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Keywords {🔍}

gnavus, ibd, gut, pubmed, patients, samples, species, article, microbiome, abundance, genes, strains, google, scholar, clade, disease, study, additional, increased, oxidative, stress, file, sequencing, ibdspecific, gene, central, facultative, anaerobes, lss, data, inflammatory, stool, cohorts, table, cas, analysis, ruminococcus, pangenome, bowel, dna, lewis, metagenomic, microbial, oxygen, healthy, controls, genomes, fig, functional, identified,

Topics {✒️}

article download pdf fluorescence-based picogreen assay fluorescence-based ribogreen assay ethanol-based wash buffers xiaofang jiang pre-computed pangenome database strain-specific pangenome haplotypes m-pva magnetic beads strain-level microbial epidemiology ibd-specific gene product inflammatory bowel disease inflammatory bowel diseases magnetic bead-based purification species-level microbial communities ibd-specific gene families strain-level identification afforded moran yassour escherichia coli showed original author ibd-specific gene involved chronic inflammatory disease strain-specific genes involved colony forming units privacy choices/manage cookies search mini bead beater-8 human microbiome project article hall gut microbial profiles tagment dna enzyme syst evol microbiol individualized microbiome signature identified ibd-specific genes allprep spin column creative commons license fecal microbiome transplants analyze large-scale sialic acid transport layer microfluidic architecture minimize reagent cost franzosa ea peroxiredoxin oxidoreductase family disease activity index specific strain variants full access specific genomic adaptations custom pangenome database comprehensive pangenome database performed pcr barcoding allowing strain-level

Questions {❓}

• In this study, we aim to address two outstanding questions in IBD: 1) How does oxidative stress in IBD shape the composition of the gut microbiome at the species and strain levels?

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WebPage:
      mainEntity:
         headline:A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
         description:Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn. We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut. This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.
         datePublished:2017-11-28T00:00:00Z
         dateModified:2017-11-28T00:00:00Z
         pageStart:1
         pageEnd:12
         license:http://creativecommons.org/publicdomain/zero/1.0/
         sameAs:https://doi.org/10.1186/s13073-017-0490-5
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            Gnavus
            Ruminococcus Gnavus
            Pangenome
            MetaPhlAn
            Facultative Anaerobes
            Human Genetics
            Metabolomics
            Bioinformatics
            Medicine/Public Health
            general
            Cancer Research
            Systems Biology
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      headline:A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
      description:Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn. We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut. This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.
      datePublished:2017-11-28T00:00:00Z
      dateModified:2017-11-28T00:00:00Z
      pageStart:1
      pageEnd:12
      license:http://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/s13073-017-0490-5
      keywords:
         Gnavus
         Ruminococcus Gnavus
         Pangenome
         MetaPhlAn
         Facultative Anaerobes
         Human Genetics
         Metabolomics
         Bioinformatics
         Medicine/Public Health
         general
         Cancer Research
         Systems Biology
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