Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing

[1]  G. Gopinath,et al.  Comparison of a PCR serotyping assay, Check&Trace assay for Salmonella, and Luminex Salmonella serotyping assay for the characterization of Salmonella enterica identified from fresh and naturally contaminated cilantro. , 2014, Food microbiology.

[2]  J. Barak,et al.  Xanthomonas perforans Colonization Influences Salmonella enterica in the Tomato Phyllosphere , 2014, Applied and Environmental Microbiology.

[3]  James R. Cole,et al.  Ribosomal Database Project: data and tools for high throughput rRNA analysis , 2013, Nucleic Acids Res..

[4]  Michael Y. Galperin,et al.  A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. , 2013, Environmental microbiology.

[5]  Rob Knight,et al.  Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere , 2013, PloS one.

[6]  S. Lindow,et al.  Resident bacteria on leaves enhance survival of immigrant cells of Salmonella enterica. , 2013, Phytopathology.

[7]  Danilo Ercolini,et al.  High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology , 2013, Applied and Environmental Microbiology.

[8]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[9]  R. Knight,et al.  Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) , 2013, BMC Microbiology.

[10]  Marc W Allard,et al.  Characterization of microflora in Latin-style cheeses by next-generation sequencing technology , 2012, BMC Microbiology.

[11]  C. Parker,et al.  The Salmonella Transcriptome in Lettuce and Cilantro Soft Rot Reveals a Niche Overlap with the Animal Host Intestine , 2012, Applied and Environmental Microbiology.

[12]  M. Allard,et al.  Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection , 2012, BMC Research Notes.

[13]  Y. Hadar,et al.  Ecology of Root Colonizing Massilia (Oxalobacteraceae) , 2012, PloS one.

[14]  C. Huttenhower,et al.  Metagenomic microbial community profiling using unique clade-specific marker genes , 2012, Nature Methods.

[15]  Paul D. Cotter,et al.  High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses , 2012, Applied and Environmental Microbiology.

[16]  J. Leveau,et al.  Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce , 2012, The ISME Journal.

[17]  Y. Sugita‐Konishi,et al.  Identification of Kudoa septempunctata as the causative agent of novel food poisoning outbreaks in Japan by consumption of Paralichthys olivaceus in raw fish. , 2012, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[18]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[19]  W. Wade,et al.  Bergey’s Manual of Systematic Bacteriology , 2012 .

[20]  William A. Walters,et al.  Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys , 2011, The ISME Journal.

[21]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

[22]  T. Klaenhammer,et al.  The impact of omic technologies on the study of food microbes. , 2011, Annual review of food science and technology.

[23]  Y. Hahn,et al.  Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food , 2011, Applied and Environmental Microbiology.

[24]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010, Bioinform..

[25]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[26]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[27]  Rob Knight,et al.  PyNAST: a flexible tool for aligning sequences to a template alignment , 2009, Bioinform..

[28]  F. Bushman,et al.  QIIME allows integration and analysis of high-throughput community sequencing data. Nat. Meth. , 2010 .

[29]  Mihai Pop,et al.  Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples , 2009, PLoS Comput. Biol..

[30]  Radhey S. Gupta,et al.  Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). , 2009, International journal of systematic and evolutionary microbiology.

[31]  G. Garrity Comprar Bergey's Manual of Systematic Bacteriology · Volume 3: The Low G + C Gram Positives | Garrity, George | 9780387950419 | Springer , 2009 .

[32]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[33]  G. Olsen,et al.  Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes , 2008, Applied and Environmental Microbiology.

[34]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[35]  D. Crowley,et al.  Bacterial Diversity in Tree Canopies of the Atlantic Forest , 2006, Science.

[36]  C. Poll,et al.  Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure. , 2006, FEMS microbiology ecology.

[37]  F. Rainey,et al.  An Introduction to the Family Clostridiaceae , 2006 .

[38]  R. Knight,et al.  UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.

[39]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[40]  W. Wenzel,et al.  Bacterial Communities Associated with Flowering Plants of the Ni Hyperaccumulator Thlaspi goesingense , 2004, Applied and Environmental Microbiology.

[41]  A. Stapleton,et al.  Ultraviolet Radiation Alters Maize Phyllosphere Bacterial Diversity , 2003, Microbial Ecology.

[42]  R. Reporter,et al.  An outbreak of Salmonella serotype Thompson associated with fresh cilantro. , 2001, The Journal of infectious diseases.

[43]  J. Wells,et al.  Salmonella Contamination Associated with Bacterial Soft Rot of Fresh Fruits and Vegetables in the Marketplace. , 1997, Plant disease.