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  • 1
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    Lifestyle of sponge symbiont phages by host prediction and correlative microscopy (2021)
    Nature Research
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    Publication Date: 2024-02-07
    Description: Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach (‘PhageFISH-CLEM‘) localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.
    Type: Article , PeerReviewed
    Format: text
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    Computational approaches to predict bacteriophage-host relationships (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-03
    Description: Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications.
    Print ISSN: 0168-6445
    Electronic ISSN: 1574-6976
    Topics: Biology
    Published by Oxford University Press
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    PAPER CURRENT
  • 3
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    SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-02
    Description: : Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools. Availability and implementation: SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS . Contact: redwards@mail.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Reference-independent comparative metagenomics using cross-assembly: crAss (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-08
    Description: Motivation: Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences. Results: Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities. Availability and implementation: crAss is available as a web server at http://edwards.sdsu.edu/crass/ , and the Perl source code can be downloaded to run as a stand-alone command line tool. Contact: dutilh@cmbi.ru.nl Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Preservation of bacterial DNA in 10-year-old guaiac FOBT cards and FIT tubes (2017)
    BMJ Publishing Group
    Details
    Publication Date: 2017-10-26
    Description: With great interest we read the article of Taylor et al in the Journal of Clinical Pathology regarding the use of guaiac faecal occult blood test (gFOBT) cards for microbiome studies. 1 gFOBT cards were found to be an easy to use option for stool collection and gained results comparable to fresh stool, even when cards were stored for up to 3 years at ambient temperature before DNA extraction. We would like to share our experience that even after 10 years of storage, gFOBT cards and faecal immunochemical test (FIT) tubes can be used to study the microbiome. Taylor et al conducted 16S rDNA amplicon sequencing for determination of outcome comparability within and between sample type and storage time. 1 Between-subject differences greatly outweighed any differences by sample collection type (fresh vs gFOBT) and time spent at ambient temperature (from 2 weeks up to 3 years after development of...
    Keywords: Open access
    Print ISSN: 0021-9746
    Electronic ISSN: 1472-4146
    Topics: Medicine
    Published by BMJ Publishing Group
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    PAPER CURRENT
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