1
|
Güven Gülhan Ü, Nikerel E, Çakır T, Erdoğan Sevilgen F, Durmuş S. Species-level identification of enterotype-specific microbial markers for colorectal cancer and adenoma. Mol Omics 2024; 20:397-416. [PMID: 38780313 DOI: 10.1039/d4mo00016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Enterotypes have been shown to be an important factor for population stratification based on gut microbiota composition, leading to a better understanding of human health and disease states. Classifications based on compositional patterns will have implications for personalized microbiota-based solutions. There have been limited enterotype based studies on colorectal adenoma and cancer. Here, an enterotype-based meta-analysis of fecal shotgun metagenomic studies was performed, including 1579 samples of healthy controls (CTR), colorectal adenoma (ADN) and colorectal cancer (CRC) in total. Gut microbiota of healthy people were clustered into three enterotypes (Ruminococcus-, Bacteroides- and Prevotella-dominated enterotypes). Reference-based enterotype assignments were performed for CRC and ADN samples, using the supervised machine learning algorithm, K-nearest neighbors. Differential abundance analyses and random forest classification were conducted on each enterotype between healthy controls and CRC-ADN groups, revealing novel enterotype-specific microbial markers for non-invasive CRC screening strategies. Furthermore, we identified microbial species unique to each enterotype that play a role in the production of secondary bile acids and short-chain fatty acids, unveiling the correlation between cancer-associated gut microbes and dietary patterns. The enterotype-based approach in this study is promising in elucidating the mechanisms of differential gut microbiome profiles, thereby improving the efficacy of personalized microbiota-based solutions.
Collapse
Affiliation(s)
- Ünzile Güven Gülhan
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, TR 34755, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Fatih Erdoğan Sevilgen
- The Institute for Data Science & Artificial Intelligence, Boğaziçi University, Istanbul, TR 34342, Turkey
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Saliha Durmuş
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| |
Collapse
|
2
|
Xiong J, Shi Z. Editorial: Environments-pathogens-the gut microbiota and host diseases. Front Microbiol 2024; 14:1357125. [PMID: 38260887 PMCID: PMC10800979 DOI: 10.3389/fmicb.2023.1357125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Affiliation(s)
- Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zunji Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| |
Collapse
|
3
|
Ruiz-Saavedra S, Arboleya S, Nogacka AM, González del Rey C, Suárez A, Diaz Y, Gueimonde M, Salazar N, González S, de los Reyes-Gavilán CG. Commensal Fecal Microbiota Profiles Associated with Initial Stages of Intestinal Mucosa Damage: A Pilot Study. Cancers (Basel) 2023; 16:104. [PMID: 38201530 PMCID: PMC10778549 DOI: 10.3390/cancers16010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Progressive intestinal mucosal damage occurs over years prior to colorectal cancer (CRC) development. The endoscopic screening of polyps and histopathological examination are used clinically to determine the risk and progression of mucosal lesions. We analyzed fecal microbiota compositions using 16S rRNA gene-based metataxonomic analyses and the levels of short-chain fatty acids (SCFAs) using gas chromatography in volunteers undergoing colonoscopy and histopathological analyses to determine the microbiota shifts occurring at the early stages of intestinal mucosa alterations. The results were compared between diagnosis groups (nonpathological controls and polyps), between samples from individuals with hyperplastic polyps or conventional adenomas, and between grades of dysplasia in conventional adenomas. Some microbial taxa from the Bacillota and Euryarchaeota phyla were the most affected when comparing the diagnosis and histopathological groups. Deeper microbiota alterations were found in the conventional adenomas than in the hyperplastic polyps. The Ruminococcus torques group was enriched in both the hyperplastic polyps and conventional adenomas, whereas the family Eggerthellaceae was enriched only in the hyperplastic polyps. The abundance of Prevotellaceae, Oscillospiraceae, Methanobacteriaceae, Streptococcaceae, Christensenellaceae, Erysipelotrichaceae, and Clostridiaceae shifted in conventional adenomas depending on the grade of dysplasia, without affecting the major SCFAs. Our results suggest a reorganization of microbial consortia involved in gut fermentative processes.
Collapse
Affiliation(s)
- Sergio Ruiz-Saavedra
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.R.-S.); (S.A.); (A.M.N.); (M.G.); (N.S.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.R.-S.); (S.A.); (A.M.N.); (M.G.); (N.S.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Alicja M. Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.R.-S.); (S.A.); (A.M.N.); (M.G.); (N.S.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Carmen González del Rey
- Department of Anatomical Pathology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain;
| | - Adolfo Suárez
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Digestive Service, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain
| | - Ylenia Diaz
- Digestive Service, Carmen and Severo Ochoa Hospital, 33819 Cangas del Narcea, Spain;
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.R.-S.); (S.A.); (A.M.N.); (M.G.); (N.S.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.R.-S.); (S.A.); (A.M.N.); (M.G.); (N.S.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Sonia González
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain
| | - Clara G. de los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (S.R.-S.); (S.A.); (A.M.N.); (M.G.); (N.S.)
- Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| |
Collapse
|