VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes DOI Creative Commons

Benjamin Hepp,

Florence Lorieux,

Augustin Degaugue

et al.

Bioinformatics, Journal Year: 2023, Volume and Issue: 39(8)

Published: Aug. 1, 2023

Abstract Motivation Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing evolutionary history, monitoring environment, creating innovative biotechnologies. However, accessing necessary data can be challenging due to a lack dedicated comparative genomic tools viral phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have computational proficiency required manipulate large amounts data. Results We developed VAPEX (Virus And Phage EXplorer), web server supported by database features user-friendly interface. This tool enables users easily perform various queries on all natural that been fully sequenced listed NCBI compendium. therefore excels producing visual depictions resolved synteny maps, one its key strengths. has ability exhibit vast array orthologous gene classes simultaneously use symbolic representation. Additionally, analyze user-submitted genomes, including those yet annotated. Availability implementation accessed from current browsers such as Chrome, Firefox, Edge, Safari, Opera. freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/.

Language: Английский

Adaptive strategies and ecological roles of phages in habitats under physicochemical stress DOI
Dan Huang, Rong Xia, Cheng‐Yi Chen

et al.

Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(9), P. 902 - 916

Published: March 2, 2024

Language: Английский

Citations

24
Bacteriophage DNA induces an interrupted immune response during phage therapy in a chicken model DOI Creative Commons
Magdalena Podlacha, Lidia Gaffke, Łukasz Grabowski

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 13, 2024

One of the hopes for overcoming antibiotic resistance crisis is use bacteriophages to combat bacterial infections, so-called phage therapy. This therapeutic approach generally believed be safe humans and animals as phages should infect only prokaryotic cells. Nevertheless, recent studies suggested that might recognized by eukaryotic cells, inducing specific cellular responses. Here we show in chickens infected with Salmonella enterica treated a cocktail, are initially animal cells viruses, however, cGAS-STING pathway (one two major pathways innate antiviral response) blocked at stage IRF3 transcription factor phosphorylation. inhibition due inability RNA polymerase III recognize DNA produce dsRNA molecules which necessary stimulate large protein complex indispensable phosphorylation, indicating mechanism response impairment.

Language: Английский

Citations

11
An overview of signal amplification strategies and construction methods on phage-based biosensors DOI
Jiahao Wang, Yu‐Qing Zheng,

Hongkai Huang

et al.

Food Research International, Journal Year: 2024, Volume and Issue: 191, P. 114727 - 114727

Published: July 3, 2024

Language: Английский

Citations

4
Comparison of disinfection of Phi6 virus bacteriophage on fomites by various methods and a prototype for IR application DOI
Baki Karaböce, Rauf Hamid, Evren Saban

et al.

Thermal Science and Engineering Progress, Journal Year: 2025, Volume and Issue: unknown, P. 103477 - 103477

Published: March 1, 2025

Language: Английский

Citations

0
Iron-based microbial interactions: the role of iron metabolism in the cheese ecosystem DOI Creative Commons
Rina Mekuli,

Mahtab Shoukat,

Éric Dugat‐Bony

et al.

Journal of Bacteriology, Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

ABSTRACT Iron is involved in various microbial metabolisms and interactions an essential micronutrient for most microorganisms. This review focuses on the cheese ecosystem, which iron sparse (median concentration of 2.9 mg/kg based a literature survey) limited bioavailability due to presence metal-binding agents matrix. Cheese microorganisms overcome this low by producing and/or importing ferric iron-specific chelators called siderophores. We introduce these siderophores their specific transporters, play key role ecological metabolism. discuss impact all major taxa (fungi, bacteria, viruses) functional groups (starters, ripening microorganisms, pathogens) present interacting cheese, from community individual levels. describe ways cheese-ripening use effects limitation metabolic pathways, including tricarboxylic acid (TCA) cycle amino-acid biosynthesis. The ecosystem relevant situ model improving our understanding biochemistry its putative microbe–microbe interactions. Yet, highlights critical gaps iron’s fundamental biochemical perspectives applied microbiology, with broader implications quality, safety, organoleptic properties cheese.

Language: Английский

Citations

0
ВЛИЯНИЕ ПРИМЕНЕНИЯ ИНГАЛЯЦИОННОЙ БАКТЕРИОФАГ-ТЕРАПИИ НА ИММУННУЮ СИСТЕМУ У ДЕТЕЙ ПРИ ЛЕЧЕНИИ ОСТРОГО ТОНЗИЛЛИТА DOI
Gulmira Ramzitdinovna Nasirova, Sh. T. Тurdieva

Международный журнал научной педиатрии, Journal Year: 2025, Volume and Issue: 4(2), P. 900 - 906

Published: April 18, 2025

Актуальность. Своевременное диагностирование и лечение острого тонзиллит (ОТ) у детей остаётся одним из актуальных направлений амбулаторно-поликлинической помощи. Вместе с тем, в последние годы актуальным направлением педиатрии становится внедрение методов лечения применением бактериофагов. Цель исследования. Анализ влияние ингаляционной бактериофаг терапии (ИБТ) на местную иммунную систему ОТ. Материалы методы Исследование проводилось основе рандомизированного контролируемого метода. Были обследованы 212 возрасте от 4 до 15 лет ОТ, 110 практически здоровых (контрольная группа). В первую группу вошли 107 больных получавшие стандартное общее лечение. Вторую составили 105 детей, получавших совместно стандартным лечением, ингаляционную терапию (ИБТ). Иммунологическое исследование включали определение sIgA TNF-α. ИБТ проводилась использованием пиобактериофага PLC (РФ). Результаты. У ОТ наблюдали первые сутки заболевания снижение уровня (у младшего возраста - 40,9%, подростков 41,9%). При к шестому суткам обеих возрастных группах отмечали повышение 96,9%, пациентов не данный показатель составил среднем 80,7%. Аналогичные изменения наблюдались при исследовании Уровень TNF-α, который был высоким острой фазе заболевания, постепенно снижался процессе лечения. На третье ИБТ, TNF-α снизился 11,0%, шестой день 17%, первоначального уровня. Заключение. Применение комплексном лечении острым тонзиллитом фоне улучшения показателей местного иммунитета 16,3% способствовало положительному сдвигу клинических признаков 1,39 раза (p≤0,05).

