Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice

Plant‐microbiome interactions under a changing world: responses, consequences, and perspective

(2022) Pankaj Trivedi et al.   NEW PHYTOLOGIST

Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions

(2022) Basavantraya N. Devanna et al.   Journal of Fungi

Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm

(2021) Mohamed Mannaa et al.   Plants-Basel

Harnessing the plant microbiome to promote the growth of agricultural crops

(2021) Janie Zhang et al.   MICROBIOLOGICAL RESEARCH

Specific modulation of the root immune system by a community of commensal bacteria

(2021) Paulo J. P. L. Teixeira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward understanding microbiota homeostasis in the plant kingdom

(2021) Bradley C. Paasch et al.   PLoS Pathogens

An Overview of Metabolic Activity, Beneficial and Pathogenic Aspects of Burkholderia Spp.

(2021) Hazem S. Elshafie et al.   Metabolites

Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions

(2021) Ankit T. Hinsu et al.   Scientific Reports

Disease-induced changes in plant microbiome assembly and functional adaptation

(2021) Min Gao et al.   Microbiome

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

(2020) Jasmine Chong et al.   Nature Protocols

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria

(2020) Qiulong Hu et al.   npj Biofilms and Microbiomes

Insect herbivory reshapes a native leaf microbiome

(2020) Parris T. Humphrey et al.   Nature Ecology & Evolution

Microbiome: Insect Herbivory Drives Plant Phyllosphere Dysbiosis

(2020) Wenke Smets et al.   CURRENT BIOLOGY

Rhizosphere Microbiome Assembly and Its Impact on Plant Growth

(2020) Qian Qu et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot

(2020) Samson Musonerimana et al.   MICROBIAL ECOLOGY

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Microbiome-Mediated Stress Resistance in Plants

(2020) Hongwei Liu et al.   TRENDS IN PLANT SCIENCE

Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions

(2020) Manoj Kaushal et al.   Microorganisms

Exploring Rice Root Microbiome; The Variation, Specialization and Interaction of Bacteria and Fungi In Six Tropic Savanna Regions in Ghana

(2020) Makoto Kanasugi et al.   Sustainability

Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

(2020) Lukas Beule et al.   PeerJ

Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches

(2020) Chunxu Song et al.   Frontiers in Bioengineering and Biotechnology

The Healthy Microbiome—What Is the Definition of a Healthy Gut Microbiome?

(2020) Fergus Shanahan et al.   GASTROENTEROLOGY

Evidence for the plant recruitment of beneficial microbes to suppress soil‐borne pathogens

(2020) Hongwei Liu et al.   NEW PHYTOLOGIST

Model of rice blast disease under tropical climate conditions

(2020) Sarinya Kirtphaiboon et al.   CHAOS SOLITONS & FRACTALS

A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

(2019) Stéphane Compant et al.   Journal of Advanced Research

Plant growth promotion driven by a novel Caulobacter strain

(2019) Dexian Luo et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Pantoea: a newly identified causative agent for leaf blight disease in rice

(2019) Febri Doni et al.   Journal of Plant Diseases and Protection

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Microbiota-mediated disease resistance in plants

(2019) Nathan Vannier et al.   PLoS Pathogens

Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient

(2019) Nadine Praeg et al.   Frontiers in Microbiology

An Ecological Loop: Host Microbiomes across Multitrophic Interactions

(2019) Hongwei Liu et al.   TRENDS IN ECOLOGY & EVOLUTION

The Pathobiome in Animal and Plant Diseases

(2019) David Bass et al.   TRENDS IN ECOLOGY & EVOLUTION

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

(2019) Selma Vieira et al.   ISME Journal

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants

(2019) Chun-Juan Dong et al.   PLoS One

Bacterial and fungal diversity in rhizosphere and bulk soil under different long-term tillage and cereal/legume rotation

(2019) Eunice Essel et al.   SOIL & TILLAGE RESEARCH

Potential of Pantoea dispersa as an effective biocontrol agent for black rot in sweet potato

(2019) Lingmin Jiang et al.   Scientific Reports

Rhizobia: from saprophytes to endosymbionts

(2018) Philip Poole et al.   NATURE REVIEWS MICROBIOLOGY

Assembly and ecological function of the root microbiome across angiosperm plant species

