A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants

Diazotroph Paenibacillus triticisoli BJ-18 Drives the Variation in Bacterial, Diazotrophic and Fungal Communities in the Rhizosphere and Root/Shoot Endosphere of Maize

(2021) Yongbin Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype

(2021) Nejc Stopnisek et al.   ISME Journal

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online

(2021) Tong Chen et al.   Journal of Genetics and Genomics

A Simple in situ Assay to Assess Plant-Associative Bacterial Nitrogenase Activity

(2021) Timothy L. Haskett et al.   Frontiers in Microbiology

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota

(2021) Kathrin Wippel et al.   Nature Microbiology

The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves

(2021) Sebastian Pfeilmeier et al.   Nature Microbiology

Defining and quantifying the core microbiome: Challenges and prospects

(2021) Alexander T. Neu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental Factors Influencing Phyllosphere Bacterial Communities in Giant Pandas’ Staple Food Bamboos

(2021) Juejie Long et al.   Frontiers in Microbiology

Culture-Dependent and Culture-Independent Characterization of the Olive Xylem Microbiota: Effect of Sap Extraction Methods

(2020) Manuel Anguita-Maeso et al.   Frontiers in Plant Science

Applying the core microbiome to understand host-microbe systems

(2020) Alice Risely   JOURNAL OF ANIMAL ECOLOGY

Plant–microbiome interactions: from community assembly to plant health

(2020) Pankaj Trivedi et al.   NATURE REVIEWS MICROBIOLOGY

Crop microbiome and sustainable agriculture

(2020) Brajesh K. Singh et al.   NATURE REVIEWS MICROBIOLOGY

A suite of complementary biocontrol traits allows a native consortium of root-associated bacteria to protect their host plant from a fungal sudden-wilt disease

(2019) Rakesh Santhanam et al.   MOLECULAR ECOLOGY

Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit

(2019) Marcelo Bueno Batista et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants

(2019) Imran Afzal et al.   MICROBIOLOGICAL RESEARCH

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

(2019) Jingying Zhang et al.   NATURE BIOTECHNOLOGY

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

FEAST: fast expectation-maximization for microbial source tracking

(2019) Liat Shenhav et al.   NATURE METHODS

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

(2019) Keara L. Grady et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

Field study reveals core plant microbiota and relative importance of their drivers

(2018) Kelly Hamonts et al.   ENVIRONMENTAL MICROBIOLOGY

16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products

(2018) MIYO NAKANO   JOURNAL OF FOOD PROTECTION

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

(2018) Allen Van Deynze et al.   PLOS BIOLOGY

The structure and function of the global citrus rhizosphere microbiome

(2018) Jin Xu et al.   Nature Communications

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simplified and representative bacterial community of maize roots

(2017) Ben Niu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

(2016) Jiwoong Kim et al.   BMC BIOINFORMATICS

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance inArabidopsis

(2015) Xuehua Zhong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

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Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome onTriticumandBrassicaseeds

(2014) Matthew G. Links et al.   NEW PHYTOLOGIST

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

The Plant Vascular System: Evolution, Development and FunctionsF

(2013) William J. Lucas et al.   Journal of Integrative Plant Biology

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The Human Microbiome: Our Second Genome

(2012) Elizabeth A. Grice et al.   Annual Review of Genomics and Human Genetics

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

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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

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A PCR-based toolbox for the culture-independent quantification of total bacterial abundances in plant environments

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biological nitrogen fixation in maize (Zea mays L.) by 15N isotope-dilution and identification of associated culturable diazotrophs

(2008) Adriana Montañez et al.   BIOLOGY AND FERTILITY OF SOILS

Properties of bacterial endophytes and their proposed role in plant growth

(2008) Pablo R. Hardoim et al.   TRENDS IN MICROBIOLOGY