Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

(2019) Bojk A. Berghuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extracellular DNA in natural environments: features, relevance and applications

(2018) Magdalena Nagler et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

(2018) Daniel H. Huson et al.   Biology Direct

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

(2018) Cindy J. Castelle et al.   CELL

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

(2018) Stephanie A. Eichorst et al.   ENVIRONMENTAL MICROBIOLOGY

Potential for primary productivity in a globally-distributed bacterial phototroph

(2018) E. D. Graham et al.   ISME Journal

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

(2018) Rekha Seshadri et al.   NATURE BIOTECHNOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation

(2018) Ohana Y. A. Costa et al.   Frontiers in Microbiology

Focused Metabolism of β-Glucans by the Soil Bacteroidetes Species Chitinophaga pinensis

(2018) Lauren S. McKee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Importance of Revisiting Legionellales Diversity

(2018) Olivier Duron et al.   TRENDS IN PARASITOLOGY

Hidden diversity of soil giant viruses

(2018) Frederik Schulz et al.   Nature Communications

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

(2018) Chirag Jain et al.   Nature Communications

Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling Bacteroidetes

(2018) Marcel Taillefer et al.   mSystems

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

(2017) Salvador Lladó et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

The trajectory of microbial single-cell sequencing

(2017) Tanja Woyke et al.   NATURE METHODS

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

The whole-soil carbon flux in response to warming

(2017) Caitlin E. Hicks Pries et al.   SCIENCE

Giant viruses with an expanded complement of translation system components

(2017) Frederik Schulz et al.   SCIENCE

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

(2017) Ramunas Stepanauskas et al.   Nature Communications

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples

(2017) Feiqiao Brian Yu et al.   eLife

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

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

Comparative genomic analysis reveals the environmental impacts on two Arcticibacter strains including sixteen Sphingobacteriaceae species

(2017) Liang Shen et al.   Scientific Reports

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

(2016) Keith Mewis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

The bright side of microbial dark matter: lessons learned from the uncultivated majority

(2016) Lindsey Solden et al.   CURRENT OPINION IN MICROBIOLOGY

Strategies to improve reference databases for soil microbiomes

(2016) Jinlyung Choi et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Chlamydia cell biology and pathogenesis

(2016) Cherilyn Elwell et al.   NATURE REVIEWS MICROBIOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Scaling laws predict global microbial diversity

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

After All, Only Millions?

(2016) Rudolf Amann et al.   mBio

The Underestimation of Global Microbial Diversity

(2016) Jay T. Lennon et al.   mBio

Microbial diversity drives multifunctionality in terrestrial ecosystems

(2016) Manuel Delgado-Baquerizo et al.   Nature Communications

Giant Viruses of Amoebas: An Update

(2016) Sarah Aherfi et al.   Frontiers in Microbiology

Back to the Future of Soil Metagenomics

(2016) Joseph Nesme et al.   Frontiers in Microbiology

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

(2016) Emily B. Graham et al.   Frontiers in Microbiology

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Microbiology

A new view of the tree of life

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

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae

(2015) Isabelle Pagnier et al.   Biology Direct

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

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

Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria

(2015) Frederik Schulz et al.   Scientific Reports

Reconstructing each cell's genome within complex microbial communities—dream or reality?

(2015) Scott Clingenpeel et al.   Frontiers in Microbiology

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

(2015) Tom O. Delmont et al.   Frontiers in Microbiology

Long-term forest soil warming alters microbial communities in temperate forest soils

(2015) Kristen M. DeAngelis et al.   Frontiers in Microbiology

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

(2015) Dongwan D. Kang et al.   PeerJ

Genomic Potential for Polysaccharide Deconstruction in Bacteria

(2014) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803

(2014) Antje Kabisch et al.   ISME Journal

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

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

Structure and function of enzymes acting on chitin and chitosan

(2013) Ingunn A. Hoell et al.   Biotechnology & Genetic Engineering Reviews

Ecology of marine Bacteroidetes: a comparative genomics approach

(2013) Beatriz Fernández-Gómez et al.   ISME Journal

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

(2013) Ilias Lagkouvardos et al.   ISME Journal

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

(2013) J. S. McLean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Distribution of Potential Cellulases in Bacteria

(2012) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Comparative Genomics Suggests an Independent Origin of Cytoplasmic Incompatibility in Cardinium hertigii

(2012) Thomas Penz et al.   PLoS Genetics

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Microbial mediation of carbon-cycle feedbacks to climate warming

(2011) Jizhong Zhou et al.   Nature Climate Change

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Environmental and Gut Bacteroidetes: The Food Connection

(2011) François Thomas et al.   Frontiers in Microbiology

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T)

(2010) Tijana Glavina Del Rio et al.   Standards in Genomic Sciences

The Genome of the Amoeba Symbiont "Candidatus Amoebophilus asiaticus" Reveals Common Mechanisms for Host Cell Interaction among Amoeba-Associated Bacteria

(2009) S. Schmitz-Esser et al.   JOURNAL OF BACTERIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Evolutionary Convergence and Nitrogen Metabolism in Blattabacterium strain Bge, Primary Endosymbiont of the Cockroach Blattella germanica

(2009) Maria J. López-Sánchez et al.   PLoS Genetics

Chlamydiae as Symbionts in Eukaryotes

(2008) Matthias Horn   Annual Review of Microbiology

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One