Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

The rise of diversity in metabolic platforms across the Candidate Phyla Radiation

(2020) Alexander L. Jaffe et al.   BMC BIOLOGY

An archaeal symbiont-host association from the deep terrestrial subsurface

(2019) Katrin Schwank et al.   ISME Journal

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Unexpected host dependency of Antarctic Nanohaloarchaeota

(2019) Joshua N. Hamm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromulinavorax destructans, a pathogen of microzooplankton that provides a window into the enigmatic candidate phylum Dependentiae

(2019) Christoph M. Deeg et al.   PLoS Pathogens

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

(2019) Karissa L. Cross et al.   NATURE BIOTECHNOLOGY

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

(2019) Raphaël Méheust et al.   Nature Communications

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

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

(2018) Cindy J. Castelle et al.   CELL

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog

(2018) Joshua D. Sackett et al.   PLoS One

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

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

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

(2018) Jessica K. Jarett et al.   Microbiome

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

(2018) Olivia S. Hershey et al.   Frontiers in Microbiology

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1)

(2017) Rosa León-Zayas et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative modeling of gene and genome evolution roots the archaeal tree of life

(2017) Tom A. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ

(2017) Olga V. Golyshina et al.   Nature Communications

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

Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

(2017) Eric D. Becraft et al.   Frontiers in Microbiology

Towards a balanced view of the bacterial tree of life

(2017) Frederik Schulz et al.   Microbiome

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

(2017) Cindy J. Castelle et al.   Scientific Reports

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

(2017) Susanne Krause et al.   Scientific Reports

The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere

(2016) Benjamin I. Jelen et al.   Annual Review of Microbiology

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

(2016) Roland Hatzenpichler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases

(2016) Schara Safarian et al.   SCIENCE

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

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

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

(2016) Marcel Huntemann et al.   Standards in Genomic Sciences

A new view of the tree of life

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

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

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

(2015) Isabelle Pagnier et al.   Biology Direct

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

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

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

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage

(2015) Yun Kit Yeoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

The bioenergetic costs of a gene

(2015) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shedding light on microbial dark matter: a TM6 bacterium as natural endosymbiont of a free-living amoeba

(2015) Vincent Delafont et al.   Environmental Microbiology Reports

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

(2015) William C. Nelson et al.   Frontiers in Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

(2013) Mircea Podar et al.   Biology Direct

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

“Candidatus Sonnebornia yantaiensis”, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea)

(2013) Jun Gong et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

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

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

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

The cytochrome bd respiratory oxygen reductases

(2011) Vitaliy B. Borisov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Extreme genome reduction in symbiotic bacteria

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

A Bioinformatics Classifier and Database for Heme-Copper Oxygen Reductases

(2011) Filipa L. Sousa et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Evolution of the haem copper oxidases superfamily: a rooting tale

(2009) Simonetta Gribaldo et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Multiple Evolutionary Histories of Dioxygen Reductases: Implications for the Origin and Evolution of Aerobic Respiration

(2008) C. Brochier-Armanet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell

(2008) Y. Hongoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA