Multiscale Evolutionary Dynamics of Host-Associated Microbiomes.

No abstract is available for this paper.

• Publication year

  2018

• Venue

  Cell

• Publication date

  2018-03-08

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1016/j.cell.2018.02.015PMID 29522743PMCID PMC5846202
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Toward a quantitative understanding of antibiotic resistance evolution.

  2017cited by this paper
• Bacteriophages Contribute to the Spread of Antibiotic Resistance Genes among Foodborne Pathogens of the Enterobacteriaceae Family – A Review

  2017cited by this paper
• The resilience of the intestinal microbiota influences health and disease

  2017cited by this paper
• The Dynamics of Molecular Evolution Over 60,000 Generations

  2017cited by this paper
• Adaptation to public goods cheats in Pseudomonas aeruginosa

  2017cited by this paper
• Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models

  2017cited by this paper
• Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

  2017cited by this paper
• metaSPAdes: a new versatile metagenomic assembler.

  2017cited by this paper
• Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes

  2017cited by this paper
• Evolution of Stenotrophomonas maltophilia in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study

  2017cited by this paper
• Using long‐term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin‐treated mouse gut

  2017influential reference
• Bacterial colonization and succession in a newly opened hospital

  2017cited by this paper
• Genetically engineered probiotic for the treatment of phenylketonuria (PKU); assessment of a novel treatment in vitro and in the PAHenu2 mouse model of PKU

  2017cited by this paper
• Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut

  2017cited by this paper
• Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii

  2017cited by this paper
• Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment

  2017influential reference
• Next-generation approaches to understand and combat the antibiotic resistome

  2017cited by this paper
• Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

  2017cited by this paper
• dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

  2017cited by this paper
• Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease

  2017cited by this paper
• Social wasps are a Saccharomyces mating nest

  2016cited by this paper
• RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics

  2016cited by this paper
• Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

  2016cited by this paper
• Interconnected microbiomes and resistomes in low-income human habitats

  2016cited by this paper
• Temporal Stability of the Human Skin Microbiome.

  2016cited by this paper
• The rapid spread of carbapenem-resistant Enterobacteriaceae.

  2016cited by this paper
• Tempo and mode of genome evolution in a 50,000-generation experiment

  2016cited by this paper
• Mobile genes in the human microbiome are structured from global to individual scales

  2016cited by this paper
• Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

  2016cited by this paper
• Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells

  2016cited by this paper
• Single-cell genome sequencing: current state of the science

  2016cited by this paper
• Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance.

  2016cited by this paper
• Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children

  2016cited by this paper
• MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.

  2016cited by this paper
• Diet–microbiota interactions as moderators of human metabolism

  2016cited by this paper
• Stretching a graphene nanoribbon

  2016cited by this paper
• Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling

  2016cited by this paper
• Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005–2010

  2016cited by this paper
• Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization

  2016cited by this paper
• Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small‐colony variants with increased fitness in vivo and antibiotic collateral sensitivity

  2016cited by this paper
• Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans.

  2016cited by this paper
• Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

  2015cited by this paper
• Tracking Strains in the Microbiome: Insights from Metagenomics and Models

  2015cited by this paper
• C. difficile Infection: Changing Epidemiology and Management Paradigms

  2015cited by this paper
• An evaluation of the accuracy and speed of metagenome analysis tools

  2015cited by this paper
• Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

  2015cited by this paper
• The evolution of drug resistance in clinical isolates of Candida albicans

  2015cited by this paper
• Black Queen evolution: the role of leakiness in structuring microbial communities.

  2015cited by this paper
• The yin and yang of bacterial resilience in the human gut microbiota.

  2014cited by this paper
• Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study.

  2014cited by this paper
• Functional Heterologous Protein Expression by Genetically Engineered Probiotic Yeast Saccharomyces boulardii

  2014cited by this paper
• Persistent Gut Microbiota Immaturity in Malnourished Bangladeshi Children

  2014cited by this paper
• Library preparation methods for next-generation sequencing: tone down the bias.

  2014cited by this paper
• Biogeography and individuality shape function in the human skin metagenome

  2014cited by this paper
• Fecal Microbiota Transplantation for Clostridium difficile Infection: The Ochsner Experience.

