Challenges and Approaches in Microbiome Research: From Fundamental to Applied

Towards utilization of the human genome and microbiome for personalized nutrition

(2018) Stavros Bashiardes et al.   CURRENT OPINION IN BIOTECHNOLOGY

The soil microbiome — from metagenomics to metaphenomics

(2018) Janet K Jansson et al.   CURRENT OPINION IN MICROBIOLOGY

Human Perturbation of the Global Phosphorus Cycle: Changes and Consequences

(2018) Zengwei Yuan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota

(2018) Nanna B Svenningsen et al.   ISME Journal

Disease-induced assemblage of a plant-beneficial bacterial consortium

(2018) Roeland L. Berendsen et al.   ISME Journal

Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms

(2018) Ma del Carmen Orozco-Mosqueda et al.   MICROBIOLOGICAL RESEARCH

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

(2018) Elena Martino et al.   NEW PHYTOLOGIST

An ecological perspective on managing weeds during the great selection for herbicide resistance

(2018) Muthukumar V Bagavathiannan et al.   PEST MANAGEMENT SCIENCE

Emerging microbial biocontrol strategies for plant pathogens

(2018) Sharifah Farhana Syed Ab Rahman et al.   PLANT SCIENCE

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

New live screening of plant-nematode interactions in the rhizosphere

(2018) Felicity E. O’Callaghan et al.   Scientific Reports

Design of synthetic bacterial communities for predictable plant phenotypes

(2018) Sur Herrera Paredes et al.   PLOS BIOLOGY

COREMIC: a web-tool to search for a niche associated CORE MICrobiome

(2018) Richard R. Rodrigues et al.   PeerJ

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

(2018) Kyle Hartman et al.   Microbiome

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

(2018) Kateryna Zhalnina et al.   Nature Microbiology

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

(2017) Panagiotis S Adam et al.   ISME Journal

Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils

(2017) Juan D. Castillo et al.   MICROBIAL ECOLOGY

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

(2017) Salvador Lladó et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genomic features of bacterial adaptation to plants

(2017) Asaf Levy et al.   NATURE GENETICS

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Bacterial Biosensors for in Vivo Spatiotemporal Mapping of Root Secretion

(2017) Francesco Pini et al.   PLANT PHYSIOLOGY

Live imaging of root–bacteria interactions in a microfluidics setup

(2017) Hassan Massalha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community

(2017) Yi Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil

(2017) Honggui Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Plant Breeding Goes Microbial

(2017) Zhong Wei et al.   TRENDS IN PLANT SCIENCE

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

(2017) Bradon R. McDonald et al.   mBio

Bottom-up effects on herbivore-induced plant defences: a case study based on compositional patterns of rhizosphere microbial communities

(2017) Emilio Benítez et al.   Scientific Reports

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

(2017) Shany Ofaim et al.   Frontiers in Microbiology

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization

(2017) Wayne Dawson et al.   Frontiers in Microbiology

A New Approach to Modify Plant Microbiomes and Traits by Introducing Beneficial Bacteria at Flowering into Progeny Seeds

(2017) Birgit Mitter et al.   Frontiers in Microbiology

Root Hair Mutations Displace the Barley Rhizosphere Microbiota

(2017) Senga Robertson-Albertyn et al.   Frontiers in Plant Science

Deciphering composition and function of the root microbiome of a legume plant

(2017) Kyle Hartman et al.   Microbiome

The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens

(2017) Daria Rybakova et al.   Microbiome

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil

(2017) Ahmed Elhady et al.   PLoS One

A Microplate Reader-Based System for Visualizing Transcriptional Activity During in vivo Microbial Interactions in Space and Time

(2017) Rosanna C. Hennessy et al.   Scientific Reports

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles

(2016) Yang Li et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent

(2016) Kei Hiruma et al.   CELL

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes

(2016) Tillmann Lueders et al.   CURRENT OPINION IN BIOTECHNOLOGY

Stable isotope probing of carbon flow in the plant holobiont

(2016) Feth el Zahar Haichar et al.   CURRENT OPINION IN BIOTECHNOLOGY

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria

(2016) Ian D. E. A. Lidbury et al.   ENVIRONMENTAL MICROBIOLOGY

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

(2016) Thilo Muth et al.   Expert Review of Proteomics

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns

(2016) Emma Timmins-Schiffman et al.   ISME Journal

Harnessing Insect–Microbe Chemical Communications To Control Insect Pests of Agricultural Systems

(2016) John J. Beck et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Multiplicity of Sulfate and Molybdate Transporters and Their Role in Nitrogen Fixation inRhizobium leguminosarumbv.viciaeRlv3841

(2016) Guojun Cheng et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management

(2016) R. Poudel et al.   PHYTOPATHOLOGY

Soil immune responses

(2016) J. M. Raaijmakers et al.   SCIENCE

The next green movement: Plant biology for the environment and sustainability

(2016) J. M. Jez et al.   SCIENCE

An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability

(2016) S. Franz Bender et al.   TRENDS IN ECOLOGY & EVOLUTION

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

(2016) Stéphane Hacquard et al.   Nature Communications

Advances in biodiversity: metagenomics and the unveiling of biological dark matter

(2016) Robert J. Robbins et al.   Standards in Genomic Sciences

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

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

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Planetary Boundaries: Exploring the Safe Operating Space for Humanity

(2016) Johan Rockström et al.   ECOLOGY AND SOCIETY

Association of Shifting Populations in the Root Zone Microbiome of Millet with Enhanced Crop Productivity in the Sahel Region (Africa)

(2015) Spencer J. Debenport et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

(2015) Nuria Bonilla et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Functional distinctness in the exoproteomes of marineSynechococcus

(2015) Joseph A. Christie-Oleza et al.   ENVIRONMENTAL MICROBIOLOGY

An analysis ofPseudomonasgenomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota

(2015) T. H. Mauchline et al.   ENVIRONMENTAL MICROBIOLOGY

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

(2015) Andrzej Tkacz et al.   ISME Journal

Role of root microbiota in plant productivity

(2015) A. Tkacz et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

(2015) Pablo R. Hardoim et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The Plant Microbiome at Work

(2015) Klaus Schlaeppi et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

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

Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping

(2015) Rakesh Santhanam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

(2015) S. L. Lebeis et al.   SCIENCE

Engineering Microbiomes to Improve Plant and Animal Health

(2015) U.G. Mueller et al.   TRENDS IN MICROBIOLOGY

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

Exometabolite niche partitioning among sympatric soil bacteria

(2015) Richard Baran et al.   Nature Communications

Manipulating the banana rhizosphere microbiome for biological control of Panama disease

(2015) Chao Xue et al.   Scientific Reports

Editorial: Above-belowground interactions involving plants, microbes and insects

(2015) Ana Pineda et al.   Frontiers in Plant Science

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

(2015) Qiong Wang et al.   Microbiome

Associations with rhizosphere bacteria can confer an adaptive advantage to plants

(2015) Cara H. Haney et al.   Nature Plants

Metaproteomics of complex microbial communities in biogas plants

(2015) Robert Heyer et al.   Microbial Biotechnology

Root microbiome relates to plant host evolution in maize and other Poaceae

(2014) Marie-Lara Bouffaud et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring the functional soil-microbe interface and exoenzymes through soil metaexoproteomics

(2014) Ashley S Johnson-Rollings et al.   ISME Journal

Selection on soil microbiomes reveals reproducible impacts on plant function

(2014) Kevin Panke-Buisse et al.   ISME Journal

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria

(2014) I. Lidbury et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial seed endophytes: genera, vertical transmission and interaction with plants

(2014) Sascha Truyens et al.   Environmental Microbiology Reports

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Genome-wide association study of Arabidopsis thaliana leaf microbial community

(2014) Matthew W. Horton et al.   Nature Communications

Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria

(2014) Maxime Bruto et al.   Scientific Reports

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

(2014) Pierre-Marc Delaux et al.   PLoS Genetics

Structure and Functions of the Bacterial Microbiota of Plants

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

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

(2013) Etienne Yergeau et al.   ISME Journal

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

Application of Natural Blends of Phytochemicals Derived from the Root Exudates ofArabidopsisto the Soil Reveal That Phenolic-related Compounds Predominantly Modulate the Soil Microbiome

(2013) Dayakar V. Badri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome

(2013) Matthew G. Bakker et al.   MOLECULAR ECOLOGY

Speak, friend and enter: signalling systems that promote beneficial symbiotic associations in plants

(2013) Giles E. D. Oldroyd   NATURE REVIEWS MICROBIOLOGY

Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline

(2013) Sally Hilton et al.   PLoS One

In vivogene expression ofPseudomonas putida KT2440 in the rhizosphere of different plants

(2013) Matilde Fernández et al.   Microbial Biotechnology

Crop Productivity and Nutrient Dynamics in a Shrub ()–Based Farming System of the Sahel

(2012) E. L. Dossa et al.   AGRONOMY JOURNAL

Manipulating the soil microbiome to increase soil health and plant fertility

(2012) Jacqueline M. Chaparro et al.   BIOLOGY AND FERTILITY OF SOILS

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

Exoproteomics: exploring the world around biological systems

(2012) Jean Armengaud et al.   Expert Review of Proteomics

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

(2012) Timothy J Williams et al.   ISME Journal

Application of metatranscriptomics to soil environments

(2012) Lilia C. Carvalhais et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

(2012) Thilo Muth et al.   Molecular BioSystems

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Transparent Soil for Imaging the Rhizosphere

(2012) Helen Downie et al.   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

The rhizosphere microbiome and plant health

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

Meeting the demand for crop production: the challenge of yield decline in crops grown in short rotations

(2011) Amanda J. Bennett et al.   BIOLOGICAL REVIEWS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

The Path to Personalized Medicine

(2010) Margaret A. Hamburg et al.   NEW ENGLAND JOURNAL OF MEDICINE

Culture-independent molecular techniques for soil microbial ecology

(2010) Penny R. Hirsch et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Ecology and Evolution of Microbes that Manipulate Host Reproduction

(2009) Jan Engelstädter et al.   Annual Review of Ecology Evolution and Systematics

Endophytic bacteria in cacti seeds can improve the development of cactus seedlings

(2009) M. Esther Puente et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Human alteration of the global nitrogen and phosphorus soil balances for the period 1970-2050

(2009) A. F. Bouwman et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates

(2009) Shirley A. Micallef et al.   JOURNAL OF EXPERIMENTAL BOTANY

Carbon flow in the rhizosphere: carbon trading at the soil–root interface

(2009) D. L. Jones et al.   PLANT AND SOIL

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea

(2008) Sarah M Sowell et al.   ISME Journal

The role of conservation agriculture in sustainable agriculture

(2007) P. R Hobbs et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES