Year: 2012
Type: article
Abstract: Eukaryotic microorganisms are important but understudied components of the human microbiome. Here we present a pipeline for analysis of deep sequencing data on single cell eukaryotes. We designed a new 18S rRNA gene-specific PCR primer set and compared a published rRNA gene internal transcribed spacer (ITS) gene primer set. Amplicons were tested against 24 specimens from defined eukaryotes and eight well-characterized human stool samples. A software pipeline https://sourceforge.net/projects/brocc/ was developed for taxonomic attribution, validated against simulated data, and tested on pyrosequence data. This study provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples.
Source: Genome biology
Institutions: University of Pennsylvania, University of Michigan
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,490
Funders: Howard Hughes Medical Institute, Pennsylvania Department of Health, University of Pennsylvania, Crohn's and Colitis Foundation, National Institutes of Health, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Center for Research Resources
Awards: Training in Emerging Infectious Diseases, Dietary Patterns and the Course of Inflammatory Bowel Disease, G256492535, G4420274321, Institutional Clinical and Translational Science Award, Microbial Pathogenesis and Genomics, Immune modulation by intestinal cell differentiation, Functional Biology of Intestinal Epithelial Cells in Food Allergy, Diet, Genetic Factors, and the Gut Microbiome in Crohn's Disease, Epithelial cell regulation of intestinal immune homeostasis, Purchase of the Roche GS SLX Sequencing System, Regulation of mucosal immunity by neuronal pathways, Center for Molecular Studies in Digestive and Liver Diseases
OpenAlex ID: W2166559909