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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 -
Communications Biology May 2024Phage replication can be studied using various approaches, including measuring the optical density (OD) of a bacterial culture in a liquid medium in the presence of...
Phage replication can be studied using various approaches, including measuring the optical density (OD) of a bacterial culture in a liquid medium in the presence of phages. A few quantitative methods are available to measure and compare the efficiency of phages by using a single index based on the analysis of OD curves. However, these methods are not always applicable to non-canonical OD curves. Using the concept of center of area (centroid), we developed a metric called Centroid Index (CI), sensitive to the trend of the growth curves (OD distribution) including bacterial regrowth, which is not considered by the methods already available. We also provide a user-friendly software to facilitate the calculation of CI. This method offers an alternative and more precise way to determine phage efficiency by considering the OD variations over time, which may help in the selection of phages for biocontrol applications.
Topics: Bacteriophages; Software; Bacteria; Escherichia coli; Virus Replication
PubMed: 38822127
DOI: 10.1038/s42003-024-06379-z -
The Bone & Joint Journal Jun 2024
Topics: Humans; Phage Therapy; Bacteriophages
PubMed: 38821504
DOI: 10.1302/0301-620X.106B6.BJJ-2023-0878.R2 -
International Journal of Biological... May 2024Bacteria and virus infections have posed a great threat to public health and personnel safety. For realizing rapid sterilization of the bacteria and virus, electrical...
Bacteria and virus infections have posed a great threat to public health and personnel safety. For realizing rapid sterilization of the bacteria and virus, electrical stimulation sterilization was adopted to endow cellulose fibers with instantaneous antibacterial and antiviral properties. In the proposed strategy, the fiber is fluffed by mechanical refining, and then by means of the hydrogen bond between hydroxyl and aniline, the polyaniline (PANI) directionally grows vertically along the fine fibers via in-situ oxidative polymerization. Benefiting from the conductive polyaniline nanorod arrays on the fiber stem, the paper made from PANI modified refined fibers (PANI/BCF/P) exhibited excellent antibacterial and antiviral activity, the inhibition rates against S. aureus, E. coli, and bacteriophage MS2 can up to 100 %, 100 %, and 99.89 %, respectively when a weak voltage (2.5 V) was applied within 20 min. This study provides a feasible path for plant fiber to achieve efficient antibacterial and antiviral activity with electrical stimulation, which is of great significance for the preparation of electroactive antibacterial and antiviral green health products.
PubMed: 38821299
DOI: 10.1016/j.ijbiomac.2024.132772 -
Life Sciences May 2024Emergence of antimicrobial-resistant bacteria (AMR) is one of the health major problems worldwide. The scientists are looking for a novel method to treat infectious... (Review)
Review
Emergence of antimicrobial-resistant bacteria (AMR) is one of the health major problems worldwide. The scientists are looking for a novel method to treat infectious diseases. Phage therapy is considered a suitable approach for treating infectious diseases. However, there are different challenges in this way. Some biological aspects can probably influence on therapeutic results and further investigations are necessary to reach a successful phage therapy. Bacteriophage activity can influence by bacterial defense system. Bacterial extracellular vesicles (BEVs) are one of the bacterial defense mechanisms which can modify the results of bacteriophage activity. BEVs have the significant roles in the gene transferring, invasion, escape, and spreading of bacteriophages. In this review, the defense mechanisms of bacteria against bacteriophages, especially BEVs secretion, the hidden linkage of BEVs and bacteriophages, and its possible consequences on the bacteriophage activity as well phage therapy will be discussed.
PubMed: 38821215
DOI: 10.1016/j.lfs.2024.122749 -
Water Research May 2024The widespread use of graphene family nanomaterials (GFNs) in mass production has resulted in their release into the atmosphere, soil and water environment through...
The widespread use of graphene family nanomaterials (GFNs) in mass production has resulted in their release into the atmosphere, soil and water environment through various processes. Among these, the water environment is particularly affected by GFN pollution. Our previous study has demonstrated the impact of graphene oxide (GO) on bacteria-phage interactions in natural systems. However, the effects of amino-functionalized GO with a positive charge on bacteria-phage interactions in aquatic environments remain unclear. In the present study, we found that amino-functionalized graphene oxide (AGO) (0.05 mg/mL) inhibited the growth of Pseudomonas aeruginosa Y12. Furthermore, treating P. aeruginosa Y12 and phage with AGO (0.05 mg/mL) led to a reduced ratio of phage to bacteria, indicating that AGO can inhibit phage infection of bacteria. Additionally, the acidic environment exacerbated this effect by promoting electrostatic adsorption between the positively charged AGO and the negatively charged phage. Finally, a field water body intervention experiment showed that the richness and diversity of bacterial communities in six water samples changed due to AGO exposure, as revealed by Illumina analysis based on the bacterial 16S rRNA gene. These findings offer valuable insights into the environmental impacts of GFNs.
PubMed: 38820731
DOI: 10.1016/j.watres.2024.121840 -
Veterinary Microbiology May 2024Non-aureus staphylococci (NAS) are an essential group of bacteria causing antimicrobial resistant intramammary infections in livestock, particularly dairy cows....
Non-aureus staphylococci (NAS) are an essential group of bacteria causing antimicrobial resistant intramammary infections in livestock, particularly dairy cows. Therefore, bacteriophages emerge as a potent bactericidal agent for NAS mastitis. This study aimed to obtain NAS-specific bacteriophages using bacterial strains isolated from cows with mastitis, subsequently evaluating their morphological, genomic, and lytic characteristics. Four distinct NAS bacteriophages were recovered from sewage or the environment of Chinese dairy farms; PT1-1, PT94, and PT1-9 were isolated using Staphylococcus chromogenes and PT1-4 using Staphylococcus gallinarum. Both PT1-1 (24/54, 44 %) and PT94 (28/54, 52 %) had broader lysis than PT1-4 (3/54, 6 %) and PT1-9 (10/54, 19 %), but PT1-4 and PT1-9 achieved cross-species lysis. All bacteriophages had a short latency period and good environmental tolerance, including surviving at pH=4-10 and at 30-60℃. Except for PT1-9, all bacteriophages had excellent bactericidal efficacy within 5 h of co-culture with host bacteria in vitro at various multiplicity of infection (MOIs). Based on whole genome sequencing, average nucleotide identity (ANI) analysis of PT1-1 and PT94 can be classified as the same species, consistent with whole-genome synteny analysis. Although motifs shared by the 4 bacteriophages differed little from those of other bacteriophages, a phylogenetic tree based on functional proteins indicated their novelty. Moreover, based on whole genome comparisons, we inferred that cross-species lysis of bacteriophage may be related to the presence of "phage tail fiber." In conclusion 4 novel NAS bacteriophages were isolated; they had good biological properties and unique genomes, with potential for NAS mastitis therapy.
PubMed: 38820726
DOI: 10.1016/j.vetmic.2024.110133 -
Science Advances May 2024Despite great progress in the field, chronic () infections remain a major cause of mortality in patients with cystic fibrosis (pwCF), necessitating treatment with...
Despite great progress in the field, chronic () infections remain a major cause of mortality in patients with cystic fibrosis (pwCF), necessitating treatment with antibiotics. Pf is a filamentous bacteriophage produced by and acts as a structural element in biofilms. Pf presence has been associated with antibiotic resistance and poor outcomes in pwCF, although the underlying mechanisms are unclear. We have investigated how Pf and sputum biopolymers impede antibiotic diffusion using pwCF sputum and fluorescent recovery after photobleaching. We demonstrate that tobramycin interacts with Pf and sputum polymers through electrostatic interactions. We also developed a set of mathematical models to analyze the complex observations. Our analysis suggests that Pf in sputum reduces the diffusion of charged antibiotics due to a greater binding constant associated with organized liquid crystalline structures formed between Pf and sputum polymers. This study provides insights into antibiotic tolerance mechanisms in chronic infections and may offer potential strategies for novel therapeutic approaches.
Topics: Sputum; Static Electricity; Anti-Bacterial Agents; Pseudomonas aeruginosa; Humans; Cystic Fibrosis; Pseudomonas Infections; Tobramycin; Diffusion; Biofilms; Bacteriophages
PubMed: 38820163
DOI: 10.1126/sciadv.adl5576 -
Methods in Molecular Biology (Clifton,... 2024Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered... (Comparative Study)
Comparative Study
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
Topics: Genome, Viral; Bacteriophages; Genomics; Phylogeny; Computational Biology; Metagenomics
PubMed: 38819567
DOI: 10.1007/978-1-0716-3838-5_14 -
Communications Biology May 2024The Anopheles gambiae 1000 Genomes (Ag1000G) Consortium previously utilized deep sequencing methods to catalogue genetic diversity across African An. gambiae...
The Anopheles gambiae 1000 Genomes (Ag1000G) Consortium previously utilized deep sequencing methods to catalogue genetic diversity across African An. gambiae populations. We analyzed the complete datasets of 1142 individually sequenced mosquitoes through Microsoft Premonition's Bayesian mixture model based (BMM) metagenomics pipeline. All specimens were confirmed as either An. gambiae sensu stricto (s.s.) or An. coluzzii with a high degree of confidence ( > 98% identity to reference). Homo sapiens DNA was identified in all specimens indicating contamination may have occurred either at the time of specimen collection, preparation and/or sequencing. We found evidence of vertebrate hosts in 162 specimens. 59 specimens contained validated Plasmodium falciparum reads. Human hepatitis B and primate erythroparvovirus-1 viral sequences were identified in fifteen and three mosquito specimens, respectively. 478 of the 1,142 specimens were found to contain bacterial reads and bacteriophage-related contigs were detected in 27 specimens. This analysis demonstrates the capacity of metagenomic approaches to elucidate important vector-host-pathogen interactions of epidemiological significance.
Topics: Animals; Anopheles; Metagenomics; Genome, Insect; Mosquito Vectors; Humans; Genetic Variation; Plasmodium falciparum; Metagenome
PubMed: 38816486
DOI: 10.1038/s42003-024-06337-9