Challenges and Approaches in Microbiome Research: From Fundamental to Applied
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Title
Challenges and Approaches in Microbiome Research: From Fundamental to Applied
Authors
Keywords
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Journal
Frontiers in Plant Science
Volume 9, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2018-08-17
DOI
10.3389/fpls.2018.01205
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Note: Only part of the references are listed.- Towards utilization of the human genome and microbiome for personalized nutrition
- (2018) Stavros Bashiardes et al. CURRENT OPINION IN BIOTECHNOLOGY
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- (2018) Janet K Jansson et al. CURRENT OPINION IN MICROBIOLOGY
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- (2018) Zengwei Yuan et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
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- (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
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- (2016) J. M. Jez et al. SCIENCE
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- (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
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- (2016) Matthew T. Agler et al. PLOS BIOLOGY
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- (2015) Spencer J. Debenport et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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- (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
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- (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
- 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
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