Metagenomic sequencing combined with flow cytometry facilitated a novel microbial risk assessment framework for bacterial pathogens in municipal wastewater without cultivation

[1]  Xiang Li,et al.  Microorganisms as bio‐filters to mitigate greenhouse gas emissions from high‐altitude permafrost revealed by nanopore‐based metagenomics , 2022, iMeta.

[2]  R. Tenreiro,et al.  Stalking Mycobacterium bovis in the total environment: FLOW-FISH & FACS to detect, quantify, and sort metabolically active and quiescent cells in complex matrices. , 2022, Journal of hazardous materials.

[3]  R. Lan,et al.  Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off. , 2021, Water research.

[4]  Tong Zhang,et al.  Rapid absolute quantification of pathogens and ARGs by nanopore sequencing. , 2021, The Science of the total environment.

[5]  Dieter M. Tourlousse,et al.  Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements , 2021, Microbiome.

[6]  N. Boon,et al.  Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products. , 2020, Environmental microbiology.

[7]  R. Starke,et al.  16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys , 2020, Microbial ecology.

[8]  K. Jeffrey,et al.  Illuminating the human virome in health and disease , 2020, Genome Medicine.

[9]  Thomas Bleazard,et al.  Developing standards for the microbiome field , 2020, Microbiome.

[10]  Kevin V. Thomas,et al.  First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community , 2020, Science of The Total Environment.

[11]  Y. P. Chua,et al.  Quantitative Microbial Risk Assessment of Drinking Water Quality to Predict the Risk of Waterborne Diseases in Primary-School Children , 2020, International journal of environmental research and public health.

[12]  Christopher E. L. Owens,et al.  Implementation of quantitative microbial risk assessment (QMRA) for public drinking water supplies: Systematic review. , 2020, Water research.

[13]  Yang Bai,et al.  Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome , 2019, Plant communications.

[14]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[15]  S. Bae,et al.  A culture-dependent and metagenomic approach of household drinking water from the source to point of use in a developing country , 2019, Water research X.

[16]  Sarika Tiwari,et al.  Assessment of enteroviruses from sewage water and clinical samples during eradication phase of polio in North India , 2018, Virology Journal.

[17]  Ted Wong,et al.  Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis , 2018, Nature Communications.

[18]  Falk Hildebrand,et al.  Structure and function of the global topsoil microbiome , 2018, Nature.

[19]  M. Doebeli,et al.  Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem , 2018, Microbiome.

[20]  Dieter M. Tourlousse,et al.  Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing , 2016, Nucleic acids research.

[21]  Raymond Lo,et al.  CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database , 2016, Nucleic Acids Res..

[22]  A. Dalsgaard,et al.  Toxigenic Vibrio cholerae O1 in vegetables and fish raised in wastewater irrigated fields and stabilization ponds during a non-cholera outbreak period in Morogoro, Tanzania: an environmental health study , 2016, BMC Research Notes.

[23]  Frederik Hammes,et al.  Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge , 2016, Front. Microbiol..

[24]  P. Simmonds,et al.  The use of human sewage screening for community surveillance of hepatitis E virus in the UK , 2015, Journal of medical virology.

[25]  Siu-Ming Yiu,et al.  Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2015, GigaScience.

[26]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[27]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[28]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[29]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[30]  Tiong Gim Aw,et al.  Detection of pathogens in water: from phylochips to qPCR to pyrosequencing , 2011, Current Opinion in Biotechnology.

[31]  Jian Yang,et al.  VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors , 2011, Nucleic Acids Res..

[32]  M. Roivainen,et al.  Role of environmental poliovirus surveillance in global polio eradication and beyond , 2011, Epidemiology and Infection.

[33]  Gertjan Medema,et al.  Quantitative microbial risk assessment of distributed drinking water using faecal indicator incidence and concentrations. , 2007, Journal of water and health.

[34]  Steve Pedley,et al.  Quantitative microbial risk assessment to estimate health risks attributable to water supply: can the technique be applied in developing countries with limited data? , 2006, Journal of water and health.

[35]  L. Riemann,et al.  Optimization of DNA extraction for quantitative marine bacterioplankton community analysis , 2004 .

[36]  K. Abd-Elsalam Non-gel based techniques for plant pathogen genotyping. , 2003, Acta microbiologica Polonica.