  2014cited by this paper
• Diet and the intestinal microbiome: associations, functions, and implications for health and disease.

  2014cited by this paper
• Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

  2014cited by this paper
• Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

  2014cited by this paper
• Empirical fitness landscapes and the predictability of evolution

  2014cited by this paper
• Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

  2014cited by this paper
• Bacteria from diverse habitats colonize and compete in the mouse gut.

  2014cited by this paper
• When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness

  2014cited by this paper
• Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

  2013cited by this paper
• Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

  2013cited by this paper
• Diet rapidly and reproducibly alters the human gut microbiome

  2013cited by this paper
• Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

  2013cited by this paper
• Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

  2013influential reference
• The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

  2013cited by this paper
• The broader context of antibiotic resistance: zinc feed supplementation of piglets increases the proportion of multi-resistant Escherichia coli in vivo.

  2013cited by this paper
• Occurrence of the Transferable Copper Resistance Gene tcrB among Fecal Enterococci of U.S. Feedlot Cattle Fed Copper-Supplemented Diets

  2013cited by this paper
• Duodenal infusion of donor feces for recurrent Clostridium difficile.

  2013cited by this paper
• Horizontal gene transfer in fungi.

  2012cited by this paper
• Space-efficient and exact de Bruijn graph representation based on a Bloom filter

  2012cited by this paper
• Long-Term Follow-Up of Colonoscopic Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection

  2012cited by this paper
• Fundamentals of Microbial Community Resistance and Resilience

  2012cited by this paper
• Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

  2012cited by this paper
• Human gut microbiome viewed across age and geography

  2012cited by this paper
• Genomic variation landscape of the human gut microbiome

  2012cited by this paper
• Ecology drives a global network of gene exchange connecting the human microbiome

  2011cited by this paper
• Dynamics of Mutator and Antibiotic-Resistant Populations in a Pharmacokinetic/Pharmacodynamic Model of Pseudomonas aeruginosa Biofilm Treatment

  2011cited by this paper
• Bacterial hypermutation: clinical implications.

  2011cited by this paper
• Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

  2011cited by this paper
• Eating for two: how metabolism establishes interspecies interactions in the gut.

  2011cited by this paper
• Second-Order Selection for Evolvability in a Large Escherichia coli Population

  2011cited by this paper
• Fecal Flora Reconstitution for Recurrent Clostridium difficile Infection: Results and Methodology

  2010cited by this paper
• Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

  2010cited by this paper
• Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

  2010cited by this paper
• Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics.

  2007influential reference
• Effect of fermented milk intake on plasmid transfer and on the persistence of transconjugants in the digestive tract of gnotobiotic mice

  2004cited by this paper
• 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

  2002cited by this paper
• Mercury released from dental "silver" fillings provokes an increase in mercury- and antibiotic-resistant bacteria in oral and intestinal floras of primates

  1993cited by this paper

• Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease

  2025cites this paper
• Describing the Persistence Landscape for Introducing Microbes into Complex Communities

  2025influential citation
• Gut microbiota drives structural variation of exogenous probiotics to enhance colonization

  2025cites this paper
• Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping

  2025cites this paper
• Rationally designed microbial communities in agri-food production systems: from research to market

  2025cites this paper
• Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change

  2025cites this paper
• Microbial electrochemical composting reduced the risk of antibiotic resistance genes

  2025cites this paper
• Native and invasive raccoon populations host distinct microbiomes that may facilitate invasion

  2025cites this paper
• Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series

  2025cites this paper
• Host Phylogeny Shapes Gut Microbiota and Predicted Functions in Captive Artiodactyls

  2025cites this paper
• The Microbiota and Evolution of Obesity

  2024cites this paper
• Multi-step pathway engineering in probiotic Saccharomyces boulardii for abscisic acid production in the gut

  2024cites this paper
• Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model

  2024cites this paper
• Implications of blood type in personalised microbiome therapy

  2024cites this paper
• Host genetic regulation of human gut microbial structural variation

  2024cites this paper
• Association between gut microbiota and glioblastoma: a Mendelian randomization study

