An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli

Jin, Menglu; Chen, Jingchao; Zhao, Xueyang; Hu, Guoru; Wang, Hailei; Li, Zhi; Chen, Wei-Hua

doi:10.1128/spectrum.01271-22

Cited by 13 publications

(11 citation statements)

References 65 publications

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“…Moreover, we also observed a similar elevated proportion of lytic phages within two rumen viral genome dataset (RVD and moose rumen [26]). Lytic phages are often isolated from the sewage [22]; our results thus provided better alternatives for lytic phage isolation.…”

Section: Discussionmentioning

confidence: 80%

“…Bacteriophages (phages) are a critical component of the ruminant GIT microbiome and play crucial roles in shaping microbial composition [19]. In addition, phages hold great promise for the precision manipulation of the bacteriome (i.e., the bacterial and archaeal microbes) because of their narrow microbial-host range (i.e., often at species and even strain levels [20,21]), providing alternative ways to suppress pathogenic bacterial/archaeal species [22] and control methane emissions [16,23]. The lifestyles of viruses can be broadly classi ed into two categories: lytic and lysogenic.…”

Section: Introductionmentioning

confidence: 99%

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A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

Wu,

Gao,

Sun

et al. 2024

Preprint

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Background: Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from ten sites along the GIT of eight ruminant species. Results: We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. Conclusions: The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants.

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Section: Discussionmentioning

confidence: 80%

Section: Introductionmentioning

confidence: 99%

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

Wu,

Gao,

Sun

et al. 2024

Preprint

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“…Importantly, the virulent conversion of a prophage was performed by DNA rebooting in this study. While virulent conversion can also be possible by removing the lysogeny control region of the prophage in the host genome by genome engineering and following phage induction ( Tinoco et al, 2016 ; Jin et al, 2022 ), genome engineering is applicable to only a few microorganisms. On the contrary, phage rebooting is based on the assembly of phage DNA fragments and following rebooting of synthetic phages in non-native host, and will be applicable for a wide variety of phages.…”

Section: Discussionmentioning

confidence: 99%

Precise microbiome engineering using natural and synthetic bacteriophages targeting an artificial bacterial consortium

Tanaka,

Sugiyama,

Sato

et al. 2024

Front. Microbiol.

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In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising method to elucidate the functions of targeted bacteria in microbiomes. However, few methods to selectively kill target microorganisms in the microbiome without affecting the growth of nontarget microorganisms are available. In this study, we focused on the host-specific lytic ability of virulent phages and validated their potency for precise microbiome engineering. In an artificial microbiome consisting of Escherichia coli, Pseudomonas putida, Bacillus subtilis, and Lactiplantibacillus plantarum, the addition of bacteriophages infecting their respective host strains specifically reduced the number of these bacteria more than 102 orders. Remarkably, the reduction in target bacteria did not affect the growth of nontarget bacteria, indicating that bacteriophages were effective tools for precise microbiome engineering. Moreover, a virulent derivative of the λ phage was synthesized from prophage DNA in the genome of λ lysogen by in vivo DNA assembly and phage-rebooting techniques, and E. coli-targeted microbiome engineering was achieved. These results propose a novel approach for precise microbiome engineering using bacteriophages, in which virulent phages are synthesized from prophage DNA in lysogenic strains without isolating phages from environmental samples.

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“…Next, we amplified and cultured the purified phage in the host strain L. plantarum CNGBCC 1800069. After 6 h of incubation, the phage genome was extracted by following a standard phenol-chloroform protocol ( 57 , 58 ). Briefly, cultures were centrifuged twice at 8,000 × g for 15 min at 4°C and filtered with a 0.22-μm filter membrane.…”

Section: Methodsmentioning

confidence: 99%

Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces

et al. 2023

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As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum ) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population.

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An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli

Cited by 13 publications

References 65 publications

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

Precise microbiome engineering using natural and synthetic bacteriophages targeting an artificial bacterial consortium

Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces

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