Bacteriophages articles within Nature Communications

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  • Article
    | Open Access

    Some phages use plasmid-encoded conjugation proteins as receptors to infect their bacterial hosts, making their host range dependent on horizontal transfer of the plasmid. Here, the authors present a method for identification of new plasmid-dependent phages, and find that they are common and abundant in wastewater and their genetic diversity is largely unexplored.

    • Natalia Quinones-Olvera
    • , Siân V. Owen
    •  & Michael Baym

  • Article
    | Open Access

    Bacteriophage can be used to target bacterial infection and used as a therapeutic approach for antibiotic resistant bacteria. Here the authors show that the use of bacteriophage to target antibiotic resistant bacteria in a mouse model of infection can induce phage specific immune responses and may impair their therapeutic efficacy.

    • Julia D. Berkson
    • , Claire E. Wate
    •  & Paul E. Carlson Jr.

  • Article
    | Open Access

    Here, the authors structurally characterise the interaction between Acinetobacter phage AP205 and the type IV Acinetobacter pili using cryo-electron microscopy, uncovering the mechanistic determinants of this interaction.

    • Ran Meng
    • , Zhongliang Xing
    •  & Junjie Zhang

  • Article
    | Open Access

    The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Here, authors present the high-resolution cryo-EM structure of its intact tail machine, and identify multiple hydrolytic and binding modules.

    • Rong-Cheng Yu
    • , Feng Yang
    •  & Cong-Zhao Zhou

  • Comment
    | Open Access

    Reporting in Nature Communications, Huo and colleagues provide three-dimensional structures of a bacterial immune defense system called Gabija. This work builds on recently published structural and functional studies and contributes strong evidence that protein assembly formation is essential for antiviral function.

    • Eirene Marie Q. Ednacot
    •  & Benjamin R. Morehouse

  • Article
    | Open Access

    Bacteriophages have great potential in both medicine and biotechnology. Here the authors present PHEIGES, a cell-free method for phage genome engineering, synthesis and selection based on T7, which allows direct selection of engineered and mutant phages without compartmentalization.

    • Antoine Levrier
    • , Ioannis Karpathakis
    •  & Vincent Noireaux

  • Article
    | Open Access

    Bacterial capsules provide protection against the environment, including host immune systems. Authors swap capsule loci in Klebsiella pneumoniae to reveal the role of these sugar coats against plasmid conjugation and phage infection, showing that the serotype is a key player in regulating conjugation rates, and phage susceptibility.

    • Matthieu Haudiquet
    • , Julie Le Bris
    •  & Olaya Rendueles

  • Article
    | Open Access

    Gut ecosystem colonization impacts lifelong health. Here, authors track mother-infant gut viruses over time, reveal feeding’s influence on early viral colonization, and demonstrate the co-transmission of bacteriophages and bacteria from mothers to infants.

    • Sanzhima Garmaeva
    • , Trishla Sinha
    •  & Alexandra Zhernakova

  • Article
    | Open Access

    Here, the authors present a metagenomic catalogue of the early-life human gut virome including 160,478 non-redundant DNA and RNA viral sequences from 8,130 gut virus-like particles enriched or bulk metagenomes in the first three years of life.

    • Shuqin Zeng
    • , Alexandre Almeida
    •  & Shaopu Wang

  • Article
    | Open Access

    The role of viruses in environmental methane cycling is still largely unclear. Here, Zhong et al. analyse metagenomics data to identify auxiliary metabolic genes related to methane metabolism within viral contigs. They found that the potential viral impacts on methane production and oxidation varies by habitat.

    • Zhi-Ping Zhong
    • , Jingjie Du
    •  & Matthew B. Sullivan

  • Article
    | Open Access

    Bacteria have evolved various defence mechanisms to protect themselves against viral infection. Here, Patel et al. identify a type of antiviral defence that blocks virion assembly, thus preventing formation of infectious virions and allowing destruction of the infected cell.

    • Pramalkumar H. Patel
    • , Véronique L. Taylor
    •  & Karen L. Maxwell

  • Article
    | Open Access

    The diverse functional roles of ribozymes (RNAs with enzymatic activity) continue to be uncovered. Here, the authors identify and characterize a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes – termed Theta ribozymes -, which they show process viral tRNA transcripts, and appearing crucial for lytic gene expression in recoded phages.

    • Kasimir Kienbeck
    • , Lukas Malfertheiner
    •  & Roland K. O. Sigel

  • Article
    | Open Access

    Phage-plasmids are mobile genetic elements that transfer horizontally between bacterial cells as viruses, and vertically within bacterial lineages as plasmids. Here, Pfeifer & Rocha show that phage-plasmids can mediate gene transfer across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.

