Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

Modeling trophic dependencies and exchanges among insects’ bacterial symbionts in a host-simulated environment

(2018) Itai Opatovsky et al.   BMC GENOMICS

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter

(2017) Marc Garcia-Garcera et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics

(2017) Craig W. Herbold et al.   ENVIRONMENTAL MICROBIOLOGY

Long-Term Persistence of Pesticides and TPs in Archived Agricultural Soil Samples and Comparison with Pesticide Application

(2017) Aurea C. Chiaia-Hernandez et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Simultaneous biodegradation of three mononitrophenol isomers by a tailor-made microbial consortium immobilized in sequential batch reactors

(2017) H. Fu et al.   LETTERS IN APPLIED MICROBIOLOGY

Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics

(2017) Andreas H. Keller et al.   MICROBIAL ECOLOGY

Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes

(2017) Xing Huang et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics

(2017) Krupa M. Parmar et al.   Frontiers in Microbiology

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

(2017) Shany Ofaim et al.   Frontiers in Microbiology

The human microbiome and metabolomics: Current concepts and applications

(2016) Eric Banan-Mwine Daliri et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Principles for designing synthetic microbial communities

(2016) Nathan I Johns et al.   CURRENT OPINION IN MICROBIOLOGY

Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community

(2016) Nir Friedman et al.   ENVIRONMENTAL MICROBIOLOGY

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Synthetic Ecology of Microbes: Mathematical Models and Applications

(2016) Ali R. Zomorrodi et al.   JOURNAL OF MOLECULAR BIOLOGY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

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

(2016) Karthik Anantharaman et al.   Nature Communications

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Metabolic interactions in microbial communities: untangling the Gordian knot

(2015) Olga Ponomarova et al.   CURRENT OPINION IN MICROBIOLOGY

Analysis of the core genome and pangenome of P seudomonas putida

(2015) Zulema Udaondo et al.   ENVIRONMENTAL MICROBIOLOGY

“Omics” Insights into PAH Degradation toward Improved Green Remediation Biotechnologies

(2015) Abdelhak El Amrani et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils

(2014) J. Jiang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

(2013) Danilo Ercolini   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

(2013) Mallory Embree et al.   ISME Journal

Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide

(2013) Kai Chen et al.   MOLECULAR MICROBIOLOGY

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

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

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

(2013) Harish Nagarajan et al.   Nature Communications

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

Bacterial community dynamics during the preferential degradation of aromatic hydrocarbons by a microbial consortium

(2012) Hernando Pactao Bacosa et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Alkaline extracellular reduction: isolation and characterization of an alkaliphilic and halotolerant bacterium, Bacillus pseudofirmus MC02

(2012) C. Ma et al.   JOURNAL OF APPLIED MICROBIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Species Interactions Alter Evolutionary Responses to a Novel Environment

(2012) Diane Lawrence et al.   PLOS BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Stable coexistence of two Caldicellulosiruptor species in a de novo constructed hydrogen-producing co-culture

(2011) Ahmad A Zeidan et al.   Microbial Cell Factories

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Cesiribacter andamanensis gen. nov., sp. nov., isolated from a soil sample from a mud volcano

(2010) T. N. R. Srinivas et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Atrazine induces complete feminization and chemical castration in male African clawed frogs (Xenopus laevis)

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

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Current statistical issues inWeed Research

(2010) A ONOFRI et al.   WEED RESEARCH

Atrazine degradation by a simple consortium of Klebsiella sp. A1 and Comamonas sp. A2 in nitrogen enriched medium

(2009) Chunyu Yang et al.   BIODEGRADATION

Persistence of 14C-labeled atrazine and its residues in a field lysimeter soil after 22years

(2009) Nicolai D. Jablonowski et al.   ENVIRONMENTAL POLLUTION

Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing

(2009) Seong Woon Roh et al.   ISME Journal

Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds

(2009) Agnieszka Mrozik et al.   MICROBIOLOGICAL RESEARCH

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Extractable atrazine and its metabolites in agricultural soils from the temperate humid zone

(2008) J. Mahía et al.   ENVIRONMENTAL GEOCHEMISTRY AND HEALTH

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Biodegradation of aged polycyclic aromatic hydrocarbons (PAHs) by microbial consortia in soil and slurry phases

(2007) Xiaojun Li et al.   JOURNAL OF HAZARDOUS MATERIALS