Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

[1]  Harris H. Wang,et al.  Metagenomic engineering of the mammalian gut microbiome in situ , 2018, Nature Methods.

[2]  A. Wood,et al.  Temporal dynamics of bacteria-plasmid coevolution under antibiotic selection , 2018, The ISME Journal.

[3]  A. Schramm,et al.  Intracellular nitrate in sediments of an oxygen-deficient marine basin is linked to pelagic diatoms. , 2018, FEMS microbiology ecology.

[4]  J. Lloyd,et al.  NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction , 2018, FEMS microbiology ecology.

[5]  Johannes Cairns,et al.  Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes , 2018, Communications Biology.

[6]  S. Sørensen,et al.  Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community , 2018 .

[7]  J. Prescott,et al.  History and Current Use of Antimicrobial Drugs in Veterinary Medicine. , 2017, Microbiology spectrum.

[8]  M. Brockhurst,et al.  Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species , 2017, FEMS microbiology ecology.

[9]  Hannah R. Meredith,et al.  Persistence and reversal of plasmid-mediated antibiotic resistance , 2017, Nature Communications.

[10]  R. MacLean,et al.  Fitness Costs of Plasmids: a Limit to Plasmid Transmission , 2017, Microbiology spectrum.

[11]  S. Sørensen,et al.  Deciphering conjugative plasmid permissiveness in wastewater microbiomes , 2017, Molecular ecology.

[12]  Samuel S. Hunter,et al.  Compensatory mutations improve general permissiveness to antibiotic resistance plasmids , 2017, Nature Ecology & Evolution.

[13]  Stephen R. Lindemann,et al.  Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach , 2017, Front. Microbiol..

[14]  M. Popowska,et al.  Occurrence and Variety of β-Lactamase Genes among Aeromonas spp. Isolated from Urban Wastewater Treatment Plant , 2017, Front. Microbiol..

[15]  M. Desvaux,et al.  InlL from Listeria monocytogenes Is Involved in Biofilm Formation and Adhesion to Mucin , 2017, Front. Microbiol..

[16]  G. Dantas,et al.  Next-generation approaches to understand and combat the antibiotic resistome , 2017, Nature Reviews Microbiology.

[17]  Virgilio Gómez-Rubio,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[18]  P. Piccaluga,et al.  Unveiling Another Missing Piece in EBV-Driven Lymphomagenesis: EBV-Encoded MicroRNAs Expression in EBER-Negative Burkitt Lymphoma Cases , 2017, Front. Microbiol..

[19]  Christian Munck,et al.  Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts , 2016, Molecular biology and evolution.

[20]  A. Wood,et al.  Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities , 2016, Proceedings of the National Academy of Sciences.

[21]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[22]  Luke S P Moore,et al.  Antimicrobials: access and sustainable eff ectiveness 2 Understanding the mechanisms and drivers of antimicrobial resistance , 2015 .

[23]  A. Olaniran,et al.  Antimicrobial resistance and virulence signatures of Listeria and Aeromonas species recovered from treated wastewater effluent and receiving surface water in Durban, South Africa , 2015, BMC Microbiology.

[24]  A. Spiers,et al.  Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum , 2015, Current Biology.

[25]  Jinling Huang,et al.  Horizontal gene transfer: building the web of life , 2015, Nature Reviews Genetics.

[26]  A. Spiers,et al.  Environmentally co‐occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context‐dependent fitness effects , 2015, Environmental microbiology.

[27]  R. MacLean,et al.  The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach , 2014, Evolutionary applications.

[28]  B. Smets,et al.  Protocol for Evaluating the Permissiveness of Bacterial Communities Toward Conjugal Plasmids by Quantification and Isolation of Transconjugants , 2014 .

[29]  S. Sørensen,et al.  Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community , 2014, The ISME Journal.

[30]  M. Popowska,et al.  The prevalence of antibiotic resistance genes among Aeromonas species in aquatic environments , 2014, Annals of Microbiology.

