82 M. anserisalpingitidis whole genomes. The VIBRANT software was used as a novel approach to further investigate the possibility of prophages in the sequences. The commonly used softwares found prophage-like sequences in the strains, but the results were inconclusive. The VIBRANT search resulted in multiple hits, and many of them were over 10,000 base pairs (bp). These putative prophages are comparable in size to the few described mycoplasma phages. The translated coding DNA sequences of the putative prophages were checked with protein BLAST. The functions of the proteins found by the BLASTP search are common among bacteriophages. The BLASTN search of the sequences found that many of these were more similar to the M. anatis NCTC 10156 strain, rather than the available M. anserisalpingitidis strains. The initial screening pointed at the presence of novel bacteriophages in the M. anserisalpingitidis and M. anatis strains. The VIBRANT search results were very similar to each other and none of these sequences were part of the core genome of M. anserisalpingitidis, with a few exceptions. The VIBRANT analysis explored presumably intact, novel prophages.
Topics: Mycoplasma; Prophages
PubMed: 33932611
DOI: 10.1016/j.meegid.2021.104886 -
NPJ Biofilms and Microbiomes Oct 2023Elimination of specific enteropathogenic microorganisms is critical to gut health. However, the complexity of the gut community makes it challenging to target specific...
Elimination of specific enteropathogenic microorganisms is critical to gut health. However, the complexity of the gut community makes it challenging to target specific bacterial organisms. Accumulating evidence suggests that various foods can change the abundance of intestinal bacteria by modulating prophage induction. By using pathogenic Escherichia coli (E. coli) ATCC 25922 as a model in this research, we explored the potential of dietary modulation of prophage induction and subsequent bacterial survival. Among a panel of sugars tested in vitro, D-xylose was shown to efficiently induce prophages in E. coli ATCC 25922, which depends, in part, upon the production of D-lactic acid. In an enteric mouse model, prophage induction was found to be further enhanced in response to propionic acid. Dietary D-xylose increased the proportion of Clostridia which converted D-lactic acid to propionic acid. Intestinal propionic acid levels were diminished, following either oral gavage with the dehydrogenase gene (ldhA)-deficient E. coli ATCC 25922 or depletion of intestinal Clostridia by administration of streptomycin. D-Xylose metabolism and exposure to propionic acid triggered E. coli ATCC 25922 SOS response that promoted prophage induction. E. coli ATCC 25922 mutant of RecA, a key component of SOS system, exhibited decreased phage production. These findings suggest the potential of using dietary components that can induce prophages as antimicrobial alternatives for disease control and prevention by targeted elimination of harmful gut bacteria.
Topics: Mice; Animals; Bacteriophages; Escherichia coli; Xylose; Prophages; Lactic Acid
PubMed: 37821428
DOI: 10.1038/s41522-023-00445-w -
Frontiers in Microbiology 2022Prophages have long been regarded as an important contributor to the evolution of and Verotoxin-producing (VTEC), members of the that cause millions of cases of...
Prophages have long been regarded as an important contributor to the evolution of and Verotoxin-producing (VTEC), members of the that cause millions of cases of foodborne illness in North America. In . Typhimurium, prophages provide many of the genes required for invasion; similarly, in VTEC, the Verotoxin-encoding genes are located in cryptic prophages. The ability of prophages to quickly acquire and lose genes have driven their rapid evolution, leading to highly diversified populations of phages that can infect distantly-related bacterial hosts. To defend against foreign genetic materials (i.e., phages), bacteria have evolved Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immunity, consisting of variable spacer regions that match short nucleic acid sequences of invaders previously encountered. The number of spacer regions varies widely amongst , and there is currently no clear consensus if the accumulation of spacers is linked to genomic prophage abundance. Given the immense prophage diversity and contribution to bacterial host phenotypes, we analyzed the prophage sequences within 118 strains of and VTEC, 117 of which are of agricultural origin. Overall, 130 unique prophage sequences were identified and they were found to be remarkably diverse with <50% nucleotide similarity, particularly with the Gifsy-1 group which was identified in several serovars and interestingly, a strain of VTEC. Additionally, we identified a novel plasmid-like phage that carried antibiotic resistance and bacteriocin resistance genes. The strains analyzed carried at least six distinct spacers which did not possess homology to prophages identified in the same genome. In fact, only a fraction of all identified spacers (14%) possessed significant homology to known prophages. Regression models did not discern a correlation between spacer and prophage abundance in our strains, although the relatively high number of spacers in our strains (an average of 27 in and 19 in VTEC) suggest that high rates of infection may occur in agricultural niches and be a contributing driver in bacterial evolution. Cumulatively, these results shed insight into prophage diversity of and VTEC, which will have further implications when informing development of phage therapies against these foodborne pathogens.
