Published in BMC Genomics on January 19, 2010
Mobile genes in the human microbiome are structured from global to individual scales. Nature (2016) 2.02
'Blooming' in the gut: how dysbiosis might contribute to pathogen evolution. Nat Rev Microbiol (2013) 1.45
Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One (2011) 1.41
Horizontal gene exchange in environmental microbiota. Front Microbiol (2011) 1.39
The human gut resistome. Philos Trans R Soc Lond B Biol Sci (2015) 1.10
Community-wide plasmid gene mobilization and selection. ISME J (2013) 1.03
Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence (2013) 1.03
Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes. Gut Microbes (2013) 1.02
The relBE2Spn toxin-antitoxin system of Streptococcus pneumoniae: role in antibiotic tolerance and functional conservation in clinical isolates. PLoS One (2010) 1.00
The human gut mobile metagenome: a metazoan perspective. Gut Microbes (2011) 0.99
Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences. Nat Commun (2013) 0.97
Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14. PLoS One (2012) 0.96
Establishment of a tractable genetic transformation system in Veillonella spp. Appl Environ Microbiol (2012) 0.92
Functional metagenomics for the investigation of antibiotic resistance. Virulence (2014) 0.90
Diverse broad-host-range plasmids from freshwater carry few accessory genes. Appl Environ Microbiol (2013) 0.90
Integrating '-omics' and natural product discovery platforms to investigate metabolic exchange in microbiomes. Curr Opin Chem Biol (2010) 0.80
Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome. Bioeng Bugs (2012) 0.80
Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG. Proteins (2010) 0.80
Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations. MBio (2015) 0.80
The rumen plasmidome: A genetic communication hub for the rumen microbiome. Mob Genet Elements (2012) 0.76
Strategies and approaches in plasmidome studies-uncovering plasmid diversity disregarding of linear elements? Front Microbiol (2015) 0.76
The Dynamic Interactions between Salmonella and the Microbiota, within the Challenging Niche of the Gastrointestinal Tract. Int Sch Res Notices (2014) 0.75
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform (2004) 72.40
Diversity of the human intestinal microbial flora. Science (2005) 49.64
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 44.35
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
Host-bacterial mutualism in the human intestine. Science (2005) 26.39
Comparative metagenomics of microbial communities. Science (2005) 25.88
Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A (1998) 21.41
Microbial gene identification using interpolated Markov models. Nucleic Acids Res (1998) 20.26
Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell (2006) 18.83
Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol (1999) 16.09
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res (2007) 13.08
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut (2005) 10.95
Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev (2004) 10.67
Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell (2006) 9.64
The gut flora as a forgotten organ. EMBO Rep (2006) 7.42
Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol (2003) 6.65
Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res (2005) 6.61
The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell (2003) 6.01
RelE, a global inhibitor of translation, is activated during nutritional stress. Proc Natl Acad Sci U S A (2001) 4.10
Plasmid and chromosome partitioning: surprises from phylogeny. Mol Microbiol (2000) 4.01
Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA. J Mol Biol (2003) 3.76
Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol Rev (1995) 3.75
Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol (2004) 3.64
Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl Environ Microbiol (2001) 3.56
RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol Microbiol (2003) 3.32
Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol (2007) 3.29
Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet (2009) 3.03
New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol (2003) 2.77
Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A (2008) 2.53
The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A (2008) 2.33
Why are antibiotic resistance genes so resistant to elimination? Antimicrob Agents Chemother (1997) 2.32
Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res (2003) 2.31
Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob Agents Chemother (2007) 2.23
Increased persistence in Escherichia coli caused by controlled expression of toxins or other unrelated proteins. J Bacteriol (2006) 2.19
Occurrence of the new tetracycline resistance gene tet(W) in bacteria from the human gut. Antimicrob Agents Chemother (2000) 2.05
Recovery of new integron classes from environmental DNA. FEMS Microbiol Lett (2001) 1.76
Evidence for natural horizontal transfer of tetQ between bacteria that normally colonize humans and bacteria that normally colonize livestock. Appl Environ Microbiol (1994) 1.75
Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl Environ Microbiol (2001) 1.74
Novel tetracycline resistance gene, tet(32), in the Clostridium-related human colonic anaerobe K10 and its transmission in vitro to the rumen anaerobe Butyrivibrio fibrisolvens. Antimicrob Agents Chemother (2001) 1.59
Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Mol Microbiol (2008) 1.59
Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proc Natl Acad Sci U S A (2000) 1.55
Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods (2006) 1.50
Chromosomal toxin-antitoxin systems may act as antiaddiction modules. J Bacteriol (2008) 1.46
Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria. Antimicrob Agents Chemother (2006) 1.42
