Strain-level diversity drives alternative community types in millimetre-scale granular biofilms

[1]  Alan McNally,et al.  Why prokaryotes have pangenomes , 2017, Nature Microbiology.

[2]  K. Pollard,et al.  An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography , 2016, Genome research.

[3]  M. Doebeli,et al.  Decoupling function and taxonomy in the global ocean microbiome , 2016, Science.

[4]  Otto X. Cordero,et al.  Microbial interactions and community assembly at microscales. , 2016, Current opinion in microbiology.

[5]  Gérard Govaert,et al.  Rmixmod: The R Package of the Model-Based Unsupervised, Supervised and Semi-Supervised Classification Mixmod Library , 2015 .

[6]  Rob Knight,et al.  ConStrains identifies microbial strains in metagenomic datasets , 2015, Nature Biotechnology.

[7]  Tong Zhang,et al.  Dominant and novel clades of Candidatus Accumulibacter phosphatis in 18 globally distributed full-scale wastewater treatment plants , 2015, Scientific Reports.

[8]  Connor T. Skennerton,et al.  Expanding our view of genomic diversity in Candidatus Accumulibacter clades. , 2015, Environmental microbiology.

[9]  C. Holliger,et al.  Optimization of operation conditions for the startup of aerobic granular sludge reactors biologically removing carbon, nitrogen, and phosphorous. , 2014, Water research.

[10]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[11]  C. Holliger,et al.  Aerobic Granules: Microbial Landscape and Architecture, Stages, and Practical Implications , 2014, Applied and Environmental Microbiology.

[12]  Otto X. Cordero,et al.  Explaining microbial genomic diversity in light of evolutionary ecology , 2014, Nature Reviews Microbiology.

[13]  Jiajie Zhang,et al.  PEAR: a fast and accurate Illumina Paired-End reAd mergeR , 2013, Bioinform..

[14]  Aaron Marc Saunders,et al.  ‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity , 2013, The ISME Journal.

[15]  C. Holliger,et al.  Identification of trigger factors selecting for polyphosphate- and glycogen-accumulating organisms in aerobic granular sludge sequencing batch reactors. , 2013, Water research.

[16]  Diana R. Nemergut,et al.  Patterns and Processes of Microbial Community Assembly , 2013, Microbiology and Molecular Reviews.

[17]  T. Neu,et al.  Assessment of bacterial and structural dynamics in aerobic granular biofilms , 2013, Front. Microbiol..

[18]  Curtis Huttenhower,et al.  A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets , 2013, PLoS Comput. Biol..

[19]  Alison S. Waller,et al.  Genomic variation landscape of the human gut microbiome , 2012, Nature.

[20]  S. Tringe,et al.  Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal , 2013, The ISME Journal.

[21]  J. Raes,et al.  Microbial interactions: from networks to models , 2012, Nature Reviews Microbiology.

[22]  Otto X. Cordero,et al.  Population Genomics of Early Events in the Ecological Differentiation of Bacteria , 2012, Science.

[23]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[24]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[25]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[26]  C. Holliger,et al.  Dynamics of Microbial Community Structure of and Enhanced Biological Phosphorus Removal by Aerobic Granules Cultivated on Propionate or Acetate , 2011, Applied and Environmental Microbiology.

[27]  S. Hubbell,et al.  The unified neutral theory of biodiversity and biogeography at age ten. , 2011, Trends in ecology & evolution.

[28]  S. Hubbell The Unified Neutral Theory of Biodiversity and Biogeography (MPB-32) , 2011 .

[29]  P. Bork,et al.  Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data , 2011, Molecular systems biology.

[30]  S. Ebrahimi,et al.  Performance and microbial community composition dynamics of aerobic granular sludge from sequencing batch bubble column reactors operated at 20 °C, 30 °C, and 35 °C , 2010, Applied Microbiology and Biotechnology.

[31]  M. Reis,et al.  Assessing the abundance and activity of denitrifying polyphosphate accumulating organisms through molecular and chemical techniques. , 2010, Water science and technology : a journal of the International Association on Water Pollution Research.

[32]  E. Virginia Armbrust,et al.  pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree , 2010, BMC Bioinformatics.

[33]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[34]  K. McMahon,et al.  Denitrification capabilities of two biological phosphorus removal sludges dominated by different "Candidatus Accumulibacter" clades. , 2009, Environmental microbiology reports.

[35]  Allan Konopka,et al.  What is microbial community ecology? , 2009, The ISME Journal.

[36]  David R. Riley,et al.  Comparative genomics: the bacterial pan-genome. , 2008, Current opinion in microbiology.

[37]  P. Hugenholtz,et al.  Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. , 2008, Environmental microbiology.

[38]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .

[39]  R. Tibshirani,et al.  Sparse inverse covariance estimation with the graphical lasso. , 2008, Biostatistics.

[40]  K. McMahon,et al.  “Candidatus Accumulibacter” Population Structure in Enhanced Biological Phosphorus Removal Sludges as Revealed by Polyphosphate Kinase Genes , 2007, Applied and Environmental Microbiology.

[41]  J. Keasling,et al.  Polyphosphate kinase genes from full-scale activated sludge plants , 2007, Applied Microbiology and Biotechnology.

[42]  Rampal S Etienne,et al.  A neutral sampling formula for multiple samples and an 'exact' test of neutrality. , 2007, Ecology letters.

[43]  Philip D Marsh,et al.  Dental plaque as a biofilm and a microbial community – implications for health and disease , 2006, BMC oral health.

[44]  S. Nee,et al.  Quantifying the roles of immigration and chance in shaping prokaryote community structure. , 2006, Environmental microbiology.

[45]  James H. Brown,et al.  Microbial biogeography: putting microorganisms on the map , 2006, Nature Reviews Microbiology.

[46]  Chanathip Pharino,et al.  Genotypic Diversity Within a Natural Coastal Bacterioplankton Population , 2005, Science.

[47]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[48]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[49]  J. Aitchison,et al.  Biplots of Compositional Data , 2002 .

[50]  Olivier Gascuel,et al.  Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle , 2002, WABI.

[51]  J. R. van der Meer,et al.  Enrichment, phylogenetic analysis and detection of a bacterium that performs enhanced biological phosphate removal in activated sludge. , 1999, Systematic and applied microbiology.

[52]  Pj Davoll,et al.  Marine snow aggregates: life history sequence and microbial community of abandoned larvacean houses from Monterey Bay, California , 1986 .

[53]  J. Tisdall,et al.  Organic matter and water‐stable aggregates in soils , 1982 .

[54]  B. Levin,et al.  Genetic diversity and structure in Escherichia coli populations. , 1980, Science.