Environmental Science › Ecology

Bacteriophages and microbial interactions

Works Count: 111981

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Description

This cluster of papers explores the ecology, evolution, and applications of viruses in various ecosystems, with a focus on bacteriophages, marine viruses, viromes, and their potential therapeutic and nanotechnological implications.

Keywords

Virus; Ecology; Bacteriophage; Metagenomics; Marine; Evolution; Therapy; Genomics; Microbiome; Nanoparticles

Nucleotide sequence of bacteriophage G4 DNA

1978-11-01

G N Godson , B. G. Barrell , Rodger Staden +1 more

Marine viruses — major players in the global ecosystem

2007-09-14

Curtis A. Suttle

[1] Production of single-stranded plasmid DNA

1987-01-01

Jeffrey Vieira , Joachim Messing

Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes

1986-05-01

F. William Studier , Barbara A. Moffatt

CAT constructions with multiple unique restriction sites for the functional analysis of eukaryotic promoters and regulatory elements

1987-01-01

Bruno Luckow , Günther Schütz

The coding region of the bacterial chloramphenicol acetyltransferase (CAT) gene is widely used as an indicator gene in gene transfer experiments dealing with regulation of transcription in eukaryotes.Chimaeric CAT fusion … The coding region of the bacterial chloramphenicol acetyltransferase (CAT) gene is widely used as an indicator gene in gene transfer experiments dealing with regulation of transcription in eukaryotes.Chimaeric CAT fusion genes are especially useful because no endogenous CAT activity is present in eukaryotic cells and because CAT enzyme activity can be monitored by a rapid and sensitive assay (1).In order to simplify the construction of hybrid CAT genes, we have constructed the plasmids pBLCAT2 and pBLCAT3.The coding region of the CAT gene as well as the small t intron and polyadenylation signals from SV40 were inserted into the polylinker region of the high copy number plasmid pUC18 (2).Unique BgHI and Xhol restriction sites were introduced upstream of the CAT coding region by insertion of synthetic linkers.A BamHI site at the 3' end of the transcription unit was converted into a dam methylation sensitive Clal site by partial digestion with BamHI, filling -in and re -ligation.In the promoterless construction pBLCAT3 eight unique restriction sites are suitable for insertion of different eukaryotic promoters at the 5' end of the CAT gene.Four additional unique restriction sites make the insertion of regulatory signals 3' of the CAT gene possible and enable the excision of the intact fusion gene from the prokaryotic vector.The presence of die Herpes simplex virus tk promoter in pBLCAT2 permits die analysis of the effects of putative regulatory elements on a heterologous eukaryotic promoter.A BamHI/Bglll fragment from the HSV tk linker scanning mutant LS -115/ -105 (3) spanning the promoter from -105 to +51 was inserted into the corresponding restriction sites of pBLCAT3 thereby generating pBLCAT2.The modified polylinker regions at the 5' and the 3' ends have been sequenced and compiled sequences for both plasmids are available on request.

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Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

2010-05-21

Daniel G. Gibson , John I. Glass , Carole Lartigue +7 more

We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell … We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase.

1986-11-01

Thomas R. Fuerst , Edward G. Niles , F. William Studier +1 more

DNA coding for bacteriophage T7 RNA polymerase was ligated to a vaccinia virus transcriptional promoter and integrated within the vaccinia virus genome. The recombinant vaccinia virus retained infectivity and stably … DNA coding for bacteriophage T7 RNA polymerase was ligated to a vaccinia virus transcriptional promoter and integrated within the vaccinia virus genome. The recombinant vaccinia virus retained infectivity and stably expressed T7 RNA polymerase in mammalian cells. Target genes were constructed by inserting DNA segments that code for beta-galactosidase or chloramphenicol acetyltransferase into a plasmid with bacteriophage T7 promoter and terminator regions. When cells were infected with the recombinant vaccinia virus and transfected with plasmids containing the target genes, the latter were expressed at high levels. Chloramphenicol acetyltransferase activity was 400-600 times greater than that observed with conventional mammalian transient-expression systems regulated either by the enhancer and promoter regions of the Rous sarcoma virus long terminal repeat or by the simian virus 40 early region. The vaccinia/T7 hybrid virus forms the basis of a simple, rapid, widely applicable, and efficient mammalian expression system.

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Rapid evolution of a protein in vitro by DNA shuffling

1994-08-01

Willem P.C. Stemmer

A new antibiotic kills pathogens without detectable resistance

2015-01-05

Losee L. Ling , Tanja Schneider , Aaron J. Peoples +7 more

Bacteriophage resistance mechanisms

2010-03-29

Simon J. Labrie , Julie Samson , Sylvain Moineau

A rapid alkaline extraction procedure for screening recombinant plasmid DNA

1979-11-24

H.C. Birnboim , Janine Doly

A procedure for extracting plasmid DNA from bacterial cells is described. The method is simple enough to permit the analysis by gel electrophoresis of 100 or more clones per day … A procedure for extracting plasmid DNA from bacterial cells is described. The method is simple enough to permit the analysis by gel electrophoresis of 100 or more clones per day yet yields plasmid DNA which is pure enough to be digestible by restriction enzymes. The principle of the method is selective alkaline denaturation of high molecular weight chromosomal DNA while covalently closed circular DNA remains double-stranded. Adequate pH control is accomplished without using a pH meter. Upon neutralization, chromosomal DNA renatures to form an insoluble clot, leaving plasmid DNA in the supernatant. Large and small plasmid DNAs have been extracted by this method.

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Supercoil Sequencing: A Fast and Simple Method for Sequencing Plasmid DNA

1985-04-01

Ellson Y. Chen , Peter H. Seeburg

A method for obtaining sequence information directly from plasmid DNA is presented. The procedure involves the rapid preparation of clean supercoiled plasmid DNA from small bacterial cultures, its complete denaturation … A method for obtaining sequence information directly from plasmid DNA is presented. The procedure involves the rapid preparation of clean supercoiled plasmid DNA from small bacterial cultures, its complete denaturation by alkali, and sequence determination using oligodeoxyribonucleotide-primed enzymatic DNA synthesis in the presence of dideoxynucleoside triphosphates. The advantages of the method include speed, simplicity, avoidance of additional cloning steps into single-stranded phage M13 vectors, and hence applicability to sequencing large numbers of samples.

Analysis of bacteriophage T7 early RNAs and proteins on slab gels

1973-09-01

F. William Studier

Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors

1985-01-01

Celeste Yanisch-Perron , Jeffrey Vieira , Joachim Messing

A rapid boiling method for the preparation of bacterial plasmids

1981-06-01

David S. Holmes , Michael E. Quigley

Entropic Elasticity of λ-Phage DNA

1994-09-09

Carlos Bustamante , John F. Marko , Eric D. Siggia +1 more

A system for shotgun DNA sequencing

1981-01-01

Joachim Messing , Roberto Crea , Peter H. Seeburg

A multipurpose cloning site has been introduced into the gene for B-galactosidase (s-D-galactosidegalactohydrolase, EC 3.21.23)on the single-stranded DMA phage M13mp2 (Gronenborn, B. and Messing, J., (1978) Nature ^72, 375-377) with … A multipurpose cloning site has been introduced into the gene for B-galactosidase (s-D-galactosidegalactohydrolase, EC 3.21.23)on the single-stranded DMA phage M13mp2 (Gronenborn, B. and Messing, J., (1978) Nature ^72, 375-377) with the use of synthetic DNA.The site contributes 14 additional codons and does not affect the ability of the lac gene product to undergo intracistronic complementation.Two restriction endonuclease cleavage sites in the viral gene II ware removed by singls base-pair mutations.Using the new phage M13mp7, DNA fragments generated by cleavage with a variety of different restriction endonucleases can be cloned directly.The nucleotide sequences of the cloned DNAs can be determined rapidly by DNA synthesis using chain terminators and a synthetic oligonucleotide primer complementary to 15 bases preceeding the new array of restriction sites.

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Nucleotide sequence of the rightward operator of phage lambda.

1975-03-01

Tom Maniatis , Andrea Jeffrey , Dennis G. Kleid

The sequence of 72 base pairs of the rightward operator (O-R) of bacteriophage lambda is presented as determined with simple and rapid methods for direct DNA sequencing. The sequence of … The sequence of 72 base pairs of the rightward operator (O-R) of bacteriophage lambda is presented as determined with simple and rapid methods for direct DNA sequencing. The sequence of an operator mutant is also described. The methods are of general use in sequencing DNA fragments with unique 5' ends up to 50 base pairs in length. Previous experiments have shown that this operator contains multiple sites recognized by the lambda phage repressor. We believe we have identified three of these sites.

