Characterisation of coliphage K30, a bacteriophage specific for<i>Escherichia coli</i>capsular serotype K30

Whitfield, Christopher; Lam, M. Y. C.

doi:10.1111/j.1574-6968.1986.tb01823.x

Cited by 21 publications

(4 citation statements)

References 20 publications

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“…Unfortunately for the bacterium, phages have at least two mechanisms to circumvent this protective layer. First, the MPG itself may provide a receptor for the phage, as has been well described for various E. coli capsules (51, 86,134). Second, phages often encode depolymerases (hydrolases or lyases) capable of degrading the capsule, allowing the phage to tunnel through the thick CPS layer and bind to receptors on the bacterial surface (8,86).…”

Section: Exclusion Of Pathogensmentioning

confidence: 99%

The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology

Porter

Martens

2017

Annu. Rev. Microbiol.

200

128

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The human intestine harbors a dense microbial ecosystem (microbiota) that is different between individuals, dynamic over time, and critical for aspects of health and disease. Dietary polysaccharides directly shape the microbiota because of a gap in human digestive physiology, which is equipped to assimilate only proteins, lipids, simple sugars, and starch, leaving nonstarch polysaccharides as major nutrients reaching the microbiota. A mutualistic role of gut microbes is to digest dietary complex carbohydrates, liberating host-absorbable energy via fermentation products. Emerging data indicate that polysaccharides play extensive roles in host-gut microbiota symbiosis beyond dietary polysaccharide digestion, including microbial interactions with endogenous host glycans and the importance of microbial polysaccharides. In this review, we consider multiple mechanisms through which polysaccharides mediate aspects of host-microbe symbiosis in the gut, including some affecting health. As host and microbial metabolic pathways are intimately connected with diet, we highlight the potential to manipulate this system for health.

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Section: Exclusion Of Pathogensmentioning

confidence: 99%

The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology

Porter

Martens

2017

Annu. Rev. Microbiol.

200

128

View full text Add to dashboard Cite

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“…Therefore, the DTR and, by proxy, the start of the genome can be inferred from the read mapping. Moreover, due to the highly conserved nature of the genomes, all przondoviruses had almost the same starting sequence as the well-curated enterobacterial phage K30 (accession HM480846) [67], making the beginning relatively easy to find. As a result, considerable time was spent on re-orienting the short-read-only assemblies to be unidirectional and to have the same starting sequence.…”

Section: Resultsmentioning

confidence: 99%

“…Where specified, publicly available phage genomes used for comparative genomics were derived from these studies [20,[66][67][68][69][70][71][72][73][74][75][76][77][78], listed in Table S6, and downloaded from the GenBank database.…”

Section: Comparative Genomicsmentioning

confidence: 99%

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

et al. 2023

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Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50–60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.

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“…Therefore, the DTR and by proxy, the start of the genome can be inferred from the read mapping. Moreover, due to the highly conserved nature of the genomes, all przondoviruses had almost the same starting sequence as the well-curated Enterobacteria phage K30 (accession HM480846) (67), making the beginning relatively easy to find. As a result, considerable time was spent on re-orienting the short-read-only assemblies to be unidirectional and to have the same starting sequence.…”

Section: Comparison Of Hyppa With Traditional Short-read-only Assemblymentioning

confidence: 99%

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Elek

Brown

Viet

et al. 2023

Preprint

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Bacteriophages (phages) within the Przondovirus genus are T7-like podoviruses belonging to the Studiervirinae subfamily, within the Autographiviridae family and have a highly conserved genome organisation. The genome size of these phages ranges from 37 kb to 42 kb, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA - a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.

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Characterisation of coliphage K30, a bacteriophage specific forEscherichia colicapsular serotype K30

Cited by 21 publications

References 20 publications

The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology

The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

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