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Human Microbiome Compendium: large-scale curation and processing ofhuman microbiome datasets

Award Number: R01LM013863
ORGANIZATION: NATIONAL LIBRARY OF MEDICINE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/15/2022
PERIOD OF PERFORMANCE END DATE: 07/31/2030

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Human Microbiome Compendium: large-scale curation and processing ofhuman microbiome datasets - Project Summary Mounting evidence shows the microbial communities living in (and on) the human body play a key role in the etiology of disease. A major obstacle in the field is the dearth of reliable methods for extracting meaningful signals from small, noisy, intercorrelated, and highly variable microbiome datasets. Enhancing the ability of researchers to generate robust characterizations of the complex relationship between microbiota and their hosts will support novel, more reliable diagnosis of disease and bring the field one step closer to finding the causal links underlying microbiome-based therapeutics. With previous NIH support, we built the Human Microbiome Compendium, the largest integrated dataset of amplicon sequencing data available to date. We propose here to use state-of-the- art machine learning approaches to annotate publicly available microbiome data at an unprecedented level of detail and scale. In addition to expanding the dataset itself with hundreds of thousands of samples, we will standardize metadata across projects and infer additional information about samples using the publications describing them. In addition to making this public data more accessible to others by performing the computationally expensive tasks associated with processing the raw data, these samples will be paired with metadata unavailable from the repositories currently storing the data: Users will be able to characterize samples and projects using standardized terms, plus technical factors and phenotypic information inferred from publications. We propose to evaluate relationships between microbiome composition and host phenotype, organized into a microbial knowledgebase. We will combine these sequencing-based conclusions with host– microbe relationships derived from parsing microbiology literature, using novel annotations and our unmatched sample size to find ecological dynamics that have until now been hidden in the noise. We will also use the compendium to build transfer-learning models that can improve the power of independent microbiome studies by incorporating insights from the compendium. These data and tools will be distributed across multiple channels, including a web application where users will be able to upload data to be evaluated alongside compendium data in real time. The proposed studies will expand the first comprehensive aggregation of the microbiome datasets available via the SRA, generate novel annotations for samples and projects, and provide a new interface for searching NCBI databases for microbiome data using standardized ontologies and compositional information. The resulting compendium will encourage the use of publicly available data and inform new microbiome analysis tools. Results from this study will be a starting point to identification of microbiome biomarkers for disease and the development of novel therapeutic approaches.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $359,883 )
2026	2026	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Medical Library Assistance	000	5	7/1/2026	COMPETING CONTINUATION	$359,883
														Subtotal = $359,883

Issue Date FY: 2025 ( Subtotal = $335,931 )
2025	2025	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Medical Library Assistance	000	4	7/30/2025	NON-COMPETING CONTINUATION	$335,931
														Subtotal = $335,931

Issue Date FY: 2024 ( Subtotal = $335,931 )
2024	2024	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Medical Library Assistance	000	3	7/25/2024	NON-COMPETING CONTINUATION	$335,931
														Subtotal = $335,931

Issue Date FY: 2023 ( Subtotal = $335,931 )
2023	2023	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Medical Library Assistance	000	2	7/20/2023	NON-COMPETING CONTINUATION	$335,931
														Subtotal = $335,931

Issue Date FY: 2022 ( Subtotal = $368,475 )
2022	2022	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Medical Library Assistance	000	1	9/9/2022	NEW	$368,475
														Subtotal = $368,475

Grand Total All Awards = $1,736,151

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Human Microbiome Compendium: large-scale curation and processing ofhuman microbiome datasets

Award Number: R01LM013863

ORGANIZATION: NATIONAL LIBRARY OF MEDICINE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/15/2022

PERIOD OF PERFORMANCE END DATE: 07/31/2030

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