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Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage lambda and Mu

1976-07-01

M J Casadaban

Calcium-dependent bacteriophage DNA infection

1970-10-01

M. Mandel , Akiko Higa

Transduction of linked genetic characters of the host by bacteriophage P1

1955-07-01

E. S. Lennox

Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing

1980-10-01

Frederick Sanger , Alan Coulson , B. G. Barrell +2 more

RNA-guided genetic silencing systems in bacteria and archaea

2012-02-01

Blake Wiedenheft , Samuel H. Sternberg , Jennifer A. Doudna

A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments

1982-10-01

Joachim Messing , Jeffrey Vieira

Filamentous Fusion Phage: Novel Expression Vectors That Display Cloned Antigens on the Virion Surface

1985-06-14

George P. Smith

Foreign DNA fragments can be inserted into filamentous phage gene III to create a fusion protein with the foreign sequence in the middle. The fusion protein is incorporated into the … Foreign DNA fragments can be inserted into filamentous phage gene III to create a fusion protein with the foreign sequence in the middle. The fusion protein is incorporated into the virion, which retains infectivity and displays the foreign amino acids in immunologically accessible form. These "fusion phage" can be enriched more than 1000-fold over ordinary phage by affinity for antibody directed against the foreign sequence. Fusion phage may provide a simple way of cloning a gene when an antibody against the product of that gene is available.

Physical Principles in the Construction of Regular Viruses

1962-01-01

D. L. D. Caspar , A. Klug

There are two key facts about viruses from which all consideration of their structure and functional organization must proceed. The first is that the essential infective agent of all viruses … There are two key facts about viruses from which all consideration of their structure and functional organization must proceed. The first is that the essential infective agent of all viruses is a high molecular weight nucleic acid component— either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Second, the nucleic acid molecule is contained in a protective package which serves to transmit this infectious agent in a functionally intact state through space and time to a susceptible host.

Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase

1990-08-03

Craig Tuerk , Larry Gold

High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound … High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.

Viruses in the sea

2005-09-01

Curtis A. Suttle

Virioplankton: Viruses in Aquatic Ecosystems

2000-03-01

K. Eric Wommack , Rita R. Colwell

SUMMARY The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest … SUMMARY The discovery that viruses may be the most abundant organisms in natural waters, surpassing the number of bacteria by an order of magnitude, has inspired a resurgence of interest in viruses in the aquatic environment. Surprisingly little was known of the interaction of viruses and their hosts in nature. In the decade since the reports of extraordinarily large virus populations were published, enumeration of viruses in aquatic environments has demonstrated that the virioplankton are dynamic components of the plankton, changing dramatically in number with geographical location and season. The evidence to date suggests that virioplankton communities are composed principally of bacteriophages and, to a lesser extent, eukaryotic algal viruses. The influence of viral infection and lysis on bacterial and phytoplankton host communities was measurable after new methods were developed and prior knowledge of bacteriophage biology was incorporated into concepts of parasite and host community interactions. The new methods have yielded data showing that viral infection can have a significant impact on bacteria and unicellular algae populations and supporting the hypothesis that viruses play a significant role in microbial food webs. Besides predation limiting bacteria and phytoplankton populations, the specific nature of virus-host interaction raises the intriguing possibility that viral infection influences the structure and diversity of aquatic microbial communities. Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities.

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PHAST: A Fast Phage Search Tool

2011-06-14

You Zhou , Yong Liang , Karlene H. Lynch +2 more

PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA … PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage 'cornerstone' feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage 'quality' and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at ( http://phast.wishartlab.com ).

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Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4

1970-08-01

Ulrich K. Laemmli

The complete genome sequence of the Gram-positive bacterium Bacillus subtilis

1997-11-01

Frank Kunst , Naotaka Ogasawara , Ivan Moszer +7 more

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a … Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

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Shape effects of filaments versus spherical particles in flow and drug delivery

2007-03-25

Yan Geng , Paul Dalhaimer , Shenshen Cai +4 more

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Complete Nucleotide Sequence of the Escherichia coli Plasmid pBR322

1979-01-01

J G Sutcliffe

I have determined the 4362-nucleotide-pair sequence of the plasmid cloning vector pBR322 using the DNA-sequencing technique of Maxam and Gilbert (1977). The DNA structure has several interesting features that lead … I have determined the 4362-nucleotide-pair sequence of the plasmid cloning vector pBR322 using the DNA-sequencing technique of Maxam and Gilbert (1977). The DNA structure has several interesting features that lead to testable predictions.

The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

2000-02-01

Julian Parkhill , Brendan W. Wren , Karen Mungall +7 more

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Genome sequencing in microfabricated high-density picolitre reactors

2005-07-31

Marcel Margulies , Michael D. Miller , William E. Altman +7 more

The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system … The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine. The race is on for a big prize: the job of providing the world's DNA sequencing laboratories with the successor to the 'Sanger-based' technology that gave us the first wave of genome sequences. One technology in the frame is that produced by 454 Life Sciences Corporation of Branford, Connecticut. Today's technology reads 67,000 base pairs per hour; this new approach is 100 times faster, reading 6 million base pairs per hour. The improved performance results from using picolitre-sized chemical reactors, enhanced light-emitting sequencing chemistries and complex informatics. Further miniaturization of the system is planned. Such leaps in technology may one day make it possible to analyse an individual's genome before designing therapy: the ultimate in personalized medicine.

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Rapid extraction of bacterial genomic DNA with guanidium thiocyanate

1989-04-01

D.G. Pitcher , Nicholas A. Saunders , Robert J. Owen

A method is described for the rapid isolation and purification of bacterial genomic DNA. A total of 215 bacterial strains representing species of Campylobacter, Corynebacterium, Escherichia, Legionella, Neisseria, Staphylococcus and … A method is described for the rapid isolation and purification of bacterial genomic DNA. A total of 215 bacterial strains representing species of Campylobacter, Corynebacterium, Escherichia, Legionella, Neisseria, Staphylococcus and Streptococcus, were lysed with guanidium thiocyanate. DNA was prepared using just three other reagents and one high-speed centrifugation step. The method, which was applicable to both Gram-positive and Gram-negative bacteria, eliminated endogenous nuclease activity and avoided the need for phenol, RNase and protease treatments. The DNA was of high purity, high molecular mass and double-stranded.

DNA sequencing with chain-terminating inhibitors

1977-12-01

Frederick Sanger , S. Nicklen , Alan Coulson

A new method for determining nucleotide sequences in DNA is described. It is similar to the "plus and minus" method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. … A new method for determining nucleotide sequences in DNA is described. It is similar to the "plus and minus" method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2',3'-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage varphiX174 and is more rapid and more accurate than either the plus or the minus method.

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Rapid and simple method for purification of nucleic acids

1990-03-01

René Boom , C. J. A. Sol , M M Salimans +3 more

We have developed a simple, rapid, and reliable protocol for the small-scale purification of DNA and RNA from, e.g., human serum and urine. The method is based on the lysing … We have developed a simple, rapid, and reliable protocol for the small-scale purification of DNA and RNA from, e.g., human serum and urine. The method is based on the lysing and nuclease-inactivating properties of the chaotropic agent guanidinium thiocyanate together with the nucleic acid-binding properties of silica particles or diatoms in the presence of this agent. By using size-fractionated silica particles, nucleic acids (covalently closed circular, relaxed circular, and linear double-stranded DNA; single-stranded DNA; and rRNA) could be purified from 12 different specimens in less than 1 h and were recovered in the initial reaction vessel. Purified DNA (although significantly sheared) was a good substrate for restriction endonucleases and DNA ligase and was recovered with high yields (usually over 50%) from the picogram to the microgram level. Copurified rRNA was recovered almost undegraded. Substituting size-fractionated silica particles for diatoms (the fossilized cell walls of unicellular algae) allowed for the purification of microgram amounts of genomic DNA, plasmid DNA, and rRNA from cell-rich sources, as exemplified for pathogenic gram-negative bacteria. In this paper, we show representative experiments illustrating some characteristics of the procedure which may have wide application in clinical microbiology.

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Maturation of the head of bacteriophage T4

1973-11-01

Ulrich K. Laemmli , Manuel Favre

Antigen — Antibody Reactions In Gels

1949-09-01

Örjan Ouchterlony

CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes

2007-03-22

Rodolphe Barrangou , Christophe Fremaux , Hélène Deveau +5 more

Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophages. We … Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophages. We found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences. Removal or addition of particular spacers modified the phage-resistance phenotype of the cell. Thus, CRISPR, together with associated cas genes, provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.

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Bacteriophages

1959-01-01

Mark Hancock Adams

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Embracing the unknown: disentangling the complexities of the soil microbiome

2017-08-21

Noah Fierer

Cleavage of structural proteins during the assemble of the head of bacterio-phage T4

1970-01-01

Ulrich K. Laemmli

Improved metagenomic analysis with Kraken 2

2019-11-28

Derrick E. Wood , Jennifer Lu , Ben Langmead

Abstract Although Kraken’s k -mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken … Abstract Although Kraken’s k -mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.

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Methods for general and molecular bacteriology

1994-01-01

Philipp Gerhardt

Methodology for General and Molecular Microbiology Morphology Light microscopy Determinative and cytological light microscopy Electron microscopy Cell fractionation Antigen-antibody reactions Growth: Physicochemical factors in growth Nutrition and media Enrichment and … Methodology for General and Molecular Microbiology Morphology Light microscopy Determinative and cytological light microscopy Electron microscopy Cell fractionation Antigen-antibody reactions Growth: Physicochemical factors in growth Nutrition and media Enrichment and isolation Solid, liquid/solid and semisolid culture Liquid culture Growth measurement Culture preservation Molecular Genetics: Gene mutation Gene transfer in Gram-negative bacteria Gene transfer in Gram-positive bacteria Plasmids Transposon mutagenesis Gene cloning and expression Polymerase chain reaction Nucleic acid analysis Metabolism: Physical analysis Chemical analysis Enzymatic activity Permeability and transport Systematics: Phenotypic characterization DNA sequence similarities Ribosomal RNA hybridization and gene sequencing Nucleic acid probes General Methods: Laboratory safety Photography Records and reports

[Phage therapy for multidrug-resistant

2025-06-25

Jia Wu , Jun Wang | PubMed

Acinetobacter baumannii is a Gram-negative opportunistic pathogen widely distributed in hospital settings. It can survive for a long time and cause a variety of infections, including pneumonia, septicemia, urinary tract … Acinetobacter baumannii is a Gram-negative opportunistic pathogen widely distributed in hospital settings. It can survive for a long time and cause a variety of infections, including pneumonia, septicemia, urinary tract infections, and meningitis. The bacterium demonstrates extensive resistance, particularly to critical antibiotics like carbapenems and polymyxins, posing a serious threat to the recovery of severely ill patients. Carbapenem-resistant A. baumannii has been designated as a pathogen of critical priority on the World Health Organization (WHO) Bacterial Pathogen Priority List, requiring urgent development of new therapeutic agents. Phages, as a novel biological control approach, exhibit substantial potential in combating A. baumannii infections due to their specific ability to infect and lyse bacteria. This review highlights the application and potential of phages and phage-derived enzymes against multidrug-resistant A. baumannii, considering the epidemiological trends of A. baumannii in China, with the aim of providing innovative insights and strategies for phage therapy of drug-resistant bacterial infections.

[Methodological breakthroughs and challenges in research of soil phage microecology].

2025-06-25

Xiaofang Wang , Shuo Wang , Keming Yang +4 more | PubMed

Phages, as obligate bacterial and archaeal parasites, constitute a virus group of paramount ecological significance due to their exceptional abundance and genetic diversity. These biological entities serve as critical regulators … Phages, as obligate bacterial and archaeal parasites, constitute a virus group of paramount ecological significance due to their exceptional abundance and genetic diversity. These biological entities serve as critical regulators in Earth's ecosystems, driving biogeochemical cycles, energy fluxes, and ecosystem services across terrestrial and marine environments. Within soil microbiomes, phages function as microbial "dark matter," maintaining the soil-plant system balance through precise modulation of the microbial community structure and functional dynamics. Despite the growing research interests in soil phages in recent years, the proportion of such studies in environmental virology remains disproportionately low, which is primarily attributed to researchers' limited familiarity with the research methodologies for phage microecology, incomplete technical frameworks, and inherent challenges posed by soil environmental complexity. To address these challenges, this review synthesizes cutting-edge methodologies for soil phage investigation from four aspects: (1) tangential flow filtration (TFF)-based phage enrichment strategies; (2) integrated quantification approaches combining double-layer agar plating, epifluorescence microscopy, and flow cytometry; (3) multi-omics analytical pipelines leveraging metagenomics and viromics datasets; and (4) computational frameworks merging machine learning algorithms with eco-evolutionary theory for deciphering phage-host interaction networks. Through comparative analysis of methodological principles, technical merits, and application scopes, we establish a comprehensive workflow for soil phage research. Future research in this field should prioritize: (1) construction of soil phage resource libraries, (2) exploration of RNA phages based on transcriptomes, (3) functional characterization of unknown genes, and (4) deep integration and interaction validation of multi-omics data. This systematic methodological synthesis provides critical technical references for addressing fundamental challenges in characterizing soil phages regarding the community structure, functional potential, and interaction mechanisms with hosts.

Proteomic analysis reveals phage-driven metabolic shifts and biofilm disruption in methicillin-resistant Staphylococcus aureus (MRSA)

2025-06-25

Khulood Hamid Dakheel , Raha Abdul Rahim , Jameel R. Al‐Obaidi +4 more | World Journal of Microbiology and Biotechnology

Methicillin-resistant Staphylococcus aureus (MRSA) biofilms pose a severe risk to public health, showing resistance to standard antibiotics, which drives the need for novel antibacterial strategies. Bacteriophages have emerged as potential … Methicillin-resistant Staphylococcus aureus (MRSA) biofilms pose a severe risk to public health, showing resistance to standard antibiotics, which drives the need for novel antibacterial strategies. Bacteriophages have emerged as potential agents against biofilms, especially through their phage-encoded enzymes that disrupt the biofilm matrix, enhancing bacterial susceptibility. In this study, two bacteriophages, UPMK_1 and UPMK_2, were propagated on MRSA strains t127/4 and t223/20, respectively. Biofilms formed by these strains were treated with phages at specified concentrations, followed by protein extraction and analysis. Comparative proteomic profiling was performed using one-dimensional and two-dimensional SDS-PAGE, with protein identification facilitated by MALDI-TOF/TOF MS spectrometry, to observe biofilm degradation effects. Proteomic analysis revealed that phage treatment induced significant changes in biofilm protein expression, particularly with upregulated ribosome-recycling factors and elongation factors linked to enhanced protein synthesis, reflecting a reactivation of amino acid metabolism in the treated biofilms. This was marked by upregulated intracellular proteases like CIpL, which play a role in protein refolding and degradation, critical for phage progeny production and biofilm disruption. Phage treatment demonstrated notable effects on the metabolic and protein synthesis pathways within MRSA biofilms, suggesting that phages can redirect bacterial cellular processes to favour biofilm breakdown. This indicates the potential of bacteriophages as a viable adjunct to traditional antimicrobial approaches, particularly in combating antibiotic-resistant infections like MRSA. The study underscores the efficacy of bacteriophages as anti-biofilm agents, offering a promising strategy to weaken biofilms and combat antibiotic resistance through targeted disruption of bacterial metabolic pathways and biofilm integrity.

A novel phage phaST4: Characterization and its protective potential against Aeromonas hydrophila infection in swamp eels

2025-06-25

Jianfen Wu , Lifei Chen , Sixuan Wu +5 more | Aquaculture Reports

In-silico Innovative mRNA Vaccine Development Using Multi-Epitopes of SopD Protein for Enteric Fever Caused by Salmonella enterica

2025-06-25

Aaiza Mumtaz , Muhammad Umair , Hadia Hussain +2 more | Jordan Journal of Pharmaceutical Sciences

An increase in antibiotic resistance has created significant challenges in treating Salmonella enterica infections. Consequently, various vaccines have been developed as practical alternatives to antibiotics for preventing S. enterica infections. … An increase in antibiotic resistance has created significant challenges in treating Salmonella enterica infections. Consequently, various vaccines have been developed as practical alternatives to antibiotics for preventing S. enterica infections. mRNA vaccine technology is rapidly advancing as a replacement for conventional methods due to its high efficiency, low cost, and ability to elicit a strong humoral immune response. This research aims to develop a novel mRNA vaccine against S. enterica using immunoinformatics approaches. The protein SopD was selected, and its suitable epitopes were identified. These epitopes were evaluated to ensure they are antigenic, non-allergenic, and non-toxic. Subsequently, the epitopes were linked using appropriate linkers to create a vaccine construct. This construct was further analyzed and subjected to molecular docking with the Toll-like receptor TLR3 using the HDock server. Molecular dynamics (MD) simulations showed that the vaccine construct is stable based on RMSD and RMSF parameters. Immune simulation indicated the vaccine’s efficacy, and it was successfully cloned using the SnapGene tool. Finally, a multi-epitope protein was modeled and optimized. The results demonstrated that the vaccine construct is effective, non-allergenic, non-toxic, and successfully cloned. Overall, the findings suggest that the designed mRNA vaccine construct could be a promising candidate for S. enterica treatment, pending validation through in vitro techniques such as ELISA and in vivo testing in animal models.

