Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

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

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

Communication between viruses guides lysis–lysogeny decisions

(2017) Zohar Erez et al.   NATURE

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

Origins and challenges of viral dark matter

(2017) Siddharth R. Krishnamurthy et al.   VIRUS RESEARCH

Exploring the under-investigated “microbial dark matter” of drinking water treatment plants

(2017) Antonia Bruno et al.   Scientific Reports

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes

(2017) Violette Da Cunha et al.   PLoS Genetics

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities

(2017) R. E. Danczak et al.   Microbiome

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

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

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea

(2017) Blair G. Paul et al.   Nature Microbiology

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

(2017) Karel Sedlar et al.   Computational and Structural Biotechnology Journal

An introduction to niche construction theory

(2016) Kevin Laland et al.   EVOLUTIONARY ECOLOGY

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

(2016) Marco Fondi et al.   Genome Biology and Evolution

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

New CRISPR–Cas systems from uncultivated microbes

(2016) David Burstein et al.   NATURE

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

(2016) Karthik Anantharaman et al.   Nature Communications

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Lokiarchaeon is hydrogen dependent

(2016) Filipa L. Sousa et al.   Nature Microbiology

A new view of the tree of life

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

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

(2016) Kevin R. Theis et al.   mSystems

Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life

(2015) Philippe Lopez et al.   Biology Direct

Archaeal ancestors of eukaryotes: not so elusive any more

(2015) Eugene V. Koonin   BMC BIOLOGY

Mining the microbial dark matter

(2015) Corie Lok   NATURE

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

(2015) Christopher T. Brown et al.   NATURE

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents

(2015) Scott F. Gilbert et al.   NATURE REVIEWS GENETICS

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

(2015) Jimmy H. Saw et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?

(2015) David Moreira et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rethinking evolutionary individuality

(2015) Marc Ereshefsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

(2015) Blair G. Paul et al.   Nature Communications

The Hologenome Concept: Helpful or Hollow?

(2015) Nancy A. Moran et al.   PLOS BIOLOGY

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

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

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

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities

(2015) Aleksandra Checinska et al.   Microbiome

Remote homology and the functions of metagenomic dark matter

(2015) Briallen Lobb et al.   Frontiers in Genetics

A brief history of the discovery of hyperthermophilic life

(2013) Karl O. Stetter   BIOCHEMICAL SOCIETY TRANSACTIONS

Carl R. Woese (1928–2012)

(2013) W. Ford Doolittle   CURRENT BIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

An archaeal origin of eukaryotes supports only two primary domains of life

(2013) Tom A. Williams et al.   NATURE

“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

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Reclassification of Giant Viruses Composing a Fourth Domain of Life in the New Order Megavirales

(2012) Philippe Colson et al.   INTERVIROLOGY

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

(2012) E. Bapteste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

The Origins of Cooperative Bacterial Communities

(2012) J. L. Sachs et al.   mBio

Mimivirus shows dramatic genome reduction after intraamoebal culture

(2011) M. Boyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Enigmatic, ultrasmall, uncultivated Archaea

(2010) B. J. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental methods for studying microbial survival in extraterrestrial environments

(2009) Karen Olsson-Francis et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Organophosphorus-degrading bacteria: ecology and industrial applications

(2008) Brajesh K. Singh   NATURE REVIEWS MICROBIOLOGY