Murine colitis reveals a disease-associated bacteriophage community.

Abstract:

:The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbours a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence-independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease, establishing a platform for investigating phage involvement in IBD.

journal_name

Nat Microbiol

journal_title

Nature microbiology

authors

Duerkop BA,Kleiner M,Paez-Espino D,Zhu W,Bushnell B,Hassell B,Winter SE,Kyrpides NC,Hooper LV

doi

10.1038/s41564-018-0210-y

subject

Has Abstract

pub_date

2018-09-01 00:00:00

pages

1023-1031

issue

9

issn

2058-5276

pii

10.1038/s41564-018-0210-y

journal_volume

3

pub_type

杂志文章
  • Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    abstract::Host adaptation is a key factor contributing to the emergence of new bacterial, viral and parasitic pathogens. Many pathogens are considered promiscuous because they cause disease across a range of host species, while others are host-adapted, infecting particular hosts(1). Host adaptation can potentially progress to h...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2015.23

    authors: Klemm EJ,Gkrania-Klotsas E,Hadfield J,Forbester JL,Harris SR,Hale C,Heath JN,Wileman T,Clare S,Kane L,Goulding D,Otto TD,Kay S,Doffinger R,Cooke FJ,Carmichael A,Lever AM,Parkhill J,MacLennan CA,Kumararatne D,Douga

    更新日期:2016-01-25 00:00:00

  • Environmental drivers of a microbial genomic transition zone in the ocean's interior.

    abstract::The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea 1,2 . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertai...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-017-0008-3

    authors: Mende DR,Bryant JA,Aylward FO,Eppley JM,Nielsen T,Karl DM,DeLong EF

    更新日期:2017-10-01 00:00:00

  • Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer.

    abstract::CRISPR-Cas adaptive immune systems protect bacteria and archaea against their invading genetic parasites, including bacteriophages/viruses and plasmids. In response to this immunity, many phages have anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas targeting. To date, anti-CRISPR genes have primarily been discovered...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-020-0692-2

    authors: Mahendra C,Christie KA,Osuna BA,Pinilla-Redondo R,Kleinstiver BP,Bondy-Denomy J

    更新日期:2020-04-01 00:00:00

  • Growth control switch by a DNA-damage-inducible toxin-antitoxin system in Caulobacter crescentus.

    abstract::Bacterial toxin-antitoxin systems (TASs) are thought to respond to various stresses, often inducing growth-arrested (persistent) sub-populations of cells whose housekeeping functions are inhibited. Many such TASs induce this effect through the translation-dependent RNA cleavage (RNase) activity of their toxins, which ...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2016.8

    authors: Kirkpatrick CL,Martins D,Redder P,Frandi A,Mignolet J,Chapalay JB,Chambon M,Turcatti G,Viollier PH

    更新日期:2016-02-22 00:00:00

  • Author Correction: A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature microbiology

    pub_type: 已发布勘误

    doi:10.1038/s41564-019-0584-5

    authors: Cartmell A,Muñoz-Muñoz J,Briggs JA,Ndeh DA,Lowe EC,Baslé A,Terrapon N,Stott K,Heunis T,Gray J,Yu L,Dupree P,Fernandes PZ,Shah S,Williams SJ,Labourel A,Trost M,Henrissat B,Gilbert HJ

    更新日期:2019-11-01 00:00:00

  • A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation.

    abstract::Glycans are major nutrients for the human gut microbiota (HGM). Arabinogalactan proteins (AGPs) comprise a heterogenous group of plant glycans in which a β1,3-galactan backbone and β1,6-galactan side chains are conserved. Diversity is provided by the variable nature of the sugars that decorate the galactans. The mecha...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-018-0258-8

    authors: Cartmell A,Muñoz-Muñoz J,Briggs JA,Ndeh DA,Lowe EC,Baslé A,Terrapon N,Stott K,Heunis T,Gray J,Yu L,Dupree P,Fernandes PZ,Shah S,Williams SJ,Labourel A,Trost M,Henrissat B,Gilbert HJ

    更新日期:2018-11-01 00:00:00

  • Mini viral RNAs act as innate immune agonists during influenza virus infection.

    abstract::The molecular processes that determine the outcome of influenza virus infection in humans are multifactorial and involve a complex interplay between host, viral and bacterial factors1. However, it is generally accepted that a strong innate immune dysregulation known as 'cytokine storm' contributes to the pathology of ...

    journal_title:Nature microbiology

    pub_type: 信件

    doi:10.1038/s41564-018-0240-5

    authors: Te Velthuis AJW,Long JC,Bauer DLV,Fan RLY,Yen HL,Sharps J,Siegers JY,Killip MJ,French H,Oliva-Martín MJ,Randall RE,de Wit E,van Riel D,Poon LLM,Fodor E

    更新日期:2018-11-01 00:00:00

  • TRIM23 mediates virus-induced autophagy via activation of TBK1.

    abstract::Autophagy and interferon (IFN)-mediated innate immunity are critical antiviral defence mechanisms, and recent evidence indicated that tripartite motif (TRIM) proteins are important regulators of both processes. Although the role of TRIM proteins in modulating antiviral cytokine responses has been well established, muc...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-017-0017-2

    authors: Sparrer KMJ,Gableske S,Zurenski MA,Parker ZM,Full F,Baumgart GJ,Kato J,Pacheco-Rodriguez G,Liang C,Pornillos O,Moss J,Vaughan M,Gack MU

    更新日期:2017-11-01 00:00:00

  • Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice.

    abstract::Inflammasomes are signalling platforms that are assembled in response to infection or sterile inflammation by cytosolic pattern recognition receptors. The consequent inflammasome-triggered caspase-1 activation is critical for the host defence against pathogens. During infection, NLRP3, which is a pattern recognition r...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-020-00832-5

    authors: Dufies O,Doye A,Courjon J,Torre C,Michel G,Loubatier C,Jacquel A,Chaintreuil P,Majoor A,Guinamard RR,Gallerand A,Saavedra PHV,Verhoeyen E,Rey A,Marchetti S,Ruimy R,Czerucka D,Lamkanfi M,Py BF,Munro P,Visvikis O,

    更新日期:2021-01-11 00:00:00

  • Epstein-Barr virus ncRNA from a nasopharyngeal carcinoma induces an inflammatory response that promotes virus production.

    abstract::The Epstein-Barr virus M81 strain, isolated from a nasopharyngeal carcinoma, induces potent spontaneous virus production in infected B cells. We found that the M81 non-coding Epstein-Barr-encoded RNA EBER2, which carries polymorphisms that are mainly restricted to viruses found in endemic nasopharyngeal carcinomas, ma...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-019-0546-y

    authors: Li Z,Tsai MH,Shumilov A,Baccianti F,Tsao SW,Poirey R,Delecluse HJ

    更新日期:2019-12-01 00:00:00

  • Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform.

    abstract::The development of new drug regimens that allow rapid, sterilizing treatment of tuberculosis has been limited by the complexity and time required for genetic manipulations in Mycobacterium tuberculosis. CRISPR interference (CRISPRi) promises to be a robust, easily engineered and scalable platform for regulated gene si...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2016.274

    authors: Rock JM,Hopkins FF,Chavez A,Diallo M,Chase MR,Gerrick ER,Pritchard JR,Church GM,Rubin EJ,Sassetti CM,Schnappinger D,Fortune SM

    更新日期:2017-02-06 00:00:00

  • SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities.

    abstract::Bacteria have evolved diverse mechanisms to fend off predation by bacteriophages. We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component. Here, we describe an unusual SspABCD-SspE P...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-020-0700-6

    authors: Xiong X,Wu G,Wei Y,Liu L,Zhang Y,Su R,Jiang X,Li M,Gao H,Tian X,Zhang Y,Hu L,Chen S,Tang Y,Jiang S,Huang R,Li Z,Wang Y,Deng Z,Wang J,Dedon PC,Chen S,Wang L

    更新日期:2020-07-01 00:00:00

  • Modulation of membrane phosphoinositide dynamics by the phosphatidylinositide 4-kinase activity of the Legionella LepB effector.

    abstract::Legionella pneumophila, the causative bacterium for Legionnaires' disease, hijacks host membrane trafficking for the maturation of the Legionella-containing vacuole (LCV). The LCV membrane mainly contains PtdIns4P, which is important for anchoring many secreted Legionella effectors onto the LCV. Here, we identify a cr...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2016.236

    authors: Dong N,Niu M,Hu L,Yao Q,Zhou R,Shao F

    更新日期:2016-12-12 00:00:00

  • Protective antibodies against Eastern equine encephalitis virus bind to epitopes in domains A and B of the E2 glycoprotein.

    abstract::Eastern equine encephalitis virus (EEEV) is a mosquito-transmitted alphavirus with a high case mortality rate in humans. EEEV is a biodefence concern because of its potential for aerosol spread and the lack of existing countermeasures. Here, we identify a panel of 18 neutralizing murine monoclonal antibodies (mAbs) ag...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-018-0286-4

    authors: Kim AS,Austin SK,Gardner CL,Zuiani A,Reed DS,Trobaugh DW,Sun C,Basore K,Williamson LE,Crowe JE Jr,Slifka MK,Fremont DH,Klimstra WB,Diamond MS

    更新日期:2019-01-01 00:00:00

  • Erratum: Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein.

    abstract::This corrects the article DOI: 10.1038/nmicrobiol.2016.155. ...

    journal_title:Nature microbiology

    pub_type: 已发布勘误

    doi:10.1038/nmicrobiol.2017.107

    authors: Buffalo CZ,Bahn-Suh AJ,Hirakis SP,Biswas T,Amaro RE,Nizet V,Ghosh P

    更新日期:2017-06-12 00:00:00

  • Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence.

    abstract::The evolution of antibiotic resistance is a major threat to society and has been predicted to lead to 10 million casualties annually by 2050(1). Further aggravating the problem, multidrug tolerance in bacteria not only relies on the build-up of resistance mutations, but also on some cells epigenetically switching to a...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2016.20

    authors: Van den Bergh B,Michiels JE,Wenseleers T,Windels EM,Boer PV,Kestemont D,De Meester L,Verstrepen KJ,Verstraeten N,Fauvart M,Michiels J

    更新日期:2016-03-07 00:00:00

  • Evolution of host adaptation in the Salmonella typhoid toxin.

    abstract::The evolution of virulence traits is central for the emergence or re-emergence of microbial pathogens and for their adaptation to a specific host 1-5 . Typhoid toxin is an essential virulence factor of the human-adapted bacterial pathogen Salmonella Typhi 6,7 , the cause of typhoid fever in humans 8-12 . Typhoid toxin...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-017-0033-2

    authors: Gao X,Deng L,Stack G,Yu H,Chen X,Naito-Matsui Y,Varki A,Galán JE

    更新日期:2017-12-01 00:00:00

  • Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli.

    abstract::Tigecycline is one of the last-resort antibiotics to treat complicated infections caused by both multidrug-resistant Gram-negative and Gram-positive bacteria1. Tigecycline resistance has sporadically occurred in recent years, primarily due to chromosome-encoding mechanisms, such as overexpression of efflux pumps and r...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-019-0496-4

    authors: Sun J,Chen C,Cui CY,Zhang Y,Liu X,Cui ZH,Ma XY,Feng Y,Fang LX,Lian XL,Zhang RM,Tang YZ,Zhang KX,Liu HM,Zhuang ZH,Zhou SD,Lv JN,Du H,Huang B,Yu FY,Mathema B,Kreiswirth BN,Liao XP,Chen L,Liu YH

    更新日期:2019-09-01 00:00:00

  • Bacillus subtilis cell diameter is determined by the opposing actions of two distinct cell wall synthetic systems.

    abstract::Rod-shaped bacteria grow by adding material into their cell wall via the action of two spatially distinct enzymatic systems: the Rod complex moves around the cell circumference, whereas class A penicillin-binding proteins (aPBPs) do not. To understand how the combined action of these two systems defines bacterial dime...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-019-0439-0

    authors: Dion MF,Kapoor M,Sun Y,Wilson S,Ryan J,Vigouroux A,van Teeffelen S,Oldenbourg R,Garner EC

    更新日期:2019-08-01 00:00:00

  • Phosphatidic acid governs natural egress in Toxoplasma gondii via a guanylate cyclase receptor platform.

    abstract::Toxoplasma gondii establishes a lifelong chronic infection in humans and animals1. Host cell entry and egress are key steps in the lytic cycle of this obligate intracellular parasite, ensuring its survival and dissemination. Egress is temporally orchestrated, underpinned by the exocytosis of secretory organelles calle...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-018-0339-8

    authors: Bisio H,Lunghi M,Brochet M,Soldati-Favre D

    更新日期:2019-03-01 00:00:00

  • Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore-rice leaf surface interface.

    abstract::Cellular adhesion mediates many important plant-microbe interactions. In the devastating blast fungus Magnaporthe oryzae1, powerful glycoprotein-rich mucilage adhesives2 cement melanized and pressurized dome-shaped infection cells-appressoria-to host rice leaf surfaces. Enormous internal turgor pressure is directed on...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-020-0786-x

    authors: Rocha RO,Elowsky C,Pham NTT,Wilson RA

    更新日期:2020-12-01 00:00:00

  • Author Correction: Structures of the stator complex that drives rotation of the bacterial flagellum.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature microbiology

    pub_type: 已发布勘误

    doi:10.1038/s41564-020-00825-4

    authors: Deme JC,Johnson S,Vickery O,Aron A,Monkhouse H,Griffiths T,James RH,Berks BC,Coulton JW,Stansfeld PJ,Lea SM

    更新日期:2020-12-01 00:00:00

  • A humanized MDCK cell line for the efficient isolation and propagation of human influenza viruses.