  2024cites this paper
• High-Molecular-Weight Hyaluronic Acid Can Be Used as a Food Additive to Improve the Symptoms of Persistent Inflammation, Immunosuppression and Catabolism Syndrome (PICS)

  2024cites this paper
• Metagenomic coverage bias at transcription start sites is correlated with gene expression

  2024cites this paper
• Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model

  2024cites this paper
• Transgressive hybrids as hopeful holobionts

  2024cites this paper
• Doblin: Inferring dominant clonal lineages from DNA barcoding time-series

  2024cites this paper
• Patterns of microbiome composition in tsetse fly Glossina palpalis palpalis during vector control using Tiny Targets in Campo, South Cameroon

  2024cites this paper
• Impact of Altered Gut Microbiota on Ketamine-Induced Conditioned Place Preference in Mice

  2024cites this paper
• A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

  2024cites this paper
• Evolutionary Transitions of DNA Replication Origins Between Archaea and Bacteria

  2024cites this paper
• Intestinal microbiota: a new perspective on delaying aging?

  2023cites this paper
• Coadaptation mechanism of the gut microbiota and human organism to physical loading

  2023cites this paper
• Mucus-associated microbiotas among different body sites of wild tuna from the South China Sea

  2023cites this paper
• Short-Chain Fatty Acids in the Microbiota-Gut-Brain Axis: Role in Neurodegenerative Disorders and Viral Infections.

  2023cites this paper
• Regulatory Mechanisms in Biosystems

  2023cites this paper
• Deep Learning enables reliable and comprehensive profiling of invertible promoters in microbes

  2023cites this paper
• Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach

  2023cites this paper
• CCDC103 as a Prognostic Biomarker Correlated with Tumor Progression and Immune Infiltration in Glioma

  2023cites this paper
• Carotenoids and Their Health Benefits as Derived via Their Interactions with Gut Microbiota

  2022cites this paper
• New Insights into the Gut Microbiota in Neurodegenerative Diseases from the Perspective of Redox Homeostasis

  2022cites this paper
• The immunosuppressive microenvironment and immunotherapy in human glioblastoma

  2022cites this paper
• A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota

  2022cites this paper
• A microbiome abundant environment remodels the intestinal microbiota and improves resistance to obesity induced by chlorpyrifos in mice.

  2022cites this paper
• Environment-Related Genes Analysis of Limosilactobacillus fermentum Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution

  2022cites this paper
• Enhanced antibacterial activity with increasing P doping ratio in CQDs

  2022cites this paper
• Emerging Interrelationship Between the Gut Microbiome and Cellular Senescence in the Context of Aging and Disease: Perspectives and Therapeutic Opportunities

  2022cites this paper
• Detecting bacterial adaptation within individual microbiomes

  2022cites this paper
• The Biological Memory Effect in Microbial Fuel Cell Biosensors

  2022cites this paper
• Gut Microbiota and Central Nervous System Diseases: New Developments

  2022cites this paper
• Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota

  2022cites this paper
• Latent Benefits and Toxicity Risks Transmission Chain of High Dietary Copper along the Livestock-Environment-Plant-Human Health Axis and Microbial Homeostasis: A Review.

  2022cites this paper
• Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

  2022cites this paper
• Good bacteria, oxidative stress and neurological disorders: Possible therapeutical considerations.

  2022cites this paper
• The Relationship between Physical Activity, Physical Exercise, and Human Gut Microbiota in Healthy and Unhealthy Subjects: A Systematic Review

  2022cites this paper
• Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite.

  2022cites this paper
• Eco-evolutionary feedbacks in the human gut microbiome

  2022cites this paper
• Intra- and inter-species interactions drive early phases of invasion in mice gut microbiota

  2022cites this paper
• Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota

  2021cites this paper
• Modeling spatial patterns in host-associated microbial communities.

  2021cites this paper
• In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii.