    • Eugen Pfeifer
    •  & Eduardo P. C. Rocha

  • Article
    | Open Access

    Bacterial viruses (phages) are generally recognised as rapidly evolving biological entities. Here, Rozwalak et al. analyse DNA sequence datasets generated from ancient palaeofaeces and identify 298 phage genomes from the last 5300 years, including a 1300-year-old phage genome nearly identical to a present-day virus that infects human gut bacteria.

    • Piotr Rozwalak
    • , Jakub Barylski
    •  & Andrzej Zielezinski

  • Article
    | Open Access

    Phage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here, Barcia-Cruz et al. identify a family of satellites, named PICMIs, that are characterized by reduced gene content and are broadly distributed in marine bacteria of the family Vibrionaceae.

    • Rubén Barcia-Cruz
    • , David Goudenège
    •  & Frédérique Le Roux

  • Article
    | Open Access

    Bacteria use various defense systems to protect themselves from phage infection, and phages have evolved diverse counter-defense measures to overcome host defenses. Here, the authors use protein structural similarity and gene co-occurrence analyses for identification of new anti-phage and counter-defense systems.

    • Ning Duan
    • , Emily Hand
    •  & Akintunde Emiola

  • Article
    | Open Access

    Short prokaryotic Argonaute and Sir2 proteins function as an antivirus system. Here the authors describe structures of SPARSA (a heterodimer of Sir2-APAZ and prokaryotic Argonaute) with and without template DNA and guide RNA, providing structural basis of its assembly and activation by the recognition of the invading virus.

    • Xiangkai Zhen
    • , Xiaolong Xu
    •  & Songying Ouyang

  • Article
    | Open Access

    Bacteriophages have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. Here, Maffei et al. show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates; however, a particular phage can directly replicate and induce the lysis of deep-dormant hosts.

    • Enea Maffei
    • , Anne-Kathrin Woischnig
    •  & Alexander Harms

  • Article
    | Open Access

    This study uses high-throughput chromosome conformation capture (Hi-C) to identify phage–host relationships in soil. By coupling Hi-C with DNA and RNA sequencing, the authors demonstrate the impact of soil drying on phage–host interactions and the downstream effects on abundances and interspecies interactions within bacterial communities.

    • Ruonan Wu
    • , Michelle R. Davison
    •  & Kirsten S. Hofmockel

  • Article
    | Open Access

    Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, Yi et al. present a systematic catalogue and analysis of genomic sequences from marine prokaryotes and their proviruses, thus contributing to a better understanding of the ecology of these microorganisms.

    • Yi Yi
    • , Shunzhang Liu
    •  & Huahua Jian

  • Article
    | Open Access

    Bacteriophages (phages) can modify the gut microbiome to benefit human health. Here, the authors report the results of a double blind, randomized, placebo-controlled trial, showing that faecal filtrate transplantation (FFT), containing phages from lean healthy donors, is safe and improves glycemic variability in patients with metabolic syndrome, while shifting the gut phage composition.

    • Koen Wortelboer
    • , Patrick A. de Jonge
    •  & Hilde Herrema

  • Article
    | Open Access

    Filamentous phages are micrometer long and encapsulate their circular ssDNA genome with five coat proteins. Here, authors report the cryo-EM structure of a mini M13 phage and the results reveal the coat protein assembly and structure of the ssDNA genome.

    • Qi Jia
    •  & Ye Xiang

  • Article
    | Open Access

    Although diagnosis of urinary tract infections has improved through the use of point-of-care molecular technologies, they are however limited by poor specificity and / or sensitivity, and requirement of laboratory resources. In this work, the authors develop a bacteriophage-based diagnostic assay for the detection of prevalent uropathogens.

    • Susanne Meile
    • , Jiemin Du
    •  & Samuel Kilcher

  • Article
    | Open Access

    Here, the authors report the isolation and genetic characterization of 25 unique crAss-like phages (termed “crAssBcn”) infecting Bacteroides intestinalis, and show that CrAssBcn phages are commonly found in fecal samples from people around the globe, indicating their wide distribution.

    • María Dolores Ramos-Barbero
    • , Clara Gómez-Gómez
    •  & Maite Muniesa

  • Article
    | Open Access

    Previous studies have shown that high alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) in the intestinal microbiome could be one of the causes of non-alcoholic fatty liver disease (NAFLD). Here, the authors show the effectiveness of phage in mice with HiAlc Kpn-induced NAFLD indicating phage therapy targeting gut microbiota may be an alternative to antibiotics, with potential efficacy and safety.

