Published in Proc Natl Acad Sci U S A on March 21, 2011
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Diversity, stability and resilience of the human gut microbiota. Nature (2012) 9.09
Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol (2012) 5.66
The long-term stability of the human gut microbiota. Science (2013) 5.15
Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell (2014) 4.25
Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol (2011) 3.97
How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol (2012) 3.65
Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30
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Metagenomics and personalized medicine. Cell (2011) 2.00
Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol (2013) 1.97
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Culturing captures members of the soil rare biosphere. Environ Microbiol (2012) 1.48
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Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol (2013) 1.45
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res (2012) 1.45
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Inflammatory bowel disease as a model for translating the microbiome. Immunity (2014) 1.39
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The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev (2014) 1.34
Exercise attenuates PCB-induced changes in the mouse gut microbiome. Environ Health Perspect (2013) 1.33
Gut microbiota and diabetes: from pathogenesis to therapeutic perspective. Acta Diabetol (2011) 1.30
Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One (2013) 1.27
Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Sci Transl Med (2015) 1.27
Contribution of diet to the composition of the human gut microbiota. Microb Ecol Health Dis (2015) 1.27
Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide. MBio (2015) 1.26
The potter's wheel: the host's role in sculpting its microbiota. Cell Mol Life Sci (2011) 1.25
Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut Microbes (2012) 1.23
Microbiota-mediated inflammation and antimicrobial defense in the intestine. Annu Rev Immunol (2015) 1.23
Understanding vaginal microbiome complexity from an ecological perspective. Transl Res (2012) 1.19
Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res (2013) 1.19
Is the gut microbiota a new factor contributing to obesity and its metabolic disorders? J Obes (2012) 1.16
A pig model of the human gastrointestinal tract. Gut Microbes (2013) 1.15
Standardised animal models of host microbial mutualism. Mucosal Immunol (2014) 1.13
Short-term effect of antibiotics on human gut microbiota. PLoS One (2014) 1.12
The human gut resistome. Philos Trans R Soc Lond B Biol Sci (2015) 1.10
Getting started with microbiome analysis: sample acquisition to bioinformatics. Curr Protoc Hum Genet (2014) 1.09
The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes. J Mol Biol (2014) 1.07
Experimental approaches for defining functional roles of microbes in the human gut. Annu Rev Microbiol (2013) 1.06
Obesity and its associated disease: a role for microbiota? Neurogastroenterol Motil (2012) 1.03
Diet, microbiota and autoimmune diseases. Lupus (2014) 1.02
Mining the human gut microbiota for effector strains that shape the immune system. Immunity (2014) 1.00
Activation of HIF-1α and LL-37 by commensal bacteria inhibits Candida albicans colonization. Nat Med (2015) 0.99
Emerging insights on intestinal dysbiosis during bacterial infections. Curr Opin Microbiol (2013) 0.99
Microbial brokers of insect-plant interactions revisited. J Chem Ecol (2013) 0.98
Equine stomachs harbor an abundant and diverse mucosal microbiota. Appl Environ Microbiol (2012) 0.94
Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthesis pathways. Appl Environ Microbiol (2015) 0.94
Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome. Cell Metab (2014) 0.94
Anthropology of microbes. Proc Natl Acad Sci U S A (2012) 0.93
Fame and future of faecal transplantations--developing next-generation therapies with synthetic microbiomes. Microb Biotechnol (2013) 0.93
The interplay between the gut microbiota and the immune system. Gut Microbes (2014) 0.93
The bacterial chemical repertoire mediates metabolic exchange within gut microbiomes. Curr Opin Microbiol (2011) 0.91
Bacteriotherapy for the treatment of intestinal dysbiosis caused by Clostridium difficile infection. Curr Opin Microbiol (2013) 0.90
Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans. MBio (2015) 0.90
Accounting for reciprocal host-microbiome interactions in experimental science. Nature (2016) 0.90
Beyond phylotyping: understanding the impact of gut microbiota on host biology. Neurogastroenterol Motil (2013) 0.90
The Shift of an Intestinal "Microbiome" to a "Pathobiome" Governs the Course and Outcome of Sepsis Following Surgical Injury. Shock (2016) 0.90
Molecular studies neglect apparently gram-negative populations in the human gut microbiota. J Clin Microbiol (2013) 0.89
Meat-metabolizing bacteria in atherosclerosis. Nat Med (2013) 0.89
Functional metagenomic investigations of the human intestinal microbiota. Front Microbiol (2011) 0.88
Identifying strains that contribute to complex diseases through the study of microbial inheritance. Proc Natl Acad Sci U S A (2015) 0.88
Candida albicans Inhibits Pseudomonas aeruginosa Virulence through Suppression of Pyochelin and Pyoverdine Biosynthesis. PLoS Pathog (2015) 0.88
Replenishing our defensive microbes. Bioessays (2013) 0.87
Divergent mechanisms of interaction of Helicobacter pylori and Campylobacter jejuni with mucus and mucins. Infect Immun (2013) 0.86
Social behavior shapes the chimpanzee pan-microbiome. Sci Adv (2016) 0.85
Exposing to cadmium stress cause profound toxic effect on microbiota of the mice intestinal tract. PLoS One (2014) 0.85
Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development. Proc Natl Acad Sci U S A (2015) 0.85
Sputum microbiota associated with new, recurrent and treatment failure tuberculosis. PLoS One (2013) 0.84
From next-generation sequencing to systematic modeling of the gut microbiome. Front Genet (2015) 0.84
Obesity and the gut microbiome: Striving for causality. Mol Metab (2012) 0.83
Pathways and functions of gut microbiota metabolism impacting host physiology. Curr Opin Biotechnol (2015) 0.83
An evolving perspective about the origins of childhood undernutrition and nutritional interventions that includes the gut microbiome. Ann N Y Acad Sci (2014) 0.82
Gut microbiota and hematopoietic stem cell transplantation: where do we stand? Bone Marrow Transplant (2016) 0.81
Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS One (2013) 0.81
Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer. Gut Microbes (2014) 0.81
Metagenomic surveys of gut microbiota. Genomics Proteomics Bioinformatics (2015) 0.81
Molecular phenotyping of infection-associated small non-coding RNAs. Philos Trans R Soc Lond B Biol Sci (2016) 0.81
