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

Items per page:

1 - 5 of 1070

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

Similar Datasets

Project description:On going efforts are directed at understanding the mutualism between the gut microbiota and the host in breast-fed versus formula-fed infants. Due to the lack of tissue biopsies, no investigators have performed a global transcriptional (gene expression) analysis of the developing human intestine in healthy infants. As a result, the crosstalk between the microbiome and the host transcriptome in the developing mucosal-commensal environment has not been determined. In this study, we examined the host intestinal mRNA gene expression and microbial DNA profiles in full term 3 month-old infants exclusively formula fed (FF) (n=6) or breast fed (BF) (n=6) from birth to 3 months. Host mRNA microarray measurements were performed using isolated intact sloughed epithelial cells in stool samples collected at 3 months. Microbial composition from the same stool samples was assessed by metagenomic pyrosequencing. Both the host mRNA expression and bacterial microbiome phylogenetic profiles provided strong feature sets that clearly classified the two groups of babies (FF and BF). To determine the relationship between host epithelial cell gene expression and the bacterial colony profiles, the host transcriptome and functionally profiled microbiome data were analyzed in a multivariate manner. From a functional perspective, analysis of the gut microbiota's metagenome revealed that characteristics associated with virulence differed between the FF and BF babies. Using canonical correlation analysis, evidence of multivariate structure relating eleven host immunity / mucosal defense-related genes and microbiome virulence characteristics was observed. These results, for the first time, provide insight into the integrated responses of the host and microbiome to dietary substrates in the early neonatal period. Our data suggest that systems biology and computational modeling approaches that integrate “-omic” information from the host and the microbiome can identify important mechanistic pathways of intestinal development affecting the gut microbiome in the first few months of life. KEYWORDS: infant, breast-feeding, infant formula, exfoliated cells, transcriptome, metagenome, multivariate analysis, canonical correlation analysis 12 samples, 2 groups