Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data
Charles E. Robertson,J. Kirk Harris,Brandie D. Wagner,David Granger,Kathy Browne,Beth Tatem,Leah M. Feazel,Kristin Park,Norman R. Pace,Daniel N. Frank +9 more
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TLDR
The subject of this manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.Abstract:
Summary: Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.
Availability and Implementation: Explicet is implemented in C++ via the Qt framework and supported in native code on all major operating systems (Windows, Macintosh, Linux). The source code, documents and tutorials are freely available under an open-source license at www.explicet.org.
Contact: ude.revnedcu@knarf.leinadread more
Citations
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An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia
Stephanie M. Dillon,Eric J. Lee,Cassandra V. Kotter,Gregory L. Austin,Z Dong,Daniel K. Hecht,Sara Gianella,Basile Siewe,Davey M. Smith,Alan L. Landay,Charles E. Robertson,Daniel N. Frank,Cara C. Wilson +12 more
TL;DR: Observations suggest that an important relationship exists between altered mucosal bacterial communities and intestinal inflammation during chronic HIV-1 infection, as well as with levels of systemic T-cell activation, inflammation, and microbial translocation.
Journal ArticleDOI
Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes
Aimon K. Alkanani,Naoko Hara,Peter A. Gottlieb,Diana Ir,Charles E. Robertson,Brandie D. Wagner,Daniel N. Frank,Daniel N. Frank,Danny Zipris +8 more
TL;DR: Results from a study performed in subjects with islet autoimmunity living in the U.S. suggest that altered intestinal microbiota may be associated with disease susceptibility.
Journal ArticleDOI
Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys.
Sofie Thijs,Michiel Op De Beeck,Bram Beckers,Sascha Truyens,Vincent Stevens,Jonathan D. Van Hamme,Nele Weyens,Jaco Vangronsveld +7 more
TL;DR: Insilico evaluation of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies.
Journal ArticleDOI
Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea
Isabel Moreno-Indias,Marta Torres,Josep M. Montserrat,Lidia Sánchez-Alcoholado,Fernando Cardona,Francisco J. Tinahones,David Gozal,Valeryi A. Poroyko,Daniel Navajas,María Isabel Queipo-Ortuño,Ramon Farré +10 more
TL;DR: Faecal microbiota composition and diversity are altered as a result of intermittent hypoxia realistically mimicking OSA, suggesting the possibility that physiological interplays between host and gut microbiota could be deregulated in OSA.
Journal ArticleDOI
The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD.
Taylor K. Soderborg,Sarah E. Clark,Christopher E. Mulligan,Rachel C. Janssen,Lyndsey Babcock,Diana Ir,Bridget E. Young,Bridget E. Young,Nancy F. Krebs,Dominick J. Lemas,Dominick J. Lemas,Linda K. Johnson,Tiffany L. Weir,Laurel L. Lenz,Daniel N. Frank,Teri L. Hernandez,Kristine A. Kuhn,Angelo D'Alessandro,Linda A. Barbour,Karim C. El Kasmi,Jacob E. Friedman +20 more
TL;DR: Functional evidence is provided supporting a causative role of maternal obesity-associated infant dysbiosis in childhood obesity and NAFLD by showing that maternal Obesity-shaped infant gut microbiome induces macrophage dysfunction, inflammation, and diet-induced metabolic disease in germ-free mice.
References
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
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TL;DR: This topographical and temporal survey of body sites from 10 healthy human individuals sampled over time provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin.
Journal ArticleDOI
Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity
Janet Markle,Daniel N. Frank,Steven M. Mortin-Toth,Charles E. Robertson,Leah M. Feazel,Ulrike Rolle-Kampczyk,Martin von Bergen,Kathy D. McCoy,Andrew J. Macpherson,Jayne S. Danska +9 more
TL;DR: It is demonstrated that early-life microbial exposures determine sex hormone levels and modify progression to autoimmunity in the nonobese diabetic (NOD) mouse model of type 1 diabetes (T1D), and Colonization by commensal microbes elevated serum testosterone and protected NOD males from T1D.
Journal ArticleDOI
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
Justin Kuczynski,Jesse Stombaugh,William A. Walters,Antonio Gonzalez,J. Gregory Caporaso,Rob Knight +5 more
TL;DR: The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities.
Journal ArticleDOI
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
TL;DR: The functions implemented by barcrawl and bartab are described and a proof-of-concept case study of both programs in which barcoded rRNA primers were designed and validated by high-throughput sequencing are presented.
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