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| Open AccessMicrobial adaptation to spaceflight is correlated with bacteriophage-encoded functions
Viruses that infect bacteria shape microbial communities. Here, authors show that this may hold for bacteria isolated from the International Space Station, with spacefaring viruses correlated to host adaptation to the spaceflight environment.
- Iris Irby
- & Jared T. Broddrick
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Article
| Open AccessLong-read powered viral metagenomics in the oligotrophic Sargasso Sea
The Sargasso Sea is a natural laboratory for understanding future conditions of warmer oceans and associated nutrient limitation. Here, the authors combined short- and long-read sequencing to survey Sargasso Sea viral communities.
- Joanna Warwick-Dugdale
- , Funing Tian
- & Ben Temperton
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Article
| Open AccessMolecular basis of bacterial DSR2 anti-phage defense and viral immune evasion
The defense-associated sirtuin 2 (DSR2) system protects bacteria from phages by depleting NAD+. Here, authors elucidate the molecular mechanisms underlying DSR2 assembly, activation, and inhibition, providing important insights into bacterial anti-phage defense.
- Jiafeng Huang
- , Keli Zhu
- & Ang Gao
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Article
| Open AccessGlobally occurring pelagiphage infections create ribosome-deprived cells
SAR11 bacteria and their phages are abundant in the oceans. Here the authors quantify the number of phage-infected SAR11 cells using microscopy techniques and discover phage-infected cells without any detectable ribosomes. They hypothesize that ribosomal RNA may be used for the synthesis of phage genomes.
- Jan D. Brüwer
- , Chandni Sidhu
- & Bernhard M. Fuchs
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| Open AccessDiverse and abundant phages exploit conjugative plasmids
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
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| Open AccessPhage-specific immunity impairs efficacy of bacteriophage targeting Vancomycin Resistant Enterococcus in a murine model
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.
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Article
| Open AccessStructural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system
The bacterial DSR2 defense system counters phage invasion by depleting NAD+. Here, Zhang et al. reveal molecular mechanisms underlying phage-mediated activation and repression of DSR2, enhancing our understanding of the bacterial-phage arms race.
- Jun-Tao Zhang
- , Xiao-Yu Liu
- & Ning Jia
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Article
| Open AccessStructural basis of Acinetobacter type IV pili targeting by an RNA virus
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
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Article
| Open AccessStructure of the intact tail machine of Anabaena myophage A-1(L)
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
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| Open AccessAn OLD protein teaches us new tricks: prokaryotic antiviral defense
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
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Article
| Open AccessPHEIGES: all-cell-free phage synthesis and selection from engineered genomes
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
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| Open AccessCapsules and their traits shape phage susceptibility and plasmid conjugation efficiency
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
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Article
| Open AccessTransmission and dynamics of mother-infant gut viruses during pregnancy and early life
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
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| Open AccessA metagenomic catalog of the early-life human gut virome
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
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Article
| Open AccessViral potential to modulate microbial methane metabolism varies by habitat
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
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Article
| Open AccessAnti-phage defence through inhibition of virion assembly
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
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| Open AccessIdentification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages
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
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Article
| Open AccessPhage-plasmids promote recombination and emergence of phages and plasmids
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
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| Open AccessExploiting lung adaptation and phage steering to clear pan-resistant Pseudomonas aeruginosa infections in vivo
In this work, authors utilise a pan-resistant Pseudomonas aeruginosa in vivo infection model to demonstrate antibiotic re-sensitisation with bacteriophage therapy.
- Eleri A. Ashworth
- , Rosanna C. T. Wright
- & Joanne L. Fothergill
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| Open AccessAn extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano
Sonani et al. report the cryo-EM structures of the Milano phage tail, unraveling the mechanism of its flexible-to-rigid transformation, the inter-chain disulfide network hindering tail contraction and the structural organization of receptor binding proteins.
- Ravi R. Sonani
- , Lee K. Palmer
- & Edward H. Egelman
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| Open AccessUltraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces
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
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| Open AccessPhage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages
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
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| Open AccessStructure-guided discovery of anti-CRISPR and anti-phage defense proteins
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
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Article
| Open AccessStructural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system
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
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Article
| Open AccessTail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail
The authors describe the structure and function of two evolutionarily diverged RNA polymerases of a thermophilic phage. One of the polymerases is fused to the phage tape measure protein, a virion component dictating the length of the phage tail.
- Anastasiia Chaban
- , Leonid Minakhin
- & Maria L. Sokolova
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Article
| Open AccessPhage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication
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
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| Open AccessHi-C metagenome sequencing reveals soil phage–host interactions
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
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| Open AccessDistantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps
Receptor binding proteins in bacteriophage tails mediate host recognition and thus infectivity. Here Gonzalez et al. identify a receptor binding module shared by different phages that all use receptor binding tail fibers that are transiently capped by their chaperones.
- Rafael Gonzalez-Serrano
- , Riccardo Rosselli
- & Matthew Dunne
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| Open AccessA systematic analysis of marine lysogens and proviruses
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
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Article
| Open AccessPhage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety
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
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Article
| Open AccessCryo-EM structure of a bacteriophage M13 mini variant
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
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Article
| Open AccessInterrogating the viral dark matter of the rumen ecosystem with a global virome database
Here, by mining 975 published rumen metagenomes for viral sequences, the authors construct a global rumen virome database (RVD), providing a resource for characterization of viral diversity, virus-host linkages, and potential roles in affecting rumen functions.
- Ming Yan
- , Akbar Adjie Pratama
- & Zhongtang Yu
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Article
| Open AccessEngineered reporter phages for detection of Escherichia coli, Enterococcus, and Klebsiella in urine
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
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| Open AccessCharacterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution
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
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| Open AccessPersonalized aerosolised bacteriophage treatment of a chronic lung infection due to multidrug-resistant Pseudomonas aeruginosa
Köhler et al. document the treatment, and clinical improvement, of a male patient with a life-threatening chronic multi-drug resistant Pseudomonas aeruginosa infection with aerosolized personalized phage therapy, in combination with intravenous antibiotic treatment.
- Thilo Köhler
- , Alexandre Luscher
- & Christian van Delden
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Article
| Open AccessBacteriophage targeting microbiota alleviates non-alcoholic fatty liver disease induced by high alcohol-producing Klebsiella pneumoniae
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
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Article
| Open AccessDesign of bacteriophage T4-based artificial viral vectors for human genome remodeling
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
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Article
| Open AccessHighly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution
Viruses in built environments raise public health concerns. By analyzing diverse samples, Du et al. provide evidence that virus–host interactions occur frequently in built environments and that viruses are integral members of built environment microbiomes.
- Shicong Du
- , Xinzhao Tong
- & Patrick K. H. Lee
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Article
| Open AccessA contractile injection system is required for developmentally regulated cell death in Streptomyces coelicolor
Bacteria can use extracellular contractile injection systems (eCISs) to inject toxic proteins into eukaryotic cells. Here, Vladimirov et al. provide evidence that the main role of eCISs in Streptomyces is not to attack other species, but to modulate the complex Streptomyces developmental process.
- Maria Vladimirov
- , Ruo Xi Zhang
- & Alan R. Davidson
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Article
| Open AccessTopical phage therapy in a mouse model of Cutibacterium acnes-induced acne-like lesions
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
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Article
| Open AccessThe ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice
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
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Article
| Open AccessMultistep diversification in spatiotemporal bacterial-phage coevolution
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
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Article
| Open AccessSelf-assembling nanofibrous bacteriophage microgels as sprayable antimicrobials targeting multidrug-resistant bacteria
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
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Article
| Open AccessCryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution
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
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Article
| Open AccessCryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper
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
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Article
| Open AccessHigh-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers
The jumbo contractile bacteriophage, Kp24, has been isolated from clinical strains of Klebsiella pneumonia. Here, the authors present structural and functional insight into the capsid, tail and tail fibres and how this impacts infectivity.
- Ruochen Ouyang
- , Ana Rita Costa
- & Ariane Briegel
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Article
| Open AccessNicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE
SspABCD–SspE is a phosphorothioation-sensing bacterial defence system. Here, authors find that SspE exploits DNA phosphorothioation-binding preference to modulate its biochemical activities for the self/nonself discrimination and phage resistance.
- Haiyan Gao
- , Xinqi Gong
- & Lianrong Wang
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Article
| Open AccessResponse of soil viral communities to land use changes
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
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Article
| Open AccessBacteriophage-antibiotic combination therapy against extensively drug-resistant Pseudomonas aeruginosa infection to allow liver transplantation in a toddler
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