Abstract：
:Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.
journal_name
Nat Microbioljournal_title
Nature microbiologyauthors
Džunková M,Low SJ,Daly JN,Deng L,Rinke C,Hugenholtz Pdoi
10.1038/s41564-019-0526-2subject
Has Abstractpub_date
2019-12-01 00:00:00pages
2192-2203issue
12issn
2058-5276pii
10.1038/s41564-019-0526-2journal_volume
4pub_type
杂志文章abstract：:How does knowing the evolutionary history of microorganisms affect our analysis of microbiological datasets? Depending on the research question, the common ancestry of microorganisms can be a source of confounding variation, or a scaffolding used for inference. For example, when performing regression on traits, common...
journal_title：Nature microbiology
pub_type： 杂志文章,评审
doi：10.1038/s41564-018-0156-0
更新日期：2018-06-01 00:00:00
abstract：:The sexually transmitted pathogen Neisseria gonorrhoeae is regarded as being on the way to becoming an untreatable superbug. Despite its clinical importance, little is known about its emergence and evolution, and how this corresponds with the introduction of antimicrobials. We present a genome-based phylogeographical ...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-019-0501-y
更新日期：2019-11-01 00:00:00
abstract：:In the version of this Article originally published, author Carolina Falcón Garcia's name was coded wrongly, resulting in it being incorrect when exported to citation databases. This has now been corrected, though no visible changes will be apparent. ...
journal_title：Nature microbiology
pub_type： 已发布勘误
doi：10.1038/s41564-018-0350-0
更新日期：2019-02-01 00:00:00
abstract：:Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon. The toxins are large (308 and 270 kDa, respectively), homo...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/nmicrobiol.2015.2
更新日期：2016-01-11 00:00:00
abstract：:Zika virus (ZIKV) is associated with neonatal microcephaly and Guillain-Barré syndrome1,2. While progress has been made in understanding the causal link between ZIKV infection and microcephaly3-9, the life cycle and pathogenesis of ZIKV are less well understood. In particular, there are conflicting reports on the role...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-017-0092-4
更新日期：2018-03-01 00:00:00
abstract：:CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection1. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases2. While the essential requirements for immune activity are well under...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-020-0691-3
更新日期：2020-05-01 00:00:00
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
更新日期：2016-03-07 00:00:00
abstract：:Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur molecules, a signalling molecule1, a key nutrient for marine microorganisms2,3 and the major precursor for gaseous dimethyl sulfide (DMS). DMS, another infochemical in signalling pathways4, is important in global sulfur cycling2 and aff...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/nmicrobiol.2017.9
更新日期：2017-02-13 00:00:00
abstract：: ...
journal_title：Nature microbiology
pub_type： 社论
doi：10.1038/s41564-018-0320-6
更新日期：2018-12-01 00:00:00
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
更新日期：2017-01-23 00:00:00
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
更新日期：2017-05-22 00:00:00
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
更新日期：2019-12-01 00:00:00
abstract：:In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective. ...
journal_title：Nature microbiology
pub_type： 已发布勘误
doi：10.1038/s41564-018-0114-x
更新日期：2018-03-01 00:00:00
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
更新日期：2017-11-01 00:00:00
abstract：:Phylogenetic and geological evidence supports the hypothesis that life on Earth originated in thermal environments and conserved energy through methanogenesis or sulfur reduction. Here we describe two populations of the deeply rooted archaeal phylum Korarchaeota, which were retrieved from the metagenome of a circumneu...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-019-0362-4
更新日期：2019-04-01 00:00:00
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
更新日期：2016-05-27 00:00:00
abstract：:In structured environments, antibiotic-producing microorganisms can gain a selective advantage by inhibiting nearby competing species1. However, despite their genetic potential2,3, natural isolates often make only small amounts of antibiotics, and laboratory evolution can lead to loss rather than enhancement of antibi...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/nmicrobiol.2016.175
更新日期：2016-09-26 00:00:00
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
更新日期：2020-07-01 00:00:00
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
更新日期：2017-12-01 00:00:00
abstract：: ...
journal_title：Nature microbiology
pub_type： 社论
doi：10.1038/s41564-019-0408-7
更新日期：2019-03-01 00:00:00
abstract：:Clostridium difficile infection (CDI) is mediated by two major exotoxins, toxin A (TcdA) and toxin B (TcdB), that damage the colonic epithelial barrier and induce inflammatory responses. The function of the colonic vascular barrier during CDI has been relatively understudied. Here we report increased colonic vascular ...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-018-0300-x
更新日期：2019-02-01 00:00:00
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/s41564-020-0679-z
更新日期：2020-03-01 00:00:00
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
更新日期：2020-12-01 00:00:00
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
更新日期：2019-08-01 00:00:00
abstract：:Retroviral infection involves the reverse transcription of the viral RNA genome into DNA, which is subsequently integrated into the host cell genome. Human immunodeficiency virus type 1 (HIV-1) and other lentiviruses mediate the infection of non-dividing cells through the ability of the capsid protein1 to engage the c...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-020-0735-8
更新日期：2020-09-01 00:00:00
abstract：:Immune responses in insects are differentially triggered depending on the infection route used by the pathogen. In most studies involving Drosophila melanogaster and viruses, infection is done by injection, while oral infection, which is probably the most common route of viral entry in nature, remains unexplored. Here...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-018-0265-9
更新日期：2018-12-01 00:00:00
abstract：:The temporal dynamics of phytoplankton growth and activity have large impacts on fluxes of matter and energy, yet obtaining in situ metabolic measurements of sufficient resolution for even dominant microorganisms remains a considerable challenge. We performed Lagrangian diel sampling with synoptic measurements of popu...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/nmicrobiol.2017.118
更新日期：2017-07-31 00:00:00
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
更新日期：2020-04-01 00:00:00
abstract：:Pathogenic bacteria are armed with potent effector proteins that subvert host signalling processes during infection1. The activities of bacterial effectors and their associated roles within the host cell are often poorly understood, particularly for Chlamydia trachomatis2, a World Health Organization designated neglec...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/s41564-018-0271-y
更新日期：2018-12-01 00:00:00
abstract：:As they proliferate, fungi expose antigens at their cell surface that are potent stimulators of the innate immune response, and yet the commensal fungus Candida albicans is able to colonize immuno competent individuals. We show that C. albicans may evade immune detection by presenting a moving immunological target. We...
journal_title：Nature microbiology
pub_type： 杂志文章
doi：10.1038/nmicrobiol.2016.238
更新日期：2016-12-12 00:00:00
