Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

[1]  Fatima Iftikhar Shah,et al.  Eminent Industrial and Biotechnological Applications of Laccases from Bacterial Source: a Current Overview , 2022, Applied Biochemistry and Biotechnology.

[2]  B. Simmons,et al.  A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities , 2021, Scientific Reports.

[3]  H. Drost,et al.  Sensitive protein alignments at tree-of-life scale using DIAMOND , 2021, Nature Methods.

[4]  U. Karaoz,et al.  A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae , 2021, Scientific Reports.

[5]  Sean P. Gilmore,et al.  Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes , 2021, Nature Microbiology.

[6]  J. Gharechahi,et al.  Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen , 2020, The ISME Journal.

[7]  B. Simmons,et al.  Whole-Genome Sequence of Brevibacillus borstelensis SDM, Isolated from a Sorghum-Adapted Microbial Community , 2020, Microbiology Resource Announcements.

[8]  Dmitry Antipov,et al.  Using SPAdes De Novo Assembler , 2020, Current protocols in bioinformatics.

[9]  Otto X. Cordero,et al.  Context-dependent dynamics lead to the assembly of functionally distinct microbial communities , 2020, Nature Communications.

[10]  D. Cowan,et al.  Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes , 2020, Scientific Reports.

[11]  V. Eijsink,et al.  Polysaccharide degradation by lytic polysaccharide monooxygenases. , 2019, Current opinion in structural biology.

[12]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[13]  S. Sunagawa,et al.  Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere , 2019, Nature Ecology & Evolution.

[14]  Jack P. Wang,et al.  Quantitative fermentation of unpretreated transgenic poplar by Caldicellulosiruptor bescii , 2019, Nature Communications.

[15]  R. White,et al.  Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle , 2019, Nature Microbiology.

[16]  M. Dal Bello,et al.  Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities , 2019, Life.

[17]  Daniel R. Amor,et al.  Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities. , 2019 .

[18]  M. Strous,et al.  Designer microbiomes for environmental, energy and health biotechnology. , 2018, Current opinion in microbiology.

[19]  B. Simmons,et al.  A bacterial pioneer produces cellulase complexes that persist through community succession , 2017, Nature Microbiology.

[20]  B. Nidetzky,et al.  Single-molecule study of oxidative enzymatic deconstruction of cellulose , 2017, Nature Communications.

[21]  D. Jiménez,et al.  Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia. , 2017, Trends in microbiology.

[22]  N. Baliga,et al.  Robustness of a model microbial community emerges from population structure among single cells of a clonal population , 2017, Environmental microbiology.

[23]  C. T. Anderson,et al.  Acetyl Bromide Soluble Lignin (ABSL) Assay for Total Lignin Quantification from Plant Biomass. , 2017, Bio-protocol.

[24]  J. Setubal,et al.  Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics , 2016, Scientific Reports.

[25]  S. Sattler,et al.  Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries , 2016, Biotechnology for Biofuels.

[26]  E. Bayer,et al.  Toward combined delignification and saccharification of wheat straw by a laccase-containing designer cellulosome , 2016, Proceedings of the National Academy of Sciences.

[27]  Daniel H. Huson,et al.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data , 2016, PLoS Comput. Biol..

[28]  J. Fuhrman,et al.  Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. , 2016, Environmental microbiology.

[29]  Blake A. Simmons,et al.  MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets , 2016, Bioinform..

[30]  Vincent Lombard,et al.  Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization , 2016, Applied and Environmental Microbiology.

[31]  Eoin L. Brodie,et al.  Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee , 2015, Nature Communications.

[32]  D. Haltrich,et al.  Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation , 2015, Nature Communications.

[33]  R. Parsons,et al.  Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton , 2015 .

[34]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[35]  Taichi E. Takasuka,et al.  Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). , 2014, ACS chemical biology.

[36]  Michelle C. Y. Chang,et al.  Exploring bacterial lignin degradation. , 2014, Current opinion in chemical biology.

[37]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[38]  B. Simmons,et al.  Community dynamics of cellulose-adapted thermophilic bacterial consortia. , 2013, Environmental microbiology.

[39]  S. Tringe,et al.  Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass , 2013, PloS one.

[40]  B. Henrissat,et al.  Characterization of salt-adapted secreted lignocellulolytic enzymes from the mangrove fungus Pestalotiopsis sp. , 2013, Nature Communications.

[41]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[42]  Chao-Hsun Yang,et al.  A 24.7-kDa copper-containing oxidase, secreted by Thermobifida fusca, significantly increasing the xylanase/cellulase-catalyzed hydrolysis of sugarcane bagasse , 2013, Applied Microbiology and Biotechnology.

[43]  M. Rose,et al.  From nature to the laboratory: the impact of founder effects on adaptation , 2012, Journal of evolutionary biology.

[44]  Daniel J. Cosgrove,et al.  Comparative structure and biomechanics of plant primary and secondary cell walls , 2012, Front. Plant Sci..

[45]  J. Keasling,et al.  Microbial engineering for the production of advanced biofuels , 2012, Nature.

[46]  Xin Chen,et al.  dbCAN: a web resource for automated carbohydrate-active enzyme annotation , 2012, Nucleic Acids Res..

[47]  H. Flint,et al.  Microbial degradation of complex carbohydrates in the gut , 2012, Gut microbes.

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

[49]  Lutz Wobbe,et al.  Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii , 2012, Nature Communications.

[50]  Jizhong Zhou,et al.  Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2 , 2011, mBio.

[51]  J. VanderGheynst,et al.  Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass , 2011, Applied and Environmental Microbiology.

[52]  Ye Deng,et al.  Functional Molecular Ecological Networks , 2010, mBio.

[53]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010, Bioinform..

[54]  M. Borodovsky,et al.  Ab initio gene identification in metagenomic sequences , 2010, Nucleic acids research.

[55]  W. Silver,et al.  Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities , 2010, BioEnergy Research.

[56]  S. Sattler,et al.  Efficacy of singular and stacked brown midrib 6 and 12 in the modification of lignocellulose and grain chemistry. , 2010, Journal of agricultural and food chemistry.

[57]  G. Bergstrom,et al.  An optimized microplate assay system for quantitative evaluation of plant cell wall–degrading enzyme activity of fungal culture extracts , 2009, Biotechnology and bioengineering.

[58]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[59]  Richard A. Kerr,et al.  Global Warming Is Changing the World , 2007, Science.

[60]  G. Stephanopoulos.  Challenges in Engineering Microbes for Biofuels Production , 2007, Science.

[61]  David K. Johnson,et al.  Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production , 2007, Science.

[62]  M. Galbe,et al.  Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production , 2007 .

[63]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[64]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[65]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[66]  Julie D Thompson,et al.  Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.

[67]  John Aitchison,et al.  Principles of compositional data analysis , 1994 .