Biosynthetic potential of the global ocean microbiome

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

(2021) Satria A Kautsar et al.   GigaScience

Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations

(2021) Mukan Ji et al.   ISME Journal

Mining genomes to illuminate the specialized chemistry of life

(2021) Marnix H. Medema et al.   NATURE REVIEWS GENETICS

Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis

(2021) Fredarla S. Miller et al.   Nature Communications

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

(2021) Silvia G. Acinas et al.   Communications Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

(2020) R. A. Barco et al.   mBio

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

(2020) Matthew R. Olm et al.   mSystems

Landornamides: Antiviral Ornithine‐Containing Ribosomal Peptides Discovered through Genome Mining

(2020) Nina M. Bösch et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

(2020) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Tara Oceans: towards global ocean ecosystems biology

(2020) Shinichi Sunagawa et al.   NATURE REVIEWS MICROBIOLOGY

The Natural Polypeptides as Significant Elastase Inhibitors

(2020) Shabir Ahmad et al.   Frontiers in Pharmacology

BiG-FAM: the biosynthetic gene cluster families database

(2020) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

Enzymatic methylation of the amide bond

(2020) Haigang Song et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease

(2019) Silvia C Bobeica et al.   eLife

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Random coil shifts of posttranslationally modified amino acids

(2019) Anne C. Conibear et al.   JOURNAL OF BIOMOLECULAR NMR

Scientists’ warning to humanity: microorganisms and climate change

(2019) Ricardo Cavicchioli et al.   NATURE REVIEWS MICROBIOLOGY

A microbial factory for defensive kahalalides in a tripartite marine symbiosis

(2019) Jindong Zan et al.   SCIENCE

Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2)

(2019) Lewis M. Ward et al.   Frontiers in Microbiology

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential

(2019) Katherine Gregory et al.   Microorganisms

Genome mining- and synthetic biology-enabled production of hypermodified peptides

(2019) Agneya Bhushan et al.   Nature Chemistry

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

A computational framework to explore large-scale biosynthetic diversity

(2019) Jorge C. Navarro-Muñoz et al.   Nature Chemical Biology

Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology

(2019) Sandra Wiegand et al.   Nature Microbiology

Promoter Activation in Δhfq Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing

(2019) Edna Bode et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics

(2019) Maria G. Pachiadaki et al.   CELL

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

Natural noncanonical protein splicing yields products with diverse β-amino acid residues

(2018) Brandon I. Morinaka et al.   SCIENCE

A global ocean atlas of eukaryotic genes

(2018) Quentin Carradec et al.   Nature Communications

AMBER: Assessment of Metagenome BinnERs

(2018) Fernando Meyer et al.   GigaScience

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Marine microbial metagenomes sampled across space and time

(2018) Steven J. Biller et al.   Scientific Data

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies

(2017) et al.   Marine Drugs

Structural Diversity, Biological Properties and Applications of Natural Products from Cyanobacteria. A Review

(2017) Sayed Shah et al.   Marine Drugs

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products

(2017) Niels S van der Velden et al.   Nature Chemical Biology

The MAR databases: development and implementation of databases specific for marine metagenomics

(2017) Terje Klemetsen et al.   NUCLEIC ACIDS RESEARCH

Retrospective analysis of natural products provides insights for future discovery trends

(2017) Cameron R. Pye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Bacterial predation: 75 years and counting!

(2016) Juana Pérez et al.   ENVIRONMENTAL MICROBIOLOGY

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

(2016) Aaron Weimann et al.   mSystems

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Interrupted adenylation domains: unique bifunctional enzymes involved in nonribosomal peptide biosynthesis

(2015) Kristin J. Labby et al.   NATURAL PRODUCT REPORTS

The enterococcal cytolysin synthetase has an unanticipated lipid kinase fold

(2015) Shi-Hui Dong et al.   eLife

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

RadicalS-Adenosyl Methionine Epimerases: Regioselective Introduction of DiverseD-Amino Acid Patterns into Peptide Natural Products

(2014) Brandon I. Morinaka et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Specialized microbial metabolites: functions and origins

(2013) Julian Davies   JOURNAL OF ANTIBIOTICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

N-Methylation of Peptides and Proteins: An Important Element for Modulating Biological Functions

(2012) Jayanta Chatterjee et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

(2012) Jonathan L Klassen et al.   BMC GENOMICS

By their genes ye shall know them: genomic signatures of predatory bacteria

(2012) Zohar Pasternak et al.   ISME Journal

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Metagenome Mining Reveals Polytheonamides as Posttranslationally Modified Ribosomal Peptides

(2012) M. F. Freeman et al.   SCIENCE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

An improvedEscherichia colidonor strain for diparental mating

(2009) Sabrina Thoma et al.   FEMS MICROBIOLOGY LETTERS