Dataset Information

Simultaneous metagenome-informed metaproteomics of the human gut microbiome, host and dietary exposome uncover functional interactomes in health & IBD

ABSTRACT: Host-microbiome-dietary interactions play crucial roles in regulating human health, yet direct functional assessment of their interplays, cross-regulations and downstream disease impacts remains challenging. We adopted metagenome-informed metaproteomics (MIM), in both mice and humans, to simultaneously explore host, dietary, and species-level microbiome interactions across diverse scenarios, including commensal and pathogen colonization, nutritional modifications, and antibiotic-induced perturbations. Implementation of MIM in murine auto-inflammation and in human IBD characterized a ‘compositional dysbiosis’ and a concomitant, species-specific ‘functional dysbiosis’ driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutrient assessment enabled determination of IBD-related consumption patterns, dietary treatment compliance and small-intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology, while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Gut Metagenome Mus Musculus (mouse)

TISSUE(S): Colon, Feces, Ileum

DISEASE(S): Crohn's Disease,Ulcerative Colitis,Inflammatory Bowel Disease

SUBMITTER: Rafael Valdes-Mas

LAB HEAD: Eran Elinav

PROVIDER: PXD057701 | Pride | 2025-08-08

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	CHECKSUM.txt	Txt
	DSS_ProteinGroups.dat.txt	Txt
	EX1_EE_16035_100_706_1_2_02052022.raw	Raw
	EX1_EE_16035_101_706_1_3_28042022.raw	Raw
	EX1_EE_16035_102_706_1_4_04052022.raw	Raw

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Publications

Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.

Valdés-Mas Rafael R Leshem Avner A Zheng Danping D Cohen Yotam Y Kern Lara L Zmora Niv N He Yiming Y Katina Corine C Eliyahu-Miller Shimrit S Yosef-Hevroni Tal T Richman Liron L Raykhel Barbara B Allswang Shira S Better Reut R Shmueli Merav M Saftien Aurelia A Cullin Nyssa N Slamovitz Fernando F Ciocan Dragos D Ouyang Kyanna S KS Mor Uria U Dori-Bachash Mally M Molina Shahar S Levin Yishai Y Atarashi Koji K Jona Ghil G Puschhof Jens J Harmelin Alon A Stettner Noa N Chen Minhu M Suez Jotham J Honda Kenya K Lieb Wolfgang W Bang Corinna C Kori Michal M Maharshak Nitsan N Merbl Yifat Y Shibolet Oren O Halpern Zamir Z Shouval Dror S DS Shamir Raanan R Franke Andre A Abdeen Suhaib K SK Shapiro Hagit H Savidor Alon A Elinav Eran E

Cell 20250120 4

Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical ...[more]

PMID: 39837331

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