    • Lin Gan
    • , Yanling Feng
    •  & Jing Yuan

  • Article
    | Open Access

    Safe delivery of genes is needed for gene therapy. Here the authors build “artificial viral vectors” (AVVs) by engineering the well-characterised structural components of bacteriophage T4: the large capacity, all-in-one, multiplex, programmable, and phage-based AVV nanomaterials have potential for gene therapy.

    • Jingen Zhu
    • , Himanshu Batra
    •  & Venigalla B. Rao

  • Article
    | Open Access

    Bacteriophage therapy is evolving as a promising approach to tackling bacterial infection, even in the case of emerging antibiotic resistance. In this work, authors present the topical application of numerous Cutibacterium acnes phage in an in vivo mouse model of acne vulgaris.

    • Amit Rimon
    • , Chani Rakov
    •  & Ronen Hazan

  • Article
    | Open Access

    To protect from host attack, numerous jumbo bacteriophages establish a micron-scale, protein-based structure to enclose their replicating DNA. Using cryoEM, the authors show that the 2D crystal enclosing this so-called phage nucleus is an assembly of tetramers linked by flexible loops and tails.

    • Eliza S. Nieweglowska
    • , Axel F. Brilot
    •  & David A. Agard

  • Article
    | Open Access

    Bacteria and their viruses coexist and coevolve in nature, but maintaining them together in the lab is challenging. Here, a spatially structured environment allowed prolonged coevolution, with bacteria and phage diversifying into multiple ecotypes, uncovering gene mechanisms affecting phage-bacteria interactions.

    • Einat Shaer Tamar
    •  & Roy Kishony

  • Article
    | Open Access

    Bacteriophage are natural antibiotic agents and provide natural building blocks for living biomaterials. Here, the authors crosslink self-organised bacteriophages to make sprayable microgels which preserves the natural antibacterial action, have tuneable auto-fluorescence and demonstrate application in food decontamination.

    • Lei Tian
    • , Leon He
    •  & Zeinab Hosseinidoust

  • Article
    | Open Access

    Structural biology investigation of conserved capsid proteins facilitates the study of virus evolution. Here, characterization of the lipid-containing ssDNA bacteriophage ΦCjT23 suggests that this phage may serve as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae.

    • Nejc Kejzar
    • , Elina Laanto
    •  & Juha T. Huiskonen

  • Article
    | Open Access

    Numerous viruses use a portal system for dsDNA entry and exit from their capsid. Here the authors report the atomic structure of phage SPP1 portal DNA gatekeeper and its mechanism of assembly. They also identify evolution breakpoints between different tailed bacteriophages morphotypes and herpesviruses.

    • Igor Orlov
    • , Stéphane Roche
    •  & Elena V. Orlova

  • Article
    | Open Access

    Soil viral communities remain understudied. Here, Liao et al. retrieve a catalogue of around sixty thousand vOTUs through a systematic viromic pipeline, and uncover the response of soil viral communities to anthropogenic land use changes.

    • Hu Liao
    • , Hu Li
    •  & Jian-Qiang Su

  • Article
    | Open Access

    In this study, authors use combinatory bacteriophage-antibiotic therapy, as treatment for extensively drug-resistant Pseudomonas aeruginosa infection in a toddler post liver transplantation. They report on the clinical and microbiological improvement, and present their investigation on how bacterial phage resistance did not result in therapeutic failure.

    • Brieuc Van Nieuwenhuyse
    • , Dimitri Van der Linden
    •  & Jean-Paul Pirnay

  • Article
    | Open Access

    E. coli phage SU10 has a short non-contractile tail. Here, the authors show that after cell binding, nozzle proteins and tail fibers of SU10 change conformation to form a nozzle that enables the delivery of the phage DNA into the bacterial cytoplasm.

    • Marta Šiborová
    • , Tibor Füzik
    •  & Pavel Plevka

  • Article
    | Open Access

    Here, Nishijima et al. perform a large-scale analysis of the human gut virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals, revealing thousands of bacteriophage genomes, virus-bacteria interactions, and describing associations with various host and environmental factors.

    • Suguru Nishijima
    • , Naoyoshi Nagata
    •  & Masahira Hattori

  • Article
    | Open Access

    HK022 put is an RNA element that inhibits transcription termination without aids from protein factors. Here, authors solved cryo-EM structures of put-associated RNA polymerase and showed the structure of putRNA and its binding to the RNA polymerase.

    • Seungha Hwang
    • , Paul Dominic B. Olinares
    •  & Jin Young Kang

  • Article
    | Open Access

    Phage contamination is a persistent problem in industrial biotechnology processes employing bacterial strains. Here, the authors report the construction of E. coli host strains with broad antiphase activities via the genomic integration of the Ssp defense system and mutations of components essential for phage infection cycles.

    • Xuan Zou
    • , Xiaohong Xiao
    •  & Sang Yup Lee

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