Using Multiplex Virtual PCR For Genetic Barcoding Of Tequatrovirus Bacteriophages DOI Open Access
O.Yu. Kiryanova, С. С. Киселев, V.V. Panyukov

et al.

Mathematical Biology and Bioinformatics, Journal Year: 2024, Volume and Issue: 19(2), P. 369 - 392

Published: Nov. 14, 2024

In this paper, we investigate the possibility of using multiplex virtual PCR method to develop approaches barcoding genomes T4-type bacteriophages. A comparison and phylogenomic analysis based on alignment-free approach was performed. dataset Tequatrovirus previously selected for pangenomic used study. The were preliminarily checked their adequate annotation and, accordingly, sequencing accuracy. study carried out 67 genomes, barcodes generated, similarity parameters determined. Based obtained data, a phylogenetic tree constructed neighbor joining method. For same set Straboviridae bacteriophage pairwise distance matriх between oligonucleotide 10-mer sets. Comparison these two trees showed differences in branching control distantly related from genera Mosigvirus Dhakavirus, branch bacteriophages genus Tequatrovirus. authors work suggested that may reflect features method, which is more applicable assessing closely than within with an identity degree less 75 %. It can be concluded allows one distinguish taxonomic groups large bacteriophages, include at level. Thus, such accurately compare viruses length about 170 kb. From practical point view, quite including compiled its basis passport use practice phage therapy.

Language: Английский

Pathogenic and Non-Pathogenic Microbes in the Wound Microbiome—How to Flip the Switch DOI Creative Commons

Sophie Charlotte Liegenfeld,

Svenja Stenzel,

Julian‐Dario Rembe

et al.

Microbiology Research, Journal Year: 2025, Volume and Issue: 16(2), P. 39 - 39

Published: Feb. 6, 2025

The wound microbiome refers to the specific community of microbes, including bacteria, fungi, and other microorganisms, that are present in around a wound. This plays crucial role healing, as it includes both healing-promoting pathogenic microbes. balance between these microbes significantly influences healing process; balanced microbial colonization can support prevent infections, while an overgrowth lead delayed processes complications. composition vary depending on type wound, cause, genetic predisposition, (social) environment. In this scope review, complex interactions will be highlighted importance non-pathogenic for discussed. addition, possible therapeutic approaches restore healthy infections addressed. A deeper understanding dynamics could open up new perspectives treatment wounds development strategies combat infections.

Language: Английский

Citations

1
Anaerobic bacteria in chronic wounds: Roles in disease, infection and treatment failure DOI

Alison Coluccio,

Francia Lopez Palomera,

Melanie A. Spero

et al.

Wound Repair and Regeneration, Journal Year: 2024, Volume and Issue: 32(6), P. 840 - 857

Published: Aug. 12, 2024

Infection is among the most common factors that impede wound healing, yet standard treatments routinely fail to resolve chronic infections. The environment largely hypoxic/anoxic, and wounds are predominantly colonised by facultative obligate anaerobic bacteria. Oxygen (O

Language: Английский

Citations

0
The healing process of diabetic ulcers correlates with changes in the cutaneous microbiota DOI Creative Commons
Emanuele Bruni, Giovanni Luca Scaglione,

Denise Tampone

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 12, 2024

Skin microbiota plays an essential role in the development and function of cutaneous immune system, maintenance skin barrier through release antimicrobial peptides, metabolism some natural products. With aim characterizing changes specifically associated with wound healing diabetic condition, we performed a 16 S rRNA gene Next Generation Sequencing swabs taken within ulcer bed ten patients before (t0) after 20 days therapy (t20) fluorescein-based galenic treatment. Considering twenty most representative genera, found at t20 increase Corynebacterium, Peptostreptococcus, Streptococcus, decrease Enterococcus, Finegoldia, Peptoniphilus genera. However, differences were not significant due to high variability among samples small patient cohort. S. aureus was abundant species t0 reduced by four patients. Comparing microbiome perilesional tissue same t0, no major observed. Taken together, our data indicate that absence antibiotic-based process ulcers is accompanied composition.

Language: Английский

Citations

0
Using Multiplex Virtual PCR For Genetic Barcoding Of Tequatrovirus Bacteriophages DOI Open Access
O.Yu. Kiryanova, С. С. Киселев, V.V. Panyukov

et al.

Mathematical Biology and Bioinformatics, Journal Year: 2024, Volume and Issue: 19(2), P. 369 - 392

Published: Nov. 14, 2024

In this paper, we investigate the possibility of using multiplex virtual PCR method to develop approaches barcoding genomes T4-type bacteriophages. A comparison and phylogenomic analysis based on alignment-free approach was performed. dataset Tequatrovirus previously selected for pangenomic used study. The were preliminarily checked their adequate annotation and, accordingly, sequencing accuracy. study carried out 67 genomes, barcodes generated, similarity parameters determined. Based obtained data, a phylogenetic tree constructed neighbor joining method. For same set Straboviridae bacteriophage pairwise distance matriх between oligonucleotide 10-mer sets. Comparison these two trees showed differences in branching control distantly related from genera Mosigvirus Dhakavirus, branch bacteriophages genus Tequatrovirus. authors work suggested that may reflect features method, which is more applicable assessing closely than within with an identity degree less 75 %. It can be concluded allows one distinguish taxonomic groups large bacteriophages, include at level. Thus, such accurately compare viruses length about 170 kb. From practical point view, quite including compiled its basis passport use practice phage therapy.

Language: Английский

Citations

0