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© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host–microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes—active ulcerative colitis, or active Crohn’s disease either with ileo-colonic or exclusive colonic localization—differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.

Details

Title
Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups
Author
Henry, Céline 1 ; Bassignani, Ariane 2   VIAFID ORCID Logo  ; Berland, Magali 3 ; Langella, Olivier 4   VIAFID ORCID Logo  ; Sokol, Harry 5 ; Juste, Catherine 6 

 PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected] (C.H.); [email protected] (A.B.); Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected] 
 PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected] (C.H.); [email protected] (A.B.); Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected]; MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected] 
 MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected] 
 PAPPSO, GQE-Le Moulon, AgroParisTech, CNRS, INRAE, Université Paris-Saclay, 91190 Gif-sur-Yvette, France; [email protected] 
 Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected]; Gastroenterology Department, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Sorbonne Université, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Service de Gastro-Entérologie et Nutrition, Hôpital Saint-Antoine, Direction de la Recherche Clinique et de l’Innovation (DRCI) de l’AP-HP, CEDEX 12, 75571 Paris, France 
 Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; [email protected] 
First page
1340
Publication year
2022
Publication date
2022
Publisher
MDPI AG
e-ISSN
20734409
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2652965002
Copyright
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.