Induction and Genomic Analysis of a Lysogenic Phage of Hafnia paralvei

Pan, Lining; Li, Dengfeng; Tong, Yigang; Lin, Wei; Qin, Weinan; Xu, Li-Hua; Zhan, Pingping

doi:10.1007/s00284-021-02698-0

Cited by 3 publications

(2 citation statements)

References 28 publications

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“…However, the scientific data available for Hafnia is still very scarce and focused on characterizing the unusual lytic phage Christian Milani and Marco Ventura contributed equally to this work. and several putative pathogenicity traits (Pan et al, 2021(Pan et al, , 2022Yin et al, 2019). Hafnia spp.…”

Section: Introductionmentioning

confidence: 99%

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Revealing the genetic traits of the foodborne microbial genus Hafnia: Implications for the human gut microbiome

Fontana,

Longhi,

Carli

et al. 2024

Environmental Microbiology

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The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host‐interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high‐quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short‐chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.

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Section: Introductionmentioning

confidence: 99%

“…Furthermore, a new member of the Hafnia genus, Hafnia paralvei , was discovered only recently (Huys et al, 2010). However, the scientific data available for Hafnia is still very scarce and focused on characterizing the unusual lytic phage and several putative pathogenicity traits (Pan et al, 2021, 2022; Yin et al, 2019). Hafnia spp.…”

Section: Introductionmentioning

confidence: 99%

Revealing the genetic traits of the foodborne microbial genus Hafnia: Implications for the human gut microbiome

Fontana,

Longhi,

Carli

et al. 2024

Environmental Microbiology

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Genomic analysis of a novel active prophage of Hafnia paralvei

Pan

Lin

et al. 2022

Arch Virol

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Relatively little is known about the prophages in Enterobacterales bacteria except Escherichia coli. A novel phage, Hafnia phage yong2, was induced from Hafnia paralvei by mitomycin C. The phage has an elliptical head of approximately 45 × 38 nm, a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546 bp double-stranded DNA with a G+C content of 49.9%, containing 59 opening reading frames (ORFs), and having at least one fixed terminus (GGGGCAGCGACA) with R=107>100. In phylogenetic analysis, Hafnia phage yong2 clustered with 4 predicted Hafnia prophages and 1 predicted Enterobacteriaceae prophage. The prophages cluster and Drexlerviridae family together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria. Bacteria of the genus Hafnia in family Hafniaceae, including Hafnia alvei and Hafnia paralvei, are normally found in food, plants, the gastrointestinal tract of animals and humans, etc [1, 2]. Rod-shaped Hafnia bacteria are facultatively anaerobic, gram-negative, considered to be an opportunistic pathogen to various animal species including fish, mammals and birds, and are capable of causing human infection under suspicion [1-4].Bacteriophages (phages) are viruses that can develop lytic or lysogenic infection in bacterial cells.

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A Novel Freshwater Cyanophage Mae-Yong1326-1 Infecting Bloom-Forming Cyanobacterium Microcystis aeruginosa

Wang

Cai

et al. 2022

Viruses

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Microcystis aeruginosa is a major harmful cyanobacterium causing water bloom worldwide. Cyanophage has been proposed as a promising tool for cyanobacterial bloom. In this study, M. aeruginosa FACHB-1326 was used as an indicator host to isolate cyanophage from Lake Taihu. The isolated Microcystis cyanophage Mae-Yong1326-1 has an elliptical head of about 47 nm in diameter and a slender flexible tail of about 340 nm in length. Mae-Yong1326-1 could lyse cyanobacterial strains across three orders (Chroococcales, Nostocales, and Oscillatoriales) in the host range experiments. Mae-Yong1326-1 was stable in stability tests, maintaining high titers at 0–40 °C and at a wide pH range of 3–12. Mae-Yong 1326-1 has a burst size of 329 PFU/cell, which is much larger than the reported Microcystis cyanophages so far. The complete genome of Mae-Yong1326-1 is a double-stranded DNA of 48, 822 bp, with a G + C content of 71.80% and long direct terminal repeats (DTR) of 366 bp, containing 57 predicted ORFs. No Mae-Yong1326-1 ORF was found to be associated with virulence factor or antibiotic resistance. PASC scanning illustrated that the highest nucleotide sequence similarity between Mae-Yong1326-1 and all known phages in databases was only 17.75%, less than 70% (the threshold to define a genus), which indicates that Mae-Yong1326-1 belongs to an unknown new genus. In the proteomic tree based on genome-wide sequence similarities, Mae-Yong1326-1 distantly clusters with three unclassified Microcystis cyanophages (MinS1, Mwe-Yong1112-1, and Mwes-Yong2). These four Microcystis cyanophages form a monophyletic clade, which separates at a node from the other clade formed by two independent families (Zierdtviridae and Orlajensenviridae) of Caudoviricetes class. We propose to establish a new family to harbor the Microcystis cyanophages Mae-Yong1326-1, MinS1, Mwe-Yong1112-1, and Mwes-Yong2. This study enriched the understanding of freshwater cyanophages.

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Induction and Genomic Analysis of a Lysogenic Phage of Hafnia paralvei

Cited by 3 publications

References 28 publications

Revealing the genetic traits of the foodborne microbial genus Hafnia: Implications for the human gut microbiome

Revealing the genetic traits of the foodborne microbial genus Hafnia: Implications for the human gut microbiome

Genomic analysis of a novel active prophage of Hafnia paralvei

A Novel Freshwater Cyanophage Mae-Yong1326-1 Infecting Bloom-Forming Cyanobacterium Microcystis aeruginosa

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