Biosynthetic potential of the global ocean microbiome

[1]  Eduardo P C Rocha,et al.  Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder. , 2017, Methods in molecular biology.

[2]  William R. Harcombe,et al.  Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis , 2021, Nature Communications.

[3]  K. Reinert,et al.  Critical Assessment of Metagenome Interpretation: the second round of challenges , 2021, Nature Methods.

[4]  B. Moore,et al.  Mining genomes to illuminate the specialized chemistry of life , 2021, Nature Reviews Genetics.

[5]  Francisco M. Cornejo-Castillo,et al.  Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities , 2021, Communications biology.

[6]  S. Sunagawa,et al.  A roadmap for metagenomic enzyme discovery , 2021, Natural product reports.

[7]  T. Williams,et al.  Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations , 2021, The ISME Journal.

[8]  Kai Blin,et al.  BiG-FAM: the biosynthetic gene cluster families database , 2020, Nucleic Acids Res..

[9]  Luis Pedro Coelho,et al.  GUNC: detection of chimerism and contamination in prokaryotic genomes , 2020, Genome Biology.

[10]  Vincent J. Denef,et al.  A genomic catalog of Earth’s microbiomes , 2020, Nature Biotechnology.

[11]  Irina R Arkhipova,et al.  Metagenome Proteins and Database Contamination , 2020, mSphere.

[12]  Justin J. J. van der Hooft,et al.  BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters , 2020, bioRxiv.

[13]  J. Naismith,et al.  Enzymatic methylation of the amide bond. , 2020, Current opinion in structural biology.

[14]  M. Saleem,et al.  The Natural Polypeptides as Significant Elastase Inhibitors , 2020, Frontiers in Pharmacology.

[15]  G. Cochrane,et al.  Tara Oceans: towards global ocean ecosystems biology , 2020, Nature Reviews Microbiology.

[16]  A. Oxenius,et al.  Landornamides, antiviral ornithine-containing ribosomal peptides discovered by proteusin mining. , 2020, Angewandte Chemie.

[17]  David J Newman,et al.  Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019. , 2020, Journal of natural products.

[18]  Donovan H Parks,et al.  GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..

[19]  J. Banfield,et al.  Consistent metagenome-derived metrics verify and define bacterial species boundaries , 2019, bioRxiv.

[20]  Sallie W. Chisholm,et al.  Charting the Complexity of the Marine Microbiome through Single-Cell Genomics , 2019, Cell.

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

[22]  Michael Y. Galperin,et al.  Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology , 2019, Nature Microbiology.

[23]  E. Thines,et al.  Promoter Activation in Δhfq Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing , 2019, Angewandte Chemie.

[24]  Luis Pedro Coelho,et al.  Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome , 2019, Cell.

[25]  Marnix H. Medema,et al.  A computational framework to explore large-scale biosynthetic diversity , 2019, Nature Chemical Biology.

[26]  P. Egli,et al.  Genome mining- and synthetic biology-enabled production of hypermodified peptides , 2019, Nature Chemistry.

[27]  T. Cardona,et al.  Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2) , 2019, Front. Microbiol..

[28]  H. Kaehlig,et al.  Random coil shifts of posttranslationally modified amino acids , 2019, Journal of Biomolecular NMR.

[29]  J. Huisman,et al.  Scientists’ warning to humanity: microorganisms and climate change , 2019, Nature Reviews Microbiology.

[30]  R. Hill,et al.  A microbial factory for defensive kahalalides in a tripartite marine symbiosis , 2019, Science.

[31]  A. Murat Eren,et al.  Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories , 2019, mBio.

[32]  Barbara I. Adaikpoh,et al.  Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential , 2019, Microorganisms.

[33]  S. Lee,et al.  antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline , 2019, Nucleic Acids Res..

[34]  Luis Pedro Coelho,et al.  Microbial abundance, activity and population genomic profiling with mOTUs2 , 2019, Nature Communications.

[35]  Feng Li,et al.  MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies , 2019, PeerJ.

[36]  S. Nair,et al.  Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease , 2019, eLife.

[37]  Edoardo Pasolli,et al.  Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle , 2019, Cell.

[38]  Lai Guan Ng,et al.  Dimensionality reduction for visualizing single-cell data using UMAP , 2018, Nature Biotechnology.

[39]  Davide Heller,et al.  eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses , 2018, Nucleic Acids Res..

[40]  A. Phillippy,et al.  High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries , 2018, Nature Communications.

[41]  T. Hackl,et al.  Marine microbial metagenomes sampled across space and time , 2018, Scientific Data.

[42]  Donovan H. Parks,et al.  A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life , 2018, Nature Biotechnology.

[43]  Changsheng Li,et al.  Genome-centric view of carbon processing in thawing permafrost , 2018, Nature.

[44]  Tom O. Delmont,et al.  Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes , 2018, Nature Microbiology.

[45]  Brian C. Thomas,et al.  Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis , 2018, Nature.

[46]  Lonnie D. Crosby,et al.  Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes , 2018, mSystems.

[47]  S. Sunagawa,et al.  Natural noncanonical protein splicing yields products with diverse β-amino acid residues , 2018, Science.

[48]  Alexander Agafonov,et al.  The MAR databases: development and implementation of databases specific for marine metagenomics , 2017, Nucleic Acids Res..

[49]  P. Bork,et al.  A global ocean atlas of eukaryotic genes , 2018, Nature Communications.

[50]  Alice C. McHardy,et al.  AMBER: Assessment of Metagenome BinnERs , 2017, bioRxiv.

