Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

(2016) Brett J. Baker et al.   Nature Microbiology

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes

(2015) Jiarong Guo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

(2015) Karthik Anantharaman et al.   ISME Journal

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils

(2015) David VanInsberghe et al.   ISME Journal

Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community

(2015) Sarahi L. Garcia et al.   MOLECULAR ECOLOGY

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

(2014) Albert Barberán et al.   ECOLOGY LETTERS

Survival of mycobacteria depends on proteasome-mediated amino acid recycling under nutrient limitation

(2014) Y. Elharar et al.   EMBO JOURNAL

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

Predicting the responsiveness of soil biodiversity to deforestation: a cross-biome study

(2014) Thomas W. Crowther et al.   GLOBAL CHANGE BIOLOGY

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Reductive genome evolution at both ends of the bacterial population size spectrum

(2014) Bérénice Batut et al.   NATURE REVIEWS MICROBIOLOGY

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cell Size Distributions of Soil Bacterial and Archaeal Taxa

(2013) Maria C. Portillo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation

(2013) Niv Sabath et al.   Genome Biology and Evolution

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

(2013) Christopher S. Miller et al.   PLoS One

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

(2013) A. Everard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

(2013) N. Fierer et al.   SCIENCE

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

(2013) R. S. Kantor et al.   mBio

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

(2012) Y. Peng et al.   BIOINFORMATICS

Oligopeptides Represent a Preferred Source of Organic N Uptake: A Global Phenomenon?

(2012) Mark Farrell et al.   ECOSYSTEMS

Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium

(2012) Paul Carini et al.   ISME Journal

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seasonality in Ocean Microbial Communities

(2012) S. J. Giovannoni et al.   SCIENCE

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

(2012) J. J. Morris et al.   mBio

The generation and maintenance of diversity in microbial communities

(2011) Noah Fierer et al.   AMERICAN JOURNAL OF BOTANY

Genome Sequence of Chthoniobacter flavus Ellin428, an Aerobic Heterotrophic Soil Bacterium

(2011) R. Kant et al.   JOURNAL OF BACTERIOLOGY

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Global patterns in belowground communities

(2009) Noah Fierer et al.   ECOLOGY LETTERS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Increased Fitness of Pseudomonas fluorescens Pf0-1 Leucine Auxotrophs in Soil

(2008) W. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

(2008) Shaobin Hou et al.   Biology Direct