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Methods for microbiome compositional data

Award Number: R01GM144351
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 03/01/2022
PERIOD OF PERFORMANCE END DATE: 11/30/2026

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Methods for microbiome compositional data - Project Summary The broad and long-term objective of this project concerns the development of novel quantitative methods and biostatistical tools for microbiome data analytics to aid in microbiome-based discovery sciences. The microbiome, also called the second genome of the human, has received much attention in the past few years. Due to its critical roles in human health and disease, the human microbiome has now been recognized as an integral part of the individualized medicine approach because it not only accounts for inter-individual variability in all aspects of a disease but also represents a potentially modifiable factor that is amenable to targeting by therapeutics. Despite those fruitful and promising findings from microbiome studies, there is no consensus in the current field as how to appropriately analyze the data, let alone the optimality and efficiency issues that have yet to be addressed. Several challenges amount to this predicament, including complex experimental designs of microbiome studies, an unknown interplay between microbiome and host, extremely sparsity and high dimensionality of the data, phylogenetic relatedness of the microbial taxa, and compositional structure of microbiome. As a result, although quite a few analytical methods and tools have been developed for microbiome data analysis, several specific gaps exist in the methodological toolbox, hindering the advance of microbiome-based biomedical sciences. To fill these gaps, this proposal aims to develop robust and powerful quantitative methods and tools for microbiome data analysis. Specifically, Aim 1 focuses on developing robust and powerful methods for differential abundance analysis in complex study designs. It will develop new methods to address zero-inflation, compositional effects and correlations in microbiome data. Aim 2 focuses on strategies to increase the power of microbiome-wide multiple testing. It proposes two new multiple testing procedures, which address confounders and phylogenetic relatedness, respectively. Aim 3 proposes to develop compositional canonical correlation analysis methods for integrating microbiome data with other omics data. Specifically, it will develop an efficient and flexible framework for integrating heterogeneous omics data with microbiome data, accounting for compositional effects and phylogenetic relatedness. Aim 4 will develop user-friendly and efficient software packages so the community can benefit maximally from methodological and scientific advances resulting from this application. The proposed methods will be evaluated using simulations, and more importantly, applications to several ongoing microbiome studies in the Center of Individualized Medicine at Mayo Clinic. The proposed quantitative methods and open-source software packages will contribute to microbiome biomarker discovery and microbiome-based mechanistic studies. All methods and tools developed under this grant will be made available free of charge to interested researchers and the public.


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 = $295,088 )
2026	2026	MAYO CLINIC	200 1ST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	000	5	1/15/2026	NON-COMPETING CONTINUATION	$295,088
														Subtotal = $295,088

Issue Date FY: 2025 ( Subtotal = $327,870 )
2025	2025	MAYO CLINIC	200 1ST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	001	4	8/6/2025	NON-COMPETING CONTINUATION	$32,787
2025	2025	MAYO CLINIC	200 1ST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	000	4	12/20/2024	NON-COMPETING CONTINUATION	$295,083
														Subtotal = $327,870

Issue Date FY: 2024 ( Subtotal = $327,860 )
2024	2024	MAYO CLINIC	200 1ST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	001	3	6/18/2024	NON-COMPETING CONTINUATION	$32,787
2024	2024	MAYO CLINIC	200 1ST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	000	3	12/22/2023	NON-COMPETING CONTINUATION	$295,073
														Subtotal = $327,860

Issue Date FY: 2023 ( Subtotal = $321,940 )
2023	2023	MAYO CLINIC	200 FIRST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	001	2	2/16/2023	NON-COMPETING CONTINUATION	$32,195
2023	2023	MAYO CLINIC	200 FIRST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	000	2	12/1/2022	NON-COMPETING CONTINUATION	$289,745
														Subtotal = $321,940

Issue Date FY: 2022 ( Subtotal = $336,579 )
2022	2022	MAYO CLINIC	200 FIRST ST SW	ROCHESTER	MN	55905	OLMSTED	USA	Biomedical Research and Research Training	000	1	2/28/2022	NEW	$336,579
														Subtotal = $336,579

Grand Total All Awards = $1,609,337

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Methods for microbiome compositional data

Award Number: R01GM144351

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 03/01/2022

PERIOD OF PERFORMANCE END DATE: 11/30/2026

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