Precision Probiotics in Agroecosystems: Multiple Strategies of Native Soil Microbiotas for Conquering the Competitor Ralstonia solanacearum

Sucrose triggers a novel signaling cascade promoting Bacillus subtilis rhizosphere colonization

(2021) Tao Tian et al.   ISME Journal

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes

(2020) Yuting Liang et al.   ENVIRONMENTAL MICROBIOLOGY

Inhibitory effect of Bifidobacterium Bifidum ATCC 29521 on colitis and its mechanism

(2020) Ahmad Ud Din et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Antibiotics of Pseudomonas protegens FD6 are essential for biocontrol activity

(2020) Q. X. Zhang et al.   AUSTRALASIAN PLANT PATHOLOGY

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Moving from probiotics to precision probiotics

(2020) Patrick Veiga et al.   Nature Microbiology

Narrow-Spectrum Antibacterial Agents—Benefits and Challenges

(2020) Richard A. Alm et al.   Antibiotics-Basel

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

(2020) Sang-Moo Lee et al.   ISME Journal

Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

(2019) Shuo Jiao et al.   mSystems

The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome

(2019) Wencong Shi et al.   Microbiome

SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

(2019) Javier Tamames et al.   Frontiers in Microbiology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Multiple-Ascending-Dose Phase 1 Clinical Study of the Safety, Tolerability, and Pharmacokinetics of CRS3123, a Narrow-Spectrum Agent with Minimal Disruption of Normal Gut Microbiota

(2019) Barbara K. Lomeli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

(2019) Víctor J. Carrión et al.   SCIENCE

OUP accepted manuscript

(2018)   BIOINFORMATICS

The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence

(2018) Francesca Mapelli et al.   ISME Journal

Disease-induced assemblage of a plant-beneficial bacterial consortium

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

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

(2018) Ling Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice

(2018) Boknam Jung et al.   Nature Communications

Persistence in Phytopathogenic Bacteria: Do We Know Enough?

(2018) Paula M. M. Martins et al.   Frontiers in Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: A Pilot Study in Patients With Irritable Bowel Syndrome

(2017) Maria Ines Pinto-Sanchez et al.   GASTROENTEROLOGY

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

Processing and targeting of proteins derived from polyprotein with 2A and LP4/2A as peptide linkers in a maize expression system

(2017) He Sun et al.   PLoS One

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes

(2017) Christian Santos-Medellín et al.   mBio

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

(2017) Hongwu Yang et al.   Frontiers in Microbiology

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome

(2017) Yunzeng Zhang et al.   Microbiome

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information

(2017) Albert Barberán et al.   mSphere

Soil immune responses

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

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

(2016) Jie Hu et al.   mBio

Temperature mediates continental-scale diversity of microbes in forest soils

(2016) Jizhong Zhou et al.   Nature Communications

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Microbial and biochemical basis of a Fusarium wilt-suppressive soil

(2015) Jae-Yul Cha et al.   ISME Journal

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover

(2015) Yuting Liang et al.   ISME Journal

Subversion of plant cellular functions by bacterial type-III effectors: beyond suppression of immunity

(2015) Alberto P. Macho   NEW PHYTOLOGIST

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Increasing aridity reduces soil microbial diversity and abundance in global drylands

(2015) Fernando T. Maestre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutualistic Interactions and Biological Invasions

(2014) Anna Traveset et al.   Annual Review of Ecology Evolution and Systematics

Induced Systemic Resistance by Beneficial Microbes

(2014) Corné M.J. Pieterse et al.   Annual Review of Phytopathology

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Bacteria can mobilize nematode-trapping fungi to kill nematodes

(2014) Xin Wang et al.   Nature Communications

A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure

(2014) Bo Sun et al.   Ecology and Evolution

Breeding for resistances to Ralstonia solanacearum

(2014) Gaëlle Huet   Frontiers in Plant Science

Accumulation of abasic sites induces genomic instability in normal human gastric epithelial cells during Helicobacter pylori infection

(2014) D Kidane et al.   Oncogenesis

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Contribution of Bacillomycin D in Bacillus amyloliquefaciens SQR9 to Antifungal Activity and Biofilm Formation

(2012) Zhihui Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Top 10 plant pathogenic bacteria in molecular plant pathology

(2012) JOHN MANSFIELD et al.   MOLECULAR PLANT PATHOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The In Planta Transcriptome of Ralstonia solanacearum: Conserved Physiological and Virulence Strategies during Bacterial Wilt of Tomato

(2012) J. M. Jacobs et al.   mBio

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon

(2010) M. C. Rea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pathogen profile update:Fusarium oxysporum

(2009) CAROLINE B. MICHIELSE et al.   MOLECULAR PLANT PATHOLOGY

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice

(2008) Lisiane B. Meira et al.   JOURNAL OF CLINICAL INVESTIGATION

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE