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Article
Open AccessMining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis
The gut microbiome plays an important role in autoimmunity including multiple sclerosis and its mouse model called experimental autoimmune encephalomyelitis (EAE). Prior studies have demonstrated that the mult...
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Article
Open AccessLimited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19
Gastrointestinal symptoms are common in COVID-19 patients but the nature of the gut immune response to SARS-CoV-2 remains poorly characterized, partly due to the difficulty of obtaining biopsy specimens from i...
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Article
Maternal infection programmes offspring immunity
A preprint by Lim et al. looks at the effects of maternal infection on long-term immunity in offspring, showing that maternal IL-6-induced signalling in mice induces epigenetic changes in fetal intestinal epit...
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Article
Open AccessInterleukin 22 disrupts pancreatic function in newborn mice expressing IL-23
Neonatal inflammatory diseases are associated with severe morbidity, but the inflammatory factors underlying them and their potential effector mechanisms are poorly defined. Here we show that necrotizing enter...
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Article
Open AccessSmall intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders
Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-sp...
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Article
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
Similar bacterial species and strains in metagenomes are resolved and linked to the plasmids that they harbor using DNA methylation analysis.
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Article
A functional genomics predictive network model identifies regulators of inflammatory bowel disease
Eric Schadt and colleagues present a predictive causal model of the immune component of inflammatory bowel disease through integration of genetic, regulatory and transcriptional data. They prioritize and valid...
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Article
Metabolic labeling puts the microbiome under the microscope
Seven years after the launch of the Human Microbiome Project, we still lack sufficient tools to visualize the microbiome in a living host. A new study provides experimental tools to label and track live anaero...
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Neutrophil ageing is regulated by the microbiome
Neutrophil ageing, which encourages inflammation and vaso-occlusion in a mouse model of sickle-cell disease, is shown to depend on the intestinal microbiota and activation of the TLR/Myd88 signalling pathways.
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Article
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
A systematic evaluation of parameters that affect short amplicons sequenced on Illumina platforms provides guidelines for how to eliminate erroneous reads and improve data interpretation.
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Open AccessLightweight genome viewer: portable software for browsing genomics data in its chromosomal context
Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standa...
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Open AccessEGenBio: A Data Management System for Evolutionary Genomics and Biodiversity
Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed E
