Published in Gut Microbes on June 12, 2012
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol (2013) 8.53
The gut microbiome modulates colon tumorigenesis. MBio (2013) 2.45
Exploring host-microbiota interactions in animal models and humans. Genes Dev (2013) 1.51
Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species. PLoS One (2013) 1.31
Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A (2013) 1.27
A pig model of the human gastrointestinal tract. Gut Microbes (2013) 1.15
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One (2013) 1.11
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units. PeerJ (2015) 1.08
Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design. FEMS Microbiol Rev (2015) 1.08
The dynamics of a family's gut microbiota reveal variations on a theme. Microbiome (2014) 1.05
Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota. Nat Immunol (2015) 0.96
Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLoS Genet (2013) 0.95
Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time. PLoS One (2015) 0.87
Experimental design considerations in microbiota/inflammation studies. Clin Transl Immunology (2016) 0.87
Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations. Appl Environ Microbiol (2014) 0.81
Temporal dynamics of the cecal gut microbiota of juvenile arctic ground squirrels: a strong litter effect across the first active season. Appl Environ Microbiol (2014) 0.80
Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods. mSystems (2016) 0.80
Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Res (2016) 0.79
Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis. Front Microbiol (2015) 0.79
Mucin-Microbiota Interaction During Postnatal Maturation of the Intestinal Ecosystem: Clinical Implications. Dig Dis Sci (2016) 0.78
Integrated community profiling indicates long-term temporal stability of the predominant faecal microbiota in captive cheetahs. PLoS One (2015) 0.76
Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird. Front Microbiol (2017) 0.75
OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units. mSphere (2017) 0.75
Investigation into Host Selection of the Cecal Acetogen Population in Rabbits after Weaning. PLoS One (2016) 0.75
Inbred Mouse Populations Exhibit Intergenerational Changes in Intestinal Microbiota Composition and Function Following Introduction to a Facility. Front Microbiol (2017) 0.75
Altered gut microbiota in female mice with persistent low body weights following removal of post-weaning chronic dietary restriction. Genome Med (2016) 0.75
Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure. Environ Microbiol (2017) 0.75
Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs). Microbiome (2015) 0.75
Macrophage dysfunction initiates colitis during weaning of infant mice lacking the interleukin-10 receptor. Elife (2017) 0.75
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
Microbial ecology: human gut microbes associated with obesity. Nature (2006) 36.98
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Enterotypes of the human gut microbiome. Nature (2011) 24.36
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res (2006) 23.67
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One (2011) 12.26
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe (2008) 11.97
Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A (2010) 9.57
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A (2010) 8.56
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun (2009) 7.48
Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics (2006) 6.99
Moving pictures of the human microbiome. Genome Biol (2011) 6.72
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A (2006) 5.04
Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol (2011) 4.57
Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol (2011) 4.55
Stability and diversity of ecosystems. Science (2007) 4.35
Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science (2011) 3.49
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
How stable is stable? Function versus community composition. Appl Environ Microbiol (1999) 3.08
A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One (2009) 3.07
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. Gut Microbes (2011) 2.37
Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05
Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing. Infect Immun (2009) 1.91
Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide. Environ Microbiol (2012) 0.94
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun (2009) 7.48
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis (2008) 6.21
Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS One (2011) 4.65
Clostridium difficile ribotype does not predict severe infection. Clin Infect Dis (2012) 4.34
Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med (2013) 3.65
Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A (2012) 3.43
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol (2008) 2.97
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology (2011) 2.60
The gut microbiome modulates colon tumorigenesis. MBio (2013) 2.45
From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev (2010) 2.42
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. Gut Microbes (2011) 2.37
The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol (2012) 2.17
Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc (2013) 2.05
Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii and related Shigella boydii strains. J Bacteriol (2005) 2.01
Significance of the microbiome in obstructive lung disease. Thorax (2012) 1.97
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe (2011) 1.97
Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy. Mol Microbiol (2004) 1.90
Alteration of the murine gut microbiota during infection with the parasitic helminth Heligmosomoides polygyrus. Inflamm Bowel Dis (2010) 1.85
Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae. Infect Immun (2012) 1.79
Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One (2007) 1.71
Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. Trends Microbiol (2012) 1.70
Colonization of the cecal mucosa by Helicobacter hepaticus impacts the diversity of the indigenous microbiota. Infect Immun (2005) 1.67
Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med (2013) 1.66
Relationship between COMLEX and USMLE scores among osteopathic medical students who take both examinations. Teach Learn Med (2010) 1.60
The microbiome of the lung. Transl Res (2012) 1.59
Perturbation of the small intestine microbial ecology by streptomycin alters pathology in a Salmonella enterica serovar typhimurium murine model of infection. Infect Immun (2009) 1.59
Antibiotic administration alters the community structure of the gastrointestinal micobiota. Gut Microbes (2010) 1.57
Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio (2015) 1.56
Depression, antidepressant medications, and risk of Clostridium difficile infection. BMC Med (2013) 1.54
Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis. Inflamm Bowel Dis (2010) 1.44
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol (2012) 1.43
Impact of enhanced Staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoS One (2012) 1.40
Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. MBio (2014) 1.40
Adaptive amplification and point mutation are independent mechanisms: evidence for various stress-inducible mutation mechanisms. PLoS Biol (2004) 1.37
Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infect Immun (2012) 1.36
The gut microbiome in health and in disease. Curr Opin Gastroenterol (2015) 1.33
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol (2008) 1.29
Cefoperazone-treated mice as an experimental platform to assess differential virulence of Clostridium difficile strains. Gut Microbes (2011) 1.29
A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis. J Allergy Clin Immunol (2012) 1.28
Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A (2013) 1.27
Application of a neutral community model to assess structuring of the human lung microbiome. MBio (2015) 1.25
Streptococcus intermedius causing infective endocarditis and abscesses: a report of three cases and review of the literature. BMC Infect Dis (2008) 1.23
Procalcitonin levels associate with severity of Clostridium difficile infection. PLoS One (2013) 1.22
Variation of the natural transformation frequency of Campylobacter jejuni in liquid shake culture. Microbiology (2003) 1.21
Pathogenesis of renal disease due to enterohemorrhagic Escherichia coli in germ-free mice. Infect Immun (2008) 1.20
Francisella tularensis genomics and proteomics. Ann N Y Acad Sci (2007) 1.18
A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome (2013) 1.17
Modulation of host immune responses by the cytolethal distending toxin of Helicobacter hepaticus. Infect Immun (2006) 1.16
Alteration of the murine gastrointestinal microbiota by tigecycline leads to increased susceptibility to Clostridium difficile infection. Antimicrob Agents Chemother (2014) 1.14
The relationship between phenotype, ribotype, and clinical disease in human Clostridium difficile isolates. Anaerobe (2013) 1.14
Disruption of the human gut microbiota following Norovirus infection. PLoS One (2012) 1.13
Understanding increased mortality in Clostridium difficile-infected older adults. Clin Infect Dis (2013) 1.13
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. FASEB J (2012) 1.10
Clostridium difficile and the microbiota. J Clin Invest (2014) 1.09
Ecological succession of bacterial communities during conventionalization of germ-free mice. Appl Environ Microbiol (2012) 1.09
Explaining unexplained diarrhea and associating risks and infections. Anim Health Res Rev (2007) 1.08
Interplay between the gastric bacterial microbiota and Candida albicans during postantibiotic recolonization and gastritis. Infect Immun (2011) 1.07
Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium. PLoS One (2007) 1.06
Poor functional status as a risk factor for severe Clostridium difficile infection in hospitalized older adults. J Am Geriatr Soc (2013) 1.05
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol (2010) 1.05
Clostridium difficile ribotype diversity at six health care institutions in the United States. J Clin Microbiol (2013) 1.04
Effect of sample storage conditions on culture-independent bacterial community measures in cystic fibrosis sputum specimens. J Clin Microbiol (2011) 1.03
Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. Microbiome (2014) 1.00
Genetic diversity of Campylobacter sp. isolates from retail chicken products and humans with gastroenteritis in Central Michigan. J Clin Microbiol (2005) 0.99
Stress-induced corticotropin-releasing hormone-mediated NLRP6 inflammasome inhibition and transmissible enteritis in mice. Gastroenterology (2013) 0.98
Challenges in IBD research: update on progress and prioritization of the CCFA's research agenda. Inflamm Bowel Dis (2013) 0.97
The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition. PLoS One (2013) 0.96
Lethal toxin is a critical determinant of rapid mortality in rodent models of Clostridium sordellii endometritis. Anaerobe (2009) 0.95
Non-toxigenic Clostridium sordellii: clinical and microbiological features of a case of cholangitis-associated bacteremia. Anaerobe (2011) 0.93
Interactions Between the Gastrointestinal Microbiome and Clostridium difficile. Annu Rev Microbiol (2015) 0.93
Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice. J Pediatr Gastroenterol Nutr (2012) 0.93
Acute infection of mice with Clostridium difficile leads to eIF2α phosphorylation and pro-survival signalling as part of the mucosal inflammatory response. Immunology (2013) 0.93
Inflammatory bowel disease causes reversible suppression of osteoblast and chondrocyte function in mice. Am J Physiol Gastrointest Liver Physiol (2009) 0.92
A clinical and epidemiological review of non-toxigenic Clostridium difficile. Anaerobe (2013) 0.91
Faecal microbiota transplantation for the treatment of recurrent Clostridium difficile infection: current promise and future needs. Curr Opin Gastroenterol (2013) 0.89
Emerging Insights into Antibiotic-Associated Diarrhea and Clostridium difficile Infection through the Lens of Microbial Ecology. Interdiscip Perspect Infect Dis (2008) 0.89
Murine models to study Clostridium difficile infection and transmission. Anaerobe (2013) 0.89
Initial insights into bacterial succession during human decomposition. Int J Legal Med (2014) 0.87
Potential role of gastrointestinal microbiota composition in prostate cancer risk. Infect Agent Cancer (2013) 0.86
Maternal micronutrients can modify colonic mucosal microbiota maturation in murine offspring. Gut Microbes (2012) 0.86
Characterization of the human gut microbiome during travelers' diarrhea. Gut Microbes (2015) 0.84
Bioactivity and bioavailability of ginsenosides are dependent on the glycosidase activities of the A/J mouse intestinal microbiome defined by pyrosequencing. Pharm Res (2012) 0.84
Colitis-induced bone loss is gender dependent and associated with increased inflammation. Inflamm Bowel Dis (2013) 0.84
The changing landscape of type 1 diabetes: recent developments and future frontiers. Curr Diab Rep (2013) 0.83
Leptin acts independently of food intake to modulate gut microbial composition in male mice. Endocrinology (2014) 0.82
Interleukin-22 and CD160 play additive roles in the host mucosal response to Clostridium difficile infection in mice. Immunology (2015) 0.81
Monotonous diets protect against acute colitis in mice: epidemiologic and therapeutic implications. J Pediatr Gastroenterol Nutr (2013) 0.80
Murine norovirus infection does not cause major disruptions in the murine intestinal microbiota. Microbiome (2013) 0.80
The role of Gr-1(+) cells and tumour necrosis factor-α signalling during Clostridium difficile colitis in mice. Immunology (2015) 0.80
Adaptive evolution and inherent tolerance to extreme thermal environments. BMC Evol Biol (2010) 0.79