Metabolic Overlap in Environmentally Diverse Microbial Communities

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

(2019) Sankha Ghatak et al.   NUCLEIC ACIDS RESEARCH

New approaches for metagenome assembly with short reads

(2019) Martin Ayling et al.   BRIEFINGS IN BIOINFORMATICS

Plant Host-Associated Mechanisms for Microbial Selection

(2019) Piet Jones et al.   Frontiers in Plant Science

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

(2018) Seong-In Na et al.   JOURNAL OF MICROBIOLOGY

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities

(2018) Eric R. Hester et al.   mSystems

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

(2018) Lindsey M. Solden et al.   Nature Microbiology

Microbial nitrogen limitation in the mammalian large intestine

(2018) Aspen T. Reese et al.   Nature Microbiology

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

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

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

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

(2016) Karthik Anantharaman et al.   Nature Communications

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

(2015) Roie Levy et al.   BMC BIOINFORMATICS

Stable and sporadic symbiotic communities of coral and algal holobionts

(2015) Eric R Hester et al.   ISME Journal

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

Microbial community transcriptional networks are conserved in three domains at ocean basin scales

(2015) Frank O. Aylward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiota of the indoor environment: a meta-analysis

(2015) Rachel I. Adams et al.   Microbiome

The Upper Respiratory Tract as a Microbial Source for Pulmonary Infections in Cystic Fibrosis. Parallels from Island Biogeography

(2014) Katrine L. Whiteson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

(2014) L. W. Kelly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The plant microbiome and its importance for plant and human health

(2014) Gabriele Berg   Frontiers in Microbiology

Macroecology of methane-oxidizing bacteria: the β-diversity ofpmoAgenotypes in tropical and subtropical rice paddies

(2013) Claudia Lüke et al.   ENVIRONMENTAL MICROBIOLOGY

Complex Interactions Among Diet, Gastrointestinal Transit, and Gut Microbiota in Humanized Mice

(2013) Purna C. Kashyap et al.   GASTROENTEROLOGY

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

(2013) Amy E Zimmerman et al.   ISME Journal

Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages

(2013) Craig E Nelson et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

(2012) R. Carr et al.   BIOINFORMATICS

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS