Published in mSphere on February 08, 2017
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97
The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A (2004) 26.56
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res (2012) 19.48
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
Metabolite profiles and the risk of developing diabetes. Nat Med (2011) 12.22
Metagenomic biomarker discovery and explanation. Genome Biol (2011) 11.29
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
BioMagResBank. Nucleic Acids Res (2007) 10.21
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature (2013) 6.45
PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics (2013) 5.61
Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab (2013) 4.88
The core gut microbiome, energy balance and obesity. J Physiol (2009) 4.45
Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem (2006) 4.29
The expanded biology of serotonin. Annu Rev Med (2009) 3.87
Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect Immun (2008) 3.68
Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell (2015) 3.67
The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab (2011) 3.54
Inhibiting peripheral serotonin synthesis reduces obesity and metabolic dysfunction by promoting brown adipose tissue thermogenesis. Nat Med (2014) 3.13
STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics (2014) 3.12
Regulation of short-chain fatty acid production. Proc Nutr Soc (2003) 3.00
The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res (2013) 2.67
Overactivation of S6 kinase 1 as a cause of human insulin resistance during increased amino acid availability. Diabetes (2005) 2.55
Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun (2014) 2.39
icoshift: A versatile tool for the rapid alignment of 1D NMR spectra. J Magn Reson (2009) 2.17
Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nat Commun (2016) 2.03
Short-chain fatty acids and ketones directly regulate sympathetic nervous system via G protein-coupled receptor 41 (GPR41). Proc Natl Acad Sci U S A (2011) 1.97
GPR41/FFAR3 and GPR43/FFAR2 as cosensors for short-chain fatty acids in enteroendocrine cells vs FFAR3 in enteric neurons and FFAR2 in enteric leukocytes. Endocrinology (2013) 1.89
The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterol Motil (2011) 1.87
Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. Int J Obes (Lond) (2014) 1.83
Antibiotic exposure in infancy and risk of being overweight in the first 24 months of life. Pediatrics (2015) 1.77
Role of the intestinal microbiota in resistance to colonization by Clostridium difficile. Gastroenterology (2014) 1.77
Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. J Proteome Res (2008) 1.67
Leucine deprivation increases hepatic insulin sensitivity via GCN2/mTOR/S6K1 and AMPK pathways. Diabetes (2011) 1.55
Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer. Nat Commun (2014) 1.47
Bile acids and the gut microbiome. Curr Opin Gastroenterol (2014) 1.45
A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice. ISME J (2013) 1.42
Helicobacter pylori arginase inhibits T cell proliferation and reduces the expression of the TCR zeta-chain (CD3zeta). J Immunol (2004) 1.37
Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure. Environ Microbiol (2012) 1.29
The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Ann Gastroenterol (2015) 1.25
Infant antibiotic exposure and the development of childhood overweight and central adiposity. Int J Obes (Lond) (2014) 1.25
Effects of gut microbes on nutrient absorption and energy regulation. Nutr Clin Pract (2012) 1.25
Antibiotics in early life and obesity. Nat Rev Endocrinol (2014) 1.25
L-arginine metabolism and its impact on host immunity against Leishmania infection. Immunol Res (2008) 1.21
MVAPACK: a complete data handling package for NMR metabolomics. ACS Chem Biol (2014) 1.19
Dietary arginine supplementation of mice alters the microbial population and activates intestinal innate immunity. J Nutr (2014) 1.12
The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids. Circ Res (2015) 1.08
Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep (2015) 1.05
Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome (2015) 1.04
Gut microbiota composition modifies fecal metabolic profiles in mice. J Proteome Res (2013) 1.03
A consensus orthogonal partial least squares discriminant analysis (OPLS-DA) strategy for multiblock Omics data fusion. Anal Chim Acta (2013) 1.00
Dietary glutamine affects mucosal functions in rats with mild DSS-induced colitis. J Nutr (2007) 0.98
Metabolomics analysis identifies intestinal microbiota-derived biomarkers of colonization resistance in clindamycin-treated mice. PLoS One (2014) 0.95
Manipulation of the gut microbiota in C57BL/6 mice changes glucose tolerance without affecting weight development and gut mucosal immunity. Res Vet Sci (2011) 0.94
Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. Trends Microbiol (2016) 0.94
Computational approaches to metabolomics. Methods Mol Biol (2010) 0.92
Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice. Sci Rep (2014) 0.92
NMR metabolomics of MTLn3E breast cancer cells identifies a role for CXCR4 in lipid and choline regulation. J Proteome Res (2012) 0.88
Lactobacillus reuteri and Escherichia coli in the human gut microbiota may predict weight gain associated with vancomycin treatment. Nutr Diabetes (2013) 0.88
Glucose metabolism: focus on gut microbiota, the endocannabinoid system and beyond. Diabetes Metab (2014) 0.88
Antibiotic use and childhood body mass index trajectory. Int J Obes (Lond) (2015) 0.87
Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health. World J Gastroenterol (2014) 0.86
Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Med (2016) 0.85
Shaping the (auto)immune response in the gut: the role of intestinal immune regulation in the prevention of type 1 diabetes. Am J Clin Exp Immunol (2013) 0.84
From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways. Mol Psychiatry (2016) 0.82
Administration of Antibiotics to Children Before Age 2 Years Increases Risk for Childhood Obesity. Gastroenterology (2016) 0.82
Immunomodulation by gut microbiota: role of Toll-like receptor expressed by T cells. J Immunol Res (2014) 0.78
Vancomycin Treatment Alters Humoral Immunity and Intestinal Microbiota in an Aged Mouse Model of Clostridium difficile Infection. J Infect Dis (2016) 0.78
Selective novel inverse agonists for human GPR43 augment GLP-1 secretion. Eur J Pharmacol (2015) 0.77
Antibiotics, obesity and the link to microbes - what are we doing to our children? BMC Med (2016) 0.77
Use of 1H NMR STD, waterLOGSY, and Langmuir monolayer techniques for characterization of drug-zein protein complexes. Eur J Pharm Biopharm (2013) 0.76
[Xenobiotics and the active gut microbiome: unknown effects unveiled]. Med Sci (Paris) (2013) 0.75
The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial. Lancet Respir Med (2014) 1.65
Combined systems approaches reveal highly plastic responses to antimicrobial peptide challenge in Escherichia coli. PLoS Pathog (2014) 0.79