Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity

Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

(2020) Kyle D. Brumfield et al.   PLoS One

Challenges of unculturable bacteria: environmental perspectives

(2020) Attila Bodor et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

(2020) Alexander Crits-Christoph et al.   ISME Journal

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

(2020) Mehmet Direnç Mungan et al.   NUCLEIC ACIDS RESEARCH

Review on natural products databases: where to find data in 2020

(2020) Maria Sorokina et al.   Journal of Cheminformatics

Synthetic-Bioinformatic Natural Product Antibiotics with Diverse Modes of Action

(2020) John Chu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA

(2020) Jingjie Hao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

New voyages to explore the natural product galaxy

(2019) Nigel J. Mouncey et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales

(2019) Regina L. Wilpiszeski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data

(2019) Krithika Arumugam et al.   Microbiome

Microbial community drivers of PK/NRP gene diversity in selected global soils

(2019) Chiara Borsetto et al.   Microbiome

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification

(2019) Florian P Breitwieser et al.   BIOINFORMATICS

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

(2019) Nicola De Maio et al.   Microbial Genomics

A computational framework to explore large-scale biosynthetic diversity

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

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

(2019) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome

(2019) Yuki Sugimoto et al.   SCIENCE

Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria

(2019) Giampiero Batani et al.   Scientific Reports

Assessing the Efficiency of Cultivation Techniques To Recover Natural Product Biosynthetic Gene Populations from Sediment

(2018) Maryam Elfeki et al.   ACS Chemical Biology

Harnessing the Properties of Natural Products

(2018) Asmaa Boufridi et al.   Annual Review of Pharmacology and Toxicology

Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces

(2018) Haitao Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

(2018) Luis M. Rodriguez-R et al.   mSystems

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Antibiotic discovery: History, methods and perspectives

(2018) Guillaume André Durand et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Using natural products for drug discovery: the impact of the genomics era

(2017) Mingzi M Zhang et al.   Expert Opinion on Drug Discovery

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale

(2017) Christophe Lemetre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria

(2017) Olaf Tyc et al.   TRENDS IN MICROBIOLOGY

An improved method suitable for isolation of high-quality metagenomic DNA from diverse soils

(2017) Sumit Kumar Verma et al.   3 Biotech

An improved method suitable for isolation of high-quality metagenomic DNA from diverse soils

(2017) Sumit Kumar Verma et al.   3 Biotech

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity

(2016) Zachary Charlop-Powers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Antibiotic drug discovery

(2016) Wolfgang Wohlleben et al.   Microbial Biotechnology

Global biogeographic sampling of bacterial secondary metabolism

(2015) Zachary Charlop-Powers et al.   eLife

The Biogeography of Putative Microbial Antibiotic Production

(2015) Hélène Morlon et al.   PLoS One

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Catchments as reactors: a comprehensive approach for water fluxes and solute turnover

(2013) Peter Grathwohl et al.   Environmental Earth Sciences

Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes

(2012) Boojala Vijay B. Reddy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges

(2012) Sheila Marie Pimentel-Elardo et al.   Marine Drugs

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

(2012) Nadine Ziemert et al.   PLoS One

Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil

(2012) Kathryn G. Eilers et al.   SOIL BIOLOGY & BIOCHEMISTRY

Challenges of Antibacterial Discovery

(2011) L. L. Silver   CLINICAL MICROBIOLOGY REVIEWS

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

(2010) C. Will et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Renaissance in antibacterial discovery from actinomycetes

(2008) R BALTZ   CURRENT OPINION IN PHARMACOLOGY