PubMed: 35935192
DOI: 10.3389/fmicb.2022.853703 -
Microbiology (Reading, England) Mar 2022subspecies serovar Typhimurium (. Typhimurium) definitive phage type 104 (DT104), . Worthington, and produce ArtAB toxin, which catalyses ADP-ribosylation of...
subspecies serovar Typhimurium (. Typhimurium) definitive phage type 104 (DT104), . Worthington, and produce ArtAB toxin, which catalyses ADP-ribosylation of pertussis toxin-sensitive G protein. ArtAB gene () is encoded on a prophage in , and prophage induction by SOS-inducing agents is associated with increases in ArtAB production . However, little is known about the expression of . Here, we showed a significant increase in transcription of DT104 within macrophage-like RAW264.7 cells. Intracellular expression of ArtAB was also observed by immunofluorescence staining. The induced expression of in DT104 and was enhanced by treatment of RAW264.7 cells with phorbol 12-myristate 13-acetate (PMA), which stimulates the production of reactive oxygen species (ROS); however, such induction was not observed in . Worthington. Upregulation of , a major regulator of oxidative stress, and a repressor of prophage induction, was observed in . Worthington within RAW264.7 cells treated with PMA but not in the DT104 strain. Although the expression of was increased, was upregulated in which lacks the gene in the incomplete -encoded prophage. Taken together, oxidative stress plays a role in the production of toxins in macrophages, and high expression levels of and are responsible for the low expression of . Therefore, strain variation in the level of expression within macrophages could be explained by differences in the oxidative stress response of bacteria and might be reflected in its virulence.
Topics: Macrophages; Prophages; Salmonella typhimurium; Virulence
PubMed: 35333707
DOI: 10.1099/mic.0.001152 -
Virus Research Apr 2023Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located...
Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located mainly within the phage tail structure. In this paper we surveyed and analysed the genomes of 506 isolated bacteriophage and prophage infecting or harboured within the genomes of the medically important Enterococcus faecalis and faecium. We highlight and characterise the major features of the genomes of phage in the morphological groups podovirus, siphovirus and myovirus, and explore their categorisation according to the new ICTV classifications, with a focus on putative extracellular lysins chiefly within tail modules. Our analysis reveals a range of potential cell-wall targeting enzyme domains that are part of tail, tape measure or other predicted base structures of these phages or prophages. These largely fall into protein domains targeting pentapeptide or glycosidic linkages within peptidoglycan but also potentially the enterococcal polysaccharide antigen (EPA) and wall teichoic acids of these species (i.e., Pectinesterases and Phosphodiesterases). Notably, there is a great variety of domain architectures that reveal the diversity of evolutionary solutions to attack the Enterococcus cell wall. Despite this variety, most phage and prophage possess a putative endopeptidase (70%), reflecting the ubiquity of this cell surface barrier. We also identified a predicted lytic transglycosylase domain belonging to the glycosyl hydrolase (GH) family 23 and present exclusively within tape measure proteins. Our data also reveal distinct features of the genomes of podo-, sipho- and myo-type viruses that most likely relate to their size and complexity. Overall, we lay a foundation for expression of recombinant TAL proteins and engineering of enterococcal and other phage that will be invaluable for researchers in this field.
Topics: Bacteriophages; Prophages; Biological Evolution; Bacteria; Enterococcus
PubMed: 36787848
DOI: 10.1016/j.virusres.2023.199073 -
Microbiome Jul 2023Porphyromonas gingivalis (hereafter "Pg") is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg...
BACKGROUND
Porphyromonas gingivalis (hereafter "Pg") is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg. Insights into the factors shaping the striking strain-level variation in Pg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. One of the key forces often shaping strain-level diversity in microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg.
RESULTS
Here we systematically addressed the question of whether Pg are infected by phages-and we found that they are. We found that prophages are common in Pg, they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg, and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain-level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures.
CONCLUSION
This work definitively establishes that phages are a major unrecognized force shaping the ecology and intra-species strain-level diversity of the well-studied oral pathogen Pg. The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly. Video Abstract.
Topics: Humans; Bacteriophages; Porphyromonas gingivalis; Prophages; Periodontal Diseases; Base Sequence
PubMed: 37491415
DOI: 10.1186/s40168-023-01607-w -
Viruses Mar 2024CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still...
CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named and ; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.
