Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations

Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida

(2019) Sujan Timilsina et al.   Frontiers in Microbiology

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

Deciphering how plant pathogenic bacteria disperse and meet: molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity

(2019) Olivier Pruvost et al.   Evolutionary Applications

Genomic sequence analysis reveals diversity of Australian Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli

(2019) R. Roach et al.   BMC GENOMICS

Molecular epidemiology of Xanthomonas perforans outbreaks in tomato from transplant to field by single-nucleotide polymorphism analysis

(2019) Peter Abrahamian et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

(2019) Apirak Wiseschart et al.   BMC MICROBIOLOGY

Independent Evolution with the Gene Flux Originating from Multiple Xanthomonas Species Explains Genomic Heterogeneity in Xanthomonas perforans

(2019) E. A. Newberry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Profiling microbial strains in urban environments using metagenomic sequencing data

(2018) Moreno Zolfo et al.   Biology Direct

Population genomics of bacterial host adaptation

(2018) Samuel K. Sheppard et al.   NATURE REVIEWS GENETICS

The type III effector AvrBsT enhances Xanthomonas perforans fitness in field-grown tomato

(2018) Peter Abrahamian et al.   PHYTOPATHOLOGY

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

(2018) Shaun P. Stice et al.   Frontiers in Microbiology

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

(2018) Luis M. Rodriguez-R et al.   mSystems

On the Road to Strain-Resolved Comparative Metagenomics

(2018) Nicola Segata   mSystems

Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans

(2018) Mustafa O. Jibrin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reclassification of Xanthomonas gardneri (ex Šutič 1957) Jones et al. 2006 as a later heterotypic synonym of Xanthomonas cynarae Trébaol et al. 2000 and description of X. cynarae pv. cynarae and X. cynarae pv. gardneri based on whole genome analyses

(2018) S. Timilsina et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature

(2018) Samuele Bovo et al.   PLoS One

Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation

(2018) Dongjuan Dai et al.   Frontiers in Microbiology

Risks Posed by Intercrops and Weeds as Alternative Hosts to Xanthomonas campestris pv. musacearum in Banana Fields

(2018) Walter Ocimati et al.   Frontiers in Plant Science

Identification of Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli crops in eastern Australia

(2017) R. Roach et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Frontiers for research on the ecology of plant-pathogenic bacteria: fundamentals for sustainability

(2017) Cindy E. Morris et al.   MOLECULAR PLANT PATHOLOGY

A Novel Phylogroup of Pseudomonas cichorii Identified Following an Unusual Disease Outbreak on Tomato

(2017) Sujan Timilsina et al.   PHYTOPATHOLOGY

Epiphytic Survival of Pantoea ananatis on Richardia scabra L. in Georgia

(2017) Bhabesh Dutta et al.   PLANT DISEASE

TALE-induced bHLH transcription factors that activate a pectate lyase contribute to water soaking in bacterial spot of tomato

(2017) Allison R. Schwartz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strain profiling and epidemiology of bacterial species from metagenomic sequencing

(2017) Davide Albanese et al.   Nature Communications

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods

(2016) Andrew D. Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

A set of PCRs for rapid identification and characterization ofPseudomonas syringaephylogroups

(2016) B. Borschinger et al.   JOURNAL OF APPLIED MICROBIOLOGY

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

Analysis of Sequenced Genomes ofXanthomonas perforansIdentifies Candidate Targets for Resistance Breeding in Tomato

(2016) Sujan Timilsina et al.   PHYTOPATHOLOGY

Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors

(2016) Jeri D. Barak et al.   Frontiers in Plant Science

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

(2015) Michael Richter 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

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Bacterial spot of tomato and pepper: diverseXanthomonasspecies with a wide variety of virulence factors posing a worldwide challenge

(2015) Neha Potnis et al.   MOLECULAR PLANT PATHOLOGY

Genetic characterization of strains named asXanthomonas axonopodispv.dieffenbachiaeleads to a taxonomic revision of theX. axonopodisspecies complex

(2015) E. C. Constantin et al.   PLANT PATHOLOGY

Co-infection alters population dynamics of infectious disease

(2015) Hanna Susi et al.   Nature Communications

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Classification and Taxonomy of Vegetable Macergens

(2015) Bukola R. Aremu et al.   Frontiers in Microbiology

Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity

(2015) Allison R. Schwartz et al.   Frontiers in Microbiology

Friends or foes: can we make a distinction between beneficial and harmful strains of the Stenotrophomonas maltophilia complex?

(2015) Gabriele Berg et al.   Frontiers in Microbiology

The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease

(2015) Roberto Buonaurio et al.   Frontiers in Plant Science

Synergisms between microbial pathogens in plant disease complexes: a growing trend

(2015) Jay Ram Lamichhane et al.   Frontiers in Plant Science

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Harnessing Population Genomics to Understand How Bacterial Pathogens Emerge, Adapt to Crop Hosts, and Disseminate

(2014) Boris A. Vinatzer et al.   Annual Review of Phytopathology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Bacterial multispecies studies and microbiome analysis of a plant disease

(2014) Daniel Passos da Silva et al.   MICROBIOLOGY-SGM

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resident Bacteria on Leaves Enhance Survival of Immigrant Cells ofSalmonella enterica

(2013) Cesar Poza-Carrion et al.   PHYTOPATHOLOGY

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SNP Design from 454 Sequencing of Podosphaera plantaginis Transcriptome Reveals a Genetically Diverse Pathogen Metapopulation with High Levels of Mixed-Genotype Infection

(2012) Charlotte Tollenaere et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

COMPETITION, COOPERATION AMONG KIN, AND VIRULENCE IN MULTIPLE INFECTIONS

(2010) Manuela López-Villavicencio et al.   EVOLUTION

Micro- and macrospatial scale analyses illustrates mixed mating strategies and extensive geneflow in populations of an invasive haploid pathogen

(2010) GUILLERMO PÉREZ et al.   MOLECULAR ECOLOGY

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences

(2009) N. Parkinson et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Pantoea ananatis: an unconventional plant pathogen

(2009) TERESA A. COUTINHO et al.   MOLECULAR PLANT PATHOLOGY

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

(2009) N. Delmotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-Infection by Two Criniviruses Alters Accumulation of Each Virus in a Host-Specific Manner and Influences Efficiency of Virus Transmission

(2008) William M. Wintermantel et al.   PHYTOPATHOLOGY