Microbial diversity in water and animal faeces: a metagenomic analysis to assess public health risk

A large scale waterborne Campylobacteriosis outbreak, Havelock North, New Zealand

(2020) Brent J. Gilpin et al.   JOURNAL OF INFECTION

Exploring bacterial pathogen community dynamics in freshwater beach sediments: A tale of two lakes

(2019) Danielle VanMensel et al.   ENVIRONMENTAL MICROBIOLOGY

Fecal Pollution: New Trends and Challenges in Microbial Source Tracking Using Next-Generation-Sequencing

(2018) Tatsuya Unno et al.   ENVIRONMENTAL MICROBIOLOGY

Fecal source tracking methods to elucidate critical sources of pathogens and contaminant microbial transport through New Zealand agricultural watersheds – A review

(2018) Megan L. Devane et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Cryptosporidium species and subtypes in animals inhabiting drinking water catchments in three states across Australia

(2018) Alireza Zahedi et al.   WATER RESEARCH

Recognizing the reagent microbiome

(2018) Marcus C. de Goffau et al.   Nature Microbiology

Relationships between chemical and microbial faecal source tracking markers in urban river water and sediments during and post-discharge of human sewage

(2018) Megan L. Devane et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Fecal source tracking and eDNA profiling in an urban creek following an extreme rain event

(2018) Zachery R. Staley et al.   Scientific Reports

Relationships between Microbial Indicators and Pathogens in Recreational Water Settings

(2018) Asja Korajkic et al.   International Journal of Environmental Research and Public Health

Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control – a comprehensive review

(2017) Thadiyam Puram Ramees et al.   VETERINARY QUARTERLY

Shotgun metagenomic sequencing reveals freshwater beach sands as reservoir of bacterial pathogens

(2017) Mahi M. Mohiuddin et al.   WATER RESEARCH

Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River

(2016) Haohao Sun et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

Effect of climate change on runoff of Campylobacter and Cryptosporidium from land to surface water

(2016) Ankie Sterk et al.   WATER RESEARCH

Public health significance of zoonotic Cryptosporidium species in wildlife: Critical insights into better drinking water management

(2016) Alireza Zahedi et al.   International Journal for Parasitology-Parasites and Wildlife

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

(2015) W. Ahmed et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identifying avian sources of faecal contamination using sterol analysis

(2015) Megan L. Devane et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Diverse Applications of Environmental DNA Methods in Parasitology

(2015) David Bass et al.   TRENDS IN PARASITOLOGY

Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring

(2015) J. Vierheilig et al.   WATER SCIENCE AND TECHNOLOGY

Human-, Ovine-, and Bovine-Specific Viral Source Tracking Tools to Discriminate Between the Major Fecal Sources in Agricultural Waters

(2015) Marta Rusiñol et al.   Food and Environmental Virology

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Fecal Source Tracking in Water by Next-Generation Sequencing Technologies Using Host-Specific Escherichia coli Genetic Markers

(2014) Ryota Gomi et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology

(2014) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

Discovering new indicators of fecal pollution

(2014) Sandra L. McLellan et al.   TRENDS IN MICROBIOLOGY

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

(2013) Danilo Ercolini   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Arcobacter in Lake Erie Beach Waters: an Emerging Gastrointestinal Pathogen Linked with Human-Associated Fecal Contamination

(2012) Cheonghoon Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Emerging pathogen Arcobacter spp. in acute gastroenteritis: molecular identification, antibiotic susceptibilities and genotyping of the isolated arcobacters

(2012) T. Kayman et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake

(2012) Christopher Staley et al.   WATER RESEARCH

Quantitative Metagenomic Analyses Based on Average Genome Size Normalization

(2011) Jeremy A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Culture-independent methods for studying environmental microorganisms: methods, application, and perspective

(2011) Can Su et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Estimated human health risks from exposure to recreational waters impacted by human and non-human sources of faecal contamination

(2010) Jeffrey A. Soller et al.   WATER RESEARCH

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

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