FORENSIC: an Online Platform for Fecal Source Identification

Highly specific sewage-derived Bacteroides qPCR assays target sewage polluted waters

(2019) Shuchen Feng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows

(2019) Jill V. Hagey et al.   Frontiers in Microbiology

Ecological and Technical Mechanisms for Cross-Reaction of Human Fecal Indicators with Animal Hosts

(2019) Shuchen Feng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2018) Tatsuya Unno et al.   ENVIRONMENTAL MICROBIOLOGY

Application of SourceTracker for Accurate Identification of Fecal Pollution in Recreational Freshwater: A Double-Blinded Study

(2018) Christopher Staley et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Rates of gut microbiome divergence in mammals

(2018) Alex H. Nishida et al.   MOLECULAR ECOLOGY

Human-Associated Lachnospiraceae Genetic Markers Improve Detection of Fecal Pollution Sources in Urban Waters

(2018) Shuchen Feng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokaryotic footprints in urban water ecosystems: A case study of urban landscape ponds in a coastal city, China

(2018) Anyi Hu et al.   ENVIRONMENTAL POLLUTION

High levels of sewage contamination released from urban areas after storm events: A quantitative survey with sewage specific bacterial indicators

(2018) Hayley T. Olds et al.   PLOS MEDICINE

Accounting for Bacterial Overlap Between Raw Water Communities and Contaminating Sources Improves the Accuracy of Signature-Based Microbial Source Tracking

(2018) Moa Hägglund et al.   Frontiers in Microbiology

Fecal source identification using random forest

(2018) Adélaïde Roguet et al.   Microbiome

Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons

(2017) Jérôme Comte et al.   ENVIRONMENTAL MICROBIOLOGY

A High-Throughput DNA-Sequencing Approach for Determining Sources of Fecal Bacteria in a Lake Superior Estuary

(2017) Clairessa M. Brown et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling

(2017) D.T. McCarthy et al.   WATER RESEARCH

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters

(2016) Rebekah Henry et al.   WATER RESEARCH

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

(2015) Jenny C. Fisher et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pathways and functions of gut microbiota metabolism impacting host physiology

(2015) Smitha Krishnan et al.   CURRENT OPINION IN BIOTECHNOLOGY

Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism

(2015) Sang Sun Yoon et al.   CURRENT OPINION IN MICROBIOLOGY

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

Sewage Reflects the Microbiomes of Human Populations

(2015) Ryan J. Newton et al.   mBio

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

A single genus in the gut microbiome reflects host preference and specificity

(2014) A Murat Eren et al.   ISME Journal

Discovering new indicators of fecal pollution

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

Population dynamics and ecology of Arcobacter in sewage

(2014) Jenny C. Fisher et al.   Frontiers in Microbiology

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Sewage reflects the distribution of human faecalLachnospiraceae

(2013) Sandra L. McLellan et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring host-microbiota interactions in animal models and humans

(2013) A. D. Kostic et al.   GENES & DEVELOPMENT

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

(2013) Jonas Ghyselinck et al.   PLoS One

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Coverage evaluation of universal bacterial primers using the metagenomic datasets

(2012) Dan-Ping Mao et al.   BMC MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations

(2011) Orin C. Shanks et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys

(2011) Patricio Jeraldo et al.   ENVIRONMENTAL MICROBIOLOGY

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Assessing Pathogen Risk to Swimmers at Non-Sewage Impacted Recreational Beaches

(2010) Mary E. Schoen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparison of molecular markers to detect fresh sewage in environmental waters

(2009) W. Ahmed et al.   WATER RESEARCH

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics