-
MSystems Jun 2022The genus includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. species frequently exchange DNA with one another,...
The genus includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect species. We also identified similar predicted prophages in genomes of different species. Additionally, we examined CRISPR-Cas targeting of each genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel prophages, several of which may infect multiple species. These findings have important implications for understanding horizontal gene transfer between members of this genus. Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
Topics: Humans; Prophages; Neisseria; Host Specificity; Bacteriophages; Genomics; Neisseria gonorrhoeae; Neisseria meningitidis
PubMed: 35418239
DOI: 10.1128/msystems.00083-22 -
Frontiers in Microbiology 2020Group B (GBS) is a gram-positive pathogen mainly affecting humans, cattle, and fishes. Mobile genetic elements play an important role in the evolution of GBS, its...
Group B (GBS) is a gram-positive pathogen mainly affecting humans, cattle, and fishes. Mobile genetic elements play an important role in the evolution of GBS, its adaptation to host species and niches, and its pathogenicity. In particular, lysogenic prophages have been associated with a high virulence of certain strains and with their ability to cause invasive infections in humans. It is therefore important to be able to accurately detect and classify prophages in GBS genomes. Several bioinformatic tools for the identification of prophages in bacterial genomes are available on-line. However, genome searches for most of these programs are affected by the composition of their reference database. Lack of databases specific to GBS results in failure to recognize all prophages in the species. Additionally, performance of these programs is affected by genome fragmentation in the case of draft genomes, leading to underestimation of the number of phages. They also prove impractical when dealing with large genome datasets and they do not offer a quick way of classifying bacteriophages. We developed a GBS-specific method to screen genome assemblies for the presence of prophages and to classify them based on a reproducible typing scheme. This was achieved through an extensive search of a vast number of high-quality GBS sequences ( = 572) originating from different host species and countries in order to build a database of phage integrase types, on which the scheme is based. The proposed typing scheme comprises 12 integration sites and sixteen prophage integrase types, including multiple subtypes per integration site and integrase genes that were not site-specific. Two putative phage-inducible chromosomal islands (PICI) and their insertion sites were also identified during the course of these analyses. Phages were common and diverse in all major clonal complexes associated with human disease and detected in isolates from every animal species and continent included in the study. This database will facilitate further work on the prevalence and role of prophages in GBS evolution, and identifies the roles of PICIs in GBS and of prophage in hypervirulent ST283 as areas for further research.
PubMed: 32983017
DOI: 10.3389/fmicb.2020.01993 -
BMC Genomics Jun 2024Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding...
BACKGROUND
Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage.
RESULTS
We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes.
CONCLUSIONS
In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.
Topics: Prophages; Phylogeny; Treponema; Genomics; Genome, Bacterial; Computational Biology; Genome, Viral; Bacteriophages
PubMed: 38824509
DOI: 10.1186/s12864-024-10461-5 -
Journal of Theoretical Biology Dec 2019Lysogens are bacterial cells that have survived after genomically incorporating the DNA of temperate bacteriophages infecting them. If an infection results in lysogeny,...
Lysogens are bacterial cells that have survived after genomically incorporating the DNA of temperate bacteriophages infecting them. If an infection results in lysogeny, the lysogen continues to grow and divide normally, seemingly unaffected by the integrated viral genome known as a prophage. However, the prophage can still have an impact on the host's phenotype and overall fitness in certain environments. Additionally, the prophage within the lysogen can activate the lytic pathway via spontaneous prophage induction (SPI), killing the lysogen and releasing new progeny phages. These new phages can then lyse or lysogenize other susceptible nonlysogens, thereby impacting the competition between lysogens and nonlysogens. In a scenario with differing growth rates, it is not clear whether SPI would be beneficial or detrimental to the lysogens since it kills the host cell but also attacks nonlysogenic competitors, either lysing or lysogenizing them. Here we study the evolutionary dynamics of a mixture of lysogens and nonlysogens and derive general conditions on SPI rates for lysogens to displace nonlysogens. We show that there exists an optimal SPI rate for bacteriophage λ and explain why it is so low. We also investigate the impact of stochasticity and conclude that even at low cell numbers SPI can still provide an advantage to the lysogens. These results corroborate recent experimental studies showing that lower SPI rates are advantageous for phage-phage competition, and establish theoretical bounds on the SPI rate in terms of ecological and environmental variables associated with lysogens having a competitive advantage over their nonlysogenic counterparts.
Topics: Computer Simulation; Lysogeny; Models, Biological; Probability; Prophages; Stochastic Processes
PubMed: 31525321
DOI: 10.1016/j.jtbi.2019.110005 -
The Journal of General and Applied... Sep 2022Site-specific recombination (SSR) systems are employed in many genetic mobile elements, including temperate phages, for their integration and excision. Recently, they...
Site-specific recombination (SSR) systems are employed in many genetic mobile elements, including temperate phages, for their integration and excision. Recently, they have also been used as tools for applications in fields ranging from basic to synthetic biology. SPβ is a temperate phage of the Siphoviridae family found in the laboratory standard Bacillus subtilis strain 168. SPβ encodes a serine-type recombinase, SprA, and recombination directionality factor (RDF), SprB. SprA catalyzes recombination between the attachment site of the phage, attP, and that of the host, attB, to integrate phage genome into the attB site of the host genome and generate attL and attR at both ends of the prophage genome. SprB works in conjunction with SprA and switches from attB/attP to attL/R recombination, which leads to excision of the prophage. In the present study, we took advantage of this highly efficient recombination system to develop a site-specific integration and excision plasmid vector, named pSSβ. It was constructed using pUC plasmid and the SSR system components, attP, sprA and sprB of SPβ. pSSβ was integrated into the attB site with a significantly high efficiency, and the resulting pSSβ integrated strain also easily eliminated pSSβ itself from the host genome by the induction of SprB expression with xylose. This report presents two applications using pSSβ that are particularly suitable for gene complementation experiments and for a curing system of SPβ prophage, that may serve as a model system for the removal of prophages in other bacteria.
Topics: Bacillus subtilis; Bacteriophages; DNA; Integrases; Prophages; Recombination, Genetic
PubMed: 35387911
DOI: 10.2323/jgam.2021.10.004 -
Viruses May 2021Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in... (Review)
Review
Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in bacteria, and currently are considered a weapon against antibiotic resistance of bacteria. Nevertheless, apart from their antibacterial activity, phages may act as modulators of mammalian immune responses. In this paper, we focus on temperate phages able to execute the lysogenic development, which may shape animal or human immune response by influencing various processes, including phagocytosis of bacterial invaders and immune modulation of mammalian host cells.
Topics: Animals; Bacteriophages; Eukaryotic Cells; Host Microbial Interactions; Humans; Immunity; Immunomodulation; Lysogeny; Prophages
PubMed: 34071422
DOI: 10.3390/v13061013 -
MSystems Feb 2020Methicillin-resistant (MRSP) is a major cause of soft tissue infections in dogs and occasionally infects humans. Hypervirulent multidrug-resistant (MDR) MRSP clones...
Methicillin-resistant (MRSP) is a major cause of soft tissue infections in dogs and occasionally infects humans. Hypervirulent multidrug-resistant (MDR) MRSP clones have emerged globally. The sequence types ST71 and ST68, the major epidemic clones of Europe and North America, respectively, have spread to other regions. The genetic factors underlying the success of these clones have not been investigated thoroughly. Here, we performed a comprehensive genomic analysis of 371 isolates to dissect the differences between major clonal lineages. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, restriction-modification (RM), and CRISPR/Cas systems differs significantly among MRSP clones. The isolates with GyrA+GrlA mutations, conferring fluoroquinolone resistance, carry more of these genes than those without GyrA+GrlA mutations. ST71 and ST68 clones carry lineage-specific prophages with genes that are likely associated with their increased fitness and virulence. We have discovered that a prophage, SpST71A, is inserted within the gene of the late competence operon in the ST71 lineage. A functional is essential for natural genetic competence, which is one of the major modes of horizontal gene transfer (HGT) in bacteria. The RM and CRISPR/Cas systems, both major genetic barriers to HGT, are also lineage specific. Clones harboring CRISPR/Cas or a prophage-disrupted exhibited less genetic diversity and lower rates of recombination than clones lacking these systems. After , this is the second example of prophage-mediated competence disruption reported in any bacteria. These findings are important for understanding the evolution and clonal expansion of MDR MRSP clones. is a bacterium responsible for clinically important infections in dogs and can infect humans. In this study, we performed genomic analysis of 371 isolates to understand the evolution of antibiotic resistance and virulence in this organism. The analysis covered significant reported clones, including ST71 and ST68, the major epidemic clones of Europe and North America, respectively. We show that the prevalence of genes associated with antibiotic resistance, virulence, prophages, and horizontal gene transfer differs among clones. ST71 and ST68 carry prophages with novel virulence and antibiotic resistance genes. Importantly, site-specific integration of a prophage, SpST71A, has led to the disruption of the genetic competence operon in ST71 clone. A functional is essential for the natural uptake of foreign DNA and thus plays an important role in the evolution of bacteria. This study provides insight into the emergence and evolution of antibiotic resistance and virulence in , which may help in efforts to combat this pathogen.