[31]  S. Sørensen,et al.  454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. , 2013, FEMS microbiology ecology.

[32]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[33]  S. C. Winans,et al.  The ABCs of plasmid replication and segregation , 2012, Nature Reviews Microbiology.

[34]  M. Brockhurst,et al.  Plasmid-mediated horizontal gene transfer is a coevolutionary process. , 2012, Trends in microbiology.

[35]  Tong Zhang,et al.  Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge , 2011, PloS one.

[36]  Tong Zhang,et al.  Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. , 2011, Environmental science & technology.

[37]  J. Block,et al.  Persistence and dissemination of the multiple-antibiotic-resistance plasmid pB10 in the microbial communities of wastewater sludge microcosms. , 2011, Water research.

[38]  Klaus Peter Schliep,et al.  phangorn: phylogenetic analysis in R , 2010, Bioinform..

[39]  H. Heuer,et al.  Variation in permissiveness for broad-host-range plasmids among genetically indistinguishable isolates of Dickeya sp. from a small field plot. , 2010, FEMS microbiology ecology.

[40]  S. Abbott,et al.  The Genus Aeromonas: Taxonomy, Pathogenicity, and Infection , 2010, Clinical Microbiology Reviews.

[41]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[42]  S. Sørensen,et al.  All IncP-1 plasmid subgroups, including the novel epsilon subgroup, are prevalent in the influent of a Danish wastewater treatment plant. , 2009, Plasmid.

[43]  E. Top,et al.  Host-specific factors determine the persistence of IncP-1 plasmids , 2008 .

[44]  A. Pühler,et al.  Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. , 2007, FEMS microbiology reviews.

[45]  S. Sørensen,et al.  The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups. , 2007, Plasmid.

[46]  H. Heuer,et al.  Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host. , 2007, FEMS microbiology ecology.

[47]  P. Joyce,et al.  Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. , 2007, Microbiology.

[48]  L. Fernandes,et al.  The evolution of a conjugative plasmid and its ability to increase bacterial fitness , 2005, Biology Letters.

[49]  Jaai Kim,et al.  Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. , 2005, Biotechnology and bioengineering.

[50]  D. Livermore,et al.  Enhancement of host fitness by the sul2-coding plasmid p9123 in the absence of selective pressure. , 2004, The Journal of antimicrobial chemotherapy.

[51]  M. Mergeay,et al.  Replication functions of new broad host range plasmids isolated from polluted soils. , 2003, Research in microbiology.

[52]  Carl T. Bergstrom,et al.  Natural selection, infectious transfer and the existence conditions for bacterial plasmids. , 2000, Genetics.

[53]  B. Levin,et al.  Transitory derepression and the maintenance of conjugative plasmids. , 1986, Genetics.

[54]  R. Hedges,et al.  Resistance Plasmids of Aeromonads , 1985 .

[55]  D. E. Bradley Characteristics and function of thick and thin conjugative pili determined by transfer-derepressed plasmids of incompatibility groups I1, I2, I5, B, K and Z. , 1984, Journal of general microbiology.

[56]  F. M. Stewart,et al.  The population biology of bacterial plasmids: a priori conditions for the existence of mobilizable nonconjugative factors. , 1980, Genetics.

[57]  D. E. Bradley Determination of pili by conjugative bacterial drug resistance plasmids of incompatibility groups B, C, H, J, K, M, V, and X , 1980, Journal of bacteriology.

[58]  A C C Gibbs,et al.  Data Analysis , 2009, Encyclopedia of Database Systems.

[59]  S. Sørensen,et al.  Impact of conjugal transfer on the stability of IncP-1 plasmid pKJK5 in bacterial populations. , 2007, FEMS microbiology letters.

[60]  P. Legendre,et al.  vegan : Community Ecology Package. R package version 1.8-5 , 2007 .