Metaproteomic portrait of the healthy human gut microbiota
Abstract Gut metaproteomics can provide direct evidence of microbial functions actively expressed in the colonic environments, contributing to clarify the role of the gut microbiota in human physiology. In this study, we re-analyzed 10 fecal metaproteomics datasets of healthy individuals from differ...
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Nature Portfolio
2024-06-01
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| Series: | npj Biofilms and Microbiomes |
| Online Access: | https://doi.org/10.1038/s41522-024-00526-4 |
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| author | Alessandro Tanca Antonio Palomba Giovanni Fiorito Marcello Abbondio Daniela Pagnozzi Sergio Uzzau |
| author_facet | Alessandro Tanca Antonio Palomba Giovanni Fiorito Marcello Abbondio Daniela Pagnozzi Sergio Uzzau |
| author_sort | Alessandro Tanca |
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| description | Abstract Gut metaproteomics can provide direct evidence of microbial functions actively expressed in the colonic environments, contributing to clarify the role of the gut microbiota in human physiology. In this study, we re-analyzed 10 fecal metaproteomics datasets of healthy individuals from different continents and countries, with the aim of identifying stable and variable gut microbial functions and defining the contribution of specific bacterial taxa to the main metabolic pathways. The “core” metaproteome included 182 microbial functions and 83 pathways that were identified in all individuals analyzed. Several enzymes involved in glucose and pyruvate metabolism, along with glutamate dehydrogenase, acetate kinase, elongation factors G and Tu and DnaK, were the proteins with the lowest abundance variability in the cohorts under study. On the contrary, proteins involved in chemotaxis, response to stress and cell adhesion were among the most variable functions. Random-effect meta-analysis of correlation trends between taxa, functions and pathways revealed key ecological and molecular associations within the gut microbiota. The contribution of specific bacterial taxa to the main biological processes was also investigated, finding that Faecalibacterium is the most stable genus and the top contributor to anti-inflammatory butyrate production in the healthy gut microbiota. Active production of other mucosal immunomodulators facilitating host tolerance was observed, including Roseburia flagellin and lipopolysaccharide biosynthetic enzymes expressed by members of Bacteroidota. Our study provides a detailed picture of the healthy human gut microbiota, contributing to unveil its functional mechanisms and its relationship with nutrition, immunity, and environmental stressors. |
| format | Article |
| id | doaj-art-3b13d4b79e8a4872a278dff92c29067f |
| institution | Kabale University |
| issn | 2055-5008 |
| language | English |
| publishDate | 2024-06-01 |
| publisher | Nature Portfolio |
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| series | npj Biofilms and Microbiomes |
| spelling | doaj-art-3b13d4b79e8a4872a278dff92c29067f2025-01-05T12:10:08ZengNature Portfolionpj Biofilms and Microbiomes2055-50082024-06-0110111210.1038/s41522-024-00526-4Metaproteomic portrait of the healthy human gut microbiotaAlessandro Tanca0Antonio Palomba1Giovanni Fiorito2Marcello Abbondio3Daniela Pagnozzi4Sergio Uzzau5Department of Biomedical Sciences, University of SassariPorto Conte Ricerche, Science and Technology Park of SardiniaClinical Bioinformatic Unit, IRCCS Istituto Giannina GasliniDepartment of Biomedical Sciences, University of SassariPorto Conte Ricerche, Science and Technology Park of SardiniaDepartment of Biomedical Sciences, University of SassariAbstract Gut metaproteomics can provide direct evidence of microbial functions actively expressed in the colonic environments, contributing to clarify the role of the gut microbiota in human physiology. In this study, we re-analyzed 10 fecal metaproteomics datasets of healthy individuals from different continents and countries, with the aim of identifying stable and variable gut microbial functions and defining the contribution of specific bacterial taxa to the main metabolic pathways. The “core” metaproteome included 182 microbial functions and 83 pathways that were identified in all individuals analyzed. Several enzymes involved in glucose and pyruvate metabolism, along with glutamate dehydrogenase, acetate kinase, elongation factors G and Tu and DnaK, were the proteins with the lowest abundance variability in the cohorts under study. On the contrary, proteins involved in chemotaxis, response to stress and cell adhesion were among the most variable functions. Random-effect meta-analysis of correlation trends between taxa, functions and pathways revealed key ecological and molecular associations within the gut microbiota. The contribution of specific bacterial taxa to the main biological processes was also investigated, finding that Faecalibacterium is the most stable genus and the top contributor to anti-inflammatory butyrate production in the healthy gut microbiota. Active production of other mucosal immunomodulators facilitating host tolerance was observed, including Roseburia flagellin and lipopolysaccharide biosynthetic enzymes expressed by members of Bacteroidota. Our study provides a detailed picture of the healthy human gut microbiota, contributing to unveil its functional mechanisms and its relationship with nutrition, immunity, and environmental stressors.https://doi.org/10.1038/s41522-024-00526-4 |
| spellingShingle | Alessandro Tanca Antonio Palomba Giovanni Fiorito Marcello Abbondio Daniela Pagnozzi Sergio Uzzau Metaproteomic portrait of the healthy human gut microbiota npj Biofilms and Microbiomes |
| title | Metaproteomic portrait of the healthy human gut microbiota |
| title_full | Metaproteomic portrait of the healthy human gut microbiota |
| title_fullStr | Metaproteomic portrait of the healthy human gut microbiota |
| title_full_unstemmed | Metaproteomic portrait of the healthy human gut microbiota |
| title_short | Metaproteomic portrait of the healthy human gut microbiota |
| title_sort | metaproteomic portrait of the healthy human gut microbiota |
| url | https://doi.org/10.1038/s41522-024-00526-4 |
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