The human species is dependent for its survival upon the activities of billions of microorganisms that inhabit multiple environmental niches within and on the human body. The Human Microbiome Project (HMP) is an NIH Roadmap program designed to collect unprecedented amounts of data about the complexity of human microbial communities. The data will be generated by multiple HMP sequencing centers. To ensure that the data is maximally useful, a Data Analysis and Coordination Center (DACC) will be formed. This task will be accomplished via a multi-instiutional collaboration between five research groups with a history of close interactions, and extensive experience in a range of disciplines relevant to this project. The leaders of the five groups are: (i) Owen White, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD;(ii) Victor Markowitz, Lawrence Berkeley National Lab, Berkeley, CA;(iii) Nikos Kyrpides, DOE-Joint Genome Institute (JGI) Walnut Creek, CA;(iv) Rob Knight, Department of Chemistry and Biochemistry, University of Colorado, Boulder CO;(v) Gary Anderson, Lawrence Berkeley National Laboratory, Berkeley, CA. Construction of the DACC will be accomplished through these four specific aims: 1. Creation of a Human Microbiome Data Store (HMDS) which will contain all data collected from the HMP centers organized through standardized formats, controlled vocabularies, a Human Microbiome Project Catalog (HMPC) tracking system, and links to Standard Operating Procedures (SOPs). 2. Development of a Comprehensive Computational Analysis Pipeline which will consist of an initial core set of elements and will be expanded over time as new tools useful to metagenomic anlaysis are developed either at the DACC or elsewhere. 3. Development of a Data Integration and Analysis System (DAIS) to support Web-Based Analysis and which will employ numerous data reduction and integration systems as well as numerouse data exploration tools that will be based on similar existing resources such as those found in IMG and IMG/M. 4. Engage in community outreach and training via surveys of target user groups, workshops at relevant conferences, onsite training courses, and online tutorials and seminars.
The information generated from the HMP project will shed light on the complex communities that inhabit the human host. The importance of this cannot be overemphasized given the growing evidence of microbiotic influence upon human development, physiology, disease progression, immunity, and nutrition. The success of the HMP depends on the DACC to provide the specialized data management and analysis infrastructure which will facilitate discoveries about the microbiome that will lead to improvements in human health.
| Sinha, Rashmi; Abu-Ali, Galeb; Vogtmann, Emily et al. (2017) Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat Biotechnol 35:1077-1086 |
| Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali et al. (2017) Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550:61-66 |
| Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal et al. (2017) Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5:27 |
| Weiss, Sophie; Van Treuren, Will; Lozupone, Catherine et al. (2016) Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J 10:1669-81 |
| Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie et al. (2016) Microbial community assembly and metabolic function during mammalian corpse decomposition. Science 351:158-62 |
| Weiss, Sophie; Carter, David O; Metcalf, Jessica L et al. (2016) Carcass mass has little influence on the structure of gravesoil microbial communities. Int J Legal Med 130:253-63 |
| Markowitz, Victor M; Chen, I-Min A; Chu, Ken et al. (2014) IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res 42:D568-73 |
| Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio et al. (2014) Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J 8:1464-75 |
| Huttenhower, Curtis; Knight, Rob; Brown, C Titus et al. (2014) Advancing the microbiome research community. Cell 159:227-30 |
| Dorrestein, Pieter C; Mazmanian, Sarkis K; Knight, Rob (2014) Finding the missing links among metabolites, microbes, and the host. Immunity 40:824-32 |
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