(2018) Connor R. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

(2018) William A. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global food security – Issues, challenges and technological solutions

(2018) Ultan Mc Carthy et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

(2018) Joelle Sasse et al.   TRENDS IN PLANT SCIENCE

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Paenibacillus terrae NK3-4: A Potential Biocontrol Agent that Produces β-1,3-Glucanase

(2018) Wen Qing Yu et al.   BIOLOGICAL CONTROL

Research priorities for harnessing plant microbiomes in sustainable agriculture

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

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica

(2017) Xue-Ying Tian et al.   Frontiers in Microbiology

The Potential of Streptomyces as Biocontrol Agents against the Rice Blast Fungus, Magnaporthe oryzae (Pyricularia oryzae)

(2017) Jodi Woan-Fei Law et al.   Frontiers in Microbiology

Culture independent assessment of human milk microbial community in lactational mastitis

(2017) Shriram H. Patel et al.   Scientific Reports

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

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

Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides

(2016) Boris Jakuschkin et al.   MICROBIAL ECOLOGY

Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice ( Oryza sativa L.)

(2016) Wenfeng Wang et al.   MICROBIOLOGICAL RESEARCH

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

The Shift of an Intestinal “Microbiome” to a “Pathobiome” Governs the Course and Outcome of Sepsis Following Surgical Injury

(2016) Monika A. Krezalek et al.   SHOCK

Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis

(2016) Iris Bertani et al.   Environmental Microbiology Reports

Fermentation Conditions that Affect Clavulanic Acid Production in Streptomyces clavuligerus: A Systematic Review

(2016) Hooi-Leng Ser et al.   Frontiers in Microbiology

Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

(2015) Barbara Reinhold-Hurek et al.   Annual Review of Phytopathology

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

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

A novel method to scale up fungal endophyte isolations

(2015) Melinda Greenfield et al.   BIOCONTROL SCIENCE AND TECHNOLOGY

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

(2015) Devin Coleman-Derr et al.   NEW PHYTOLOGIST

Endophytes-assisted biocontrol: novel insights in ecology and the mode of action of Paenibacillus

(2015) Daria Rybakova et al.   PLANT AND SOIL

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rhizobium rhizoryzae sp. nov., isolated from rice roots

(2014) X.-X. Zhang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The Opposing Forces of the Intestinal Microbiome and the Emerging Pathobiome

(2014) Jennifer Defazio et al.   SURGICAL CLINICS OF NORTH AMERICA

Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics

(2014) Muriel Vayssier-Taussat et al.   Frontiers in Cellular and Infection Microbiology

Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

(2014) Susanne Schreiter et al.   Frontiers in Microbiology

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

(2013) Andrea R Ottesen et al.   BMC MICROBIOLOGY

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

(2013) Natacha Bodenhausen et al.   PLoS One

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

(2013) K. Schlaeppi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotics produced by Streptomyces

(2012) Rudi Emerson de Lima Procópio et al.   Brazilian Journal of Infectious Diseases

Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

(2012) Fredrik Bäckhed et al.   Cell Host & Microbe

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg 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

Incoming pathogens team up with harmless ‘resident’ bacteria

(2012) Vittorio Venturi et al.   TRENDS IN MICROBIOLOGY

Rice root-associated bacteria: insights into community structures across 10 cultivars

(2011) Pablo Rodrigo Hardoim et al.   FEMS MICROBIOLOGY ECOLOGY

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

(2011) Claudia Knief et al.   ISME Journal

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

The Intestinal Microbiota Plays a Role in Salmonella-Induced Colitis Independent of Pathogen Colonization

(2011) Rosana B. R. Ferreira et al.   PLoS One

Altering Host Resistance to Infections through Microbial Transplantation

(2011) Benjamin P. Willing et al.   PLoS One

Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes

(2010) M. T. Hoffman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

Fungal endophytes: diversity and functional roles

(2009) R. J. Rodriguez et al.   NEW PHYTOLOGIST

Against the grain: safeguarding rice from rice blast disease

(2009) Pari Skamnioti et al.   TRENDS IN BIOTECHNOLOGY

Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta

(2008) G. Peng et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY