Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes

Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

(2019) Hirokazu Toju et al.   Royal Society Open Science

Leaf-associated microbiomes of grafted tomato plants

(2019) Hirokazu Toju et al.   Scientific Reports

Molecular diagnosis and enrichment culture identified a septic pseudoarthrosis due to an infection with Erysipelatoclostridium ramosum

(2019) Fathiah Zakham et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Fluctuating interaction network and time-varying stability of a natural fish community

(2018) Masayuki Ushio et al.   NATURE

Role of priority effects in the early-life assembly of the gut microbiota

(2018) Daniel Sprockett et al.   Nature Reviews Gastroenterology & Hepatology

Design of synthetic bacterial communities for predictable plant phenotypes

(2018) Sur Herrera Paredes et al.   PLOS BIOLOGY

Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies

(2018) Yusuke Kitada et al.   Science Advances

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

(2018) Matej Medvecky et al.   BMC GENOMICS

Effect of co-inoculation with phosphate and potassium solubilizing bacteria on mineral uptáme and growth of pepper and cucumber

(2018) H.S. Han et al.   PLANT SOIL AND ENVIRONMENT

A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet

(2018) Chiharu Ishii et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The k-core as a predictor of structural collapse in mutualistic ecosystems

(2018) Flaviano Morone et al.   Nature Physics

Simultaneous fermentation of biomass-derived sugars to ethanol by a co-culture of an engineered Escherichia coli and Saccharomyces cerevisiae

(2018) Liang Wang et al.   BIORESOURCE TECHNOLOGY

Indirect effects drive coevolution in mutualistic networks

(2017) Paulo R. Guimarães et al.   NATURE

Identification of a novel fungus, Trichoderma asperellum GDFS1009, and comprehensive evaluation of its biocontrol efficacy

(2017) Qiong Wu et al.   PLoS One

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

Meta-Analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases

(2017) Toshifumi Osaka et al.   Nutrients

Research priorities for harnessing plant microbiomes in sustainable agriculture

(2017) Posy E. Busby et al.   PLOS BIOLOGY

Species-rich networks and eco-evolutionary synthesis at the metacommunity level

(2017) Hirokazu Toju et al.   Nature Ecology & Evolution

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Network modules and hubs in plant-root fungal biomes

(2016) Hirokazu Toju et al.   Journal of the Royal Society Interface

Ericaceous plant-fungus network in a harsh alpine-subalpine environment

(2016) H. Toju et al.   MOLECULAR ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Tracking and forecasting ecosystem interactions in real time

(2016) Ethan R. Deyle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

Networking in the Plant Microbiome

(2016) Marcel G. A. van der Heijden et al.   PLOS BIOLOGY

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

(2016) Sandrine Brugiroux et al.   Nature Microbiology

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology

(2015) Ben Stenuit et al.   CURRENT OPINION IN BIOTECHNOLOGY

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

Microbial cocktails join fecal transplants in IBD treatment trials

(2015) Mark Ratner   NATURE BIOTECHNOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Induced Systemic Resistance by Beneficial Microbes

(2014) Corné M.J. Pieterse et al.   Annual Review of Phytopathology

Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery

(2014) Samuel Bertrand et al.   BIOTECHNOLOGY ADVANCES

Order of arrival structures arbuscular mycorrhizal colonization of plants

(2014) Gijsbert D. A. Werner et al.   NEW PHYTOLOGIST

Lactobacillus rhamnosus GG Protects against Non-Alcoholic Fatty Liver Disease in Mice

(2014) Yvonne Ritze et al.   PLoS One

Assembly of complex plant–fungus networks

(2014) Hirokazu Toju et al.   Nature Communications

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

(2013) Karen De Roy et al.   ENVIRONMENTAL MICROBIOLOGY

Slowing PCR ramp speed reduces chimera formation from environmental samples

(2013) Julia L. Stevens et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics

(2013) David J. Studholme et al.   Frontiers in Plant Science

Yeast–yeast interactions revealed by aromatic profile analysis of Sauvignon Blanc wine fermented by single or co-culture of non-Saccharomyces and Saccharomyces yeasts

(2012) Mohand Sadoudi et al.   FOOD MICROBIOLOGY

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

Synthetic ecology – A way forward for sustainable algal biofuel production?

(2012) Elena Kazamia et al.   JOURNAL OF BIOTECHNOLOGY

Stability criteria for complex ecosystems

(2012) Stefano Allesina et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse

(2012) L. Dai et al.   SCIENCE

Detecting Causality in Complex Ecosystems

(2012) G. Sugihara et al.   SCIENCE

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Finding Statistically Significant Communities in Networks

(2011) Andrea Lancichinetti et al.   PLoS One

Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve

(2011) J. A. Bravo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Creating and characterizing communities of human gut microbes in gnotobiotic mice

(2010) Jeremiah J Faith et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Identification of influential spreaders in complex networks

(2010) Maksim Kitsak et al.   Nature Physics

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

Mixed fermentation for natural product drug discovery

(2009) Robin K. Pettit   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Reconsideration of Insulin Signals Induced by Improved Laboratory Animal Diets, Japanese and American Diets, in IRS-2 Deficient Mice

(2009) H. Hashimoto et al.   EXPERIMENTAL AND CLINICAL ENDOCRINOLOGY & DIABETES

Early-warning signals for critical transitions

(2009) Marten Scheffer et al.   NATURE

Azospirillum brasilense Az39 and Bradyrhizobium japonicum E109, inoculated singly or in combination, promote seed germination and early seedling growth in corn (Zea mays L.) and soybean (Glycine max L.)

(2008) Fabricio Cassán et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

In vitro activity of potential probiotic Lactobacillus murinus isolated from the dog

(2008) Karen Perelmuter et al.   JOURNAL OF APPLIED MICROBIOLOGY

Chaos in a long-term experiment with a plankton community

(2008) Elisa Benincà et al.   NATURE

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities

(2006) Farah Ahmad et al.   MICROBIOLOGICAL RESEARCH