Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

Lithologically controlled subsurface critical zone thickness and water storage capacity determine regional plant community composition

(2019) W. Jesse Hahm et al.   WATER RESOURCES RESEARCH

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria

(2019) Yu Zheng et al.   Frontiers in Microbiology

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

(2019) Chiara Borsetto et al.   Microbiome

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

(2019) Spencer Diamond et al.   Nature Microbiology

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

(2019) Dmitry Meleshko et al.   GENOME RESEARCH

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

(2019) Tess E. Brewer et al.   mBio

Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition

(2019) Dmitrii Y. Travin et al.   Nature Communications

The distinction of CPR bacteria from other bacteria based on protein family content

(2019) Raphaël Méheust et al.   Nature Communications

Quantification of the seasonal hillslope water storage that does not drive streamflow

(2018) David N. Dralle et al.   HYDROLOGICAL PROCESSES

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

Direct observations of rock moisture, a hidden component of the hydrologic cycle

(2018) Daniella M. Rempe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drainage From the Critical Zone: Lithologic Controls on the Persistence and Spatial Extent of Wetted Channels During the Summer Dry Season

(2018) S. M. Lovill et al.   WATER RESOURCES RESEARCH

Controls on the distribution and resilience of Quercus garryana : ecophysiological evidence of oak's water-limitation tolerance

(2018) W. Jesse Hahm et al.   Ecosphere

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x

(2018) Joseph K. Bedree et al.   Frontiers in Microbiology

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade

(2018) Kristina Bayer et al.   mSystems

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

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

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

Dissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analogues expressed in vivo

(2017) Taro Ozaki et al.   Nature Communications

Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C

(2017) Ruth Schmidt et al.   Scientific Reports

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

(2016) Kazutaka Katoh et al.   BIOINFORMATICS

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

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

(2016) Cristina N. Butterfield et al.   PeerJ

A new view of the tree of life

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

Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli

(2016) Pouya Javidpour et al.   PLoS One

Lasso Peptides: An Intriguing Class of Bacterial Natural Products

(2015) Julian D. Hegemann et al.   ACCOUNTS OF CHEMICAL RESEARCH

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

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

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

The Biogeography of Putative Microbial Antibiotic Production

(2015) Hélène Morlon et al.   PLoS One

Genome Mining Reveals a Minimum Gene Set for the Biosynthesis of 32-Membered Macrocyclic Thiopeptides Lactazoles

(2014) Shohei Hayashi et al.   CHEMISTRY & BIOLOGY

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

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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Chemical-biogeographic survey of secondary metabolism in soil

(2014) Z. Charlop-Powers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural products: A continuing source of novel drug leads

(2013) Gordon M. Cragg et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Diversity and abundance of phosphonate biosynthetic genes in nature

(2013) X. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery, Biosynthesis, and Engineering of Lantipeptides

(2012) Patrick J. Knerr et al.   Annual Review of Biochemistry

Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes

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

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Combinatorial biosynthesis of polyketides—a perspective

(2012) Fong T Wong et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Anaerobic Ammonium-Oxidizing Bacteria: Unique Microorganisms with Exceptional Properties

(2012) L. van Niftrik et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Rain, rock moisture dynamics, and the rapid response of perched groundwater in weathered, fractured argillite underlying a steep hillslope

(2012) Rohit Salve et al.   WATER RESOURCES RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Unexpected applications of secondary metabolites

(2010) Preeti Vaishnav et al.   BIOTECHNOLOGY ADVANCES

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Macroecological patterns in soil communities

(2010) Thibaud Decaëns   GLOBAL ECOLOGY AND BIOGEOGRAPHY

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

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

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Emerging tools for measuring and modeling the in situ activity of soil extracellular enzymes

(2008) Matthew D. Wallenstein et al.   SOIL BIOLOGY & BIOCHEMISTRY