The Butyrivibrio fibrisolvens tet(W) gene is carried on the novel conjugative transposon TnB1230, which contains duplicated nitroreductase coding sequences. J Bacteriol (2004) 1.38
Gene transfer in the gastrointestinal tract. Appl Environ Microbiol (1999) 1.29
Bacterial toxin-antitoxin gene system as containment control in yeast cells. Appl Environ Microbiol (2000) 1.21
The bacterial toxin RelE induces specific mRNA cleavage in the A site of the eukaryote ribosome. RNA (2007) 1.10
Tetracycline resistome of the organic pig gut. Appl Environ Microbiol (2009) 1.06
A new Bacteroides conjugative transposon that carries an ermB gene. Appl Environ Microbiol (2003) 1.03
Bacterial toxin RelE induces apoptosis in human cells. FEBS Lett (2002) 1.02
The application of a recently isolated strain of Bacteroides (GB-124) to identify human sources of faecal pollution in a temperate river catchment. Water Res (2007) 0.88
Transfer of conjugative plasmid pAM beta 1 from Lactococcus lactis to mouse intestinal bacteria. Lett Appl Microbiol (1996) 0.87
Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives. Lett Appl Microbiol (2007) 0.87
Distribution of the ermG gene among bacterial isolates from porcine intestinal contents. Appl Environ Microbiol (2005) 0.86
Monitoring transfer of recombinant and nonrecombinant plasmids between Lactococcus lactis strains and members of the human gastrointestinal microbiota in vivo--impact of donor cell number and diet. J Appl Microbiol (2002) 0.85
Accessing the mobile metagenome of the human gut microbiota. Mol Biosyst (2007) 0.81
Gut microbiota composition correlates with diet and health in the elderly. Nature (2012) 6.94
Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A (2010) 5.02
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One (2009) 4.93
Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut (2011) 3.42
Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J Clin Microbiol (2006) 2.93
Diversity of bifidobacteria within the infant gut microbiota. PLoS One (2012) 2.71
A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects. Nat Rev Microbiol (2012) 2.56
Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A (2008) 2.53
Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biol Psychiatry (2008) 2.52
The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol (2013) 1.87
Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J (2008) 1.70
Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. J Proteome Res (2008) 1.67
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol (2008) 1.56
Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab (2012) 1.55
Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods (2006) 1.50
Microbiomic analysis of the bifidobacterial population in the human distal gut. ISME J (2009) 1.43
Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol (2008) 1.42
A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome. Dig Dis Sci (2009) 1.39
Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Fact (2008) 1.32
Culture-independent analysis of desulfovibrios in the human distal colon of healthy, colorectal cancer and polypectomized individuals. FEMS Microbiol Ecol (2009) 1.31
Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res (2007) 1.30
Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans collected from Irish waters. Mar Biotechnol (NY) (2008) 1.30
Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environ Microbiol (2008) 1.20
Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes. Gut Microbes (2013) 1.02
Experimental bariatric surgery in rats generates a cytotoxic chemical environment in the gut contents. Front Microbiol (2011) 1.00
Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME J (2012) 0.97
Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl Microbiol Biotechnol (2007) 0.97
The gut microbiome: the role of a virtual organ in the endocrinology of the host. J Endocrinol (2013) 0.95
Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters. Mar Biotechnol (NY) (2008) 0.94
Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1. Appl Microbiol Biotechnol (2008) 0.85
Minimum taxonomic criteria for bacterial genome sequence depositions and announcements. J Microbiol Methods (2012) 0.83
Accessing the mobile metagenome of the human gut microbiota. Mol Biosyst (2007) 0.81
The contribution of 'omic'-based approaches to the study of enhanced biological phosphorus removal microbiology. FEMS Microbiol Ecol (2009) 0.79
Mining the human gut microbiome for novel stress resistance genes. Gut Microbes (2012) 0.79
A robust plate assay for detection of extracellular microbial protease activity in metagenomic screens and pure cultures. J Microbiol Methods (2012) 0.78
Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: theory and practical application to genomic and metagenomic projects. BMC Bioinformatics (2007) 0.77
Too much fat for the gut's microbiota. Gut (2012) 0.76
Metabolic, immune, and gut microbial signals mount a systems response to Leishmania major infection. J Proteome Res (2014) 0.76
Functional characterisation of Lp_2714, an EAL-domain protein from Lactobacillus plantarum. Biochem Biophys Res Commun (2011) 0.76
Inhibition of the growth of Bacillus subtilis DSM10 by a newly discovered antibacterial protein from the soil metagenome. Bioengineered (2015) 0.75
Isolation of novel bacteria able to degrade alpha-halocarboxylic acids by enrichment from environmental samples. Chemosphere (2005) 0.75
Current functional metagenomic approaches only expand the existing protease sequence space, but does not presently add any novelty to it. Curr Microbiol (2014) 0.75
Characterization of the electrochemical behavior of gastrointestinal fluids using a multielectrode sensor probe. IEEE Trans Biomed Eng (2011) 0.75
Isolation and characterization of a diverse group of phenylacetic acid degrading microorganisms from pristine soil. Chemosphere (2005) 0.75