    abstract::Here, we developed hCK, a Madin-Darby canine kidney (MDCK) cell line that expresses high levels of human influenza virus receptors and low levels of avian virus receptors. hCK cells supported human A/H3N2 influenza virus isolation and growth much more effectively than conventional MDCK or human virus receptor-overexpr...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-019-0433-6

    authors: Takada K,Kawakami C,Fan S,Chiba S,Zhong G,Gu C,Shimizu K,Takasaki S,Sakai-Tagawa Y,Lopes TJS,Dutta J,Khan Z,Kriti D,van Bakel H,Yamada S,Watanabe T,Imai M,Kawaoka Y

    更新日期:2019-08-01 00:00:00

  • Probing the metabolic heterogeneity of live Euglena gracilis with stimulated Raman scattering microscopy.

    abstract::Understanding metabolism in live microalgae is crucial for efficient biomaterial engineering, but conventional methods fail to evaluate heterogeneous populations of motile microalgae due to the labelling requirements and limited imaging speeds. Here, we demonstrate label-free video-rate metabolite imaging of live Eugl...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2016.124

    authors: Wakisaka Y,Suzuki Y,Iwata O,Nakashima A,Ito T,Hirose M,Domon R,Sugawara M,Tsumura N,Watarai H,Shimobaba T,Suzuki K,Goda K,Ozeki Y

    更新日期:2016-08-01 00:00:00

  • Tagging the type VI secretion system.

    abstract:: ...

    journal_title:Nature microbiology

    pub_type: 评论,杂志文章

    doi:10.1038/s41564-018-0277-5

    authors: Francetic O

    更新日期:2018-11-01 00:00:00

  • Pneumococcal quorum sensing drives an asymmetric owner-intruder competitive strategy during carriage via the competence regulon.

    abstract::Competition among microorganisms is a key determinant of successful host colonization and persistence. For Streptococcus pneumoniae, lower than predicted rates of co-colonizing strains suggest a competitive advantage for resident bacteria over newcomers. In light of evolutionary theory, we hypothesized that S. pneumon...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-018-0314-4

    authors: Shen P,Lees JA,Bee GCW,Brown SP,Weiser JN

    更新日期:2019-01-01 00:00:00

  • Influenza virus mRNA trafficking through host nuclear speckles.

    abstract::Influenza A virus is a human pathogen with a genome composed of eight viral RNA segments that replicate in the nucleus. Two viral mRNAs are alternatively spliced. The unspliced M1 mRNA is translated into the matrix M1 protein, while the ion channel M2 protein is generated after alternative splicing. These proteins are...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2016.69

    authors: Mor A,White A,Zhang K,Thompson M,Esparza M,Muñoz-Moreno R,Koide K,Lynch KW,García-Sastre A,Fontoura BM

    更新日期:2016-05-27 00:00:00

  • Multi-virion infectious units arise from free viral particles in an enveloped virus.

    abstract::Many animal viruses are enveloped in a lipid bilayer taken up from cellular membranes. Because viral surface proteins bind to these membranes to initiate infection, we hypothesized that free virions may also be capable of interacting with the envelopes of other virions extracellularly. Here, we demonstrate this hypoth...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2017.78

    authors: Cuevas JM,Durán-Moreno M,Sanjuán R

    更新日期:2017-05-22 00:00:00

  • Unexpected mode of engagement between enterovirus 71 and its receptor SCARB2.

    abstract::Enterovirus 71 (EV71) is a common cause of hand, foot and mouth disease-a disease endemic especially in the Asia-Pacific region1. Scavenger receptor class B member 2 (SCARB2) is the major receptor of EV71, as well as several other enteroviruses responsible for hand, foot and mouth disease, and plays a key role in cell...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/s41564-018-0319-z

    authors: Zhou D,Zhao Y,Kotecha A,Fry EE,Kelly JT,Wang X,Rao Z,Rowlands DJ,Ren J,Stuart DI

    更新日期:2019-03-01 00:00:00

  • The anti-inflammatory drug mesalamine targets bacterial polyphosphate accumulation.

    abstract::Mesalamine serves as the gold standard in treating ulcerative colitis. However, its precise mechanism(s) of action remains unclear. Here, we show that mesalamine treatment rapidly decreases polyphosphate levels in diverse bacteria, including members of the human gut microbiome. This decrease sensitizes bacteria toward...

    journal_title:Nature microbiology

    pub_type: 杂志文章

    doi:10.1038/nmicrobiol.2016.267

    authors: Dahl JU,Gray MJ,Bazopoulou D,Beaufay F,Lempart J,Koenigsknecht MJ,Wang Y,Baker JR,Hasler WL,Young VB,Sun D,Jakob U

    更新日期:2017-01-23 00:00:00