Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

SAMSA2: a standalone metatranscriptome analysis pipeline

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Microbial nutrient niches in the gut

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Oxygen as a driver of gut dysbiosis

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An investigation of parasitic infections and review of molecular characterization of the intestinal protozoa in nonhuman primates in China from 2009 to 2015

(2017) Junqiang Li et al.   International Journal for Parasitology-Parasites and Wildlife

Inflamed Intestinal Mucosa Features a Specific Epithelial Expression Pattern of Indoleamine 2,3-Dioxygenase

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Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota

(2017) Tingting Chen et al.   Scientific Reports

SAMSA: a comprehensive metatranscriptome analysis pipeline

(2016) Samuel T. Westreich et al.   BMC BIOINFORMATICS

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation

(2016) Gopanandan Parthasarathy et al.   GASTROENTEROLOGY

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

Prevotella in the gut: choose carefully

(2016) Ruth E. Ley   Nature Reviews Gastroenterology & Hepatology

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

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Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

Gut Microbiota Linked to Sexual Preference and HIV Infection

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Revisiting the Life Cycle of Dung Fungi, Including Sordaria fimicola

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Human Clostridium difficile infection: altered mucus production and composition

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Friend Turned Foe: A Role for Bacterial Sulfatases in Colitis

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Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

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Intestinal Fucose as a Mediator of Host–Microbe Symbiosis

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Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection

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Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Proteobacteria: microbial signature of dysbiosis in gut microbiota

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Immune Homeostasis in Epithelial Cells: Evidence and Role of Inflammasome Signaling Reviewed

(2015) Paul M. Peeters et al.   Journal of Immunology Research

Mucin glycan foraging in the human gut microbiome

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Idiopathic Microscopic Colitis of Rhesus Macaques: Quantitative Assessment of Colonic Mucosa

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Trimmomatic: a flexible trimmer for Illumina sequence data

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Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

(2014) Erica D. Sonnenburg et al.   Cell Metabolism

Fecal calprotectin in diagnosis and clinical assessment of inflammatory bowel disease

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PEAR: a fast and accurate Illumina Paired-End reAd mergeR

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Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis

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Nonhuman Primate Models in the Genomic Era: A Paradigm Shift

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The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

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RefSeq microbial genomes database: new representation and annotation strategy

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Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

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Indoleamine 2,3 dioxygenase in intestinal disease

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The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

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High incidence of rhesus enteric calicivirus infections and diarrhea in captive juvenile macaques: a likely association

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Therapeutic Helminth Infection of Macaques with Idiopathic Chronic Diarrhea Alters the Inflammatory Signature and Mucosal Microbiota of the Colon

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Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways

(2011) Angela Marcobal et al.   Cell Host & Microbe

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

(2011) Patricia Lepage et al.   GASTROENTEROLOGY

Absence of focally enhanced gastritis in macaques with idiopathic colitis

(2011) Amnon Sonnenberg et al.   INFLAMMATORY BOWEL DISEASES

Intestinal homeostasis and its breakdown in inflammatory bowel disease

(2011) Kevin J. Maloy et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

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The formin FRL1 (FMNL1) is an essential component of macrophage podosomes

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Persistent infection of rhesus monkeys with 'Helicobacter macacae' and its isolation from an animal with intestinal adenocarcinoma

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

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The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

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The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis

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