  2021cites this paper
• Exploring the Gut-Brain Axis for the Control of CNS Inflammatory Demyelination: Immunomodulation by Bacteroides fragilis’ Polysaccharide A

  2021cites this paper
• Anatomy promotes neutral coexistence of strains in the human skin microbiome

  2021cites this paper
• Gut Microbiota in Brain diseases

  2021cites this paper
• Targeting gut dysbiosis as a means to enhance recovery from surgical brain injury

  2021cites this paper
• An optimized culture medium to isolate Lactobacillus fermentum strains from the human intestinal tract.

  2021cites this paper
• What E. coli knows about your 1-year-old infant: Antibiotic use, lifestyle, birth mode, and siblings.

  2021cites this paper
• Neuro-Signals from Gut Microbiota: Perspectives for Brain Glioma

  2021cites this paper
• Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

  2021influential citation
• Predicting plasmid persistence in microbial communities by coarse‐grained modeling

  2021cites this paper
• Prebiotic inulin as a treatment of obesity related nonalcoholic fatty liver disease through gut microbiota: a critical review

  2021cites this paper
• Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs

  2021cites this paper
• Gut Microbiome and Cellular Senescence in the Context of Aging and Disease: An Emerging Frontier

  2021cites this paper
• GENÉTICA NA ERA ÔMICA: ANÁLISE DE TEMAS IMPORTANTES PARA A FORMAÇÃO DO DENTISTA DO FUTURO

  2021cites this paper
• Universal adaptive evolution strategy of probiotic Lactobacillus plantarum to gut selection pressure from humans, mice and zebrafish

  2021cites this paper
• The microbiome extends host evolutionary potential

  2021cites this paper
• The Impact of Gut Microbiota-Derived Metabolites in Autism Spectrum Disorders

  2021cites this paper
• P-Doped Carbon Quantum Dots with Antibacterial Activity

  2021cites this paper
• Evolutionary and dietary relationships of wild mammals based on the gut microbiome.

  2021cites this paper
• Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

  2021cites this paper
• Networked collective microbiomes and the rise of subcellular 'units of life'.

  2021cites this paper
• Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level

  2021cites this paper
• Autopoietic symbiogenesis in secondary metabolism

  2020cites this paper
• Low mutational load and high mutation rate variation in gut commensal bacteria

  2020cites this paper
• Effect of sucralose and aspartame on glucose metabolism and gut hormones.

  2020cites this paper
• Materials design by synthetic biology

  2020cites this paper
• The persistence potential of transferable plasmids

  2020cites this paper
• Colistin and amoxicillin combinatorial exposure alters the human intestinal microbiota and antibiotic resistome in the simulated human intestinal microbiota.

  2020cites this paper
• The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide

  2020cites this paper
• The effect of short-course antibiotics on the resistance profile of colonizing gut bacteria in the ICU: a prospective cohort study

  2020cites this paper
• Deploying Big Data to Crack the Genotype to Phenotype Code.

  2020cites this paper
• The Persistence Potential of Mobile Genetic Elements

  2020cites this paper
• Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster

  2020cites this paper
• The Oral Microbiome Bank of China

  2020cites this paper
• The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

  2020cites this paper
• Establishing Probiotic Saccharomyces boulardii as a Model Organism for Synthesis and Delivery of Biomolecules

  2020cites this paper
• Effect of short-course antibiotics on the antimicrobial resistance profile of colonizing gut bacteria in the ICU

  2019cites this paper
• Title: Deploying Big Data to Crack the Genotype to Phenotype Code (g2p w/ML)

  2019cites this paper
• Mucosal microbial parasites/symbionts in health and disease: an integrative overview

  2019cites this paper
• Adaptive Strategies of theCandidate Probiotic E . coli Nissle in the Mammalian Gut Graphical

  2019cites this paper
• Culture-enriched human gut microbiomes reveal core and accessory resistance genes

  2019cites this paper
• Low Mutational Load Allows for High Mutation Rate Variation in Gut Commensal Bacteria

  2019cites this paper
• Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis

  2019cites this paper
• Multi-omic Understanding of the Evolution of Xenobiotic Tolerance in Bacterial Isolates and Communities

  2019cites this paper
• Population Genetics in the Human Microbiome.

  2019cites this paper
• Effect of nutrition on neurodegenerative diseases. A systematic review

  2019cites this paper