PubMed: 32071159
DOI: 10.1128/mSystems.00684-19 -
Genes Feb 2022Whole-genome sequencing of a soil isolate , strain 7P, and its streptomycin-resistant derivative, 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp,...
Whole-genome sequencing of a soil isolate , strain 7P, and its streptomycin-resistant derivative, 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-19, respectively. In the genomes of both strains, the prophage regions Bp1 and Bp2 were identified. These include 52 ORF of prophage proteins in the Bp1 region and 38 prophages ORF in the Bp2 region. Interestingly, more than 50% of Bp1 prophage proteins are similar to the proteins of the in . The DNA region of Bp2 has 15% similarity to the DNA of the phage. Degradome analysis of the genome of both strains revealed 148 proteases of various classes. These include 60 serine proteases, 48 metalloproteases, 26 cysteine proteases, 4 aspartate proteases, 2 asparagine proteases, 3 threonine proteases, and 2 unclassified proteases. Likewise, three inhibitors of proteolytic enzymes were found. Comparative analysis of variants in the genomes of strains 7P and 3-19 showed the presence of 81 nucleotide variants in the genome 3-19. Among them, the missense mutations in the , , genes and in the upstream region of the gene were revealed. These nucleotide polymorphisms may have affected the streptomycin resistance and overproduction of extracellular hydrolases of the 3-19 strain. Finally, a plasmid DNA was found in strain 7P, which is lost in its derivative, strain 3-19. This plasmid contains five coding DNA sequencing (CDS), two regulatory proteins and three hypothetical proteins.
Topics: Bacillus pumilus; Nucleotides; Peptide Hydrolases; Prophages; Streptomycin
PubMed: 35327964
DOI: 10.3390/genes13030409 -
Cell Genomics Dec 2022The phylum includes important human pathogens like and and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity...
The phylum includes important human pathogens like and and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.
PubMed: 36778052
DOI: 10.1016/j.xgen.2022.100213 -
Microorganisms Apr 2021is the most exploited lactic acid bacterium in the wine industry and drives the malolactic fermentation of wines. Although prophage-like sequences have been identified...
is the most exploited lactic acid bacterium in the wine industry and drives the malolactic fermentation of wines. Although prophage-like sequences have been identified in the species, many are not characterized, and a global view of their integration and distribution amongst strains is currently lacking. In this work, we analyzed the complete genomes of 231 strains for the occurrence of prophages, and analyzed their size and positions of insertion. Our data show the limited variation in the number of prophages in genomes, and that six sites of insertion within the bacterial genome are being used for site-specific recombination. Prophage diversity patterns varied significantly for different host lineages, and environmental niches. Overall, the findings highlight the pervasive presence of prophages in the species, their role as a major source of within-species bacterial diversity and drivers of horizontal gene transfer. Our data also have implications for enhanced understanding of the prophage recombination events which occurred during evolution of , as well as the potential of prophages in influencing the fitness of these bacteria in their distinct niches.
PubMed: 33923461
DOI: 10.3390/microorganisms9040856