Application of fast expectation-maximization microbial source tracking to discern fecal contamination in rivers exposed to low fecal inputs

[1]  S. Mongkolsuk,et al.  The effect of quantitative polymerase chain reaction data analysis using sample amplification efficiency on microbial source tracking assay performance and source attribution. , 2020, Environmental science & technology.

[2]  L. Tang,et al.  Homogeneous selection drives antibiotic resistome in two adjacent sub-watersheds, China. , 2020, Journal of hazardous materials.

[3]  Zhisheng Yu,et al.  Validation of Bacteroidales-based microbial source tracking markers for pig fecal pollution and their application in two rivers of North China , 2020, Frontiers of Environmental Science & Engineering.

[4]  Yi Li,et al.  Source identification of phosphorus in the river-lake interconnected system using microbial community fingerprints. , 2020, Environmental research.

[5]  M. Cyterski,et al.  Microbial source tracking (MST) in Chattahoochee River National Recreation Area: Seasonal and precipitation trends in MST marker concentrations, and associations with E. coli levels, pathogenic marker presence, and land use , 2019, Water research.

[6]  M. Barra,et al.  Fecal pollution source tracking and thalassogenic diseases: The temporal-spatial concordance between maximum concentrations of human mitochondrial DNA in seawater and Hepatitis A outbreaks among a coastal population. , 2019, The Science of the total environment.

[7]  Yanguo Teng,et al.  Source identification of antibiotic resistance genes in a peri-urban river using novel crAssphage marker genes and metagenomic signatures. , 2019, Water research.

[8]  William A. Walters,et al.  Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 , 2019, Nature Biotechnology.

[9]  E. Halperin,et al.  FEAST: fast expectation-maximization for microbial source tracking , 2019, Nature Methods.

[10]  Yucheng Feng,et al.  Comparison of microbial source tracking efficacy for detection of cattle fecal contamination by quantitative PCR. , 2019, The Science of the total environment.

[11]  C. Staley,et al.  Influence of Library Composition on SourceTracker Predictions for Community-Based Microbial Source Tracking. , 2018, Environmental science & technology.

[12]  Xu Li,et al.  Characterization of Natural and Affected Environments Tracking the Sources of Antibiotic Resistance Genes in an Urban Stream during Wet Weather using Shotgun Metagenomic Analyses , 2018 .

[13]  Tong Zhang,et al.  Tracking antibiotic resistance gene pollution from different sources using machine-learning classification , 2018, Microbiome.

[14]  V. Harwood,et al.  Application of SourceTracker for Accurate Identification of Fecal Pollution in Recreational Freshwater: A Double-Blinded Study. , 2018, Environmental science & technology.

[15]  C. Staley,et al.  A High-Throughput DNA-Sequencing Approach for Determining Sources of Fecal Bacteria in a Lake Superior Estuary. , 2017, Environmental science & technology.

[16]  S. Wuertz,et al.  Bacteroidales markers for microbial source tracking in Southeast Asia. , 2017, Water research.

[17]  R. Forster,et al.  Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis) , 2016, PloS one.

[18]  D. Mccarthy,et al.  Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters. , 2016, Water research.

[19]  David Kay,et al.  Application of human and animal viral microbial source tracking tools in fresh and marine waters from five different geographical areas. , 2014, Water research.

[20]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[21]  Orin C. Shanks,et al.  Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study. , 2013, Water research.

[22]  Robert C. Edgar,et al.  UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.

[23]  S. Wei,et al.  Bacterial census of poultry intestinal microbiome. , 2013, Poultry science.

[24]  I. Rychlik,et al.  Chicken faecal microbiota and disturbances induced by single or repeated therapy with tetracycline and streptomycin , 2013, BMC Veterinary Research.

[25]  T. Edge,et al.  Comparison of Gull Feces-Specific Assays Targeting the 16S rRNA Genes of Catellicoccus marimammalium and Streptococcus spp , 2012, Applied and Environmental Microbiology.

[26]  Linda K. Dick,et al.  Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water , 2011, Applied and Environmental Microbiology.

[27]  S. Salzberg,et al.  FLASH: fast length adjustment of short reads to improve genome assemblies , 2011, Bioinform..

[28]  Rob Knight,et al.  Bayesian community-wide culture-independent microbial source tracking , 2011, Nature Methods.

[29]  Michael J Sadowsky,et al.  Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. , 2010, Environmental science & technology.

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

[31]  A. Blanch,et al.  The persistence of bifidobacteria populations in a river measured by molecular and culture techniques , 2009, Journal of applied microbiology.

[32]  R. Knight,et al.  Worlds within worlds: evolution of the vertebrate gut microbiota , 2008, Nature Reviews Microbiology.

[33]  Yan Sun,et al.  Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) , 2008, BMC 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]  Stephen B Weisberg,et al.  Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. , 2003, Journal of water and health.

[36]  Marti J. Anderson,et al.  CANONICAL ANALYSIS OF PRINCIPAL COORDINATES: A USEFUL METHOD OF CONSTRAINED ORDINATION FOR ECOLOGY , 2003 .

[37]  Katharine G. Field,et al.  A PCR Assay To Discriminate Human and Ruminant Feces on the Basis of Host Differences in Bacteroides-Prevotella Genes Encoding 16S rRNA , 2000, Applied and Environmental Microbiology.