OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients
Abstract The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enri...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-04-01
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| Series: | npj Biofilms and Microbiomes |
| Online Access: | https://doi.org/10.1038/s41522-025-00692-z |
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| author | Jinhui Yuan Boyan Sun Murong Li Congyi Yang Lingqiang Zhang Ning Chen Feng Chen Leyuan Li |
| author_facet | Jinhui Yuan Boyan Sun Murong Li Congyi Yang Lingqiang Zhang Ning Chen Feng Chen Leyuan Li |
| author_sort | Jinhui Yuan |
| collection | DOAJ |
| description | Abstract The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enriching bacterial cells from oral samples (such as saliva and mouth rinse) rich in host proteins is challenging. Here, we present an Optimized Salivary MetaProteomic sample analysis workflow (OSaMPle) to enrich salivary bacteria and reduce host-derived interferences for in-depth analysis of the oral metaproteome. Compared to a conventional approach, OSaMPle improved the identification of bacterial peptides and proteins by 3.2 folds and 1.7 folds, respectively. Furthermore, applying OSaMPle to analyze mouth rinse samples from IBD patients revealed significant alterations in bacterial protein expressions under disease conditions. Specifically, proteins involved in the fatty acid elongation pathway in Peptostreptococcus were significantly less abundant in IBD patients, whereas proteins associated with the TCA cycle in Neisseria were significantly more abundant. The OSaMPle workflow is capable of processing small-volume oral samples and adaptable to high-throughput automation. It holds promise as a strategy for investigating the functional responses of oral microbiomes under disease conditions and identifying disease-associated microbes with their proteins, providing critical insights for detecting disease-related biomarkers within the oral microbiome. |
| format | Article |
| id | doaj-art-2737f2935f32464b81aebfbf3d40e651 |
| institution | OA Journals |
| issn | 2055-5008 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Biofilms and Microbiomes |
| spelling | doaj-art-2737f2935f32464b81aebfbf3d40e6512025-08-20T02:30:20ZengNature Portfolionpj Biofilms and Microbiomes2055-50082025-04-0111111410.1038/s41522-025-00692-zOSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patientsJinhui Yuan0Boyan Sun1Murong Li2Congyi Yang3Lingqiang Zhang4Ning Chen5Feng Chen6Leyuan Li7State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsCentral Laboratory, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical DevicesDepartment of Gastroenterology, Peking University People’s HospitalState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsDepartment of Gastroenterology, Peking University People’s HospitalCentral Laboratory, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical DevicesState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsAbstract The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enriching bacterial cells from oral samples (such as saliva and mouth rinse) rich in host proteins is challenging. Here, we present an Optimized Salivary MetaProteomic sample analysis workflow (OSaMPle) to enrich salivary bacteria and reduce host-derived interferences for in-depth analysis of the oral metaproteome. Compared to a conventional approach, OSaMPle improved the identification of bacterial peptides and proteins by 3.2 folds and 1.7 folds, respectively. Furthermore, applying OSaMPle to analyze mouth rinse samples from IBD patients revealed significant alterations in bacterial protein expressions under disease conditions. Specifically, proteins involved in the fatty acid elongation pathway in Peptostreptococcus were significantly less abundant in IBD patients, whereas proteins associated with the TCA cycle in Neisseria were significantly more abundant. The OSaMPle workflow is capable of processing small-volume oral samples and adaptable to high-throughput automation. It holds promise as a strategy for investigating the functional responses of oral microbiomes under disease conditions and identifying disease-associated microbes with their proteins, providing critical insights for detecting disease-related biomarkers within the oral microbiome.https://doi.org/10.1038/s41522-025-00692-z |
| spellingShingle | Jinhui Yuan Boyan Sun Murong Li Congyi Yang Lingqiang Zhang Ning Chen Feng Chen Leyuan Li OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients npj Biofilms and Microbiomes |
| title | OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients |
| title_full | OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients |
| title_fullStr | OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients |
| title_full_unstemmed | OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients |
| title_short | OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients |
| title_sort | osample workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients |
| url | https://doi.org/10.1038/s41522-025-00692-z |
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