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Bacterial Metatranscriptomics from Human Tissues to Resolve Contributions of Host and Microbial Pathways to Health and Disease

Award Number: R01DK149061
ORGANIZATION: NATIONAL INSTITUTE OF DIABETES & DIGESTIVE & KIDNEY DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/21/2026
PERIOD OF PERFORMANCE END DATE: 06/30/2030

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Bacterial Metatranscriptomics from Human Tissues to Resolve Contributions of Host and Microbial Pathways to Health and Disease - PROJECT SUMMARY Tissue-associated microbes play fundamental roles in human health and disease, shaping host immunity, barrier integrity, and metabolism. Although DNA-level analyses are beginning to shed light on some aspects of the roles these tissue microbes may play, understanding their true functional significance of host-microbe interactions requires insights at the gene-expression (RNA) level. However, obtaining these RNA-level insights on microbes in human tissues has been a formidable challenge because bacterial RNAs are unstable and represent <0.1 % of total nucleic acids in tissue, their fragile expression profiles are distorted by standard processing, and the field lacks tools for rigorous and reproducible analysis of low-abundance microbes. Thus, many questions are left unanswered regarding the molecular mechanism of host-microbe interactions – particularly in complex diseases. For example, perianal Crohn’s disease (pCD) is a chronic, debilitating inflammatory bowel disease with no cure and no preventive strategies. Immune and microbial factors are strongly implicated in pCD pathogenesis, but previous studies struggled to define the drivers of pCD, and none have simultaneously investigated gene expression of the host and microbes directly in tissues from pCD patients. This technology-development R01 aims to overcome the current barriers to performing rigorous and reproducible simultaneous analyses of human and microbial gene expression by developing T-BEAM (Tissue‑associated Bacteria Enrichment for Analysis by Metatranscriptomics), a tool for stabilizing bacterial and host RNA, removing >99.9% host nucleic acids, and simultaneously capturing microbial and host transcriptomes from a single biopsy. We have three Specific Aims: Aim 1: Optimize T‑BEAM in germ‑free tissues spiked with defined bacterial communities to establish conditions that (i) preserve bacterial transcriptional profiles, (ii) reduce host nucleic acids >1,000-fold, and (iii) retain bacterial RNA. Aim 2: Rigorously validate and determine limits of detection and quantification for T‑BEAM in vivo using (i) a monocolonized model and (ii) the human‑relevant hCom2 bacterial consortium. Aim 3: Apply T‑BEAM to biopsies from patients with subclinical pCD (and matched controls) to identify microbial and host genes and pathways that are unique to subclinical pCD and that predict radiological progression of subclinical pCD. This final aim demonstrates the clinical feasibility of the technology and will produce the first experimentally validated set of microbial and host genes and pathways whose joint expression patterns are associated with earliest, actionable stage of pCD. Ultimately, T-BEAM will advance human health by producing validated data that will enable—using both human intelligence and artificial intelligence—rigorous, reproducible RNA-level analyses of both microbes and the host in human tissues. Such studies are urgently needed to improve diagnostics and therapeutics for the many human diseases with poorly understood tissue-associated microbial contributions.


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 = $661,126 )
2026	2026	CALIFORNIA INSTITUTE OF TECHNOLOGY	1200 E CALIFORNIA BLVD	PASADENA	CA	91125	LOS ANGELES	USA	Diabetes, Digestive, and Kidney Diseases Extramural Research	000	1	8/20/2026	NEW	$661,126
														Subtotal = $661,126

Grand Total All Awards = $661,126

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Bacterial Metatranscriptomics from Human Tissues to Resolve Contributions of Host and Microbial Pathways to Health and Disease

Award Number: R01DK149061

ORGANIZATION: NATIONAL INSTITUTE OF DIABETES & DIGESTIVE & KIDNEY DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/21/2026

PERIOD OF PERFORMANCE END DATE: 06/30/2030

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