[51]  Kuiwu Wang,et al.  Structural Diversity, Biological Properties and Applications of Natural Products from Cyanobacteria. A Review † , 2017, Marine drugs.

[52]  Johannes Söding,et al.  MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.

[53]  Donovan H. Parks,et al.  Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life , 2017, Nature Microbiology.

[54]  L. Dijkhuizen,et al.  Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus , 2017, BMC Genomics.

[55]  Natalia N. Ivanova,et al.  Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea , 2017, Nature Biotechnology.

[56]  Y. P. Paudel,et al.  Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies , 2017, Marine drugs.

[57]  J. Banfield,et al.  dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication , 2017, The ISME Journal.

[58]  Elaina D. Graham,et al.  The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans , 2017, Scientific Data.

[59]  A. von Haeseler,et al.  UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.

[60]  M. Künzler,et al.  Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products. , 2017, Nature chemical biology.

[61]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[62]  William H. Gerwick,et al.  Retrospective analysis of natural products provides insights for future discovery trends , 2017, Proceedings of the National Academy of Sciences.

[63]  Michael Richter,et al.  Catalytic Alkylation Using a Cyclic S-Adenosylmethionine Regeneration System. , 2017, Angewandte Chemie.

[64]  Alexander Lex,et al.  UpSetR: an R package for the visualization of intersecting sets and their properties , 2017, bioRxiv.

[65]  Leland McInnes,et al.  hdbscan: Hierarchical density based clustering , 2017, J. Open Source Softw..

[66]  David K. Smith,et al.  ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data , 2017 .

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

[68]  Luis Pedro Coelho,et al.  Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper , 2016, bioRxiv.

[69]  Eric P. Nawrocki,et al.  NCBI prokaryotic genome annotation pipeline , 2016, Nucleic acids research.

[70]  Brian C. Thomas,et al.  A new view of the tree of life , 2016, Nature Microbiology.

[71]  Alice C. McHardy,et al.  From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer , 2016, mSystems.

[72]  J. Muñoz-Dorado,et al.  Bacterial predation: 75 years and counting! , 2016, Environmental microbiology.

[73]  Tom O. Delmont,et al.  Anvi’o: an advanced analysis and visualization platform for ‘omics data , 2015, PeerJ.

[74]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[75]  Luis Pedro Coelho,et al.  Structure and function of the global ocean microbiome , 2015, Science.

[76]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[77]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[78]  Anders F. Andersson,et al.  Binning metagenomic contigs by coverage and composition , 2014, Nature Methods.

[79]  H. Bode,et al.  Radical S-adenosyl methionine epimerases: regioselective introduction of diverse D-amino acid patterns into peptide natural products. , 2014, Angewandte Chemie.

[80]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[81]  Christian Rinke,et al.  An environmental bacterial taxon with a large and distinct metabolic repertoire , 2014, Nature.

[82]  A. Demain,et al.  Microbial Enzymes: Tools for Biotechnological Processes , 2014, Biomolecules.

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

[84]  Alexandros Stamatakis,et al.  Metagenomic species profiling using universal phylogenetic marker genes , 2013, Nature Methods.

[85]  P. Bork,et al.  Accurate and universal delineation of prokaryotic species , 2013, Nature Methods.

[86]  J. Davies,et al.  Specialized microbial metabolites: functions and origins , 2013, The Journal of Antibiotics.

[87]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[88]  Horst Kessler,et al.  N-methylation of peptides and proteins: an important element for modulating biological functions. , 2013, Angewandte Chemie.

[89]  U. Gophna,et al.  By their genes ye shall know them: genomic signatures of predatory bacteria , 2012, The ISME Journal.

[90]  Jörn Piel,et al.  Metagenome Mining Reveals Polytheonamides as Posttranslationally Modified Ribosomal Peptides , 2012, Science.

[91]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[92]  C. Currie,et al.  Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation , 2012, BMC Genomics.

[93]  Stephan Frickenhaus,et al.  Average genome size: a potential source of bias in comparative metagenomics , 2010, The ISME Journal.

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

[95]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[96]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[97]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[98]  M. Schobert,et al.  An improved Escherichia coli donor strain for diparental mating. , 2009, FEMS microbiology letters.

[99]  D. Mazel,et al.  Construction of a Vibrio splendidus Mutant Lacking the Metalloprotease Gene vsm by Use of a Novel Counterselectable Suicide Vector , 2006, Applied and Environmental Microbiology.

[100]  Feng Chen,et al.  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups , 2005, Nucleic Acids Res..

[101]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

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

[103]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[104]  H. Anke,et al.  Omphalotin, a new cyclic peptide with potent nematicidal activity from Omphalotus olearius. II. Isolation and structure determination. , 1997 .

[105]  B. Arison,et al.  Characterization of methyltransferase and hydroxylase genes involved in the biosynthesis of the immunosuppressants FK506 and FK520 , 1996, Journal of Bacteriology.

[106]  U. Hofmann,et al.  Syntheses of Metabolites of S‐Carboxymethyl‐L‐cysteine and S‐Methyl‐L‐cysteine and of Some Isotopically Labelled (2H, 13C) Analogues , 1990, Archiv der Pharmazie.

[107]  D. R. Crist,et al.  Use of NOE difference spectra to determine configurations and conformations of imidate esters , 1987 .

[108]  W. Walter,et al.  Unusual 13C/77se couplings in the 13C NMR spectra of selenoimidates , 1985 .

[109]  Supplemental Information 2: Kyoto Encyclopedia of genes and genomes. , 2022 .