Topics: Genome, Viral; Bacteriophages; Phylogeny; Viral Proteins; Retroelements; Genetic Variation; Prophages; DNA, Viral; DNA Primase; Genomics; RNA-Directed DNA Polymerase
PubMed: 38675856
DOI: 10.3390/v16040513 -
Frontiers in Cellular and Infection... 2023is a model quorum sensing (QS) pathogen with three interconnected QS circuits that control the production of virulence factors and antibiotic tolerant biofilms. The QS...
is a model quorum sensing (QS) pathogen with three interconnected QS circuits that control the production of virulence factors and antibiotic tolerant biofilms. The QS system of is responsible for the biosynthesis of diverse 2-alkyl-4-quinolones (AQs), of which 2-heptyl-4-hydroxyquinoline (HHQ) and 2-heptyl-3-hydroxy-4()-quinolone (PQS) function as QS signal molecules. Transcriptomic analyses revealed that HHQ and PQS influenced the expression of multiple genes via PqsR-dependent and -independent pathways whereas 2-heptyl-4-hydroxyquinoline -oxide (HQNO) had no effect on transcriptome. HQNO is a cytochrome inhibitor that causes programmed cell death and autolysis. However, mutants unable to synthesize HQNO undergo autolysis when grown as colony biofilms. The mechanism by which such autolysis occurs is not understood. Through the generation and phenotypic characterization of multiple PAO1 mutants producing altered levels of AQs in different combinations, we demonstrate that mutation of results in the accumulation of HHQ which in turn leads to Pf4 prophage activation and consequently autolysis. Notably, the effect of HHQ on Pf4 activation is not mediated its cognate receptor PqsR. These data indicate that the synthesis of HQNO in PAO1 limits HHQ-induced autolysis mediated by Pf4 in colony biofilms. A similar phenomenon is shown to occur in cystic fibrosis (CF) isolates, in which the autolytic phenotype can be abrogated by ectopic expression of .
Topics: Humans; Quinolones; Quorum Sensing; Pseudomonas aeruginosa; Prophages; Biofilms; Autolysis
PubMed: 37305419
DOI: 10.3389/fcimb.2023.1183681 -
Journal of Bioinformatics and... Apr 2021This paper proposes a new algorithm for prophage loci prediction in bacteria. Prophages are defined in Bioinformatics as viral nucleotide sequences that are found...
This paper proposes a new algorithm for prophage loci prediction in bacteria. Prophages are defined in Bioinformatics as viral nucleotide sequences that are found intermixed with host nucleotide sequences in bacteria. The proposed algorithm uses machine learning patterns and processing methodologies in order to provide a highly efficient system for loci prediction, thereby reducing the time-space complexity required unlike others of its class. In the training phase, a pattern database is constructed from raw nucleotide sequences of both bacteria and viruses obtained from a training set. In the prediction phase, the aforementioned database is used along with Particle Swarm Optimization (PSO) to predict the probable loci of prophages in a test set of bacterial nucleotide sequences. Testing this method on raw sequences consisting of both partial and complete nucleotide sequences of various bacteria has yielded good results in predicting the loci of prophages in them. This algorithm and connected processes compare favorably in terms of predictive performance with others of its class such as PhiSpy and ProphET, while outperforming others in terms of raw processing speed, suggesting that a data-centric approach can yield comparable results while using a fraction of the resources.
Topics: Bacteria; Base Sequence; Computational Biology; Genome, Bacterial; Prophages
PubMed: 33641637
DOI: 10.1142/S0219720020500493 -
Briefings in Bioinformatics Jan 2023In the current era, one of the major challenges is to manage the treatment of drug/antibiotic-resistant strains of bacteria. Phage therapy, a century-old technique, may... (Review)
Review
In the current era, one of the major challenges is to manage the treatment of drug/antibiotic-resistant strains of bacteria. Phage therapy, a century-old technique, may serve as an alternative to antibiotics in treating bacterial infections caused by drug-resistant strains of bacteria. In this review, a systematic attempt has been made to summarize phage-based therapy in depth. This review has been divided into the following two sections: general information and computer-aided phage therapy (CAPT). In the case of general information, we cover the history of phage therapy, the mechanism of action, the status of phage-based products (approved and clinical trials) and the challenges. This review emphasizes CAPT, where we have covered primary phage-associated resources, phage prediction methods and pipelines. This review covers a wide range of databases and resources, including viral genomes and proteins, phage receptors, host genomes of phages, phage-host interactions and lytic proteins. In the post-genomic era, identifying the most suitable phage for lysing a drug-resistant strain of bacterium is crucial for developing alternate treatments for drug-resistant bacteria and this remains a challenging problem. Thus, we compile all phage-associated prediction methods that include the prediction of phages for a bacterial strain, the host for a phage and the identification of interacting phage-host pairs. Most of these methods have been developed using machine learning and deep learning techniques. This review also discussed recent advances in the field of CAPT, where we briefly describe computational tools available for predicting phage virions, the life cycle of phages and prophage identification. Finally, we describe phage-based therapy's advantages, challenges and opportunities.
Topics: Humans; Phage Therapy; Bacteriophages; Bacterial Infections; Prophages; Genomics; Bacteria; Anti-Bacterial Agents
PubMed: 36575815
DOI: 10.1093/bib/bbac574