A Two‐Component Pseudo‐Icosahedral Protein Nanocompartment with Variable Shell Composition and Irregular Tiling

2025-06-25

Cassandra A. Dutcher , Michael P. Andreas , Tobias W. Giessen | Advanced Science

Abstract Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells … Abstract Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein‐based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein‐based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral Hong Kong 97 (HK97)‐fold. Here, the characterization of a Family 2B two‐component encapsulin from Streptomyces lydicus is reported. The differential assembly behavior of the two shell components and their ability to co‐assemble into mixed shells with variable shell composition is demonstrated. The structures of both shell proteins are determined using cryo‐electron microscopy. Using 3D‐classification and cross‐linking studies, the irregular tiling of mixed shells is highlighted. This work expands the known assembly modes of HK97‐fold proteins and lays the foundation for future functional and engineering studies on two‐component encapsulins.

Broad-spectrum virus elimination by nasal mucosa-colonized wild-type Bacillus subtilis

2025-06-25

Yuchen Li , Chengjie Yang , Rongfeng Tang +7 more | Research

Characterization of a Phage vB_LZ 2044 Deriving from K1-Type Hypervirulent Klebsiella pneumoniae Efficient Against Liver Infection Mice Model

2025-06-25

Liqin Shi , Yulan Su , Zhen Li +5 more | Probiotics and Antimicrobial Proteins

Multi-omics characterization of a lytic phage targeting Listeria monocytogenes

2025-06-25

Stevan Cucić , Leena Putzeys , Maarten Boon +4 more | mSystems

ABSTRACT Listeria monocytogenes is a foodborne pathogenic bacterium that can persist in food-processing environments. Strictly lytic Listeria phages have shown promise as biosanitation and biocontrol agents. However, little is known … ABSTRACT Listeria monocytogenes is a foodborne pathogenic bacterium that can persist in food-processing environments. Strictly lytic Listeria phages have shown promise as biosanitation and biocontrol agents. However, little is known about the molecular progression of phage expression and the host gene expression profile it elicits in Listeria . In this work, the P100-like phage CKA15 was characterized using a proteogenomics-based approach to identify virion-associated proteins, Illumina-based RNA-seq to analyze time-resolved host and phage transcript abundance during infection, and ONT-cappable-seq to experimentally determine the operon structure of the phage genome. We detected 29 phage-encoded putative particle-associated proteins. During infection, a progressive decrease in host transcript abundance and an increase in phage transcript abundance are observed. The progression of phage gene expression indicates a switch in functions from hypothetical at 5 min; nucleic acid metabolism at 15; structural proteins at 25; and DNA packaging, tail assembly, and lysis at 40 min post-infection. Using ONT-cappable-seq, we identified 81 phage transcription start sites (TSS) and 66 transcription termination sites (TTS). We used motif analysis to identify two classes of promoters, corresponding to early and late infection stages. Profound changes in the host transcriptome became evident 5 min post-infection. GO enrichment and KEGG pathway analysis indicate a downregulation of host transcription factor expression and an upregulation of translation, cobalamin biosynthesis, and propanediol metabolism. This research contributes to our systems-level understanding of the infection process of a strictly lytic phage infecting an important foodborne pathogen. IMPORTANCE Listeria monocytogenes is an important foodborne pathogenic bacterium that contributes to significant mortality worldwide. Since bacteriophages have evolved diverse mechanisms to take over their host bacteria, studying phage interactions with pathogenic bacteria enables researchers to develop novel ways of controlling pathogenic bacteria and tools to study them. Detection of phage particle-associated proteins using mass spectrometry combined with transcriptomic techniques that determine the operon structure of the phage genome, time-resolved transcript abundance of phage, as well as host transcripts, comprises powerful approaches for phage characterization. Moreover, these analyses provide a starting point for hypothesis generation in relation to different aspects of the biology of phages infecting L. monocytogenes , including phage particle assembly, gene regulation, host takeover, and bacterial response to phage infection.

Structural Insights into the Regulatory Mechanisms of the Toxic Activity of Sofic in Anti-Phage Defense Systems

2025-06-24

Zhuoxi Wu , Guodong Chen , Libang He +5 more | International Journal of Molecular Sciences

The FIC domain-containing protein Sofic has recently been shown to provide robust protection to bacteria against phage infection. Sofic acts as a toxic protein, inducing abortive infection through the AMPylation … The FIC domain-containing protein Sofic has recently been shown to provide robust protection to bacteria against phage infection. Sofic acts as a toxic protein, inducing abortive infection through the AMPylation of target proteins during phage invasion. However, the molecular mechanisms regulating Sofic’s toxic activity remain elusive. In this study, we identified a small gene encoding a short protein located downstream of Sofic in the genome, named AS1 (anti-Sofic1), which functions as an antitoxic protein to counteract Sofic’s toxicity. The crystal structure of Sofic revealed that the protein functions as a dimer in solution, with dimerization being indispensable for its toxic activity. Importantly, structural analysis indicated that ATP binding induces a conformational change in the C-terminal domain (CTD) of Sofic, underscoring the critical role of the CTD in mediating its toxic effects. In vitro colony-forming assays confirmed that the interaction between the CTD and the Amylase domain is crucial for Sofic’s toxic activity. Overall, our results provide molecular insights into the regulatory mechanisms of Sofic in antiviral immunity.

Phage Therapy in Managing Multidrug-Resistant (MDR) Infections in Cancer Therapy: Innovations, Complications, and Future Directions

2025-06-24

Alice Njolke Mafe , Dietrich Büsselberg | Pharmaceutics

Multidrug-resistant (MDR) bacterial infections present a major challenge in cancer therapy, particularly for immunocompromised patients undergoing chemotherapy, radiation, or surgery. These infections often arise from prolonged antibiotic use, hospital-acquired pathogens, … Multidrug-resistant (MDR) bacterial infections present a major challenge in cancer therapy, particularly for immunocompromised patients undergoing chemotherapy, radiation, or surgery. These infections often arise from prolonged antibiotic use, hospital-acquired pathogens, and weakened immune defenses, leading to increased morbidity and mortality. As conventional antibiotics become less effective against MDR strains, there is an urgent need for alternative treatment options. This review highlights phage therapy as a promising approach to managing MDR bacterial infections in cancer patients. Once widely used, phage therapy has recently regained attention as a targeted antimicrobial strategy that can specifically eliminate harmful bacteria while preserving the beneficial microbiota. Phages work by directly lysing bacteria, disrupting biofilms, and synergizing with antibiotics to restore bacterial susceptibility. These mechanisms make phage therapy especially appealing for treating infections that complicate cancer treatments. However, the clinical application of phage therapy faces challenges such as variability in phage–host interactions, regulatory hurdles, and immune responses in patients. This review identifies gaps in current research regarding the use of phage therapy for MDR infections in cancer patients. By examining recent innovations, therapeutic mechanisms, and associated limitations, we provide valuable insights into the potential of phage therapy for improving infection management in oncology. Future research should focus on refining phage delivery methods, assessing long-term safety, and exploring combination therapies to maximize clinical efficacy. Overcoming these challenges could position phage therapy as a valuable complement to existing antimicrobial strategies in cancer care.

