An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads

Estimating Protistan Diversity Using High-Throughput Sequencing

(2015) Sarah K. Hu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water

(2015) Asja Korajkic et al.   WATER RESEARCH

Sewage Reflects the Microbiomes of Human Populations

(2015) Ryan J. Newton et al.   mBio

Collection media and delayed freezing effects on microbial composition of human stool

(2015) Roberto Flores et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys

(2014) Frédéric Mahé et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis

(2014) Yong Wang et al.   PLoS One

Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

(2014) Luisa W. Hugerth et al.   PLoS One

What is the importance of zoonotic trichomonads for human health?

(2014) Julia M. Maritz et al.   TRENDS IN PARASITOLOGY

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

(2014) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Bacterial communities on classroom surfaces vary with human contact

(2014) James F Meadow et al.   Microbiome

Trichomonas stableri n. sp., an agent of trichomonosis in Pacific Coast band-tailed pigeons (Patagioenas fasciata monilis)

(2014) Yvette A. Girard et al.   International Journal for Parasitology-Parasites and Wildlife

Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

(2013) Orin C. Shanks et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sewage reflects the distribution of human faecalLachnospiraceae

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

Responses of protists with different feeding habits to the changes of activated sludge conditions: A study based on biomass data

(2013) Bo Hu et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

A Microbial Signature Approach to Identify Fecal Pollution in the Waters Off an Urbanized Coast of Lake Michigan

(2013) Ryan J. Newton et al.   MICROBIAL ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Pyrosequencing the Canine Faecal Microbiota: Breadth and Depth of Biodiversity

(2013) Daniel Hand et al.   PLoS One

Evaluation of molecular community analysis methods for discerning fecal sources and human waste

(2013) Yiping Cao et al.   WATER RESEARCH

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Enteric Protozoa in the Developed World: a Public Health Perspective

(2012) S. M. Fletcher et al.   CLINICAL MICROBIOLOGY REVIEWS

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

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

(2012) J Gregory Caporaso et al.   ISME Journal

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The influence of fundamental design parameters on ciliates community structure in Irish activated sludge systems

(2011) Donata Dubber et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

(2011) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Identification of Ciliate Grazers of Autotrophic Bacteria in Ammonia-Oxidizing Activated Sludge by RNA Stable Isotope Probing

(2010) A. M. Moreno et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life

(2010) Laura Wegener Parfrey et al.   SYSTEMATIC BIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

(2009) Thorsten Stoeck et al.   BMC BIOLOGY

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular Characterization of the Trichomonas gallinae Morphologic Complex in the United States

(2009) Richard W. Gerhold et al.   JOURNAL OF PARASITOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs

(2008) Hege Vestheim et al.   Frontiers in Zoology