Thursday, June 19, 2025 6/19/2025

A Foundation for the Oral Microbiome and Metagenome

Award Number: R01DE016937
ORGANIZATION: NATIONAL INSTITUTE OF DENTAL AND CRANIOFACIAL RESEARCH
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 04/01/2006
PERIOD OF PERFORMANCE END DATE: 03/31/2026

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A Foundation for the Oral Microbiome and Metagenome - The major objective of the proposed research is to build a foundation of genomic information and resources for the scientific community investigating how the oral microbiome contributes to human health and disease. In prior years of this project we created the expanded Human Oral Microbiome Database (eHOMD), a web accessible taxonomic and genomic database with taxon descriptions and microbiome analysis tools. We cultivated reference strains for previously uncultured oral & nasal bacteria to facilitate in vivo and in vitro experimentation, and we leveraged the sequencing power of the Human Microbiome Project as well as our laboratory's sequencing facility to generate genome sequences for the majority of oral microbial taxa. In the proposed project period, our goal is to fill in the major remaining gaps that present a barrier to full realization of the potential of `omics technologies to drive discoveries in oral microbiology. Our strategy involves three specific aims. The first Aim encompasses improvements to eHOMD itself, including a significant expansion of eHOMD to include the viruses that infect oral & nasal microbes. To allow investigators to do more rigorous microbiome research in mice, a Mouse Oral Microbiome Database (MOMD) will be released so that investigators can accurately document the composition of their mice's oral microbiome. Completion of this aim will allow investigators to link phenotypic, clinical, genomic and bibliographic information to precisely-defined bacterial and phage taxa. The Second Aim addresses the fact that nearly one-third of the 771 eHOMD bacterial taxa have no known cultivated isolates. We will bring into cultivation strains of oral bacteria that are currently refractory to cultivation and make these strains available to the research community. For bacteria that are only sporadically abundant we will use information on abundance of uncultivated bacteria in 20 subjects to guide sampling efforts, and for bacteria that are common but difficult to grow we will use co-cultivation approaches that we have previously employed successfully to isolate and grow 30 strains of the previously uncultivable Saccharibacteria. In the third Aim we will obtain genome sequences for eHOMD taxa currently lacking genome information. Using long-read sequencing we will produce closed genomes of cultivable strains, including strains isolated in Aim 2. To provide genome coverage for remaining uncultivable taxa, we will add high quality Metagenome-Assembled Genomes (MAGs) to eHOMD. Successful completion of the three Aims of this project will increase the genomic coverage of oral and nasal taxa to the point where eHOMD is an exemplary reference database that enables studies using metagenomics, transcriptomics, proteomics, and metabolomics to understand the interactions of oral microbes with one another and with their host. The genome information, tools, and strains generated by this project will serve as a permanent foundation and resource for investigations on the role of the oral microbiome in human health and disease.


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: 2025 ( Subtotal = $1,200,286 )
2025	2025	ADA FORSYTH INSTITUTE, INC.	245 1ST ST 17TH FLOOR	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	000	20	3/10/2025	NON-COMPETING CONTINUATION	$1,080,257
2025	2025	ADA FORSYTH INSTITUTE, INC.	245 1ST ST 17TH FLOOR	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	001	20	5/8/2025	NON-COMPETING CONTINUATION	$120,029
														Subtotal = $1,200,286

Issue Date FY: 2024 ( Subtotal = $1,181,303 )
2024	2024	ADA FORSYTH INSTITUTE, INC.	245 1ST ST 17TH FLOOR	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	000	19	4/19/2024	NON-COMPETING CONTINUATION	$1,084,871
2024	2024	ADA FORSYTH INSTITUTE, INC.	245 1ST ST 17TH FLOOR	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	001	19	6/18/2024	NON-COMPETING CONTINUATION	$96,432
														Subtotal = $1,181,303

Issue Date FY: 2023 ( Subtotal = $1,573,114 )
2023	2023	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	000	18	3/1/2023	NON-COMPETING CONTINUATION	$1,255,465
2023	2023	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	001	18	9/20/2023	SUPPLEMENT FOR EXPANSION	$317,649
														Subtotal = $1,573,114

Issue Date FY: 2022 ( Subtotal = $1,678,271 )
2022	2022	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	002	17	4/22/2022	NON-COMPETING CONTINUATION	$116,834
2022	2022	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	003	17	8/24/2022	NON-COMPETING CONTINUATION	$0
2022	2022	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	001	17	3/23/2022	NON-COMPETING CONTINUATION	$1,168,314
2022	2021	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	000	16	10/17/2021	COMPETING CONTINUATION	$393,123
														Subtotal = $1,678,271

Issue Date FY: 2021 ( Subtotal = $1,413,241 )
2021	2021	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	003	16	9/24/2021	COMPETING CONTINUATION	-$441,482
2021	2021	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	002	16	8/11/2021	SUPPLEMENT FOR EXPANSION	$488,025
2021	2021	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	000	16	3/8/2021	COMPETING CONTINUATION	$925,216
2021	2021	FORSYTH DENTAL INFIRMARY FOR CHILDREN	245 FIRST ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Oral Diseases and Disorders Research	001	16	8/7/2021	COMPETING CONTINUATION	$441,482
														Subtotal = $1,413,241

Issue Date FY: 2011 ( Subtotal = $873,321 )
2011	2011	Forsyth Dental Infirmary for Children Forsyth Institute	140 FENWAY	BOSTON	MA	02115	SUFFOLK	USA	Oral Diseases and Disorders Research	000	6	2/28/2011	COMPETING CONTINUATION	$866,484
2011	2011	Forsyth Dental Infirmary for Children Forsyth Institute	140 FENWAY	BOSTON	MA	02115	SUFFOLK	USA	Oral Diseases and Disorders Research	001	6	3/31/2011	COMPETING CONTINUATION	$6,837
														Subtotal = $873,321

Grand Total All Awards = $7,919,536

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A Foundation for the Oral Microbiome and Metagenome

Award Number: R01DE016937

ORGANIZATION: NATIONAL INSTITUTE OF DENTAL AND CRANIOFACIAL RESEARCH

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 04/01/2006

PERIOD OF PERFORMANCE END DATE: 03/31/2026

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