Language: Русский

Citations

0
Resistance differences of representative model microorganisms in different disinfection processes: ZIF-67, UVC and ozone DOI Creative Commons

Xiang Zheng,

Yang Qing-wen,

Jincheng Xia

et al.

Water Cycle, Journal Year: 2024, Volume and Issue: 5, P. 259 - 265

Published: Jan. 1, 2024

Due to their inherent nature, each type of microorganism exhibits unique resistance various disinfection processes. Disinfection with nanomaterials represents a promising technology that has garnered significant interest. Among them, ZIF material antibacterial and antiviral activities, ZIF-67 is new nanomaterial can effectively kill bacteria viruses, the potential for large-scale use. Therefore, in this paper, we investigate differences between techniques (employing ZIF-67) traditional inactivation (e.g., ultraviolet-C ozone). Phage MS2 PhiX174 respective host E. coli were chosen as representative microorganisms. Our findings indicate phages exhibit greater than bacteria, but different show specific effects on three Considering differences, choosing appropriate based characteristics disinfected substances practical selection essential.

Language: Английский

Citations

2
The comparison of the antioxidant, antibacterial and antiviral potential of Polish fir honeydew and Manuka honeys DOI Creative Commons
Dorota Grabek-Lejko, Michał Miłek, Małgorzata Dżugan

et al.

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

Published: Dec. 28, 2024

Abstract The aim of the present study was to compare antioxidant, antibacterial and antiviral activities Podkarpackie coniferous honeydew honey Manuka honey. quality tested samples (honeydew-12 Manuka-4) regarding standard evaluated as well additional indicators (methylglyoxal, total phenolics HPTLC phenolic profile, antioxidant potential, glucose oxidase activity, hydrogen peroxide) were compared. Antibacterial potential analyzed against Gram-positive ( S. aureus B. cereus ) Gram-negative E. coli enterica bacteria. Antiviral activity different RNA (phi6, MS2) DNA (T7, phiX174) bacteriophages considered “viral surrogates” determined. Based on determined physicochemical parameters good honeys confirmed, excluding two samples. content polyphenolic compounds in ranged from 583.87 1102.42 mg gallic acid/kg strongly correlated with properties. Moreover, for strongest these comparable However, obtained profiles completely than which exhibited bands (Rf = 0.74 0.52). Honeydew characterized by a strong properties most all MICs (minimal inhibitory concentrations) 15–35% 8–15% honeys, respectively. demonstrated mainly even higher honey, especially MS2 virus. results suggest that controlled may be natural substance used combat viral bacterial diseases.

Language: Английский

Citations

1
Inactivating Host Bacteria for Characterization and Use of Phages DOI Creative Commons
James P. Chambers,

Elena T. Wright,

Barbara Hunter

et al.

Biophysica, Journal Year: 2023, Volume and Issue: 3(4), P. 558 - 568

Published: Sept. 27, 2023

Phage characterization for research and therapy can involve newly isolated phages propagated in pathogenic bacteria. If so, requires safety-managing the In current study, we adapt a common inexpensive reagent, PrimeStore (Longhorn Vaccines Diagnostics, San Antonio, TX, USA), to safety-manage bacteria 20 min by selectively inactivating No bacterial survivors are observed among >109 per ml representative of both Gram-negative (Escherichia coli) Gram-positive (Bacillus thuringiensis). This procedure causes no detected inactivation podophage T3, myophage T4 siphophage 0105phi7-2. Margins safety concentration exist phage non-inactivation. Thus, general applicability is expected. Subsequent dialysis used block long-term effects on phages. Nonetheless, comparable tests should be performed each strain/phage. Electron microscopy thin sections reveals inactivation-altered cytoplasm non-disintegrated envelope (ghosts). Ghosting E. coli includes re-arrangement release endotoxin. The activity released endotoxin >99% reduced after subsequent dialysis, which also removes components. B. thuringiensis apparent phase separation within cytoplasm. primary application envisaged biophysical other screening infectious disease.

Language: Английский

Citations

1
Thermal and Chemical Inactivation of Bacillus Phage BM-P1 DOI Creative Commons
Xia Chen, Can Zhang, Jing Guo

et al.

Journal of Food Protection, Journal Year: 2024, Volume and Issue: 87(3), P. 100223 - 100223

Published: Jan. 18, 2024

Bacillus spp. are often used as probiotics; however, they can be infected by phages, leading to significant economic losses. Biocidal and thermal treatments considered rapid effective methods for controlling microbial contamination. To prevent viral contamination in industrial dairy production, the impact of temperature biocides on viability methylotrophic phage BM-P1 was assessed. The results demonstrated that reconstituted skim milk (RSM) a medium showed most protective effect BM-P1. Treatment at 90°C 5 min or 72°C 10 inactivated it nondetectable levels from initial titer 7.19 ± 0.11 log, regardless culture medium. Sodium hypochlorite exhibited best inactivating effect, which could reduce below detection level 4 50 ppm. Additionally, treatment with 75% ethanol 20 50% isopropanol 30 achieve inactivation levels. peracetic acid limited; even when treated highest concentration (0.45%) 60 min, only 2.47 0.17 log reduction observed. This study may provide some theoretical basis data support establishing measures against phages.

Language: Английский

Citations

0