Bacteriophage Discovery and Genomics

Hatfull, Graham F.

doi:10.1007/978-3-319-40598-8_6-1

Cited by 3 publications

(3 citation statements)

References 40 publications

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“…This makes mycobacteria medically relevant (e.g., Mycobacterium tuberculosis) as it consists of hosts for phage isolation that can be used with few biocontainment precautions (especially Mycobacterium smegmatis). The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) [107,108] and the Phage Hunters Integrating Research and Education (PHIRE) programs [109,110] successfully integrated phage isolation into mentoring young scientists and providing large collections of phages that infect Actinobacteria (the bacterial phylum that includes genus Mycobacterium). As a consequence, M. smegmatis-infecting phages represent the largest collection in the world of well-characterized virus isolates infecting a single microbial host.…”

Section: Well-developed Soil-virus Systemsmentioning

confidence: 99%

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

et al. 2020

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The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.

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Section: Well-developed Soil-virus Systemsmentioning

confidence: 99%

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

et al. 2020

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“…Dedrick et al [52] treated a 15-year-old cystic-fibrosis, lung-transplant recipient for a disseminated M. abscessus infection using a three-phage cocktail (BPs, Muddy, and ZoeJ). Phages were derived from the SEA-PHAGES program [118], with BPs and ZoeJ modified using combinations of recombinant genetics and selection. Phages were supplied predominantly intravenously, twice daily for 32 weeks with a dose of 3 × 10 9 PFU.…”

Section: Dedrick Et Al 2019 M Abscessus Disseminated Infectionmentioning

confidence: 99%

Phage Therapy in the 21st Century: Is There Modern, Clinical Evidence of Phage-Mediated Efficacy?

2021

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Many bacteriophages are obligate killers of bacteria. That this property could be medically useful was first recognized over one hundred years ago, with 2021 being the 100-year anniversary of the first clinical phage therapy publication. Here we consider modern use of phages in clinical settings. Our aim is to answer one question: do phages serve as effective anti-bacterial infection agents when used clinically? An important emphasis of our analyses is on whether phage therapy-associated anti-bacterial infection efficacy can be reasonably distinguished from that associated with often coadministered antibiotics. We find that about half of 70 human phage treatment reports—published in English thus far in the 2000s—are suggestive of phage-mediated anti-bacterial infection efficacy. Two of these are randomized, double-blinded, infection-treatment studies while 14 of those studies, in our opinion, provide superior evidence of a phage role in observed treatment successes. Roughly three-quarters of these potentially phage-mediated outcomes are based on microbiological as well as clinical results, with the rest based on clinical success. Since many of these phage treatments are of infections for which antibiotic therapy had not been successful, their collective effectiveness is suggestive of a valid utility in employing phages to treat otherwise difficult-to-cure bacterial infections.

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“…Genome mosaicism of viruses has been reported between bacterial phages and archaeal head-tail viruses. To date, there have been no reports on viruses infecting crenarchaeota (9,44).…”

Section: Agv1 Genomic Features Of and Host Genomic Interactionsmentioning

confidence: 99%

Isolation and characterization of novel temperate virusAeropyrumglobular virus 1 infecting hyperthermophilic archaeonAeropyrum

Yumiya¹,

Fukuyama

Sako

et al. 2021

Preprint

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We isolate a novel archaeal temperate virus named Aeropyrum globular virus 1 (AGV1) from the host Aeropyrum culture. Reproduction of AGV1 was induced by adding 20 mM tris acetate buffer to exponentially growing host cells. Negatively stained virions showed spherical morphology (60 2 nm in diameter) similar to Globuloviridae viruses. The double-stranded circular DNA genome of AGV1 contains 18,222 bp encoding 34 open-reading frames. No ORFs showed significant similarity with Globuloviridae viruses. AGV1 shares three genes, including an integrase gene, with reported spindle-shaped temperate viruses. However we couldnt detect its integration site in the host genome. Moreover AGV1 seemed not to replicate autonomously because there are no origin recognition boxes in the genome. qPCR results showed that the genome copy number of AGV1 was lower than that of the host genome (1/1000 copies per host genome). Upon the addition of tris-acetate buffer, a steep increase in the AGV1 genome copy number (9.5 to 26 copies per host genome at 2 days post-treatment) was observed although clustered regularly interspaced short palindromic repeat (CRISPR) elements of the host genome showed significant matches with AGV1 protospacers. Our findings suggest that AGV1 is a novel globular virus exhibiting an unstable carrier state in the growing host and in that way AGV1 can escape from the host defense system and propagate under stressful host conditions.

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Bacteriophage Discovery and Genomics

Cited by 3 publications

References 40 publications

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

Phage Therapy in the 21st Century: Is There Modern, Clinical Evidence of Phage-Mediated Efficacy?

Isolation and characterization of novel temperate virusAeropyrumglobular virus 1 infecting hyperthermophilic archaeonAeropyrum

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