Related references
Note: Only part of the references are listed.Plant secondary metabolites altering root microbiome composition and function
Anna Koprivova et al.
CURRENT OPINION IN PLANT BIOLOGY (2022)
Camalexin accumulation as a component of plant immunity during interactions with pathogens and beneficial microbes
Ngoc Huu Nguyen et al.
PLANTA (2022)
Multifaceted roles of flavonoids mediating plant-microbe interactions
Lanxiang Wang et al.
MICROBIOME (2022)
Two-way microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging
Shifra Steinberg et al.
ISME JOURNAL (2021)
Pinpointing secondary metabolites that shape the composition and function of the plant microbiome
Richard P. Jacoby et al.
JOURNAL OF EXPERIMENTAL BOTANY (2021)
Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria
Elhanan Tzipilevich et al.
CELL HOST & MICROBE (2021)
Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution
Daniel Dar et al.
SCIENCE (2021)
Recent advances in tools to map the microbiome
Hao Shi et al.
CURRENT OPINION IN BIOMEDICAL ENGINEERING (2021)
Spatial metabolomics of in situ host-microbe interactions at the micrometre scale
Benedikt Geier et al.
NATURE MICROBIOLOGY (2020)
Short-range interactions govern the dynamics and functions of microbial communities
Alma Dal Co et al.
NATURE ECOLOGY & EVOLUTION (2020)
Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries
Dongyeop Kim et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Spatial Ecology of the Human Tongue Dorsum Microbiome
Steven A. Wilbert et al.
CELL REPORTS (2020)
Oral Microbiome Geography: Micron-Scale Habitat and Niche
Jessica L. Mark Welch et al.
CELL HOST & MICROBE (2020)
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis
Christopher J. Harbort et al.
CELL HOST & MICROBE (2020)
Revealing the in vivo growth and division patterns of mouse gut bacteria
Liyuan Lin et al.
SCIENCE ADVANCES (2020)
Highly multiplexed spatial mapping of microbial communities
Hao Shi et al.
NATURE (2020)
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH
Chee-Huat Linus Eng et al.
NATURE (2019)
Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells
Kook Hui Ryu et al.
PLANT PHYSIOLOGY (2019)
Bacterial surface colonization, preferential attachment and fitness under periodic stress
Maor Grinberg et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
A specialized metabolic network selectively modulates Arabidopsis root microbiota
Ancheng C. Huang et al.
SCIENCE (2019)
Spatial metagenomic characterization of microbial biogeography in the gut
Ravi U. Sheth et al.
NATURE BIOTECHNOLOGY (2019)
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Evan Bolyen et al.
NATURE BIOTECHNOLOGY (2019)
Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains
Anna Koprivova et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome
Mathias J. E. E. E. Voges et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms
Michael Lukumbuzya et al.
FRONTIERS IN MICROBIOLOGY (2019)
The Landscape of Genetic Content in the Gut and Oral Human Microbiome
Braden T. Tierney et al.
CELL HOST & MICROBE (2019)
A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome
Alessandra Riva et al.
NATURE COMMUNICATIONS (2019)
Host Specificity and Spatial Distribution Preference of Three Pseudomonas Isolates
Nesli Tovi et al.
FRONTIERS IN MICROBIOLOGY (2019)
Fluorescence in situ hybridization, a complementary molecular tool for the clinical diagnosis of infectious diseases by intracellular and fastidious bacteria
Elsa Prudent et al.
FEMS MICROBIOLOGY REVIEWS (2019)
Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?
Joelle Sasse et al.
TRENDS IN PLANT SCIENCE (2018)
Multiplexed protein maps link subcellular organization to cellular states
Gabriele Gut et al.
SCIENCE (2018)
Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces
Hannes Schmidt et al.
FRONTIERS IN ENVIRONMENTAL SCIENCE (2018)
A communal catalogue reveals Earth's multiscale microbial diversity
Luke R. Thompson et al.
NATURE (2017)
Profiling the transcriptome with RNA SPOTs
Chee-Huat Linus Eng et al.
NATURE METHODS (2017)
Dispersal limitation promotes the diversification of the mammalian gut microbiota
Andrew H. Moeller et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice
Jessica L. Mark Welch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Live imaging of root-bacteria interactions in a microfluidics setup
Hassan Massalha et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Mobilization of Iron by Plant-Borne Coumarins
Huei Hsuan Tsai et al.
TRENDS IN PLANT SCIENCE (2017)
The Gut Microbiome: Connecting Spatial Organization to Function
Carolina Tropini et al.
CELL HOST & MICROBE (2017)
MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells
Mario P. Schimak et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)
Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes
Muhammad Saleem et al.
MICROBIAL ECOLOGY (2016)
Gut biogeography of the bacterial microbiota
Gregory P. Donaldson et al.
NATURE REVIEWS MICROBIOLOGY (2016)
Microbial interactions and community assembly at microscales
Otto X. Cordero et al.
CURRENT OPINION IN MICROBIOLOGY (2016)
Nanoscale imaging of RNA with expansion microscopy
Fei Chen et al.
NATURE METHODS (2016)
Spatial structure, cooperation and competition in biofilms
Carey D. Nadell et al.
NATURE REVIEWS MICROBIOLOGY (2016)
In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus
Sheel Shah et al.
NEURON (2016)
Biogeography of a human oral microbiome at the micron scale
Jessica L. Mark Welch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization
Jeffrey R. Moffitt et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research
Tim Richter-Heitmann et al.
FRONTIERS IN MICROBIOLOGY (2016)
VSEARCH: a versatile open source tool for metagenomics
Torbjorn Rognes et al.
PEERJ (2016)
Multiplexed Spectral Imaging of 120 Different Fluorescent Labels
Alex M. Valm et al.
PLOS ONE (2016)
Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat
Akitomo Kawasaki et al.
PLOS ONE (2016)
Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417
Roeland L. Berendsen et al.
BMC GENOMICS (2015)
Quantitative Imaging of Gut Microbiota Spatial Organization
Kristen A. Earle et al.
CELL HOST & MICROBE (2015)
Functional overlap of the Arabidopsis leaf and root microbiota
Yang Bai et al.
NATURE (2015)
Spatially resolved, highly multiplexed RNA profiling in single cells
Kok Hao Chen et al.
SCIENCE (2015)
Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
Sarah L. Lebeis et al.
SCIENCE (2015)
Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for Accurate Identification
Erik S. Wright et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2014)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization
Mitja N. P. Remus-Emsermann et al.
ENVIRONMENTAL MICROBIOLOGY (2014)
Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescence in situ hybridization
Hannes Schmidt et al.
FEMS MICROBIOLOGY ECOLOGY (2014)
Rhizosphere microbiome assemblage is affected by plant development
Jacqueline M. Chaparro et al.
ISME JOURNAL (2014)
Single-cell in situ RNA profiling by sequential hybridization
Eric Lubeck et al.
NATURE METHODS (2014)
Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing
David Berry et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota
Davide Bulgarelli et al.
NATURE (2012)
mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models for In Silico Evaluation of Oligonucleotide Probes for Fluorescence In Situ Hybridization
L. Safak Yilmaz et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)
Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging
Alex M. Valm et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Cell identity mediates the response of Arabidopsis roots to abiotic stress
Jose R. Dinneny et al.
SCIENCE (2008)
Development of thermodynamic models for simulating probe dissociation profiles in fluorescence in situ hybridization
L. Safak Yilmaz et al.
BIOTECHNOLOGY AND BIOENGINEERING (2007)
Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)
M Watt et al.
ENVIRONMENTAL MICROBIOLOGY (2006)
ARB:: a software environment for sequence data
W Ludwig et al.
NUCLEIC ACIDS RESEARCH (2004)
Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria
A Pernthaler et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2004)
Multiplex FISH analysis of a six-species bacterial biofilm
T Thurnheer et al.
JOURNAL OF MICROBIOLOGICAL METHODS (2004)
Differential survival of solitary and aggregated bacterial cells promotes aggregate formation on leaf surfaces
JM Monier et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)