Fast and accurate in silico antigen typing with Kaptive 3

2025-06-24

Thomas D. Stanton , Marit A. K. Hetland , Iren H. Löhr +2 more | Microbial Genomics

Surface polysaccharides are common antigens in priority pathogens and therefore attractive targets for novel control strategies such as vaccines, monoclonal antibody and phage therapies. Distinct serotypes correspond to diverse polysaccharide … Surface polysaccharides are common antigens in priority pathogens and therefore attractive targets for novel control strategies such as vaccines, monoclonal antibody and phage therapies. Distinct serotypes correspond to diverse polysaccharide structures that are encoded by distinct biosynthesis gene clusters; e.g. the Klebsiella pneumoniae species complex (KpSC) K- and O-loci encode the synthesis machinery for the capsule (K) and outer-lipopolysaccharides (O), respectively. We previously presented Kaptive and Kaptive 2, programmes to identify K- and O-loci directly from KpSC genome assemblies (later adapted for Acinetobacter baumannii ), enabling sero-epidemiological analyses to guide vaccine and phage therapy development. However, for some KpSC genome collections, Kaptive (v≤2) was unable to type a high proportion of K-loci. Here, we identify the cause of this issue as assembly fragmentation and present a new version of Kaptive (v3) to circumvent this problem, reduce processing times and simplify output interpretation. We compared the performance of Kaptive v2 and Kaptive v3 for typing genome assemblies generated from subsampled Illumina read sets (decrements of 10× depth), for which a corresponding high-quality completed genome was also available to determine the ‘true’ loci ( n =549 KpSC, n =198 A . baumannii ). Both versions of Kaptive showed high rates of agreement to the matched true locus amongst ‘typeable’ locus calls (≥96% for ≥20× read depth), but Kaptive v3 was more sensitive, particularly for low-depth assemblies (at <40× depth, v3 ranged 0.85–1 vs v2 0.09–0.94) and/or typing KpSC K-loci (e.g. 0.97 vs 0.82 for non-subsampled assemblies). Overall, Kaptive v3 was also associated with a higher rate of optimal outcomes; i.e. loci matching those in the reference database were correctly typed, and genuine novel loci were reported as untypeable (73–98% for v3 vs 7–77% for v2 for KpSC K-loci). Kaptive v3 was >1 order of magnitude faster than Kaptive v2, making it easy to analyse thousands of assemblies on a desktop computer, facilitating broadly accessible in silico serotyping that is both accurate and sensitive. The Kaptive v3 source code is freely available on GitHub ( https://github.com/klebgenomics/Kaptive ), and has been implemented in Kaptive Web ( https://kaptive-web.erc.monash.edu/ ).

Evolutionary dynamics and research hotspots of phage applications against Acinetobacter baumannii infections from the past to the new era

2025-06-24

Ping Jiang , Xiaoqin Luo , Jing Zhao +3 more | Frontiers in Microbiology

Background Acinetobacter baumannii is a common hospital pathogen that poses a serious clinical challenge due to its rapidly increasing resistance to antibiotics. Phage therapy has been successfully used to treat … Background Acinetobacter baumannii is a common hospital pathogen that poses a serious clinical challenge due to its rapidly increasing resistance to antibiotics. Phage therapy has been successfully used to treat antibiotic resistant A. baumannii infections. The aim of this study was to comprehensively assess the current status and trend of research on the application of phages in A. baumannii infections through bibliometric analysis. Methods Studies on phages and A. baumannii infections were searched in the Web of Science Core Collection database and relevant articles were selected for inclusion in the study based on the inclusion criteria. Bibliometric and visual analysis of the included publications were performed using VOSviewer and CiteSpace software. Results A total of 264 studies were included. There is an increasing trend in the number of publications per year from 2010 to 2024. China was the leading country with 35.98% of the total publications. Tzu Chi University and Lin, Nien-Tsung were the most influential institution and author, respectively. The journal with the highest H-index was Frontiers in Microbiology, and Viruses-Basel was the most prolific journal. Antimicrobial Agents and Chemotherapy was the most cited journal. Phages endolysin and phage therapy were found to be the widely researched aspects, biofilm, phage resistance and synergistic effect are recent research hotspots. Conclusion In the last decade or so, this is the first bibliometric study that systematically describes the research hotspots and development trends on phages in A. baumannii infections. Research hotspots should be given more attention.

Development of a colloidal gold immunochromatographic strip to detect equine infectious anemia virus

2025-06-24

Jianzhong Wang , Jicheng Qiu , Mengmeng Wang +3 more | Virology Journal

Synergistic efficacy of phages along with vancomycin for eradication of vancomycin-resistant Enterococcus faecalis biofilms

2025-06-23

Minakshi Sahu , Ranjeet Kumar Vishwakarma , Subhash Lal Karn +1 more | World Journal of Virology

The upsurge of antibiotic resistance is a significant challenge to public health, and the dry pipeline of new antibiotics has prompted the discovery of alternative treatment approaches. Enterococcus faecalis (E. … The upsurge of antibiotic resistance is a significant challenge to public health, and the dry pipeline of new antibiotics has prompted the discovery of alternative treatment approaches. Enterococcus faecalis (E. faecalis) isolates are often multidrug-resistant, posing challenges to antibiotic therapy. Bacteriophage therapy is being explored as an alternative method to treat the growing population of antibiotic-resistant infections. Nevertheless, many inherent limitations of phages diminish their therapeutic utility, notably the restricted host range and quick development of mutants. The specific types and quantities of bacteriophages and antibiotics may be crucial in generating the optimal phage-antibiotic synergy. To optimize the doses, order, and timing to optimize the synergy of phages and vancomycin on different bacteria states. A volume of 180 μL of E. faecalis bacteria in the logarithmic growth phase, with a concentration of approximately 1 × 108 colony forming units (CFUs)/mL, was introduced onto a microtitre plate. Subsequently, 20 μL of phage suspension (1 × 106 PFUs/mL), vancomycin (16 µg/mL), or a combination of both was introduced into the designated wells in the specified sequence and incubated at 37 °C for 48 hours. The number of live bacteria was counted at different time points using standardized CFU counting protocols. The biofilm model demonstrated that combining phages with vancomycin can eradicate the biofilm. Sequential therapy, involving phage application 8 hours before the antibiotic at a concentration of 108 PFUs/mL, proved the most efficient in eliminating the biofilms and killing the planktonic form of E. faecalis. The combination of phage ɸEFP01 at a higher concentration with a subinhibitory concentration of vancomycin yields a synergistic antibacterial outcome on E. faecalis strain resistant to vancomycin.

Refinement of the Reference Viral Database (RVDB) for improving bioinformatics analysis of virus detection by high-throughput sequencing (HTS)

2025-06-23

Pei-Ju Chin , Jaysheel Bhavsar , Trent J. Bosma +3 more | mSphere

All biological products are required to demonstrate the absence of adventitious viruses (AVs), which may be inadvertently introduced at different steps involved in the manufacturing process. The currently recommended in … All biological products are required to demonstrate the absence of adventitious viruses (AVs), which may be inadvertently introduced at different steps involved in the manufacturing process. The currently recommended in vitro and in vivo virus detection assays have limitations for broad detection and are lengthy and laborious. Additionally, the use of animals is discouraged by the global 3 R's initiative for replacement, reduction, and refinement. High-throughput or next-generation sequencing (HTS/NGS) technologies can rapidly detect known and novel viruses in biological materials. There are, however, challenges for HTS detection of AVs due to differential abundance of viral sequences in public databases, which led to the creation of a non-redundant, Reference Viral Database (RVDB) containing all viral, viral-like, and viral-related sequences, with a reduced cellular sequence content. In this paper, we describe improvements in RVDB, which include the transition of RVDB production scripts from the original Python 2 to Python 3 codebase, updating the semantic pipeline to remove misannotated non-viral sequences and irrelevant viral sequences, use of taxonomy for the removal of phages, and inclusion of a quality-check step for SARS-CoV-2 genomes to exclude low-quality sequences. Additionally, RVDB website updates include search tools for exploring the database sequences and implementation of an automatic pipeline for providing annotation information to distinguish non-viral and viral sequences in the database. These updates for refining RVDB are expected to enhance HTS bioinformatics by reducing the computational time and increasing the accuracy for virus detection.IMPORTANCEHigh-throughput sequencing (HTS) has emerged as an advanced technology for demonstrating the safety of biological products. HTS can be used as an alternative adventitious virus detection method for replacing the currently recommended in vivo and PCR assays and supplementing or replacing the in vitro cell culture assays. However, HTS bioinformatics analysis for broad virus detection, including both known and novel viruses, depends on using a comprehensive and accurately annotated database. In this study, we have refined our original comprehensive Reference Virus Database (RVDB) for greater accuracy of virus detection with a reduced computational burden. Additionally, the production script for automating the generation of RVDB was updated to facilitate reliable database production and timely availability.

Frenemy: adaptive temperate phage_SAP_1432 supports Staphylococcus aureus survival in changing temperatures

2025-06-23

Ting-ting Liu , Pengcheng Gao , Jinjie Cui +4 more | Microbiology Spectrum

It is important to understand how the presence of pathogens could benefit the survival of their hosts during climate change. In this study, we investigated the influence of the heat-resistant … It is important to understand how the presence of pathogens could benefit the survival of their hosts during climate change. In this study, we investigated the influence of the heat-resistant temperate phage phage_SAP_1432 on its bacterial host Staphylococcus aureus Q1432 at different temperatures. Thermal host performance curves at a multiplicity of infection of 0.001 showed that the phage killed the bacterium efficiently from 20 to 39°C and from 47 to 50°C. However, the phage resulted in a 41.2% increase in the maximal growth rate for the host bacterium from 1.53 (95% confidence interval [CI]: 1.42-1.63) in the absence of phage_SAP_1432 to 2.16 (95% CI: 2.02-2.37) in its presence, along with a shift in the optimum temperature from 41.0°C to 44.1°C. In the absence of phage, the maximum survival temperature of S. aureus Q1432 was 51°C, but after co-culture with phage_SAP_1432, a few bacteria survived at 55°C-80°C. Lysogenesis occurred more easily at lower temperatures; the percentage of lysogenesis increased with phage concentration, while the maximum growth rate of the host decreased. Our findings provide new evidence that heat-resistant temperate phages can benefit the survival of their bacterial host at specific temperatures, giving a new perspective on the effects of co-evolution of heat-resistant temperate phages and bacterial hosts in an era of global climate change. Understanding pathogen-host interactions is crucial for predicting climate change impacts on microbial ecosystems. This study examined the heat-resistant temperate phage_SAP_1432 and its effects on Staphylococcus aureus Q1432 at various temperatures. Phage_SAP_1432 enhanced the thermal performance and survival at high temperatures of its host at a low MOI. This mutual benefit demonstrates the adaptive advantages phages provide in changing thermal environments. As global temperatures rise, such phage-host interactions may play a critical role in microbial survival and evolution. Our research highlights the potential for phages to act as allies, offering a new perspective on the co-evolution of heat-resistant temperate phages and their bacterial hosts.

DNA virus-host patterns in lake and marine environments over the last glacial cycle

2025-06-23

Christiane Boeckel , Simeon Lisovski , Kathleen R. Stoof‐Leichsenring +4 more

Viruses are crucial to population control, biogeochemical cycling, and host evolution, making them essential for ecosystem function. Here, we explore long-term virus-host interactions in lake and marine environments across the … Viruses are crucial to population control, biogeochemical cycling, and host evolution, making them essential for ecosystem function. Here, we explore long-term virus-host interactions in lake and marine environments across the late Pleistocene and Holocene. We analysed sedimentary ancient DNA (sedaDNA) from five Siberian lakes and four Subarctic/Antarctic marine cores to infer past DNA virus taxa from metagenomic sequences. Viruses accounted for 0.089% (357,161 reads) of mapped reads across 2,084 taxa. Virus communities differ between lakes and marine sites, with lakes dominated by Caudoviricetes and marine environments featuring Caudoviricetes and Algavirales. Each time series shows compositional changes in virus communities from the Pleistocene to the Holocene, supporting the inference that sedaDNA can reconstruct time-resolved ancient viral assemblages. Among the most abundant viruses, we identified 83 virus-host pairs known from published literature to infect bacterial, archaeal, or eukaryotic hosts, and assessed their associations using co-variation patterns. Over millennia, virus-host co-variations are particularly stable in marine systems, especially for phytoplankton-infecting viruses. However, in the Bering Sea, we find a lack of virus-host correlation, likely because an Arctic Pelagibacter strain expanded rapidly after the Bering Strait opened, potentially due to absent viral infection. Antagonistic patterns also appear between bacteriophages and hosts, possibly linked to shifts between lytic and lysogenic cycles in response to environmental changes. This study shows that sedaDNA can reveal ancient viral community structures and long-term ecological patterns, highlighting the value of ancient viromes in understanding ecosystem-specific responses to environmental change.

Phage-based microbiome manipulation elucidates interactions within community context

2025-06-21

Tomas Hessler , Dawn Chiniquy , Benjamin A. Adler +7 more | bioRxiv (Cold Spring Harbor Laboratory)

Testing microbial interaction hypotheses remains a major challenge in microbiome research. Bacteriophages have the potential to probe organism-organism interactions within complex microbiomes, yet are rarely used for this purpose. Here, … Testing microbial interaction hypotheses remains a major challenge in microbiome research. Bacteriophages have the potential to probe organism-organism interactions within complex microbiomes, yet are rarely used for this purpose. Here, we isolated nine narrow host range phages that replicate in several ecologically important Variovorax species. As Variovorax CL14 degrades the plant root-stunting hormone auxin, we used phages to eliminate V. CL14 from a rhizosphere consortium and reestablished the stunted root phenotype. We used three of the phages to deplete another Variovorax, SCN45, from complex communities to test correlation network-based hypotheses of thiamine interdependencies. Genome-resolved metagenomics revealed that specific taxa decreased in relative abundance following Variovorax depletion and could be rescued by thiamine supplementation. Thus, we confirmed thiamine production as the mechanistic basis for interdependence. These experiments lay the foundation for research that employs wildtype and engineered phages to test interaction hypotheses and for targeted microbiome manipulation.

Engineering Escherichia coli FAD synthetase for the biosynthesis of FAD nucleotide analogues results in aminoglycoside antibiotic tolerance

2025-06-21

Amrita B. Hazra , Arnab Mukherjee , Ateek Shah +7 more | bioRxiv (Cold Spring Harbor Laboratory)

The presence of the adenosine moiety in flavin adenine dinucleotide (FAD), nicotimanide adenine dinculeotide, coenzyme A, and S-adenosylmethionine cofactors is intriguing as it appears to play no direct catalytic role. … The presence of the adenosine moiety in flavin adenine dinucleotide (FAD), nicotimanide adenine dinculeotide, coenzyme A, and S-adenosylmethionine cofactors is intriguing as it appears to play no direct catalytic role. In FAD biosynthesis, the bifunctional FAD synthetase catalyzes FMN adenylation using ATP via its FMN adenylyltransferase (FMNAT) domain. Substituting ATP with alternative nucleotides in this reaction would enable the synthesis of FAD nucleotide analogues. This study explores nucleotide selectivity of the Escherichia coli FMNAT domain. Mutant enzyme variants were engineered which produce FAD analogues. Chromosomal substitution of the wild-type E. coli FAD synthetase with a mutated version resulted in the intracellular synthesis of FAD analogues and conferred increased tolerance to aminoglycoside antibiotics. These findings validate the FMNAT domain loop as a viable site for cofactor engineering, with potential synthetic biology applications. Finally, the observed correlation between FAD analogue production and antibiotic tolerance reveals that there exist novel metabolic mechanisms underlying bacterial resistance.

Atomistic simulations of intact virus capsids: A computational challenge worth the scientific payoff

2025-06-21

Carolina Pérez-Segura , Juan R. Perilla , Jodi A. Hadden‐Perilla | Current Opinion in Structural Biology

All-atom molecular dynamics (MD) simulations of intact virus capsids provide unparalleled insights into the functional motions of these complex macromolecular assemblies. Despite the computational challenges of simulating multimillion-atom systems, these … All-atom molecular dynamics (MD) simulations of intact virus capsids provide unparalleled insights into the functional motions of these complex macromolecular assemblies. Despite the computational challenges of simulating multimillion-atom systems, these simulations uniquely reveal the structural basis for emergent properties, including collective motions, allostery, selective permeability, and mechanical responses that are inaccessible through experimental methods. Capsid simulations also drive technological advancements in MD methodologies, analysis tools, and multiscale modeling, fostering broader innovations in structural biology and biophysics. Given next-generation computational resources, MD simulations will continue to illuminate virus biology, support antiviral drug discovery, and enhance preparedness for emerging viral diseases. Here, atomistic simulations of complete capsid assemblies are reviewed, and their role in elucidating fundamental principles of virus function and therapeutic targeting is discussed. Altogether, MD of intact capsids is a computational challenge worth the payoff.

Isolation and complete genome sequence of a novel Mycobacterium phage MS619

2025-06-21

Qiqi Zhao , Shi Xinpu , M. Liu +1 more | Virus Genes

PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB

2025-06-20

Jennifer J. Readshaw , Lindsey Doyle , Maria Puiu +7 more | PubMed

BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The … BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX Types harbour multiple protein subunits (between four and eight) and all encode a conserved putative phosphatase, PglZ, and an equally conserved, putative ATPase, BrxC. Almost all BREX systems also contain a site-specific methyltransferase, PglX. Despite having determined the structure and fundamental biophysical and biochemical behaviours of several BREX factors (including the PglX methyltransferase, the BrxL effector, the BrxA DNA-binding protein, and a commonly-associated transcriptional regulator, BrxR), the mechanism by which BREX impedes phage replication remains largely undetermined. In this study, we identified a stable BREX sub-complex of PglZ:BrxB, generated and validated a structural model of that protein complex, and assessed the biochemical activity of PglZ from BREX, revealing it to be a metal-dependent nuclease. PglZ can cleave cyclic oligonucleotides, linear oligonucleotides, plasmid DNA and both non-modified and modified linear phage genomes. PglZ nuclease activity has no obvious role in BREX-dependent methylation, but does contribute to BREX phage defence. BrxB binding does not impact PglZ nuclease activity. These data contribute to our growing understanding of BREX phage defence.

Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation

2025-06-20

Shuai Ji , Freed Ahmad , Baizhao Peng +4 more | Microbiome

Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment … Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear. The gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis. Gut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages. FMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes. Video Abstract.

Milk promotes the development of complex, protein-rich biofilms in Staphylococcus aureus and limits the efficacy of phage-based eradication strategies

2025-06-20

Seila Agún , Lucía Fernández , Ana Rodrı́guez +1 more | LWT

Characterization and genome analyses of the novel phages targeting extraintestinal Escherichia coli clones ST131 and ST410

2025-06-20

Md Shamsuzzaman , Yoon-Jung Choi , Shukho Kim +1 more | International Microbiology

Correction to 'Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance'.

2025-06-20

| PubMed

The Ability of Bacteriophages to Reduce Biofilms Produced by Pseudomonas aeruginosa Isolated from Corneal Infections

2025-06-20

Kuma Diriba , Dinesh Subedi , Naresh Kumar +1 more | Antibiotics

Pseudomonas aeruginosa (P. aeruginosa) is a common antibiotic-resistant pathogen, posing significant public health threats worldwide. It is a major cause of ocular infections, mostly linked to contact lens wear. P. … Pseudomonas aeruginosa (P. aeruginosa) is a common antibiotic-resistant pathogen, posing significant public health threats worldwide. It is a major cause of ocular infections, mostly linked to contact lens wear. P. aeruginosa often produces biofilm during infections, and these are also associated with antibiotic resistance. Bacteriophage (phage) therapy is emerging as a promising approach for treating multidrug-resistant P. aeruginosa. Objective: This study aimed to assess the antibiofilm effects of six phages against P. aeruginosa biofilms isolated from patients with corneal infections. Method: This study examined P. aeruginosa strains for their ability to form biofilms using crystal violet assay. Six P. aeruginosa bacteriophages (DiSu1 to DiSu6) were used, which were isolated from sewage water in Melbourne, Australia. Spot tests were used to assess phage sensitivity. The effect of phages against P. aeruginosa strains was determined using time–kill assay and efficiency of plating. The ability of phage to inhibit biofilm formation over 24 h or reduce preformed biofilms was also studied and confirmed using confocal laser scanning microscopy with Live/Dead staining. Result: After 24 h of incubation, all tested P. aeruginosa strains formed moderate to strong biofilms. All P. aeruginosa strains were sensitive to at least four of the six phages. The highest level of bacterial growth inhibition in the liquid infection model was observed when phages were applied at a multiplicity of infection (MOI) of 100. Certain bacteria/phage combinations were able to inhibit biofilm formation over 24 h, with the combination of strain PA235 and phage DiSu3 producing the highest inhibition (83%) at a MOI of 100. This was followed by the combinations of PA223/DiSu3 (56%), and PA225/DiSu5 (52%). For the reduction in preformed biofilms, the best combinations were PA235 (90%), PA221 (61%), and PA213 and PA225 (57% each), all with DiSu3 after 3 h. However, exposing the biofilm with phages for over 24 h appeared to promote phage resistance as there was evidence of biofilm growth, with the only combination still showing a significant reduction being PA221/DiSu3 (58%) at MOI of 100. Conclusions: This study showed that the effect of phages against P. aeruginosa is concentration (MOI) dependent. Phages at higher MOI have the ability to disrupt, inhibit, and reduce P. aeruginosa biofilms. However, prolonged exposure of the biofilm with phages appeared to promote phage resistance. To enhance phage efficacy and address this form of resistance, further studies utilizing phage cocktails or a combination of phages and antibiotics is warranted.

Viral whole-genome sequences of Pseudomonas jumbo phages, ΦNK1 and ΦBrmt, from sewage water in Japan

2025-06-20

Jumpei Fujiki , Tomohiro Nakamura , Natsuko Ichikawa +5 more | Microbiology Resource Announcements

ABSTRACT Jumbo phages have potentials for uncovering phage diversity. Here, we report the complete genome sequences of two Pseudomonas jumbo phages, ΦNK1 and ΦBrmt, isolated from waste water in Japan. … ABSTRACT Jumbo phages have potentials for uncovering phage diversity. Here, we report the complete genome sequences of two Pseudomonas jumbo phages, ΦNK1 and ΦBrmt, isolated from waste water in Japan. To explore their molecular characteristics, whole phage genomes were sequenced and assembled via the short- and long-read platforms.

A novel genus of virulent phage targeting Acinetobacter baumannii: Efficacy and safety in a murine model of pulmonary infection

2025-06-20

JiaWang Wang , Huan Hu , Qingqing Wang +6 more | PLoS Pathogens

Acinetobacter baumannii is a notable opportunistic pathogen responsible for severe hospital-acquired infections, with multidrug-resistant strains posing significant treatment challenges. Phage therapy, which employs bacteriophages as natural bacterial antagonists, has gained … Acinetobacter baumannii is a notable opportunistic pathogen responsible for severe hospital-acquired infections, with multidrug-resistant strains posing significant treatment challenges. Phage therapy, which employs bacteriophages as natural bacterial antagonists, has gained renewed attention as a promising solution to combat antibiotic-resistant infections. In this study, we isolated and characterized a novel virulent phage, vB_AbaS_qsb1, which specifically lyses A.baumannii . Phylogenetic and genomic analyses indicate that vB_AbaS_qsb1 is the founding member of a previously unreported genus, which we propose to name Acinibactriovirus , with Acinibactriovirus lysinus as the type species. vB_AbaS_qsb1 demonstrated robust stability across diverse temperature and pH ranges, a short latent period, and no known virulence or antibiotic resistance genes within its 54,713 bp dsDNA genome. Safety assessments showed that high-dose vB_AbaS_qsb1 induced no adverse effects in mice, with histopathology confirming its safety profile. Therapeutic experiments further indicated that vB_AbaS_qsb1 provided at least 50% protection against A.baumannii -induced pneumonia, significantly reducing bacterial loads and inflammation markers, while maintaining high phage titers in lung tissue.This study introduces vB_AbaS_qsb1 as a promising candidate for phage therapy against A.baumannii , offering both innovative insights and a valuable framework for future isolation, genomic characterization, and efficacy evaluation of phages targeting antibiotic-resistant bacteria.

A type IV pili-mediated mutualism between two co-resident temperate archaeal viruses and their host

2025-06-20

Jialin Xiang , Ravi R. Sonani , Yangyang Wang +7 more | Cell Reports

Underestimated roles of phages in biological wastewater treatment systems: Recent advances and challenges

2025-06-20

Wenxuan Huang , Feng Wang , Yinglong Su +2 more | Journal of Hazardous Materials

Metagenomic analysis reveals gut phage diversity across three mammalian models

2025-06-20

Menghao Yu , Yunmeng Chu , Yong-ming Wang +5 more | Microbiome

The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown. … The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown. We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (> = 60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota. Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.

Structure of the virulence-associated Neisseria meningitidis filamentous bacteriophage MDAΦ

2025-06-20

Jan Böhning , Miles Graham , Mathieu Coureuil +5 more | Proceedings of the National Academy of Sciences

Neisseria meningitidis is a human commensal bacterium that can opportunistically invade the bloodstream and cross the blood–brain barrier, where it can cause septicemia and meningitis. These diseases, if left untreated, … Neisseria meningitidis is a human commensal bacterium that can opportunistically invade the bloodstream and cross the blood–brain barrier, where it can cause septicemia and meningitis. These diseases, if left untreated, can be lethal within hours. Hyperinvasive N. meningitidis strains often express a genomically encoded filamentous bacteriophage called MDAΦ, which promotes colonization of mucosal host surfaces to facilitate bacterial invasion. How this phage is organized and how it promotes biofilm formation and infection at the molecular level is unclear. Here, we present an electron cryomicroscopy structure of the MDA phage, showing that MDAΦ is a class I filamentous inovirus, with the major capsid protein (MCP) arranged within the phage as a highly curved and densely packed α-helix. Comparison with other filamentous bacteriophages offers clues about inoviral genome encapsidation mechanisms, providing a framework for understanding the evolutionary diversity of inoviruses. A disordered, N-terminal segment in the MCP presents hydrophobic patches on the surface of assembled phage particles, which, together with electron cryotomography data of phage bundles, furnishes a structural rationale for phage–phage interactions that were seen previously in an epithelium adhesion infection model of N. meningitidis . Taken together, our results shed light on the structure, organization, and higher-order assembly of a biomedically relevant phage encoded in the genome of a human pathogen. Molecular insights gleaned from this study increase our understanding of phage evolution, phage-mediated bacterial adhesion, and pathogenicity.

Investigating the novel Escherichia coli bacteriophage Jgk1 as a potential antimicrobial agent

2025-06-20

Mengxin Gong , Mingyuan Li , Jilian Wang +2 more | International Microbiology

A lytic vibriophage as a potential biocontrol agent against vibriosis in aquaculture

2025-06-19

Yunlan Yang , Wanxuan Zhong , Haifeng Ding +7 more | Fish & Shellfish Immunology

A semi-mechanistic Pharmacokinetic/Pharmacodynamic model for quantifying phage-antibiotic synergy against Pseudomonas aeruginosa

2025-06-19

Omar Assafiri , Qixuan Hong , Sandra Morales +2 more | Expert Opinion on Drug Delivery

Multidrug-resistant (MDR) Pseudomonas aeruginosa is among the top three pathogens urgently needing new treatments. Phage therapy offers an alternative to antibiotics by auto-dosing and by targeting bacteria that are resistant … Multidrug-resistant (MDR) Pseudomonas aeruginosa is among the top three pathogens urgently needing new treatments. Phage therapy offers an alternative to antibiotics by auto-dosing and by targeting bacteria that are resistant to conventional antibiotics, and combining phages with antibiotics may overcome shortcomings of monotherapy. We developed a novel semi-mechanistic pharmacokinetic/pharmacodynamic (PK/PD) model based on static in vitro time-kill data evaluating ciprofloxacin (CIPRO; 0-128 µg/mL) and bacteriophage PEV31 (0.01-100 MOI) individually and in combination against MDR P. aeruginosa strain FADDI-PA001. Additionally, a Shiny-based interactive application was designed to simulate and visualize the impact of varying concentrations of phage and antibiotic treatments, facilitating real-time regimen optimization. Monotherapy with either CIPRO or PEV31 inhibited bacterial growth for less than 8 h before regrowth occurred; complete eradication was achieved only at high CIPRO concentrations (64 and 128 µg/mL). In combination (with CIPRO doses above 2 µg/mL), PEV31 and CIPRO acted synergistically, reducing bacterial levels below 102 CFU/mL at 24 h. The final PK/PD model which included a phage-bacteria-interaction term and implemented CIPRO's effect as a power-model successfully captured the observed time-kill-data for both monotherapy and combination therapy. These promising findings support further in vivo validation and mechanistic studies to advance combination therapy for MDR pathogens. Our integrated approach paves way for clinical translation.

Bacteriophage-based veterinary products: aligning regulatory framework and development challenges for market integration

2025-06-19

Céline Antoine , D.M. Mackay , Paul J. Midtlyng +5 more | Biologicals

Effects of dietary supplementation of Bacillus subtilis and bacteriophage on water quality, carcass traits and muscle growth of Magang Geese

2025-06-19

Yong Li , Yongquan Luo , Yuanhao Han +7 more | Research Square (Research Square)

<title>Abstract</title> Presence of <italic>Escherichia coli</italic> and <italic>Salmonella</italic> causes poor bath water quality, which is an important factor plaguing the development of the goose farming industry. As these bacteria release stable … <title>Abstract</title> Presence of <italic>Escherichia coli</italic> and <italic>Salmonella</italic> causes poor bath water quality, which is an important factor plaguing the development of the goose farming industry. As these bacteria release stable endotoxins like Lipopolysaccharide (LPS), which can affects goose farming by impairing their immune health. <italic>Bacillus subtilis</italic> is a non-toxic Gram-positive probiotic that can decompose organic matter in water, improves feed efficiency in animals, inhibit harmful bacteria, and enhances the animal growth. Bacteriophages are virus which can specifically kill bacteria, reduce their numbers in the environment. To evaluate the effects of dietary supplementation of <italic>Bacillus subtilis</italic> and bacteriophage on Magang geese's carcass traits, skeletal muscle weight percentage, myogenic gene and immunity factor gene mRNA expression during different rearing stages, 288 one-day old Magang geese were divied into 4 groups with with 6 replicates. The dietary treatments were group A, basal diet (with no treatment), group B, basal diet with 5.0×1010 PFU/L bacteriophage at a concentration of 1/103, group C, basal diet with 5.0×109 CFU/kg <italic>Bacillus subtilis</italic> and group D, basal diet with bacteriophage and <italic>Bacillus subtilis</italic> in combination same as group B and C. The results indicated that dietary supplementation of <italic>Bacillus subtilis</italic> and bacteriophage or their combination significantly increased wing length, tibia length and live weight on 60 d, reduced the levels of feeding environment water endotoxin as well as blood endotoxin in all stages, and suppressed the levels of <italic>Escherichia coli</italic>, <italic>Salmonella</italic>, and total bacterial colony in the water. It may also play a role in promoting muscle production through the mRNA and protein expression of muscle-associated factors (<italic>MYOD</italic>, <italic>MYOG</italic>, <italic>MYH1</italic>), insulin like growth factor (<italic>IGF-1</italic>) and reducing the mRNA and protein expression of inflammatory factors (<italic>TNF-α</italic>, <italic>IL-6</italic>), which may promote the growth of myofiber diameter and improve growth performance. These findings may guide new strategies to improve goose productivity and immunity, provide new eco-friendly methods to manage farming environments and thereby reducing the use of antibiotics.

Bacteria–phage (co)evolution is constrained in a synthetic community across multiple bacteria–phage pairs

2025-06-19

Meaghan Castledine , Daniel Padfield , M. Corrie Schoeman +2 more | Microbiology

Bacteriophages can be important drivers of bacterial densities and, therefore, microbial community composition and function. These ecological interactions are likely to be greatly affected by evolutionary dynamics because bacteria can … Bacteriophages can be important drivers of bacterial densities and, therefore, microbial community composition and function. These ecological interactions are likely to be greatly affected by evolutionary dynamics because bacteria can rapidly evolve resistance to phage, while phage can reciprocally evolve to increase infectivity. Most studies to date have explored eco-evolutionary dynamics using isolated pairs of bacteria–phage, but in nature, multiple bacteria and phages coexist and (co)evolve simultaneously. How coevolution plays out in this context is poorly understood. Here, we examine how three coexisting soil bacteria ( Ochrobactrum sp., Pseudomonas sp. and Variovorax sp.) interact and evolve with three species-specific bacteriophages over 8 weeks of experimental evolution, both as host–parasite pairs in isolation and as a mixed community. Across all species, phage resistance evolution was inhibited in polyculture, with the most pronounced effect on Ochrobactrum . Between bacteria–phage pairs, there were also substantial differences in the effect of phage on host densities and evolutionary dynamics, including whether pairs coevolved. Our results also indicate bacteria have a relative advantage over phage, with high rates of phage extinction and/or lower densities in polyculture. These contrasts emphasize the difficulty in generalizing findings from monoculture to polyculture and between model bacteria–phage pairs to wider systems. Future studies should consider how multiple bacteria and phage pairs interact simultaneously to better understand how coevolutionary dynamics happen in natural communities.