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Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J 2013; 8:1-3. [PMID: 24152717 PMCID: PMC3869023 DOI: 10.1038/ismej.2013.176] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elizabeth M Glass
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Yekaterina Dribinsky
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Robert Van Pelt
- Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Doug Wendel
- Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Andreas Wilke
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | | | - Sue Huse
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | - Mitch Sogin
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | - Rob Knight
- 1] Department of Computer Science, University of Colorado, Boulder, CO, USA [2] Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Folker Meyer
- 1] Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA [2] Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
| | - Lynn M Schriml
- Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R. Meta-analyses of studies of the human microbiota. Genome Res 2013; 23:1704-14. [PMID: 23861384 PMCID: PMC3787266 DOI: 10.1101/gr.151803.112] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ileal Crohn's disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.
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Affiliation(s)
- Catherine A Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
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McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 2012; 1:7. [PMID: 23587224 PMCID: PMC3626512 DOI: 10.1186/2047-217x-1-7] [Citation(s) in RCA: 502] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 07/12/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. FINDINGS The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. CONCLUSIONS The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.
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Affiliation(s)
- Daniel McDonald
- Biofrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Jose C Clemente
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, CO, USA
| | | | - Jai Ram Rideout
- Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
| | - Jesse Stombaugh
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, CO, USA
| | - Doug Wendel
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, CO, USA
| | | | - Susan Huse
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | | | - Rob Knight
- Biofrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, CO, USA
- Howard Hughes Medical Institute, Boulder, CO, USA
| | - J Gregory Caporaso
- Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
- Argonne National Laboratory, Argonne, IL, USA
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Abstract
Motivation: Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies. Results: TopiaryExplorer supports the visualization of very large phylogenetic trees, including features such as the automated coloring of branches by environmental data, manipulation of trees and incorporation of per-tip metadata (e.g. taxonomic labels). Availability:http://topiaryexplorer.sourceforge.net Contact:rob.knight@colorado.edu
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Affiliation(s)
- Meg Pirrung
- Department of Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA
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Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, Laederach A. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Stand Genomic Sci 2011; 4:252-6. [PMID: 21677862 PMCID: PMC3111981 DOI: 10.4056/sigs.1724282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop to facilitate collaborations among those researchers formalizing concepts in RNA, those developing RNA-related software, and those performing genome annotation and standardization. The workshop included three software presentations, extended round-table discussions, and the constitution of two new working groups, the first to address the need for better software integration and the second to discuss standardization and benchmarking of existing RNA annotation pipelines. These working groups have subsequently pursued concrete implementation of actions suggested during the discussion. Further information about the ROC and its activities can be found at http://roc.bgsu.edu/.
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Shinobu LA, Jones MM, Basinger MA, Mitchell WM, Wendel D, Razzuk A. In vivo screening of potential antidotes for chronic cadmium intoxication. J Toxicol Environ Health 1983; 12:757-65. [PMID: 6321748 DOI: 10.1080/15287398309530467] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nineteen chelating agents have been screened under identical conditions of metal loading in an attempt to establish their relative ability to mobilize cadmium from the liver and kidney in mice with chronic cadmium intoxication. The compounds investigated were divided into five groups: polyaminocarboxylic acids, monothiols, dithiols, macrocycles, and a miscellaneous category. Only 2,3-dimercaptopropanol (BAL) and sodium diethyldithiocarbamate (NaDDTC) were able to produce a statistically significant (at the 95% level) reduction in the cadmium content of the kidney. The closely related dithiols sodium 2,3-dimercaptopropane-1-sulfonate and 2,3-dimercaptosuccinic acid produced statistically significant increases in the liver cadmium contents, as did N-(2-mercaptopropionyl)-glycine. The reduction in kidney cadmium levels produced by both BAL and NaDDTC was just under 40%.
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