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A (2004) 26.56
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18
Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67
Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J (2010) 5.43
Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl Environ Microbiol (2010) 2.77
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Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail. Appl Environ Microbiol (2010) 1.51
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 44.35
Microbial ecology: human gut microbes associated with obesity. Nature (2006) 36.98
Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A (2005) 33.66
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
The human microbiome project. Nature (2007) 28.53
The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A (2004) 26.56
Host-bacterial mutualism in the human intestine. Science (2005) 26.39
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Evolution of mammals and their gut microbes. Science (2008) 21.40
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell (2006) 18.83
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
Design of a novel globular protein fold with atomic-level accuracy. Science (2003) 13.06
A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science (2003) 12.57
Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature (2008) 12.45
Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol (2008) 12.16
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe (2008) 11.97
Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature (2012) 10.74
Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci U S A (2002) 9.78
NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell (2011) 9.75
Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A (2007) 9.71
Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell (2006) 9.64
Diversity, stability and resilience of the human gut microbiota. Nature (2012) 9.09
Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science (2005) 9.08
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science (2011) 8.88
Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr (2002) 8.31
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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science (2013) 6.98
Moving pictures of the human microbiome. Genome Biol (2011) 6.72
Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67
Detecting differential usage of exons from RNA-seq data. Genome Res (2012) 6.34
Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol (2003) 6.17
Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature (2010) 5.92
Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc Natl Acad Sci U S A (2004) 5.89
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
Honor thy symbionts. Proc Natl Acad Sci U S A (2003) 5.72
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe (2008) 5.39
IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe (2007) 5.18
Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A (2004) 5.16
The long-term stability of the human gut microbiota. Science (2013) 5.15
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A (2006) 5.13
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A (2006) 5.04
Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr (2011) 4.60
Homeostasis and inflammation in the intestine. Cell (2010) 4.60
Getting a grip on things: how do communities of bacterial symbionts become established in our intestine? Nat Immunol (2004) 4.58
Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe (2010) 4.54
Immunoproliferative small intestinal disease associated with Campylobacter jejuni. N Engl J Med (2004) 4.47
The core gut microbiome, energy balance and obesity. J Physiol (2009) 4.45
Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Natl Acad Sci U S A (2008) 4.45
Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol (2006) 4.27
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med (2011) 4.24
Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe (2008) 4.14
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem (2009) 4.05
The shared antibiotic resistome of soil bacteria and human pathogens. Science (2012) 3.98
Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol (2011) 3.97
Tackling antibiotic resistance. Nat Rev Microbiol (2011) 3.95
Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science (2011) 3.49
Direct sequencing of the human microbiome readily reveals community differences. Genome Biol (2010) 3.34
The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc Natl Acad Sci U S A (2006) 3.07
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure (2008) 3.02
Cohabiting family members share microbiota with one another and with their dogs. Elife (2013) 2.92
Manipulation of a nuclear NAD+ salvage pathway delays aging without altering steady-state NAD+ levels. J Biol Chem (2002) 2.91
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc Natl Acad Sci U S A (2009) 2.91
Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A (2007) 2.79
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell (2013) 2.67
Reverse-engineering transcription control networks. Phys Life Rev (2005) 2.59
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett (2010) 2.57
Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches. J Biol Chem (2006) 2.49
Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem (2006) 2.43
Dissecting the in vivo metabolic potential of two human gut acetogens. J Biol Chem (2010) 2.42
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol (2013) 2.36
Meta-analyses of studies of the human microbiota. Genome Res (2013) 2.35
Molecular regulation of urothelial renewal and host defenses during infection with uropathogenic Escherichia coli. J Biol Chem (2001) 2.34
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The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A (2008) 2.33
Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont. J Biol Chem (2009) 2.21
Laser capture microdissection of mouse intestine: characterizing mRNA and protein expression, and profiling intermediary metabolism in specified cell populations. Methods Enzymol (2002) 2.17
Escherichia coli from urine of female patients with urinary tract infections is competent for intracellular bacterial community formation. Infect Immun (2006) 2.11
Identification of MW polyomavirus, a novel polyomavirus in human stool. J Virol (2012) 2.10
Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation. Proc Natl Acad Sci U S A (2013) 2.10
Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol (2012) 2.08
Science education. Educating future scientists. Science (2003) 1.97
Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A (2011) 1.96
Molecular characterization of mouse gastric epithelial progenitor cells. Proc Natl Acad Sci U S A (2002) 1.94
A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Proc Natl Acad Sci U S A (2006) 1.90