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@ARTICLE{ValdsMas:298168,
      author       = {R. Valdés-Mas and A. Leshem and D. Zheng and Y. Cohen and
                      L. Kern and N. Zmora and Y. He and C. Katina and S.
                      Eliyahu-Miller and T. Yosef-Hevroni and L. Richman and B.
                      Raykhel and S. Allswang and R. Better and M. Shmueli and A.
                      Saftien$^*$ and N. Cullin$^*$ and F. Slamovitz and D. Ciocan
                      and K. S. Ouyang$^*$ and U. Mor and M. Dori-Bachash and S.
                      Molina and Y. Levin and K. Atarashi and G. Jona and J.
                      Puschhof$^*$ and A. Harmelin and N. Stettner and M. Chen and
                      J. Suez and K. Honda and W. Lieb and C. Bang and M. Kori and
                      N. Maharshak and Y. Merbl and O. Shibolet and Z. Halpern and
                      D. S. Shouval and R. Shamir and A. Franke and S. K. Abdeen
                      and H. Shapiro and A. Savidor and E. Elinav$^*$},
      title        = {{M}etagenome-informed metaproteomics of the human gut
                      microbiome, host, and dietary exposome uncovers signatures
                      of health and inflammatory bowel disease.},
      journal      = {Cell},
      volume       = {188},
      number       = {4},
      issn         = {0092-8674},
      address      = {[Cambridge, Mass.]},
      publisher    = {Cell Press},
      reportid     = {DKFZ-2025-00187},
      pages        = {1062-1083.e36},
      year         = {2025},
      note         = {#LA:D480# / 2025 Feb 20;188(4):1062-1083.e36},
      abstract     = {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 and dietary contexts. Implementation of
                      MIM in murine auto-inflammation and in human inflammatory
                      bowel disease (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 nutritional MIM assessment
                      enabled the 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.},
      keywords     = {biomarker (Other) / diet (Other) / inflammatory bowel
                      disease (Other) / metagenome-informed metaproteomics (Other)
                      / microbiome (Other)},
      cin          = {D480},
      ddc          = {610},
      cid          = {I:(DE-He78)D480-20160331},
      pnm          = {314 - Immunologie und Krebs (POF4-314)},
      pid          = {G:(DE-HGF)POF4-314},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39837331},
      doi          = {10.1016/j.cell.2024.12.016},
      url          = {https://inrepo02.dkfz.de/record/298168},
}