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  1. Article ; Online: expam-high-resolution analysis of metagenomes using distance trees.

    Solari, Sean M / Young, Remy B / Marcelino, Vanessa R / Forster, Samuel C

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 20, Page(s) 4814–4816

    Abstract: Summary: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may ... ...

    Abstract Summary: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing.
    Availability and implementation: expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https://github.com/seansolari/expam.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Metagenome ; Metagenomics/methods ; Microbiota/genetics ; Software
    Language English
    Publishing date 2022-08-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac591
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease.

    D'Adamo, Gemma L / Chonwerawong, Michelle / Gearing, Linden J / Marcelino, Vanessa R / Gould, Jodee A / Rutten, Emily L / Solari, Sean M / Khoo, Patricia W R / Wilson, Trevor J / Thomason, Tamblyn / Gulliver, Emily L / Hertzog, Paul J / Giles, Edward M / Forster, Samuel C

    Cell reports. Medicine

    2023  Volume 4, Issue 7, Page(s) 101124

    Abstract: Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal ... ...

    Abstract Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade-specific metagenomic analysis identifies key, functionally distinct Enterococcus clades associated with either IBD or health. Strain-specific in vitro validation demonstrates differences in cell cytotoxicity and inflammatory signaling in intestinal epithelial cells, consistent with the colonic mucosa-specific response measured in patients with IBD. This demonstrates the importance of strain-specific phenotypes and consideration of anatomical sites in exploring the dysregulated host-bacterial interactions in IBD.
    MeSH term(s) Humans ; Inflammatory Bowel Diseases/genetics ; Colon/pathology ; Biopsy ; Intestinal Mucosa/microbiology ; Epithelial Cells/pathology
    Language English
    Publishing date 2023-07-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-3791
    ISSN (online) 2666-3791
    DOI 10.1016/j.xcrm.2023.101124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Extensive genome analysis identifies novel plasmid families in

    Gulliver, Emily L / Adams, Vicki / Marcelino, Vanessa Rossetto / Gould, Jodee / Rutten, Emily L / Powell, David R / Young, Remy B / D'Adamo, Gemma L / Hemphill, Jamia / Solari, Sean M / Revitt-Mills, Sarah A / Munn, Samantha / Jirapanjawat, Thanavit / Greening, Chris / Boer, Jennifer C / Flanagan, Katie L / Kaldhusdal, Magne / Plebanski, Magdalena / Gibney, Katherine B /
    Moore, Robert J / Rood, Julian I / Forster, Samuel C

    Microbial genomics

    2023  Volume 9, Issue 4

    Abstract: Globally, the anaerobic ... ...

    Abstract Globally, the anaerobic bacterium
    MeSH term(s) Humans ; Clostridium perfringens ; Bacterial Toxins/genetics ; Phylogeny ; Base Composition ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S ; Plasmids/genetics
    Chemical Substances Bacterial Toxins ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-04-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000995
    Database MEDical Literature Analysis and Retrieval System OnLINE

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