Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

(2019) Samiran Banerjee et al.   ISME Journal

Ecology and Evolution of Plant Microbiomes

(2019) Viviane Cordovez et al.   Annual Review of Microbiology

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

(2018) Pamela Ferretti et al.   Cell Host & Microbe

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia

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

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice

(2018) Joseph A. Edwards et al.   PLOS BIOLOGY

Geographical and Cultivar Features Differentiate Grape Microbiota in Northern Italy and Spain Vineyards

(2018) Valerio Mezzasalma et al.   Frontiers in Microbiology

What Is There in Seeds? Vertically Transmitted Endophytic Resources for Sustainable Improvement in Plant Growth

(2018) Raheem Shahzad et al.   Frontiers in Plant Science

Conservation and transmission of seed bacterial endophytes across generations following crossbreeding and repeated inbreeding of rice at different geographic locations

(2018) Denver I. Walitang et al.   MicrobiologyOpen

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

(2018) Nicholas A. Bokulich et al.   Microbiome

The wild side of plant microbiomes

(2018) Juan E. Pérez-Jaramillo et al.   Microbiome

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Transmission modes of the mammalian gut microbiota

(2018) Andrew H. Moeller et al.   SCIENCE

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?

(2018) Florent Mazel et al.   mSystems

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

(2016) Fantao Zhang et al.   BMC PLANT BIOLOGY

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

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

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The Cucurbita pepo seed microbiome: genotype-specific composition and implications for breeding

(2016) Eveline Adam et al.   PLANT AND SOIL

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

(2016) Iris Bertani et al.   Environmental Microbiology Reports

Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

(2016) Matthew Shenton et al.   Rice

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

(2016) Maggie R. Wagner et al.   Nature Communications

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

(2016) Andrew W. Brooks et al.   PLOS BIOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

(2015) R. Henrik Nilsson et al.   MICROBES AND ENVIRONMENTS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

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

The Hologenome Concept: Helpful or Hollow?

(2015) Nancy A. Moran et al.   PLOS BIOLOGY

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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

Helium: visualization of large scale plant pedigrees

(2014) Paul D Shaw et al.   BMC BIOINFORMATICS

Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize

(2014) David Johnston-Monje et al.   BMC PLANT BIOLOGY

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology

(2011) David Johnston-Monje et al.   PLoS One

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

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

Polyploid evolution in Oryza officinalis complex of the genus Oryza

(2009) Baosheng Wang et al.   BMC EVOLUTIONARY BIOLOGY