1
|
Conde‐Pérez K, Aja‐Macaya P, Buetas E, Trigo‐Tasende N, Nasser‐Ali M, Rumbo‐Feal S, Nión P, Arribas EM, Estévez LS, Otero‐Alén B, Noguera JF, Concha Á, Pardiñas‐López S, Carda‐Diéguez M, Gómez‐Randulfe I, Martínez‐Lago N, Ladra S, Aparicio LMA, Bou G, Mira Á, Vallejo JA, Poza M. The multispecies microbial cluster of Fusobacterium, Parvimonas, Bacteroides and Faecalibacterium as a precision biomarker for colorectal cancer diagnosis. Mol Oncol 2024; 18:1093-1122. [PMID: 38366793 PMCID: PMC11076999 DOI: 10.1002/1878-0261.13604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/27/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
The incidence of colorectal cancer (CRC) has increased worldwide, and early diagnosis is crucial to reduce mortality rates. Therefore, new noninvasive biomarkers for CRC are required. Recent studies have revealed an imbalance in the oral and gut microbiomes of patients with CRC, as well as impaired gut vascular barrier function. In the present study, the microbiomes of saliva, crevicular fluid, feces, and non-neoplastic and tumor intestinal tissue samples of 93 CRC patients and 30 healthy individuals without digestive disorders (non-CRC) were analyzed by 16S rRNA metabarcoding procedures. The data revealed that Parvimonas, Fusobacterium, and Bacteroides fragilis were significantly over-represented in stool samples of CRC patients, whereas Faecalibacterium and Blautia were significantly over-abundant in the non-CRC group. Moreover, the tumor samples were enriched in well-known periodontal anaerobes, including Fusobacterium, Parvimonas, Peptostreptococcus, Porphyromonas, and Prevotella. Co-occurrence patterns of these oral microorganisms were observed in the subgingival pocket and in the tumor tissues of CRC patients, where they also correlated with other gut microbes, such as Hungatella. This study provides new evidence that oral pathobionts, normally located in subgingival pockets, can migrate to the colon and probably aggregate with aerobic bacteria, forming synergistic consortia. Furthermore, we suggest that the group composed of Fusobacterium, Parvimonas, Bacteroides, and Faecalibacterium could be used to design an excellent noninvasive fecal test for the early diagnosis of CRC. The combination of these four genera would significantly improve the reliability of a discriminatory test with respect to others that use a single species as a unique CRC biomarker.
Collapse
Affiliation(s)
- Kelly Conde‐Pérez
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Pablo Aja‐Macaya
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Elena Buetas
- Genomic and Health Department, FISABIO FoundationCenter for Advanced Research in Public HealthValenciaSpain
| | - Noelia Trigo‐Tasende
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Mohammed Nasser‐Ali
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Soraya Rumbo‐Feal
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Paula Nión
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Elsa Martín‐De Arribas
- Database Laboratory, Research Center for Information and Communication Technologies (CITIC)University of A Coruña (UDC)A CoruñaSpain
| | - Lara S. Estévez
- Pathology Service and BiobankUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Begoña Otero‐Alén
- Pathology Service and BiobankUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - José F. Noguera
- Surgery ServiceUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Ángel Concha
- Pathology Service and BiobankUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Simón Pardiñas‐López
- Periodontology and Oral Surgery, Pardiñas Medical Dental Clinic – Cell Therapy and Regenerative Medicine GroupInstitute of Biomedical Research (INIBIC)A CoruñaSpain
| | - Miguel Carda‐Diéguez
- Genomic and Health Department, FISABIO FoundationCenter for Advanced Research in Public HealthValenciaSpain
| | - Igor Gómez‐Randulfe
- Medical Oncology DepartmentUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | | | - Susana Ladra
- Database Laboratory, Research Center for Information and Communication Technologies (CITIC)University of A Coruña (UDC)A CoruñaSpain
| | - Luis M. A. Aparicio
- Medical Oncology DepartmentUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Germán Bou
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Álex Mira
- Genomic and Health Department, FISABIO FoundationCenter for Advanced Research in Public HealthValenciaSpain
| | - Juan A. Vallejo
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
| | - Margarita Poza
- Microbiome and Health Group (meiGAbiome), Microbiology Research Group, Institute of Biomedical Research (INIBIC) – Interdisciplinary Center for Chemistry and Biology (CICA) – University of A Coruña (UDC) – CIBER de Enfermedades Infecciosas (CIBERINFEC‐ISCIII), Servicio de MicrobiologíaUniversity Hospital of A Coruña (CHUAC)A CoruñaSpain
- Microbiome and Health Group, Faculty of SciencesUniversity of A Coruña (UDC)A CoruñaSpain
| |
Collapse
|
2
|
Zhang L, Feng Z, Li Y, Lv C, Li C, Hu Y, Fu M, Song L. Salivary and fecal microbiota: potential new biomarkers for early screening of colorectal polyps. Front Microbiol 2023; 14:1182346. [PMID: 37655344 PMCID: PMC10467446 DOI: 10.3389/fmicb.2023.1182346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Objective Gut microbiota plays an important role in colorectal cancer (CRC) pathogenesis through microbes and their metabolites, while oral pathogens are the major components of CRC-associated microbes. Multiple studies have identified gut and fecal microbiome-derived biomarkers for precursors lesions of CRC detection. However, few studies have used salivary samples to predict colorectal polyps. Therefore, in order to find new noninvasive colorectal polyp biomarkers, we searched into the differences in fecal and salivary microbiota between patients with colorectal polyps and healthy controls. Methods In this case-control study, we collected salivary and fecal samples from 33 patients with colorectal polyps (CP) and 22 healthy controls (HC) between May 2021 and November 2022. All samples were sequenced using full-length 16S rRNA sequencing and compared with the Nucleotide Sequence Database. The salivary and fecal microbiota signature of colorectal polyps was established by alpha and beta diversity, Linear discriminant analysis Effect Size (LEfSe) and random forest model analysis. In addition, the possibility of microbiota in identifying colorectal polyps was assessed by Receiver Operating Characteristic Curve (ROC). Results In comparison to the HC group, the CP group's microbial diversity increased in saliva and decreased in feces (p < 0.05), but there was no significantly difference in microbiota richness (p > 0.05). The principal coordinate analysis revealed significant differences in β-diversity of salivary and fecal microbiota between the CP and HC groups. Moreover, LEfSe analysis at the species level identified Porphyromonas gingivalis, Fusobacterium nucleatum, Leptotrichia wadei, Prevotella intermedia, and Megasphaera micronuciformis as the major contributors to the salivary microbiota, and Ruminococcus gnavus, Bacteroides ovatus, Parabacteroides distasonis, Citrobacter freundii, and Clostridium symbiosum to the fecal microbiota of patients with polyps. Salivary and fecal bacterial biomarkers showed Area Under ROC Curve of 0.8167 and 0.8051, respectively, which determined the potential of diagnostic markers in distinguishing patients with colorectal polyps from controls, and it increased to 0.8217 when salivary and fecal biomarkers were combined. Conclusion The composition and diversity of the salivary and fecal microbiota were significantly different in colorectal polyp patients compared to healthy controls, with an increased abundance of harmful bacteria and a decreased abundance of beneficial bacteria. A promising non-invasive tool for the detection of colorectal polyps can be provided by potential biomarkers based on the microbiota of the saliva and feces.
Collapse
Affiliation(s)
- Limin Zhang
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Ziying Feng
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yinghua Li
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Cuiting Lv
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Chunchun Li
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yue Hu
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Mingsheng Fu
- Department of Gastroenterology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Liang Song
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| |
Collapse
|
3
|
Valciukiene J, Strupas K, Poskus T. Tissue vs. Fecal-Derived Bacterial Dysbiosis in Precancerous Colorectal Lesions: A Systematic Review. Cancers (Basel) 2023; 15:cancers15051602. [PMID: 36900392 PMCID: PMC10000868 DOI: 10.3390/cancers15051602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Alterations in gut microbiota play a pivotal role in the adenoma-carcinoma sequence. However, there is still a notable lack of the correct implementation of tissue and fecal sampling in the setting of human gut microbiota examination. This study aimed to review the literature and to consolidate the current evidence on the use of mucosa and a stool-based matrix investigating human gut microbiota changes in precancerous colorectal lesions. A systematic review of papers from 2012 until November 2022 published on the PubMed and Web of Science databases was conducted. The majority of the included studies have significantly associated gut microbial dysbiosis with premalignant polyps in the colorectum. Although methodological differences hampered the precise fecal and tissue-derived dysbiosis comparison, the analysis revealed several common characteristics in stool-based and fecal-derived gut microbiota structures in patients with colorectal polyps: simple or advanced adenomas, serrated lesions, and carcinomas in situ. The mucosal samples considered were more relevant for the evaluation of microbiota's pathophysiological involvement in CR carcinogenesis, while non-invasive stool sampling could be beneficial for early CRC detection strategies in the future. Further studies are required to identify and validate mucosa-associated and luminal colorectal microbial patterns and their role in CRC carcinogenesis, as well as in the clinical setting of human microbiota studies.
Collapse
|
4
|
Zhang Z, Bahaji Azami NL, Liu N, Sun M. Research Progress of Intestinal Microecology in the Pathogenesis of Colorectal Adenoma and Carcinogenesis. Technol Cancer Res Treat 2023; 22:15330338221135938. [PMID: 36740990 PMCID: PMC9903042 DOI: 10.1177/15330338221135938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Colorectal adenoma is a precancerous lesion that may progress to colorectal cancer. Patients with colorectal adenoma had a 4-fold higher risk of developing colorectal malignancy than the rest of the population, with approximately 80% of colorectal cancer originating from colorectal adenoma. Therefore, preventing the occurrence and progression of colorectal adenoma is crucial in reducing the risk for colorectal cancer. The human intestinal microecology is a complex system consisting of numerous microbial communities with a sophisticated structure. Interactions among intestinal microorganisms play crucial roles in maintaining normal intestinal structure, digestion, absorption, metabolism, and other functions. The colorectal system is the largest microbial bank or fermentation system in the human body. Studies suggest that intestinal microecological imbalance, one of the most important environmental factors, may play an essential role in the occurrence and development of colorectal adenoma and colorectal cancer. Based on the complexity of studying the gut microbiota ecosystem, its specific role in the occurrence and development of colorectal adenoma is yet to be elucidated. In addition, further studies are expected to provide new insights regarding the prevention and treatment of colorectal adenoma. This article reviews the relationship and mechanism of the diversity of the gut microbiota, the relevant inflammatory response, immune regulation, and metabolic changes in the presence of colorectal adenomas.
Collapse
Affiliation(s)
- Zhipeng Zhang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Nisma Lena Bahaji Azami
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ningning Liu
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Medical Oncology and Cancer Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Ningning Liu, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
Mingyu Sun, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Mingyu Sun
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
5
|
Zwezerijnen-Jiwa FH, Sivov H, Paizs P, Zafeiropoulou K, Kinross J. A systematic review of microbiome-derived biomarkers for early colorectal cancer detection. Neoplasia 2022; 36:100868. [PMID: 36566591 PMCID: PMC9804137 DOI: 10.1016/j.neo.2022.100868] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/24/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Increasing evidence suggests a role of the gut microbiome in the development of colorectal cancer (CRC) and that it can serve as a biomarker for early diagnosis. This review aims to give an overview of the current status of published studies regarding the microbiome as a screening tool for early CRC detection. A literature search was conducted using PubMed and EMBASE in August 2022. Studies assessing the efficacy of microbiome-derived biomarkers based on noninvasive derived samples were included. Not relevant studies or studies not specifying the stage of CRC or grouping them together in the analysis were excluded. The risk of bias for screening tools was performed using the QUADAS-2 checklist. A total of 28 studies were included, ranging from 2 to 462 for CRC and 18 to 665 advanced adenoma patient inclusions, of which only two investigated the co-metabolome as biomarker. The diagnostic performance of faecal bacteria-derived biomarkers had an AUC ranging from 0.28-0.98 for precursor lesions such as advanced adenomas and 0.54-0.89 for early CRC. Diagnostic performance based on the co-metabolome showed an AUC ranging from 0.69 - 0.84 for precursor lesions and 0.65 - 0.93 for early CRC. All models improved when combined with established clinical early detection markers such as gFOBT. A high level of heterogeneity was seen in the number of inclusions and methodology used in the studies. The faecal and oral gut microbiome has the potential to complement existing CRC screening tools, however current evidence suggests that this is not yet ready for routine clinical use.
Collapse
Affiliation(s)
- Florine H. Zwezerijnen-Jiwa
- Department of Surgery and Cancer, St. Mary's Hospital, Imperial College London, London W2 1NY, UK,Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centres, University of Amsterdam, 1105 BK Amsterdam, The Netherlands,Department of Gastroenterology, Amsterdam University Medical Centres, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Hugo Sivov
- Department of Surgery and Cancer, St. Mary's Hospital, Imperial College London, London W2 1NY, UK
| | - Petra Paizs
- Department of Surgery and Cancer, St. Mary's Hospital, Imperial College London, London W2 1NY, UK
| | - Konstantina Zafeiropoulou
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centres, University of Amsterdam, 1105 BK Amsterdam, The Netherlands,Department of Paediatric Surgery, Emma Children's Hospital, Amsterdam University Medical Centres, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - James Kinross
- Department of Surgery and Cancer, St. Mary's Hospital, Imperial College London, London W2 1NY, UK,Corresponding author at: Department of Surgery and Cancer, St. Mary's Hospital, Imperial College London, 10th Floor QEQMW, Praed Street, London, W2 1NY, UK
| |
Collapse
|
6
|
Wang T, Brown NM, McCoy AN, Sandler RS, Keku TO. Omega-3 Polyunsaturated Fatty Acids, Gut Microbiota, Microbial Metabolites, and Risk of Colorectal Adenomas. Cancers (Basel) 2022; 14:4443. [PMID: 36139601 PMCID: PMC9496906 DOI: 10.3390/cancers14184443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/02/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Omega-3 polyunsaturated fatty acids (ω-3 PUFAs) are thought to protect against colorectal adenoma (CRA) development. We aimed to further understand the underlying mechanisms by examining the relationships between ω-3 PUFAs and the gut microbiota on CRAs. We assessed the mucosal microbiota via bacterial 16S rRNA sequencing among 217 CRA cases and 218 controls who completed PUFA intake questionnaires. The overall microbial composition was assessed by α-diversity measurements (diversity, richness, and evenness). Global metabolomics was conducted using a random subset of case−control pairs (n = 50). We compared microbiota and metabolite signatures between cases and controls according to fold change (FC). Odds ratios (OR) and confidence intervals (CI) were estimated from logistic regression for associations of ω-3 PUFAs and the microbiota with CRAs. We observed an inverse association between overall ω-3 PUFA intake and CRAs, especially for short-chain ω -3 PUFAs (OR = 0.45, 95% CI: 0.21, 0.97). Such inverse associations were modified by bacterial evenness (p-interaction = 0.03). Participants with higher levels (FC > 2) of bile acid-relevant metabolites were more likely to have CRAs than the controls, and the correlation between bile acids and bacterial diversity differed by case−control status. Our findings suggest that ω-3 PUFAs are inversely associated with CRA development, and the association may be modified by gut microbiota profiles.
Collapse
Affiliation(s)
- Tengteng Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nicole M. Brown
- Center for Gastrointestinal Disease and Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Amber N. McCoy
- Center for Gastrointestinal Disease and Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert S. Sandler
- Center for Gastrointestinal Disease and Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Temitope O. Keku
- Center for Gastrointestinal Disease and Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
7
|
Reusing a prepaid health plan's fecal immunochemical tests for microbiome associations with colorectal adenoma. Sci Rep 2022; 12:14801. [PMID: 36045142 PMCID: PMC9433441 DOI: 10.1038/s41598-022-18870-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
An altered colonic microbiota probably increases colorectal adenoma (CRA) and cancer (CRC) risk, but large, unbiased fecal collections are needed to examine the relationship of gut microbiota diversity and composition to colorectal carcinogenesis. This study assessed whether fecal immunochemical tests (FITs) from CRA/CRC screening may fulfill this requirement. Using FIT, self-collected by members of Kaiser Permanente Hawaii (KPH), as well as interspersed quality control (QC) specimens, DNA was extracted and amplified to generate 16S rRNA microbiome profiles rarified at 10,000 reads. CRA/CRC were diagnosed by colonoscopy and histopathology. Covariates were from electronic KPH records. Of 921 participants’ FIT devices, 538 (58%) yielded at least 10,000 rRNA reads and 1016 species-level variants mapped to 46 genera. Of the 538 evaluable participants, 63 (11.7%) were FIT-negative per protocol, and they were considered negative for CRA/CRC. Of the 475 FIT + participants, colonoscopy and pathologic review revealed that 8 (1.7%) had CRC, 71 (14.9%) had high-risk CRA, 107 (22.5%) had low-risk CRA, and 289 (60.8%) did not have CRA/CRC. Men were 2.27-fold [95% confidence interval (CI) 1.32–3.91] more likely than women to be FIT+ . Men also had 1.96-fold (CI 1.24–3.07) higher odds of low-risk CRA, with similar trends for high-risk CRA and CRC. CRA/CRC were not associated with overweight, obesity, diabetes, or antibiotic prescriptions in this study. QC analysis across 24 batches of FIT devices revealed QC outliers in four batches. With or without exclusion of the four QC-outlier batches, as well as lenient (1000-read) rarefaction, CRA/CRC had no consistent, statistically significant associations with fecal microbiome alpha diversity, beta diversity or genera relative abundance. CRA/CRC had expected associations with male sex but not with microbiome metrics. Fecal microbiome profiling using DNA extracted from at-home collected, re-used FIT devices is feasible, albeit with substantial challenges. Using FITs for prospective microbiome studies of CRA/CRC risk should consider the impact of the current findings on statistical power and requisite sample sizes.
Collapse
|
8
|
Hou Z, Song F, Xing J, Zheng Z, Liu S, Liu Z. Comprehensive fecal metabolomics and gut microbiota for the evaluation of the mechanism of Panax Ginseng in the treatment of Qi-deficiency liver cancer. JOURNAL OF ETHNOPHARMACOLOGY 2022; 292:115222. [PMID: 35341933 DOI: 10.1016/j.jep.2022.115222] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Qi deficiency liver cancer (QDLC) is an important part of liver cancer research in traditional Chinese medicine (TCM). In the course of its treatment, Panax ginseng is often selected as the main Chinese herbal medicine, and its function has special significance in the tumor treatment of Qi deficiency constitution. However, its mechanism is not clear. AIM OF THE STUDY The research tried to evaluate the mechanism of Panax ginseng in the treatment of QDLC through fecal metabonomics and gut microbiota on the basis of previous pharmacodynamic evaluation. MATERIALS AND METHODS Firstly, biomarkers and related metabolic pathways were screened and identified by metabonomics and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Then, 16S rRNA sequencing technique was used to investigate the composition, β diversity and key differences of gut microbiota. Finally, the relationship among phenotypes, gut microbiota and fecal metabolites was comprehensively analyzed by spearman correlation coefficient. RESULTS 31 pharmacodynamic potential biomarkers and 20 synergistic potential biomarkers of effective parts of Panax ginseng on QDLC were screened and identified by fecal metabonomics. And then, 6 major metabolic pathways were searched, including bile acid biosynthesis, unsaturated fatty acid biosynthesis, tryptophan metabolism, arachidonic acid metabolism, pyrimidine metabolism, vitamin B6 metabolism. In the study of gut microbiota, at the genus level, 25 species of bacteria with significant differences of effective parts on QDLC and 23 species of bacteria with significant differences of synergistic action of ginsenosides and polysaccharides were screened. In addition, Spearman correlation analysis showed that there was a complex potential relationship among phenotype, gut microbiota and fecal metabolites during the development of QDLC and Panax ginseng intervention, which was mainly reflected in the close potential relationship between bacteria and fecal metabolites such as bile acids, unsaturated fatty acids and indole compounds. CONCLUSION Through the changes of fecal endogenous metabolites and intestinal bacteria, the mechanism of Panax ginseng on QDLC were preliminarily clarified.
Collapse
Affiliation(s)
- Zong Hou
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Fengrui Song
- Jilin Provincial Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Junpeng Xing
- Jilin Provincial Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Zhong Zheng
- Jilin Provincial Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Shu Liu
- Jilin Provincial Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| | - Zhiqiang Liu
- Jilin Provincial Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| |
Collapse
|
9
|
Lan J, Chen C, Chen L, Liu P. Intestinal Microflora Provides Biomarkers for Infertile Women with Endometrial Polyps. Biomarkers 2022; 27:579-586. [PMID: 35546106 DOI: 10.1080/1354750x.2022.2077445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Endometrial polyps (EPs) are related to infertility; however, there are no biomarkers for identification. We evaluated changes in the intestinal microflora to identify microflora-based biomarkers that may be useful for detecting EPs. Intestinal specimens were prospectively collected from 100 women: 25 infertile women with EPs (InfEP + group), 25 infertile women without EPs (InfEP- group), and 50 healthy women (Fertile group). The microbiota composition was analyzed using 16S ribosomal RNA gene amplification and the intestinal expression of selected human genes using quantitative reverse transcription polymerase chain reaction. The InfEP + group had higher proportions of Prevotella, Streptococcus, Fusobacterium, Fenollaria, and Porphyromonas than the InfEP- and Fertile groups, while the Fertile group had higher proportions of Faecalibacterium, Bacteroides, and Blautia. We constructed a microbial dysbiosis index based on the intestinal microbiota at the genus level as a predictive model. The most accurate model to predict the presence of EPs was that including the Fertile and InfEP + groups (area under the curve: 0.89, 95% confidence interval: 0.79-0.96). The InfEP- and Fertile groups had significant differences in microflora composition compared with the InfEP + group. The intestinal microflora may be a useful biomarker for identifying EPs in infertile women.
Collapse
Affiliation(s)
- Jun Lan
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Dadao North Road, Baiyun District, Guangzhou City 510000, Guangdong Province, China.,Department of Obstetrics and Gynecology, Maternal and Child Health Hospital of Dong Guan, 99 Zhenxing Road, Dongguan City, Guangdong Province, Dongguan, 523000, China
| | - Chunlin Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Dadao North Road, Baiyun District, Guangzhou City 510000, Guangdong Province, China
| | - Ling Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Dadao North Road, Baiyun District, Guangzhou City 510000, Guangdong Province, China
| | - Ping Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, 1838 Guangzhou Dadao North Road, Baiyun District, Guangzhou City 510000, Guangdong Province, China
| |
Collapse
|
10
|
Zhang SL, Han B, Mao YQ, Zhang ZY, Li ZM, Kong CY, Wu Y, Chen GQ, Wang LS. Lacticaseibacillus paracasei sh2020 induced antitumor immunity and synergized with anti-programmed cell death 1 to reduce tumor burden in mice. Gut Microbes 2022; 14:2046246. [PMID: 35259052 PMCID: PMC8920197 DOI: 10.1080/19490976.2022.2046246] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota was emerging as critical regulatory elements in shaping the outcome of cancer immunotherapy. However, the underlying mechanisms by which the gut commensal species enhance antitumor immunity remain largely unexplored. Here, we show that the gut microbiota from healthy individuals conferred considerable sensitivity to anti-PD-1 in the colorectal cancer (CRC) tumor-bearing mice, whereas gut microbiota from CRC patients failed to do so. By 16S rRNA gene sequencing, we identified Lactobacillus that was significantly increased in the mice with good response to anti-PD-1, and significantly correlated with anti-tumor immunity. After a series of screening, we isolated a novel Lacticaseibacillus strain, named L. paracasei sh2020. L. paracasei sh2020 showed the most notable anti-tumor immunity in the mice with gut dysbiosis. Mechanistically, the antitumor immune response elicited by L. paracasei sh2020 was dependent on CD8+ T cell. In vitro and in vivo studies revealed that L. paracasei sh2020 stimulation triggered the upregulated expression of CXCL10 in the tumors and subsequently enhanced CD8+ T cell recruitment. Meanwhile, the modulation of gut microbiota caused by L. paracasei sh2020 enhanced its antitumor effect and gut barrier function. Overall, our study offered novel insights into the mechanism by which gut microbiota shaped the outcome of cancer immunotherapy and, more importantly, the novel strain L. paracasei sh2020 might serve as an easy and effective way to promote anti-PD-1 effect in clinical practice.
Collapse
Affiliation(s)
- Shi-Long Zhang
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Bing Han
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Yu-Qin Mao
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Zheng-Yan Zhang
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Zhan-Ming Li
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Chao-Yue Kong
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - You Wu
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Guo-Qiang Chen
- State Key Laboratory of Oncogenes and Related Genes, and Chinese Academy of Medical Sciences Research Unit (NO.2019RU043), Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China,Guo-Qiang Chen State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Li-Shun Wang
- Center for Traditional Chinese Medicine and Gut Microbiota, Minhang Hospital, Fudan University, Shanghai, China,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China,CONTACT Li-Shun Wang Center for traditional Chinese medicine and gut microbiota, Minhang hospital, Fudan University201100, Shanghai, China
| |
Collapse
|
11
|
Yu L, Zhao G, Wang L, Zhou X, Sun J, Li X, Zhu Y, He Y, Kofonikolas K, Bogaert D, Dunlop M, Zhu Y, Theodoratou E, Li X. A systematic review of microbial markers for risk prediction of colorectal neoplasia. Br J Cancer 2022; 126:1318-1328. [PMID: 35292756 PMCID: PMC9042911 DOI: 10.1038/s41416-022-01740-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/23/2021] [Accepted: 02/03/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Substantial evidence indicates that dysbiosis of the gut microbial community is associated with colorectal neoplasia. This review aims to systematically summarise the microbial markers associated with colorectal neoplasia and to assess their predictive performance. METHODS A comprehensive literature search of MEDLINE and EMBASE databases was performed to identify eligible studies. Observational studies exploring the associations between microbial biomarkers and colorectal neoplasia were included. We also included prediction studies that constructed models using microbial markers to predict CRC and adenomas. Risk of bias for included observational and prediction studies was assessed. RESULTS Forty-five studies were included to assess the associations between microbial markers and colorectal neoplasia. Nine faecal microbiotas (i.e., Fusobacterium, Enterococcus, Porphyromonas, Salmonella, Pseudomonas, Peptostreptococcus, Actinomyces, Bifidobacterium and Roseburia), two oral pathogens (i.e., Treponema denticola and Prevotella intermedia) and serum antibody levels response to Streptococcus gallolyticus subspecies gallolyticus were found to be consistently associated with colorectal neoplasia. Thirty studies reported prediction models using microbial markers, and 83.3% of these models had acceptable-to-good discrimination (AUROC > 0.75). The results of predictive performance were promising, but most of the studies were limited to small number of cases (range: 9-485 cases) and lack of independent external validation (76.7%). CONCLUSIONS This review provides insight into the evidence supporting the association between different types of microbial species and their predictive value for colorectal neoplasia. Prediction models developed from case-control studies require further external validation in high-quality prospective studies. Further studies should assess the feasibility and impact of incorporating microbial biomarkers in CRC screening programme.
Collapse
Affiliation(s)
- Lili Yu
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gang Zhao
- Center for Disease Control and Prevention of Hangzhou, Hangzhou, China
| | - Lijuan Wang
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuan Zhou
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Sun
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinxuan Li
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingshuang Zhu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yazhou He
- Department of Oncology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Sichuan, China
| | | | - Debby Bogaert
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Yimin Zhu
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| |
Collapse
|
12
|
Smet A, Kupcinskas J, Link A, Hold GL, Bornschein J. The Role of Microbiota in Gastrointestinal Cancer and Cancer Treatment: Chance or Curse? Cell Mol Gastroenterol Hepatol 2021; 13:857-874. [PMID: 34506954 PMCID: PMC8803618 DOI: 10.1016/j.jcmgh.2021.08.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023]
Abstract
The gastrointestinal (GI) tract is home to a complex and dynamic community of microorganisms, comprising bacteria, archaea, viruses, yeast, and fungi. It is widely accepted that human health is shaped by these microbes and their collective microbial genome. This so-called second genome plays an important role in normal functioning of the host, contributing to processes involved in metabolism and immune modulation. Furthermore, the gut microbiota also is capable of generating energy and nutrients (eg, short-chain fatty acids and vitamins) that are otherwise inaccessible to the host and are essential for mucosal barrier homeostasis. In recent years, numerous studies have pointed toward microbial dysbiosis as a key driver in many GI conditions, including cancers. However, comprehensive mechanistic insights on how collectively gut microbes influence carcinogenesis remain limited. In addition to their role in carcinogenesis, the gut microbiota now has been shown to play a key role in influencing clinical outcomes to cancer immunotherapy, making them valuable targets in the treatment of cancer. It also is becoming apparent that, besides the gut microbiota's impact on therapeutic outcomes, cancer treatment may in turn influence GI microbiota composition. This review provides a comprehensive overview of microbial dysbiosis in GI cancers, specifically esophageal, gastric, and colorectal cancers, potential mechanisms of microbiota in carcinogenesis, and their implications in diagnostics and cancer treatment.
Collapse
Affiliation(s)
- Annemieke Smet
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences,Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Juozas Kupcinskas
- Institute for Digestive Research, Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany
| | - Georgina L. Hold
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, Australia
| | - Jan Bornschein
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom,Correspondence Address correspondence to: Jan Bornschein, MD, Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, United Kingdom.
| |
Collapse
|
13
|
Aprile F, Bruno G, Palma R, Mascellino MT, Panetta C, Scalese G, Oliva A, Severi C, Pontone S. Microbiota Alterations in Precancerous Colon Lesions: A Systematic Review. Cancers (Basel) 2021; 13:cancers13123061. [PMID: 34205378 PMCID: PMC8234190 DOI: 10.3390/cancers13123061] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Even with recent advances, gut microbiota is still one of the most demanding challenges that research needs to handle. In particular, given its deep impact on gastrointestinal health, microbiota could explain the development and progression of certain diseases. Moreover, it could be used as a potential predictive biomarker. Given this, the relationship between intestinal microbiota and colorectal adenoma, considered a premalignant lesion leading to carcinoma, has been deeply evaluated. This review highlights the historical and novel data on microbiota characteristics in adenoma patients to provide an updated summary of current knowledge and its limits. Abstract Gut microbiota plays an important role in human health. It may promote carcinogenesis and is related to several diseases of the gastrointestinal tract. This study of microbial dysbiosis in the etiology of colorectal adenoma aimed to investigate the possible causative role of microbiota in the adenoma–carcinoma sequence and its possible preventive role. A systematic, PRISMA-guided review was performed. The PubMed database was searched using “adenoma microbiota” and selecting original articles between January 2010 and May 2020 independently screened. A higher prevalence of Proteobacteria, Fusobacteria, and Bacteroidetes phyla was observed in the fecal luminal and mucosa-associated microbiota of patients with adenoma. However, other studies provided evidence of depletion of Clostridium, Faecalibacterium, Bacteroides and Romboutsia. Results on the relationship between adenoma endoscopic resection and microbiota were inconsistent. In conclusion, none of the analyzed studies developed a predictive model that could differentiate adenoma from non-adenoma patients, and therefore, to prevent cancer progression. The impact of adenoma’s endoscopic resection on microbiota was investigated, but the results were inconclusive. Further research in the field is required.
Collapse
Affiliation(s)
- Francesca Aprile
- Department of Translational and Precision Medicine, Gastroenterology Unit, Sapienza University of Rome, 00161 Rome, Italy; (F.A.); (G.B.); (G.S.); (C.S.)
| | - Giovanni Bruno
- Department of Translational and Precision Medicine, Gastroenterology Unit, Sapienza University of Rome, 00161 Rome, Italy; (F.A.); (G.B.); (G.S.); (C.S.)
| | - Rossella Palma
- Department of Surgical Sciences, Sapienza University of Rome, 00161 Rome, Italy; (R.P.); (C.P.)
| | - Maria Teresa Mascellino
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00161 Rome, Italy; (M.T.M.); (A.O.)
| | - Cristina Panetta
- Department of Surgical Sciences, Sapienza University of Rome, 00161 Rome, Italy; (R.P.); (C.P.)
| | - Giulia Scalese
- Department of Translational and Precision Medicine, Gastroenterology Unit, Sapienza University of Rome, 00161 Rome, Italy; (F.A.); (G.B.); (G.S.); (C.S.)
| | - Alessandra Oliva
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00161 Rome, Italy; (M.T.M.); (A.O.)
| | - Carola Severi
- Department of Translational and Precision Medicine, Gastroenterology Unit, Sapienza University of Rome, 00161 Rome, Italy; (F.A.); (G.B.); (G.S.); (C.S.)
| | - Stefano Pontone
- Department of Surgical Sciences, Sapienza University of Rome, 00161 Rome, Italy; (R.P.); (C.P.)
- Correspondence: ; Tel.: +39-06-49975568
| |
Collapse
|
14
|
Park JM, Lee WH, Seo H, Oh JY, Lee DY, Kim SJ, Hahm KB. Fecal microbiota changes with fermented kimchi intake regulated either formation or advancement of colon adenoma. J Clin Biochem Nutr 2021. [PMID: 33879965 DOI: 10.3164/jcbn.20.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gut bacteria might contribute in early stage of colorectal cancer through the development and advancement of colon adenoma, by which exploring either beneficial bacteria, which are decreased in formation or advancement of colon adenoma and harmful bacteria, which are increased in advancement of colon adenoma may result in implementation of dietary interventions or probiotic therapies to functional means for prevention. Korean fermented kimchi is one of representative probiotic food providing beneficiary microbiota and exerting significant inhibitory outcomes in both APC/Min+ polyposis model and colitis-associated cancer. Based on these backgrounds, we performed clinical trial to document the changes of fecal microbiota in 32 volunteers with normal colon, simple adenoma, and advanced colon adenoma with 10 weeks of fermented kimchi intake. Each amplicon is sequenced on MiSeq of Illumina and the sequence reads were clustered into Operational Taxonomic Units using VSEARCH and the Chao Indices, an estimator of richness of taxa per individual, were estimated to measure the diversity of each sample. Though significant difference in α or β diversity was not seen between three groups, kimchi intake significantly led to significant diversity of fecal microbiome. After genus analysis, Acinobacteria, Cyanobacteria, Clostridium sensu, Turicibacter, Gastronaeophillales, H. pittma were proven to be increased in patients with advanced colon adenoma, whereas Enterococcua Roseburia, Coryobacteriaceau, Bifidobacterium spp., and Akkermansia were proven to be significantly decreased in feces from patients with advanced colon adenoma after kimchi intake. Conclusively, fermented kimchi plentiful of beneficiary microbiota can afford significant inhibition of either formation or advancement of colon adenoma.
Collapse
Affiliation(s)
- Jong Min Park
- College of Oriental Medicine, Daejeon University School of Oriental Medicine, Daehak-ro 62, Dong-gu, Daejeon 34520, Korea
| | | | | | - Ji Young Oh
- CJ Food Research Center, Gwanggyo-ro, Yeongtong-gu, Suwon 16495, Korea
| | - Dong Yoon Lee
- CJ Food Research Center, Gwanggyo-ro, Yeongtong-gu, Suwon 16495, Korea
| | - Seong Jin Kim
- CHA Cancer Preventive Research Center, CHA Bio Complex, 330 Pangyo-dong, Bundang-gu, Seongnam, 13497, Korea
| | - Ki Baik Hahm
- CHA Cancer Preventive Research Center, CHA Bio Complex, 330 Pangyo-dong, Bundang-gu, Seongnam, 13497, Korea.,Medpacto Research Institute, Medpacto Inc., 92, Myeongdal-ro, Seocho-gu, Seoul 06668, Korea
| |
Collapse
|
15
|
Park JM, Lee WH, Seo H, Oh JY, Lee DY, Kim SJ, Hahm KB. Fecal microbiota changes with fermented kimchi intake regulated either formation or advancement of colon adenoma. J Clin Biochem Nutr 2020; 68:139-148. [PMID: 33879965 DOI: 10.3164/jcbn.20-121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/16/2020] [Indexed: 12/14/2022] Open
Abstract
Gut bacteria might contribute in early stage of colorectal cancer through the development and advancement of colon adenoma, by which exploring either beneficial bacteria, which are decreased in formation or advancement of colon adenoma and harmful bacteria, which are increased in advancement of colon adenoma may result in implementation of dietary interventions or probiotic therapies to functional means for prevention. Korean fermented kimchi is one of representative probiotic food providing beneficiary microbiota and exerting significant inhibitory outcomes in both APC/Min+ polyposis model and colitis-associated cancer. Based on these backgrounds, we performed clinical trial to document the changes of fecal microbiota in 32 volunteers with normal colon, simple adenoma, and advanced colon adenoma with 10 weeks of fermented kimchi intake. Each amplicon is sequenced on MiSeq of Illumina and the sequence reads were clustered into Operational Taxonomic Units using VSEARCH and the Chao Indices, an estimator of richness of taxa per individual, were estimated to measure the diversity of each sample. Though significant difference in α or β diversity was not seen between three groups, kimchi intake significantly led to significant diversity of fecal microbiome. After genus analysis, Acinobacteria, Cyanobacteria, Clostridium sensu, Turicibacter, Gastronaeophillales, H. pittma were proven to be increased in patients with advanced colon adenoma, whereas Enterococcua Roseburia, Coryobacteriaceau, Bifidobacterium spp., and Akkermansia were proven to be significantly decreased in feces from patients with advanced colon adenoma after kimchi intake. Conclusively, fermented kimchi plentiful of beneficiary microbiota can afford significant inhibition of either formation or advancement of colon adenoma.
Collapse
Affiliation(s)
- Jong Min Park
- College of Oriental Medicine, Daejeon University School of Oriental Medicine, Daehak-ro 62, Dong-gu, Daejeon 34520, Korea
| | | | | | - Ji Young Oh
- CJ Food Research Center, Gwanggyo-ro, Yeongtong-gu, Suwon 16495, Korea
| | - Dong Yoon Lee
- CJ Food Research Center, Gwanggyo-ro, Yeongtong-gu, Suwon 16495, Korea
| | - Seong Jin Kim
- CHA Cancer Preventive Research Center, CHA Bio Complex, 330 Pangyo-dong, Bundang-gu, Seongnam, 13497, Korea
| | - Ki Baik Hahm
- CHA Cancer Preventive Research Center, CHA Bio Complex, 330 Pangyo-dong, Bundang-gu, Seongnam, 13497, Korea.,Medpacto Research Institute, Medpacto Inc., 92, Myeongdal-ro, Seocho-gu, Seoul 06668, Korea
| |
Collapse
|
16
|
Abstract
AbstractThis article aims to provide a thorough overview of the use of Artificial Intelligence (AI) techniques in studying the gut microbiota and its role in the diagnosis and treatment of some important diseases. The association between microbiota and diseases, together with its clinical relevance, is still difficult to interpret. The advances in AI techniques, such as Machine Learning (ML) and Deep Learning (DL), can help clinicians in processing and interpreting these massive data sets. Two research groups have been involved in this Scoping Review, working in two different areas of Europe: Florence and Sarajevo. The papers included in the review describe the use of ML or DL methods applied to the study of human gut microbiota. In total, 1109 papers were considered in this study. After elimination, a final set of 16 articles was considered in the scoping review. Different AI techniques were applied in the reviewed papers. Some papers applied ML, while others applied DL techniques. 11 papers evaluated just different ML algorithms (ranging from one to eight algorithms applied to one dataset). The remaining five papers examined both ML and DL algorithms. The most applied ML algorithm was Random Forest and it also exhibited the best performances.
Collapse
|
17
|
Aydin AM, Chahoud J, Adashek JJ, Azizi M, Magliocco A, Ross JS, Necchi A, Spiess PE. Understanding genomics and the immune environment of penile cancer to improve therapy. Nat Rev Urol 2020; 17:555-570. [DOI: 10.1038/s41585-020-0359-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 02/07/2023]
|
18
|
Arabameri A, Asemani D, Teymourpour P. Detection of Colorectal Carcinoma Based on Microbiota Analysis Using Generalized Regression Neural Networks and Nonlinear Feature Selection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:547-557. [PMID: 30222584 DOI: 10.1109/tcbb.2018.2870124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To obtain a screening tool for colorectal cancer (CRC) based on gut microbiota, we seek here to identify an optimal classifier for CRC detection as well as a novel nonlinear feature selection method for determining the most discriminative microbial species. In this study, the intestinal microflora in feces of 141 patients were modeled using general regression neural networks (GRNNs) combined with the proposed feature selection method. The proposed model led to slightly higher accuracy (AUC = 0.911) than previous studies . The results show that the Clostridium scindens and Bifidobacterium angulatum are indicators of healthy gut flora and CRC happens to reduce these bacterial species. In addition, Fusobacterium gonidiaformans was found to be closely correlated with the CRC. The occurrence of colorectal adenoma was not sufficiently discriminatory based on fecal microbiota implicating that the change of colonic flora happens in the advanced phase of CRC development rather than initial adenoma. Integrating the proposed model with fecal occult blood test (FOBT), the CRC detection accuracy remained nearly unchanged (AUC = 0.915). The performance of the proposed method is validated using independent cohorts from America and Austria. Our results suggest that the proposed feature selection method combined with GRNN is potentially an accurate method for CRC detection.
Collapse
|
19
|
Sun W, Wang L, Zhang Q, Dong Q. Microbial Biomarkers for Colorectal Cancer Identified with Random Forest Model. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2020; 000:1-000. [DOI: 10.14218/erhm.2019.00026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
20
|
Grobbee EJ, Lam SY, Fuhler GM, Blakaj B, Konstantinov SR, Bruno MJ, Peppelenbosch MP, Kuipers EJ, Spaander MC. First steps towards combining faecal immunochemical testing with the gut microbiome in colorectal cancer screening. United European Gastroenterol J 2019; 8:293-302. [PMID: 32213018 PMCID: PMC7184657 DOI: 10.1177/2050640619890732] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objectives Many countries use faecal immunochemical testing (FIT) to screen for colorectal cancer. There is increasing evidence that faecal microbiota play a crucial role in colorectal cancer carcinogenesis. We assessed the possibility of measuring faecal microbial features in FIT as potential future biomarkers in colorectal cancer screening. Methods Bacterial stability over time and the possibility of bacterial contamination were evaluated using quantitative polymerase chain reaction analysis. Positive FIT samples (n = 200) of an average-risk screening cohort were subsequently analysed for universal 16S, and bacteria. Escherichia coli (E. coli), Fusobacterium nucleatum (F. nucleatum), Bacteroidetes and Faecalibacterium prausnitzii (F. prausnitzii) by qPCR. The results were compared with colonoscopy findings. Results Faecal microbiota in FIT were stably measured up to six days for E. coli (p = 0.53), F. nucleatum (p = 0.30), Bacteroidetes (p = 0.05) and F. prausnitzii (p = 0.62). Overall presence of bacterial contamination in FIT controls was low. Total bacterial load (i.e. 16S) was significantly higher in patients with colorectal cancer and high-grade dysplasia (p = 0.006). For the individual bacteria tested, no association was found with colonic lesions. Conclusions These results show that the faecal microbial content can be measured in FIT samples and remains stable for six days. Total bacterial load was higher in colorectal cancer and high-grade dysplasia. These results pave the way for further research to determine the potential role of microbiota assessment in FIT screening.
Collapse
Affiliation(s)
- Esmée J Grobbee
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Suk Yee Lam
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Blerdi Blakaj
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Sergey R Konstantinov
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Marco J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Ernst J Kuipers
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - Manon Cw Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| |
Collapse
|
21
|
Tarashi S, Siadat SD, Ahmadi Badi S, Zali M, Biassoni R, Ponzoni M, Moshiri A. Gut Bacteria and their Metabolites: Which One Is the Defendant for Colorectal Cancer? Microorganisms 2019; 7:E561. [PMID: 31766208 PMCID: PMC6920974 DOI: 10.3390/microorganisms7110561] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/22/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is a worldwide health concern which requires efficient therapeutic strategies. The mechanisms underlying CRC remain an essential subject of investigations in the cancer biology field. The evaluation of human microbiota can be critical in this regard, since the disruption of the normal community of gut bacteria is an important issue in the development of CRC. However, several studies have already evaluated the different aspects of the association between microbiota and CRC. The current study aimed at reviewing and summarizing most of the studies on the modifications of gut bacteria detected in stool and tissue samples of CRC cases. In addition, the importance of metabolites derived from gut bacteria, their relationship with the microbiota, and epigenetic modifications have been evaluated.
Collapse
Affiliation(s)
- Samira Tarashi
- Microbiology Research Center, Pasteur Institute of Iran, 1316943551 Tehran, Iran; (S.T.); (S.D.S.); (S.A.B.)
- Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, 1316943551 Tehran, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center, Pasteur Institute of Iran, 1316943551 Tehran, Iran; (S.T.); (S.D.S.); (S.A.B.)
- Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, 1316943551 Tehran, Iran
| | - Sara Ahmadi Badi
- Microbiology Research Center, Pasteur Institute of Iran, 1316943551 Tehran, Iran; (S.T.); (S.D.S.); (S.A.B.)
- Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, 1316943551 Tehran, Iran
| | - Mohammadreza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, 19857-17411 Tehran, Iran;
| | - Roberto Biassoni
- Laboratory of Molecular Medicine, IRCCS Instituto Giannina Gaslini, 16147 Genova, Italy;
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Arfa Moshiri
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, 19857-17411 Tehran, Iran;
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| |
Collapse
|
22
|
Reis SAD, da Conceição LL, Peluzio MDCG. Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease. J Med Microbiol 2019; 68:1391-1407. [PMID: 31424382 DOI: 10.1099/jmm.0.001049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tools that predict the risk of colorectal cancer are important for early diagnosis, given the high mortality rate for this cancer. The composition of the intestinal microbiota is now considered to be a risk factor for the development of colorectal cancer. This discovery has motivated a growing number of studies to identify the micro-organisms responsible for the onset and/or progression of colorectal cancer. With this in mind, this review discusses the relationship between the composition of the intestinal microbiota and colorectal cancer risk. Prospective and case-control studies indicate that the intestinal microbiota of individuals with colorectal cancer usually contains a greater proportion of bacteria responsible for gastrointestinal tract inflammatory diseases, as well as bacteria that produce toxins and carcinogenic metabolites. In contrast, there tends to be a reduced presence of butyric acid-producing bacteria, probiotic bacteria and potentially probiotic bacteria. Despite these differences, the onset and development of colorectal cancer cannot be attributed to a specific micro-organism. Thus, studies focused on the formation of the intestinal microbiota and factors that modulate its composition are important for the development of approaches for colorectal cancer prevention.
Collapse
Affiliation(s)
- Sandra Aparecida Dos Reis
- Department of Nutrition and Health, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Lisiane Lopes da Conceição
- Department of Nutrition and Health, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | | |
Collapse
|
23
|
Leung PHM, Subramanya R, Mou Q, Lee KTW, Islam F, Gopalan V, Lu CT, Lam AKY. Characterization of Mucosa-Associated Microbiota in Matched Cancer and Non-neoplastic Mucosa From Patients With Colorectal Cancer. Front Microbiol 2019; 10:1317. [PMID: 31244818 PMCID: PMC6581718 DOI: 10.3389/fmicb.2019.01317] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 05/27/2019] [Indexed: 12/21/2022] Open
Abstract
Colonic microbiota play important roles in the development of colorectal cancer. We aim to characterise the mucosa-associated microbiota in the tumour as well as the matched non-neoplastic mucosa from patients with colorectal cancer. Microbiota profiling in these samples was done using high-throughput 16S rRNA amplicon sequencing. Our results showed that the microbiota richness and diversity were similar between the tumour and non-neoplastic mucosae. Linear discriminant analysis effect size (LEfSe) analysis identified Fusobacterium and Campylobacter as the key genera of the tumour while Brevundimonas as the key genus of the non-neoplastic mucosa. In patients with shorter survival period, the relative abundance of Fusobacterium and Campylobacter was significantly higher in the tumour. Besides, regardless of the sites, tumour showed higher abundance of Fusobacterium. On the other hand, the relative abundance of Brevundimonas was significantly lower in the tumour. When validated with quantitative ddPCR, we found the absolute numbers of both Fusobacterium and F. nucleatum were significantly higher in the carcinoma from patients with shorter survival period, conventional type of adenocarcinoma in the distal portion of the large intestine (descending colon, sigmoidal colon, and rectum). In conclusion, our study showed a compositional alteration in the mucosa-associated microbiota in the tumour, which may contribute to the progression of colorectal cancer.
Collapse
Affiliation(s)
- Polly H M Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Rao Subramanya
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Qianqian Mou
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Katherine Ting-Wei Lee
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
| | - Farhadul Islam
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia.,Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Vinod Gopalan
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
| | - Cu-Tai Lu
- Department of Surgery, Gold Coast University Hospital, Gold Coast, QLD, Australia
| | - Alfred King-Yin Lam
- Pathology, School of Medicine, Gold Coast Campus, Griffith University, Gold Coast, QLD, Australia
| |
Collapse
|
24
|
Zhang B, Xu S, Xu W, Chen Q, Chen Z, Yan C, Fan Y, Zhang H, Liu Q, Yang J, Yang J, Xiao C, Xu H, Ren J. Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors. Front Genet 2019; 10:447. [PMID: 31191599 PMCID: PMC6547015 DOI: 10.3389/fgene.2019.00447] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/30/2019] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer (CRC) ranks second in cancer-associated mortality and third in the incidence worldwide. Most of CRC follow adenoma-carcinoma sequence, and have more than 90% chance of survival if diagnosed at early stage. But the recommended screening by colonoscopy is invasive, expensive, and poorly adhered to. Recently, several studies reported that the fecal bacteria might provide non-invasive biomarkers for CRC and precancerous tumors. Therefore, we collected and uniformly re-analyzed these published fecal 16S rDNA sequencing datasets to verify the association and identify biomarkers to classify and predict colorectal tumors by random forest method. A total of 1674 samples (330 CRC, 357 advanced adenoma, 141 adenoma, and 846 control) from 7 studies were analyzed in this study. By random effects model and fixed effects model, we observed significant differences in alpha-diversity and beta-diversity between individuals with CRC and the normal colon, but not between adenoma and the normal. We identified various bacterial genera with significant odds ratios for colorectal tumors at different stages. Through building random forest model with 10-fold cross-validation as well as new test datasets, we classified individuals with CRC, advanced adenoma, adenoma and normal colon. All approaches obtained comparable performance at entire OTU level, entire genus level, and the common genus level as measured using AUC. When combined all samples, the AUC of random forest model based on 12 common genera reached 0.846 for CRC, although the predication performed poorly for advance adenoma and adenoma.
Collapse
Affiliation(s)
- Bangzhou Zhang
- Department of Gastroenterology, Zhongshan Hospital Xiamen University, Xiamen, China.,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Shuangbin Xu
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Wei Xu
- Department of Gastroenterology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Qiongyun Chen
- Department of Gastroenterology, Zhongshan Hospital Xiamen University, Xiamen, China.,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Zhangran Chen
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Changsheng Yan
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Yanyun Fan
- Department of Gastroenterology, Zhongshan Hospital Xiamen University, Xiamen, China
| | | | - Qi Liu
- Department of Gastroenterology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jie Yang
- Department of Gastroenterology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jinfeng Yang
- Department of Gastroenterology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Chuanxing Xiao
- Department of Gastroenterology, Zhongshan Hospital Xiamen University, Xiamen, China.,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Hongzhi Xu
- Department of Gastroenterology, Zhongshan Hospital Xiamen University, Xiamen, China.,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Jianlin Ren
- Department of Gastroenterology, Zhongshan Hospital Xiamen University, Xiamen, China.,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| |
Collapse
|
25
|
Dadkhah E, Sikaroodi M, Korman L, Hardi R, Baybick J, Hanzel D, Kuehn G, Kuehn T, Gillevet PM. Gut microbiome identifies risk for colorectal polyps. BMJ Open Gastroenterol 2019; 6:e000297. [PMID: 31275588 PMCID: PMC6577315 DOI: 10.1136/bmjgast-2019-000297] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/23/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023] Open
Abstract
Objective To characterise the gut microbiome in subjects with and without polyps and evaluate the potential of the microbiome as a non-invasive biomarker to screen for risk of colorectal cancer (CRC). Design Presurgery rectal swab, home collected stool, and sigmoid biopsy samples were obtained from 231 subjects undergoing screening or surveillance colonoscopy. 16S rRNA analysis was performed on 552 samples (231 rectal swab, 183 stool, 138 biopsy) and operational taxonomic units (OTU) were identified using UPARSE. Non-parametric statistical methods were used to identify OTUs that were significantly different between subjects with and without polyps. These informative OTUs were then used to build classifiers to predict the presence of polyps using advanced machine learning models. Results We obtained clinical data on 218 subjects (87 females, 131 males) of which 193 were White, 21 African-American, and 4 Asian-American. Colonoscopy detected polyps in 56% of subjects. Modelling of the non-invasive home stool samples resulted in a classification accuracy >75% for Naïve Bayes and Neural Network models using informative OTUs. A naïve holdout analysis performed on home stool samples resulted in an average false negative rate of 11.5% for the Naïve Bayes and Neural Network models, which was reduced to 5% when the two models were combined. Conclusion Gut microbiome analysis combined with advanced machine learning represents a promising approach to screen patients for the presence of polyps, with the potential to optimise the use of colonoscopy, reduce morbidity and mortality associated with CRC, and reduce associated healthcare costs.
Collapse
Affiliation(s)
- Ezzat Dadkhah
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| | - Louis Korman
- Capital Digestive Care, Chevy Chase, Maryland, USA
| | | | | | | | | | | | - Patrick M Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA
| |
Collapse
|
26
|
Abstract
GOALS AND BACKGROUND This study aimed to compare differences in the fecal microbiota according to the risk of advanced colorectal neoplasia (ACN) based on a risk-score model in a large Korean cohort. STUDY Stool samples were collected from 1122 health screening recipients: 404 enrolled in the average risk (AR) group, 514 in the moderate risk (MR) group, and 204 in the high risk (HR) group, in accordance with their risk of ACN. The fecal microbiota was characterized using pyrosequencing of the V3-V4 region of the 16S rRNA genes. RESULTS The overall microbial diversity was significantly reduced with an increased risk of ACN [false discovery rate (FDR), P<0.001], and the composition was significantly different between the risk groups (Bonferroni corrected, P<0.05). On taxonomic comparison, 6 of 11 phyla and 39 of 88 genera were significantly different among the risk groups (all FDR P<0.05). These included under-representation of Bacteroides, Ruminococcus, and Bifidobacterium, and over-representation of Prevotella and Fusobacterium with an increased risk of ACN. In particular, we observed that the unknown genus of Ruminococcaceae were relatively abundant (16.2%) in the AR group and significantly depleted with an increased risk of ACN (13.5% in the HR group; FDR P<0.001). CONCLUSIONS These findings support the hypothesis that the fecal microbiota is different according to the risk of ACN. An unknown genus of Ruminococcaceae, as novel potential butyrate producers, might have a possible role in colorectal tumorigenesis in the Korean population.
Collapse
|
27
|
Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R, Wei Y. Gut microbiota in patients after surgical treatment for colorectal cancer. Environ Microbiol 2018; 21:772-783. [PMID: 30548192 PMCID: PMC7379540 DOI: 10.1111/1462-2920.14498] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
Abstract
Colorectal cancer (CRC) is a common disease worldwide that is strongly associated with the gut microbiota. However, little is known regarding the gut microbiota after surgical treatment. 16S rRNA gene sequencing was used to evaluate differences in gut microbiota among colorectal adenoma patients, CRC patients, CRC postoperative patients and healthy controls by comparing gut microbiota diversity, overall composition and taxonomic signature abundance. The gut microbiota of CRC patients, adenoma patients and healthy controls developed in accordance with the adenoma‐carcinoma sequence, with impressive shifts in the gut microbiota before or during the development of CRC. The gut microbiota of postoperative patients and CRC patients differed significantly. Subdividing CRC postoperative patients according to the presence or absence of newly developed adenoma which based on the colonoscopy findings revealed that the gut microbiota of newly developed adenoma patients differed significantly from that of clean intestine patients and was more similar to the gut microbiota of carcinoma patients than to the gut microbiota of healthy controls. The alterations of the gut microbiota between the two groups of postoperative patients corresponded to CRC prognosis. More importantly, we used the different gut microbiota as biomarkers to distinguish postoperative patients with or without newly developed adenoma, achieving an AUC value of 0.72. These insights on the changes in the gut microbiota of CRC patients after surgical treatment may allow the use of the microbiota as non‐invasive biomarkers for the diagnosis of newly developed adenomas and to help prevent cancer recurrence in postoperative patients.
Collapse
Affiliation(s)
- Ye Jin
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Yang Liu
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Lei Zhao
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Fuya Zhao
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Jing Feng
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Shengda Li
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Huinan Chen
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Jiayu Sun
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Biqiang Zhu
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Rui Geng
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Yunwei Wei
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| |
Collapse
|
28
|
Frugé AD, Van der Pol W, Rogers LQ, Morrow CD, Tsuruta Y, Demark-Wahnefried W. Fecal Akkermansia muciniphila Is Associated with Body Composition and Microbiota Diversity in Overweight and Obese Women with Breast Cancer Participating in a Presurgical Weight Loss Trial. J Acad Nutr Diet 2018; 120:650-659. [PMID: 30420171 PMCID: PMC6509025 DOI: 10.1016/j.jand.2018.08.164] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/23/2018] [Accepted: 08/28/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Akkermansia muciniphila (AM) is a gram-negative, mucin-degrading bacteria inhabiting the gastrointestinal tract associated with host phenotypes and disease states. OBJECTIVE Explore characteristics of overweight and obese female early-stage (0 to II) breast cancer patients with low AM relative abundance (LAM) vs high (HAM) enrolled in a presurgical weight-loss trial. DESIGN Secondary analysis of pooled participants in a randomized controlled trial (NCT02224807). PARTICIPANTS/SETTING During the period from 2014 to 2017, 32 female patients with breast cancer were randomized to weight-loss or attention-control arms from time of diagnosis-to-lumpectomy (mean=30±9 days). INTERVENTION All were instructed to correct nutrient deficiencies via food sources and on upper-body exercises. The weight-loss group received additional guidance to promote 0.5 to 1 kg/wk weight-loss via energy restriction and aerobic exercise. MAIN OUTCOME MEASURES At baseline and follow-up, sera, fecal samples, two-24 hour dietary recalls and dual x-ray absorptiometry were obtained. Bacterial DNA was isolated from feces and polymerase chain reaction (16S) amplified. Inflammatory cytokines were measured in sera. STATISTICAL ANALYSES PERFORMED Differences between LAM and HAM participants were analyzed using t tests and nonparametric tests. Spearman correlations explored relationships between continuous variables. RESULTS Participants were aged 61±9 years with body mass index 34.8±6. Mean AM relative abundance was 0.02% (0.007% to 0.06%) and 1.59% (0.59% to 13.57%) for LAM and HAM participants, respectively. At baseline, women with HAM vs LAM had lower fat mass (38.9±11.2 kg vs 46.4±9.0 kg; P=0.044). Alpha diversity (ie, species richness) was higher in women with HAM (360.8±84.8 vs 282.4±69.6; P=0.008) at baseline, but attenuated after weight-loss (P=0.058). At baseline, interleukin-6 level was associated with species richness (ρ=-0.471, P=0.008) and fat mass (ρ=0.529, P=0.002), but not AM. Change in total dietary fiber was positively associated with AM in LAM (ρ=0.626, P=0.002), but not HAM (ρ=0.436, P=0.180) participants. CONCLUSIONS Among women with early-stage breast cancer, body composition is associated with AM, microbiota diversity, and interleukin-6 level. AM may mediate the effects of dietary fiber in improving microbiota composition.
Collapse
|
29
|
The association between fecal microbiota and different types of colorectal polyp as precursors of colorectal cancer. Microb Pathog 2018; 124:244-249. [DOI: 10.1016/j.micpath.2018.08.035] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/14/2018] [Accepted: 08/18/2018] [Indexed: 12/22/2022]
|
30
|
Erben V, Bhardwaj M, Schrotz-King P, Brenner H. Metabolomics Biomarkers for Detection of Colorectal Neoplasms: A Systematic Review. Cancers (Basel) 2018; 10:E246. [PMID: 30060469 PMCID: PMC6116151 DOI: 10.3390/cancers10080246] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Several approaches have been suggested to be useful in the early detection of colorectal neoplasms. Since metabolites are closely related to the phenotype and are available from different human bio-fluids, metabolomics are candidates for non-invasive early detection of colorectal neoplasms. OBJECTIVES We aimed to summarize current knowledge on performance characteristics of metabolomics biomarkers that are potentially applicable in a screening setting for the early detection of colorectal neoplasms. DESIGN We conducted a systematic literature search in PubMed and Web of Science and searched for biomarkers for the early detection of colorectal neoplasms in easy-to-collect human bio-fluids. Information on study design and performance characteristics for diagnostic accuracy was extracted. RESULTS Finally, we included 41 studies in our analysis investigating biomarkers in different bio-fluids (blood, urine, and feces). Although single metabolites mostly had limited ability to distinguish people with and without colorectal neoplasms, promising results were reported for metabolite panels, especially amino acid panels in blood samples, as well as nucleosides in urine samples in several studies. However, validation of the results is limited. CONCLUSIONS Panels of metabolites consisting of amino acids in blood and nucleosides in urinary samples might be useful biomarkers for early detection of advanced colorectal neoplasms. However, to make metabolomic biomarkers clinically applicable, future research in larger studies and external validation of the results is required.
Collapse
Affiliation(s)
- Vanessa Erben
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.
| | - Megha Bhardwaj
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.
| | - Petra Schrotz-King
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany.
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
| |
Collapse
|
31
|
Chao A, Sivaram S. Important Role of Health Surveillance Systems in Community-Based Colorectal Cancer Screening. Oncologist 2018; 23:871-873. [PMID: 30049884 DOI: 10.1634/theoncologist.2018-0178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Ann Chao
- Center for Global Health, National Cancer Institute, Rockville, Maryland, USA
| | - Sudha Sivaram
- Center for Global Health, National Cancer Institute, Rockville, Maryland, USA
| |
Collapse
|
32
|
Yang Y, Xu C, Wu D, Wang Z, Wu P, Li L, Huang J, Qiu F. γδ T Cells: Crosstalk Between Microbiota, Chronic Inflammation, and Colorectal Cancer. Front Immunol 2018; 9:1483. [PMID: 29997627 PMCID: PMC6028700 DOI: 10.3389/fimmu.2018.01483] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/14/2018] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence suggests that intestinal microbiota dysbiosis and chronic inflammation contribute to colorectal cancer (CRC) development. γδ T cells represent a major innate immune cell population in the intestinal epithelium that is involved in the maintenance of gut homeostasis, inflammation regulation, and carcinogenesis. The important contributions of γδ T cells are (i) to perform a protective role in the context of barrier damage and pathogenic microorganism translocation; (ii) to exert either pro- or anti-inflammatory effects at different inflammatory stages; and (iii) to boost the crosstalk between immune cells and tumor microenvironment, inducing a cascade of suppressive immune responses. Understanding the crucial role of γδ T cells would enable us to manipulate these cells during the CRC sequence and improve the efficacy of tumor therapy.
Collapse
Affiliation(s)
- Yunben Yang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Chunjing Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Dang Wu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhen Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Pin Wu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Lili Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Jian Huang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Surgical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Fuming Qiu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
33
|
Villéger R, Lopès A, Veziant J, Gagnière J, Barnich N, Billard E, Boucher D, Bonnet M. Microbial markers in colorectal cancer detection and/or prognosis. World J Gastroenterol 2018; 24:2327-2347. [PMID: 29904241 PMCID: PMC6000297 DOI: 10.3748/wjg.v24.i22.2327] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/03/2018] [Accepted: 05/18/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer worldwide. CRC is still associated with a poor prognosis among patients with advanced disease. On the contrary, due to its slow progression from detectable precancerous lesions, the prognosis for patients with early stages of CRC is encouraging. While most robust methods are invasive and costly, actual patient-friendly screening methods for CRC suffer of lack of sensitivity and specificity. Therefore, the development of sensitive, non-invasive and cost-effective methods for CRC detection and prognosis are necessary for increasing the chances of a cure. Beyond its beneficial functions for the host, increasing evidence suggests that the intestinal microbiota is a key factor associated with carcinogenesis. Many clinical studies have reported a disruption in the gut microbiota balance and an alteration in the faecal metabolome of CRC patients, suggesting the potential use of a microbial-based test as a non-invasive diagnostic and/or prognostic tool for CRC screening. This review aims to discuss the microbial signatures associated with CRC known to date, including dysbiosis and faecal metabolome alterations, and the potential use of microbial variation markers for non-invasive early diagnosis and/or prognostic assessment of CRC and advanced adenomas. We will finally discuss the possible use of these markers as predicators for treatment response and their limitations.
Collapse
Affiliation(s)
- Romain Villéger
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
| | - Amélie Lopès
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Research Biologics, Sanofi R&D, Vitry-Sur-Seine 94400, France
| | - Julie Veziant
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Chirurgie digestive, Centre Hospitalier Universitaire, Clermont-Ferrand 63000, France
| | - Johan Gagnière
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Chirurgie digestive, Centre Hospitalier Universitaire, Clermont-Ferrand 63000, France
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Elisabeth Billard
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Delphine Boucher
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Mathilde Bonnet
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| |
Collapse
|
34
|
Amitay EL, Krilaviciute A, Brenner H. Systematic review: Gut microbiota in fecal samples and detection of colorectal neoplasms. Gut Microbes 2018; 9. [PMID: 29543545 PMCID: PMC6219654 DOI: 10.1080/19490976.2018.1445957] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer morbidity and mortality. Dysbiosis in the gut microbiota may be associated with CRC. This systematic review focuses on differences in gut microbial community between people diagnosed with CRC or adenoma and healthy individuals using fecal samples, emphasizing non-invasive fecal microbiome models for CRC early diagnosis. Nineteen studies were identified in a systematic literature search of Pubmed, Web of Science and ScienceDirect. Several bacteria were reported to differ in abundance between CRC and adenoma cases and healthy controls, with Fusobacterium the most common. Fecal multi-bacterial predictive models used to distinguish CRC patients from healthy controls had reported areas under the receiver operating curve (AUCs) in external validation populations of 0.68-0.77. Though advanced sequencing techniques could in the future complement current non-invasive methods for CRC early detection, more studies with high statistical power, comparable and reproducible methods and external validation of predictive models are needed.
Collapse
Affiliation(s)
- Efrat L. Amitay
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany,CONTACT Efrat L. Amitay, MPH, PhD, Division of Clinical Epidemiology and Aging Research (C070) German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Agne Krilaviciute
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany,Heidelberg Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany,Division of Preventive Oncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), German Cancer Research Centre (DKFZ), Heidelberg, Germany
| |
Collapse
|
35
|
Shah MS, DeSantis TZ, Weinmaier T, McMurdie PJ, Cope JL, Altrichter A, Yamal JM, Hollister EB. Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer. Gut 2018; 67:882-891. [PMID: 28341746 DOI: 10.1136/gutjnl-2016-313189] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Colorectal cancer (CRC) is the second leading cause of cancer-associated mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC and indicate transition in the adenoma-carcinoma sequence. Re-analysing raw sequence and metadata from several studies uniformly, we sought to identify a composite and generalisable microbial marker for CRC. DESIGN Raw 16S rRNA gene sequence data sets from nine studies were processed with two pipelines, (1) QIIME closed reference (QIIME-CR) or (2) a strain-specific method herein termed SS-UP (Strain Select, UPARSE bioinformatics pipeline). A total of 509 samples (79 colorectal adenoma, 195 CRC and 235 controls) were analysed. Differential abundance, meta-analysis random effects regression and machine learning analyses were carried out to determine the consistency and diagnostic capabilities of potential microbial biomarkers. RESULTS Definitive taxa, including Parvimonas micra ATCC 33270, Streptococcus anginosus and yet-to-be-cultured members of Proteobacteria, were frequently and significantly increased in stools from patients with CRC compared with controls across studies and had high discriminatory capacity in diagnostic classification. Microbiome-based CRC versus control classification produced an area under receiver operator characteristic (AUROC) curve of 76.6% in QIIME-CR and 80.3% in SS-UP. Combining clinical and microbiome markers gave a diagnostic AUROC of 83.3% for QIIME-CR and 91.3% for SS-UP. CONCLUSIONS Despite technological differences across studies and methods, key microbial markers emerged as important in classifying CRC cases and such could be used in a universal diagnostic for the disease. The choice of bioinformatics pipeline influenced accuracy of classification. Strain-resolved microbial markers might prove crucial in providing a microbial diagnostic for CRC.
Collapse
Affiliation(s)
- Manasi S Shah
- Department of Epidemiology, University of Texas School of Public Health, Houston, Texas, USA.,Bioinformatics, Second Genome Inc, South San Francisco, California, USA.,Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, HoustonTexas, USA
| | - Todd Z DeSantis
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA
| | - Thomas Weinmaier
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA
| | - Paul J McMurdie
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA.,Bioinformatics, Whole Biome Inc, San Francisco, California, USA
| | - Julia L Cope
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, HoustonTexas, USA.,Diversigen, Inc, Houston, Texas, USA
| | - Adam Altrichter
- Bioinformatics, Second Genome Inc, South San Francisco, California, USA
| | - Jose-Miguel Yamal
- Department of Epidemiology, University of Texas School of Public Health, Houston, Texas, USA
| | - Emily B Hollister
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, HoustonTexas, USA
| |
Collapse
|
36
|
Zhang Y, Kang C, Wang XL, Zhou M, Chen MT, Zhu XH, Liu K, Wang B, Zhang QY, Zhu JD, Mi MT. Dietary Factors Modulate Colonic Tumorigenesis Through the Interaction of Gut Microbiota and Host Chloride Channels. Mol Nutr Food Res 2018; 62. [DOI: 10.1002/mnfr.201700554] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/04/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Yong Zhang
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Chao Kang
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Xiao-lan Wang
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Min Zhou
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Meng-ting Chen
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Xiao-hui Zhu
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Kai Liu
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Bin Wang
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Qian-yong Zhang
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Jun-dong Zhu
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| | - Man-tian Mi
- Research center for Nutrition and Food safety; Institute of Military Preventive Medicine; Third Military Medical University; Chongqing Key Laboratory of Nutrition and Food safety; Chongqing Medical Nutrition Research Center; Chongqing P.R. China
| |
Collapse
|
37
|
陆 颖, 曾 悦, 胡 国, 王 兴. [High-throughput sequencing for analysis of structural change of intestinal microbiota in patients with colorectal adenoma]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2017; 37:1156-1163. [PMID: 28951355 PMCID: PMC6765500 DOI: 10.3969/j.issn.1673-4254.2017.09.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To investigate the taxonomic richness and diversity of gut microbiota in patients with colorectal adenoma and elucidate the role of gut microorganisms in precancerous lesions in the colon and rectum. METHOD Adenomatous tissues from 31 patients with colorectal adenoma and normal intestinal mucosal tissues from 20 healthy control subjects were collected through colonoscopy. The total bacterial genomic DNA was extracted, and the V3-V4 hypervariable region in bacterial 16S rRNA gene was amplified using polymerase chain reaction and sequenced on an Illumina MiSeq platform. RESULTS Patients with colorectal adenomas had a higher alpha diversity and richness indices compared to the healthy controls (P<0.01). The mucosal microbiota in colorectal adenoma tissue showed a distinctive structural difference from that in normal intestinal mucosal tissues. At the phylum level, a large decrease in Firmicutes with concomitant relative expansion of Proteobacteria was observed in patients with colorectal adenomas, resulting in a significant decrease in the Firmicutes/Bacteroidetes ratio (P<0.01). At the genus level, Lactococcus and Pseudomonas were enriched whereas Enterococcus, Bacillus, and Solibacillus were reduced obviously in the preneoplastic tissues (P<0.01). We also found a similar gut microbiome composition between low-grade and high-grade intraepithelial neoplasia; the ratio of Escherichia-Shigella tended to increase in high-grade intraepithelial neoplasia, but this change was not statistically significant (P%0.28). CONCLUSION Significant changes in the structure of the intestinal flora occur in patients with colorectal adenomas, indicating that the association of dysbiosis of the gut microbiota with the occurrence of a pro-oncogenic microenvironment.
Collapse
Affiliation(s)
- 颖影 陆
- />南京医科大学附属上海一院临床医学院消化内科,上海 201620Department of Gastroenterology, Shanghai General Hospital of Nanjing Medical University, Shanghai 200080, China
| | - 悦 曾
- />南京医科大学附属上海一院临床医学院消化内科,上海 201620Department of Gastroenterology, Shanghai General Hospital of Nanjing Medical University, Shanghai 200080, China
| | - 国勇 胡
- />南京医科大学附属上海一院临床医学院消化内科,上海 201620Department of Gastroenterology, Shanghai General Hospital of Nanjing Medical University, Shanghai 200080, China
| | - 兴鹏 王
- />南京医科大学附属上海一院临床医学院消化内科,上海 201620Department of Gastroenterology, Shanghai General Hospital of Nanjing Medical University, Shanghai 200080, China
| |
Collapse
|
38
|
Eklöf V, Löfgren-Burström A, Zingmark C, Edin S, Larsson P, Karling P, Alexeyev O, Rutegård J, Wikberg ML, Palmqvist R. Cancer-associated fecal microbial markers in colorectal cancer detection. Int J Cancer 2017; 141:2528-2536. [PMID: 28833079 PMCID: PMC5697688 DOI: 10.1002/ijc.31011] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/07/2017] [Accepted: 07/20/2017] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer death in the western world. An effective screening program leading to early detection of disease would severely reduce the mortality of CRC. Alterations in the gut microbiota have been linked to CRC, but the potential of microbial markers for use in CRC screening has been largely unstudied. We used a nested case–control study of 238 study subjects to explore the use of microbial markers for clbA+ bacteria harboring the pks pathogenicity island, afa‐C+ diffusely adherent Escherichia coli harboring the afa‐1 operon, and Fusobacterium nucleatum in stool as potential screening markers for CRC. We found that individual markers for clbA+ bacteria and F. nucleatum were more abundant in stool of patients with CRC, and could predict cancer with a relatively high specificity (81.5% and 76.9%, respectively) and with a sensitivity of 56.4% and 69.2%, respectively. In a combined test of clbA+ bacteria and F. nucleatum, CRC was detected with a specificity of 63.1% and a sensitivity of 84.6%. Our findings support a potential value of microbial factors in stool as putative noninvasive biomarkers for CRC detection. We propose that microbial markers may represent an important future screening strategy for CRC, selecting patients with a “high‐risk” microbial pattern to other further diagnostic procedures such as colonoscopy. What's new? Nobody looks forward to a colonoscopy, and now a pair of telltale bacteria could help people avoid them. Researchers know that microbial changes occur in colorectal cancer, and have hoped these microbial changes could provide less invasive screening tools to detect tumors. These authors conducted a nested case–control study investigating 3 bacterial markers in 238 patients. Two of the markers, clbA+ bacteria and Fusobacterium nucleatum, successfully predicted colorectal cancer with high sensitivity, particularly when tested together.
Collapse
Affiliation(s)
- Vincy Eklöf
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | | | - Carl Zingmark
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Pär Larsson
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Pontus Karling
- Department of Public Health and Clinical Medicine, Medicine, Umeå University, Umeå, Sweden
| | - Oleg Alexeyev
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Jörgen Rutegård
- Department of Surgical and Perioperative Sciences, Surgery, Umeå University, Umeå, Sweden
| | - Maria L Wikberg
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| |
Collapse
|
39
|
Abstract
Answer questions and earn CME/CNE The human body harbors enormous numbers of microbiota that influence cancer susceptibility, in part through their prodigious metabolic capacity and their profound influence on immune cell function. Microbial pathogens drive tumorigenesis in 15% to 20% of cancer cases. Even larger numbers of malignancies are associated with an altered composition of commensal microbiota (dysbiosis) based on microbiome studies using metagenomic sequencing. Although association studies cannot distinguish whether changes in microbiota are causes or effects of cancer, a causative role is supported by rigorously controlled preclinical studies using gnotobiotic mouse models colonized with one or more specific bacteria. These studies demonstrate that microbiota can alter cancer susceptibility and progression by diverse mechanisms, such as modulating inflammation, inducing DNA damage, and producing metabolites involved in oncogenesis or tumor suppression. Evidence is emerging that microbiota can be manipulated for improving cancer treatment. By incorporating probiotics as adjuvants for checkpoint immunotherapy or by designing small molecules that target microbial enzymes, microbiota can be harnessed to improve cancer care. CA Cancer J Clin 2017;67:326-344. © 2017 American Cancer Society.
Collapse
Affiliation(s)
- Aadra P. Bhatt
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biochemistry & Biophysics, Microbiology & Immunology, and the Integrated Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott J. Bultman
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
40
|
Gagnière J, Bonnin V, Jarrousse AS, Cardamone E, Agus A, Uhrhammer N, Sauvanet P, Déchelotte P, Barnich N, Bonnet R, Pezet D, Bonnet M. Interactions between microsatellite instability and human gut colonization by Escherichia coli in colorectal cancer. Clin Sci (Lond) 2017; 131:471-485. [PMID: 28093453 DOI: 10.1042/cs20160876] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Recent studies suggest that colonization of colonic mucosa by pathogenic Escherichia coli could be involved in the development of colorectal cancer (CRC), especially through the production of genotoxins such as colibactin and/or by interfering with the DNA mismatch repair (MMR) pathway that leads to microsatellite instability (MSI). The present study, performed on 88 CRC patients, revealed a significant increase in E. coli colonization in the MSI CRC phenotype. In the same way, E. coli persistence and internalization were increased in vitro in MMR-deficient cells. Moreover, we demonstrated that colibactin-producing E. coli induce inhibition of the mutL homologue 1 (MLH1) MMR proteins, which could lead to genomic instability. However, colibactin-producing E. coli were more frequently identified in microsatellite stable (MSS) CRC. The present study suggests differences in the involvement of colibactin-producing E. coli in colorectal carcinogenesis according to the CRC phenotype. Further host–pathogen interactions studies should take into account CRC phenotypes.
Collapse
Affiliation(s)
- Johan Gagnière
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
- Department of Digestive Surgery, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Virginie Bonnin
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
| | | | - Emilie Cardamone
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
| | - Allison Agus
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
- Department of Oncogenetic, Centre Jean Perrin, 63000 Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Department of Oncogenetic, Centre Jean Perrin, 63000 Clermont-Ferrand, France
| | - Pierre Sauvanet
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
- Department of Digestive Surgery, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Pierre Déchelotte
- Department of Pathology, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Nicolas Barnich
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
| | - Richard Bonnet
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
- Department of Bacteriology, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Denis Pezet
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
- Department of Digestive Surgery, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Mathilde Bonnet
- UMR 1071 Inserm/Université Clermont Auvergne, 63000 Clermont-Ferrand, France
- INRA USC-2018, 63000 Clermont-Ferrand, France
| |
Collapse
|
41
|
Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB, Ahn J. The gut microbiota in conventional and serrated precursors of colorectal cancer. MICROBIOME 2016; 4:69. [PMID: 28038683 PMCID: PMC5203720 DOI: 10.1186/s40168-016-0218-6] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/03/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Colorectal cancer is a heterogeneous disease arising from at least two precursors-the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut microbiota and colorectal cancer; however, its relationship to the different early precursors of colorectal cancer is understudied. We tested, for the first time, the relationship of the gut microbiota to specific colorectal polyp types. RESULTS Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples. Participants were categorized as CA cases (n = 144), serrated polyp cases (n = 73), or polyp-free controls (n = 323). CA cases were further classified as proximal (n = 87) or distal (n = 55) and as non-advanced (n = 121) or advanced (n = 22). Serrated polyp cases were further classified as hyperplastic polyp (HP; n = 40) or sessile serrated adenoma (SSA; n = 33). We compared gut microbiota diversity, overall composition, and normalized taxon abundance among these groups. CA cases had lower species richness in stool than controls (p = 0.03); in particular, this association was strongest for advanced CA cases (p = 0.004). In relation to overall microbiota composition, only distal or advanced CA cases differed significantly from controls (p = 0.02 and p = 0.002). In taxon-based analysis, stool of CA cases was depleted in a network of Clostridia operational taxonomic units from families Ruminococcaceae, Clostridiaceae, and Lachnospiraceae, and enriched in the classes Bacilli and Gammaproteobacteria, order Enterobacteriales, and genera Actinomyces and Streptococcus (all q < 0.10). SSA and HP cases did not differ in diversity or composition from controls, though sample size for these groups was small. Few taxa were differentially abundant between HP cases or SSA cases and controls; among them, class Erysipelotrichi was depleted in SSA cases. CONCLUSIONS Our results indicate that gut microbes may play a role in the early stages of colorectal carcinogenesis through the development of CAs. Findings may have implications for developing colorectal cancer prevention therapies targeting early microbial drivers of colorectal carcinogenesis.
Collapse
Affiliation(s)
- Brandilyn A Peters
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Christine Dominianni
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Jean A Shapiro
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Timothy R Church
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jing Wu
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - George Miller
- Department of Surgery, New York University School of Medicine, New York, NY, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
- NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | | | - Hal Freiman
- Kips Bay Endoscopy Center, New York, NY, USA
| | | | - James Salik
- Kips Bay Endoscopy Center, New York, NY, USA
| | | | - Richard B Hayes
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Jiyoung Ahn
- Department of Population Health, New York University School of Medicine, New York, NY, USA.
- NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
42
|
Frugé AD, Ptacek T, Tsuruta Y, Morrow CD, Azrad M, Desmond RA, Hunter GR, Rais-Bahrami S, Demark-Wahnefried W. Dietary Changes Impact the Gut Microbe Composition in Overweight and Obese Men with Prostate Cancer Undergoing Radical Prostatectomy. J Acad Nutr Diet 2016; 118:714-723.e1. [PMID: 27988219 DOI: 10.1016/j.jand.2016.10.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/14/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Diet and obesity influence prostate cancer risk and progression-effects that may be mediated through the gut microbiome. OBJECTIVE Our aim was to explore relationships among diet, gut microbes, and Gleason sum in overweight and obese prostate cancer patients enrolled in a presurgical weight-loss trial. DESIGN Randomized controlled trial (NCT01886677) secondary analysis. PARTICIPANTS/SETTING In 2013-2014, 40 prostate cancer patients in the southeastern United States were randomized and allocated equally to weight-loss and wait-list control arms while they awaited prostatectomy; stool samples were collected on a subset of 22 patients. INTERVENTION Registered dietitian nutritionists and exercise physiologists provided semi-weekly in-person and telephone-based guidance on calorie-restricted diets and exercise to promote an approximate weight loss of 0.91 kg/wk. MAIN OUTCOME MEASURES Baseline and follow-up 24-hour dietary recalls were conducted and analyzed (using the Automated Self-Administered 24-hour dietary recall system; National Cancer Institute, Bethesda, MD) for macronutrients, micronutrients, and food groups. Microbiome analysis targeting the V4 region of the 16S ribosomal RNA gene was performed on fecal samples. Biopsy Gleason sum data were accessed from diagnostic pathology reports. STATISTICAL ANALYSES PERFORMED Associations between dietary factors and operational taxonomic units were determined by β-diversity analysis. Wilcoxon signed rank, and Mann-Whitney U testing assessed within- and between-arm differences. Associations between Gleason sum and operational taxonomic units, and diet and operational taxonomic units, were analyzed using Spearman correlations. RESULTS At baseline, Proteobacteria (median 0.06, interquartile range 0.01 to 0.16) were abundant, with four orders positively associated with Gleason sum. Gleason sum was associated with Clostridium (ρ=.579; P=0.005) and Blautia (ρ=-0.425, P=0.049). Increased red meat consumption from baseline was associated with Prevotella (ρ=-.497; P=0.018) and Blautia (ρ=.422; P=0.039). Men who increased poultry intake had decreased Clostridiales abundance (P=0.009). CONCLUSIONS This hypothesis-generating study provides a starting point for investigating the relationships between the fecal microbiome, diet, and prostate cancer. Adequately powered studies are required to further explore and validate these findings.
Collapse
|
43
|
Hale VL, Chen J, Johnson S, Harrington SC, Yab TC, Smyrk TC, Nelson H, Boardman LA, Druliner BR, Levin TR, Rex DK, Ahnen DJ, Lance P, Ahlquist DA, Chia N. Shifts in the Fecal Microbiota Associated with Adenomatous Polyps. Cancer Epidemiol Biomarkers Prev 2016; 26:85-94. [PMID: 27672054 DOI: 10.1158/1055-9965.epi-16-0337] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Adenomatous polyps are the most common precursor to colorectal cancer, the second leading cause of cancer-related death in the United States. We sought to learn more about early events of carcinogenesis by investigating shifts in the gut microbiota of patients with adenomas. METHODS We analyzed 16S rRNA gene sequences from the fecal microbiota of patients with adenomas (n = 233) and without (n = 547). RESULTS Multiple taxa were significantly more abundant in patients with adenomas, including Bilophila, Desulfovibrio, proinflammatory bacteria in the genus Mogibacterium, and multiple Bacteroidetes species. Patients without adenomas had greater abundances of Veillonella, Firmicutes (Order Clostridia), and Actinobacteria (family Bifidobacteriales). Our findings were consistent with previously reported shifts in the gut microbiota of colorectal cancer patients. Importantly, the altered adenoma profile is predicted to increase primary and secondary bile acid production, as well as starch, sucrose, lipid, and phenylpropanoid metabolism. CONCLUSIONS These data hint that increased sugar, protein, and lipid metabolism along with increased bile acid production could promote a colonic environment that supports the growth of bile-tolerant microbes such as Bilophilia and Desulfovibrio In turn, these microbes may produce genotoxic or inflammatory metabolites such as H2S and secondary bile acids, which could play a role in catalyzing adenoma development and eventually colorectal cancer. IMPACT This study suggests a plausible biological mechanism to explain the links between shifts in the microbiota and colorectal cancer. This represents a first step toward resolving the complex interactions that shape the adenoma-carcinoma sequence of colorectal cancer and may facilitate personalized therapeutics focused on the microbiota. Cancer Epidemiol Biomarkers Prev; 26(1); 85-94. ©2016 AACR.
Collapse
Affiliation(s)
- Vanessa L Hale
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Stephen Johnson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Sean C Harrington
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brooke R Druliner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Theodore R Levin
- Division of Gastroenterology, Kaiser Permanente, Oakland, California
| | - Douglas K Rex
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Dennis J Ahnen
- Denver Department of Veterans Affairs Medical Center, University of Colorado Denver School of Medicine, Denver, Colorado
| | - Peter Lance
- University of Arizona Cancer Center, Tucson, Arizona
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, Minnesota.
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
44
|
Vogtmann E, Goedert JJ. Epidemiologic studies of the human microbiome and cancer. Br J Cancer 2016; 114:237-42. [PMID: 26730578 PMCID: PMC4742587 DOI: 10.1038/bjc.2015.465] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/30/2015] [Accepted: 11/10/2015] [Indexed: 12/17/2022] Open
Abstract
The human microbiome, which includes the collective genome of all bacteria, archaea, fungi, protists, and viruses found in and on the human body, is altered in many diseases and may substantially affect cancer risk. Previously detected associations of individual bacteria (e.g., Helicobacter pylori), periodontal disease, and inflammation with specific cancers have motivated studies considering the association between the human microbiome and cancer risk. This short review summarises microbiome research, focusing on published epidemiological associations with gastric, oesophageal, hepatobiliary, pancreatic, lung, colorectal, and other cancers. Large, prospective studies of the microbiome that employ multidisciplinary laboratory and analysis methods, as well as rigorous validation of case status, are likely to yield translational opportunities to reduce cancer morbidity and mortality by improving prevention, screening, and treatment.
Collapse
Affiliation(s)
- Emily Vogtmann
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| |
Collapse
|
45
|
Onodera H. Novel Method for Screening Colorectal Neoplasm. EBioMedicine 2015; 2:495-6. [PMID: 26288813 PMCID: PMC4535159 DOI: 10.1016/j.ebiom.2015.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 01/19/2023] Open
|