Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics

Parmar, Krupa; Gaikwad, Saurabh L.; Dhakephalkar, Prashant K.; Kothari, Ramesh; Singh, Ravindra

doi:10.3389/fmicb.2017.00559

Cited by 40 publications

(31 citation statements)

References 163 publications

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“…Advances in sequencing technologies together with improvement in platforms for genome annotation and model construction [42,[76][77][78][79] are expected to lead to in silico representation of complex microbial communities [70]. In parallel to the advent of sequencing technologies, metabolomics technologies are now rapidly emerging and in the very near future a growing number of ecosystems will be subject to an extensive profiling [78,80,81]. Simulations accuracy is expected to improve when based on a detailed description of the metabolic environmental conditions.…”

Section: Discussionmentioning

confidence: 99%

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

et al. 2018

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Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.These authors contributed equally:

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Section: Discussionmentioning

confidence: 99%

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

et al. 2018

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“…There are other similar bioinformatics tools designed to check the quality of phage DNA (identifying potential contamination by host genome), analyze the sequencing results further to determine the lifestyle, and analyze the viral ORFs, for example, CyVerse in the PCPipe available through iVirus project. Besides PHAST, there are ACCLAIM, Prophinder and PhiSpy, which are also available as tools for prophage detection [87].…”

Section: Determining Safety Of Phages In the Era Of "Omics"mentioning

confidence: 99%

“…Single cells can be isolated by various technologies, such as FACS or confocal laser scanning microscopy. Alongside this, bioinformatics tools also evolve to accommodate these technologies with subsequent analysis, for example, PIPS, a method of classification of prophages-pathogenicity islands [87]. Thus, guidelines for characterizing phages to qualify them for therapeutic use will have to rely on complex methodologies and the validation of these guidelines will most likely be a complex, multi-step process.…”

Section: Determining Safety Of Phages In the Era Of "Omics"mentioning

confidence: 99%

Application of Campylobacter jejuni Phages: Challenges and Perspectives

Ushanov

Lasareishvili

Janashia

et al. 2020

Animals

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Bacteriophages (phages) are the most abundant and diverse biological entities in the biosphere. Due to the rise of multi-drug resistant bacterial strains during the past decade, phages are currently experiencing a renewed interest. Bacteriophages and their derivatives are being actively researched for their potential in the medical and biotechnology fields. Phage applications targeting pathogenic food-borne bacteria are currently being utilized for decontamination and therapy of live farm animals and as a biocontrol measure at the post-harvest level. For this indication, the United States Food and Drug Administration (FDA) has approved several phage products targeting Listeria sp., Salmonella sp. and Escherichia coli. Phage-based applications against Campylobacter jejuni could potentially be used in ways similar to those against Salmonella sp. and Listeria sp.; however, only very few Campylobacter phage products have been approved anywhere to date. The research on Campylobacter phages conducted thus far indicates that highly diverse subpopulations of C. jejuni as well as phage isolation and enrichment procedures influence the specificity and efficacy of Campylobacter phages. This review paper emphasizes conclusions from previous findings instrumental in facilitating isolation of Campylobacter phages and improving specificity and efficacy of the isolates.

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“…We therefore applied the principle of BCP to investigate which metabolic pathway of VP AHPND is targeted during the phage Seahorse infection by fluorescence microscopy. Since phages are believed to hijack host DNA replication, RNA transcription, and protein translation pathways during the lytic cycle 41 , we focused on antibiotics that also inhibit these major pathways. Ciprofloxacin, rifampicin, and tetracycline were used as inhibitors to replication, transcription, and translation respectively.…”

Section: Phage Seahorse Infection Triggers the Condensation Of Host Nmentioning

confidence: 99%

A novel vibriophage exhibits inhibitory activity against host protein synthesis machinery

Thammatinna

Egan

Htoo

et al. 2020

Sci Rep

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Since the emergence of deadly pathogens and multidrug-resistant bacteria at an alarmingly increased rate, bacteriophages have been developed as a controlling bioagent to prevent the spread of pathogenic bacteria. One of these pathogens, disease-causing Vibrio parahaemolyticus (Vp AHPND ) which induces acute hepatopancreatic necrosis, is considered one of the deadliest shrimp pathogens, and has recently become resistant to various classes of antibiotics. Here, we discovered a novel vibriophage that specifically targets the vibrio host, VP AHPND . The vibriophage, designated Seahorse, was classified in the family Siphoviridae because of its icosahedral capsid surrounded by head fibers and a non-contractile long tail. Phage Seahorse was able to infect the host in a broad range of pH and temperatures, and it had a relatively short latent period (nearly 30 minutes) in which it produced progeny at 72 particles per cell at the end of its lytic cycle. Upon phage infection, the host nucleoid condensed and became toroidal, similar to the bacterial DNA morphology seen during tetracycline treatment, suggesting that phage Seahorse hijacked host biosynthesis pathways through protein translation. As phage Seahorse genome encodes 48 open reading frames with many hypothetical proteins, this genome could be a potential untapped resource for the discovery of phage-derived therapeutic proteins.Vibrio is a genus of motile Gram-negative bacteria that possesses a curved-rod cell shape with a single flagellum. Vibrios are abundant and diverse bacteria that are typically found in marine habitats. The genus Vibrio consists of 14 recognized clades and at least 86 different species 1 . While some of them are not pathogenic, many can cause serious health effects in both human and aquatic life. Due to the continuously rising ocean temperature, the composition of vibrio in the ocean microbiome has been reported to be higher than usual 2-4 . This vibrio-rich environment might increase the incident of a vibrio outbreak in the near future posing risks to global health 2 .Vibrio parahaemolyticus, which is one of the disease-causing Vibrio species, is pathogenic to both humans and marine animals 5 . Consumption of raw seafoods contaminated with the bacteria can cause acute gastroenteritis 5,6 . This opportunistic bacterium is also able to infect through an open wound which can lead to sepsis and, in rare cases, subsequent death in immunocompromised patients 7,8 . Moreover, V. parahaemolyticus that has acquired a plasmid encoding the deadly binary toxins PirA vp /PirB vp is even more virulent 9 . The V. parahaemolyticus strain harboring the plasmid has been found to cause a newly emerging disease in shrimp, known as acute hepatopancreatic necrosis disease (AHPND) 9 . Moreover, the AHPND-causing plasmid is also found to be transferable among other vibrios, increasing the chance of the disease spreading regionally and globally 10 . Unsurprisingly, the spread of AHPND has been reported in many countries, including China, Vietnam, Malaysia, Thailand, Me...

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Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics

Cited by 40 publications

References 163 publications

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

Application of Campylobacter jejuni Phages: Challenges and Perspectives

A novel vibriophage exhibits inhibitory activity against host protein synthesis machinery

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