Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities

Modulation of microbial community dynamics by spatial partitioning

(2022) Feilun Wu et al.   Nature Chemical Biology

Rhizosphere bacteriome structure and functions

(2022) Ning Ling et al.   Nature Communications

High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota

(2022) Rong Tan et al.   Gut Microbes

The Influence of Coalescent Microbiotic Particles From Water and Soil on the Evolution and Spread of Antimicrobial Resistance

(2022) F. Baquero et al.   Frontiers in Environmental Science

A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits

(2022) Liliane Costa Conteville et al.   Scientific Reports

Horizontal gene transfer enables programmable gene stability in synthetic microbiota

(2022) Teng Wang et al.   Nature Chemical Biology

Elevated rates of horizontal gene transfer in the industrialized human microbiome

(2021) Mathieu Groussin et al.   CELL

Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities

(2021) Aida Alonso-del Valle et al.   Nature Communications

Predicting plasmid persistence in microbial communities by coarse‐grained modeling

(2021) Teng Wang et al.   BIOESSAYS

Soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens

(2021) Dong Zhu et al.   ISME Journal

The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

(2021) Anastasia Kottara et al.   MICROBIOLOGY-SGM

Ecological and evolutionary solutions to the plasmid paradox

(2021) Michael A. Brockhurst et al.   TRENDS IN MICROBIOLOGY

Mathematical Models of Plasmid Population Dynamics

(2021) José Carlos Ramón Hernández-Beltrán et al.   Frontiers in Microbiology

Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes

(2020) Samuel Bickel et al.   Nature Communications

Mouse Genetic Background Affects Transfer of an Antibiotic Resistance Plasmid in the Gastrointestinal Tract

(2020) Logan C. Ott et al.   mSphere

Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli

(2020) Jonathan H. Bethke et al.   Science Advances

Selective and non‐selective bottlenecks as drivers of the evolution of hypermutable bacterial loci

(2020) Megan De Ste Croix et al.   MOLECULAR MICROBIOLOGY

Plasmids related to the symbiotic nitrogen fixation are not only cooperated functionally, but also may have evolved over a time span in family Rhizobiaceae

(2020) Ling-Ling Yang et al.   Genome Biology and Evolution

Oceanic Hitchhikers – Assessing Pathogen Risks from Marine Microplastic

(2020) Jake Bowley et al.   TRENDS IN MICROBIOLOGY

Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

(2020) William J Watterson et al.   eLife

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

(2020) Alyssa G. Kent et al.   Nature Communications

Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology

(2020) Masaki Shintani et al.   Frontiers in Microbiology

Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation

(2020) Na Li et al.   Microbiome

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

The founder hypothesis: A basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens

(2019) Yael Litvak et al.   PLoS Pathogens

Man-made microbial resistances in built environments

(2019) Alexander Mahnert et al.   Nature Communications

Scientists’ warning to humanity: microorganisms and climate change

(2019) Ricardo Cavicchioli et al.   NATURE REVIEWS MICROBIOLOGY

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance

(2019) Tanita Wein et al.   Nature Communications

Versatile biomanufacturing through stimulus-responsive cell–material feedback

(2019) Zhuojun Dai et al.   Nature Chemical Biology

Common principles and best practices for engineering microbiomes

(2019) Christopher E. Lawson et al.   NATURE REVIEWS MICROBIOLOGY

Microplastic pollution increases gene exchange in aquatic ecosystems

(2018) Maria Arias-Andres et al.   ENVIRONMENTAL POLLUTION

Metabolic division of labor in microbial systems

(2018) Ryan Tsoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neutral and selective dynamics in a synthetic microbial community

(2018) Nate J. Cira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell-to-cell bacterial interactions promoted by drier conditions on soil surfaces

(2018) Robin Tecon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microscale Heterogeneity of the Spatial Distribution of Organic Matter Can Promote Bacterial Biodiversity in Soils: Insights From Computer Simulations

(2018) Xavier Portell et al.   Frontiers in Microbiology

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

(2017) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistence and reversal of plasmid-mediated antibiotic resistance

(2017) Allison J. Lopatkin et al.   Nature Communications

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

(2016) James P. J. Hall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

(2016) Christopher L. Hemme et al.   mBio

Microbial communities for bioprocessing: lessons learned from nature

(2016) Xuefeng “Nick” Peng et al.   Current Opinion in Chemical Engineering

Microbial Evolution: Towards Resolving the Plasmid Paradox

(2015) R. Craig MacLean et al.   CURRENT BIOLOGY

Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

(2015) Ellie Harrison et al.   CURRENT BIOLOGY

The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community

(2015) Meghan Wymore Brand et al.   ILAR JOURNAL

Horizontal gene transfer: building the web of life

(2015) Shannon M. Soucy et al.   NATURE REVIEWS GENETICS

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine

(2015) W. Zac Stephens et al.   mBio

Analysis of Bottlenecks in Experimental Models of Infection

(2015) Sören Abel et al.   PLoS Pathogens

Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens

(2015) Emile Gluck-Thaler et al.   PLoS Pathogens

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

(2014) A. San Millan et al.   Nature Communications

Granulocytes Impose a Tight Bottleneck upon the Gut Luminal Pathogen Population during Salmonella Typhimurium Colitis

(2014) Lisa Maier et al.   PLoS Pathogens

Horizontal gene transfer in human pathogens

(2013) Mario Juhas   CRITICAL REVIEWS IN MICROBIOLOGY

Broad-host-range IncP-1 plasmids and their resistance potential

(2013) Magdalena Popowska et al.   Frontiers in Microbiology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species

(2011) Maria Smorawinska et al.   FEMS MICROBIOLOGY LETTERS

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

(2011) Sébastien Wielgoss et al.   G3-Genes Genomes Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

What traits are carried on mobile genetic elements and why?

(2010) D J Rankin et al.   HEREDITY

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages

(2009) Wataru Iwasaki et al.   PLoS Genetics