A Method article published in GenomeBiology presents MMUPHin: a novel statistical framework that allows joint normalization and meta-analysis of large microbial community profile collections with heterogeneous and complex designs.
: Table S1). Demultiplexed raw sequences were either downloaded from EBI or available locally as previously generated . Metadata were obtained either directly from the sequence repository/manuscript , or from collaborators . This resulted in a total of 5151 samples and 2179 subjects available prior to processing and quality control.We manually curated subject- and sample-specific metadata across studies to ensure consistency. Variables collected and curated include:Type of controls .
° HMP2: ileum classification kept unchanged; cecum, ascending/right-sided colon, transverse colon, descending/left-sided colon, and sigmoid colon were aggregated as colon.° Pouchitis: terminal ileum, pouch, pre-pouch ileum aggregated as ileum; sigmoid colon aggregated to colon.° RISK: terminal ileum was aggregated to ileum; rectum kept unchanged.° Location for CDs , available for BIDMC-FMT, CS-PRISM, Herfarth, Jansson-Lamendella, LSS-PRISM, and Pouchitis.
Age at diagnosis . Directly available for CS-PRISM, HMP2, LSS-PRISM, and Pouchitis, inferred as baseline age for PROTECT and RISK as these were new-onset cohorts. Gender . Available for BIDMC-FMT, CS-PRISM, Herfarth, HMP2, Jansson-Lamendella, LSS-PRISM, MucosalIBD, Pouchitis, PROTECT,
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Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi - MicrobiomeBackground Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. Results Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. Conclusions Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract
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