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Zhou D, Chen Y, Wang Z, Zhu S, Zhang L, Song J, Bai T, Hou X. Integrating clinical and cross-cohort metagenomic features: a stable and non-invasive colorectal cancer and adenoma diagnostic model. Front Mol Biosci 2024; 10:1298679. [PMID: 38455360 PMCID: PMC10919151 DOI: 10.3389/fmolb.2023.1298679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/24/2023] [Indexed: 03/09/2024] Open
Abstract
Background: Dysbiosis is associated with colorectal cancer (CRC) and adenomas (CRA). However, the robustness of diagnostic models based on microbial signatures in multiple cohorts remains unsatisfactory. Materials and Methods: In this study, we used machine learning models to screen metagenomic signatures from the respective cross-cohort datasets of CRC and CRA (selected from CuratedMetagenomicData, each disease included 4 datasets). Then select a CRC and CRA data set from the CuratedMetagenomicData database and meet the requirements of having both metagenomic data and clinical data. This data set will be used to verify the inference that integrating clinical features can improve the performance of microbial disease prediction models. Results: After repeated verification, we selected 20 metagenomic features that performed well and were stably expressed within cross-cohorts to represent the diagnostic role of bacterial communities in CRC/CRA. The performance of the selected cross-cohort metagenomic features was stable for multi-regional and multi-ethnic populations (CRC, AUC: 0.817-0.867; CRA, AUC: 0.766-0.833). After clinical feature combination, AUC of our integrated CRC diagnostic model reached 0.939 (95% CI: 0.932-0.947, NRI=30%), and that of the CRA integrated model reached 0.925 (95%CI: 0.917-0.935, NRI=18%). Conclusion: In conclusion, the integrated model performed significantly better than single microbiome or clinical feature models in all cohorts. Integrating cross-cohort common discriminative microbial features with clinical features could help construct stable diagnostic models for early non-invasive screening for CRC and CRA.
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Affiliation(s)
- Dan Zhou
- Division of Gastroenterology, Union Hospital, Tongji Medical College Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Youli Chen
- State Key Laboratory for Oncogenes and Related Genes, NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zehao Wang
- School of Management, Huazhong University of Science and Technology, Wuhan, China
| | - Siran Zhu
- Division of Gastroenterology, Union Hospital, Tongji Medical College Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Zhang
- Division of Gastroenterology, Union Hospital, Tongji Medical College Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Bai
- Division of Gastroenterology, Union Hospital, Tongji Medical College Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College Medical College, Huazhong University of Science and Technology, Wuhan, China
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Gut microbiome-modulating properties of a polyphenol-enriched dietary supplement comprised of hibiscus and lemon verbena extracts. Monitoring of phenolic metabolites. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Bai J, Barandouzi ZA, Rowcliffe C, Meador R, Tsementzi D, Bruner DW. Gut Microbiome and Its Associations With Acute and Chronic Gastrointestinal Toxicities in Cancer Patients With Pelvic Radiation Therapy: A Systematic Review. Front Oncol 2021; 11:745262. [PMID: 34938654 PMCID: PMC8685326 DOI: 10.3389/fonc.2021.745262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Aim Pelvic radiation therapy (RT) can impact the gut microbiome in patients with cancer and result in gastrointestinal (GI) toxicities. The purpose of this systematic review was to describe the effects of RT on the gut microbiome and the associations between the gut microbiome and GI toxicities in patients treated with pelvic RT. Methods PubMed, Embase, and Web of Science databases were searched from their earliest records to August 2020. The articles screening process adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The Mixed Method Assessment Tool was used to assess the methodological quality for each included study. All study findings were synthesized and presented in narrative format. Thirteen studies were included. The gut microbiome of fecal samples was analyzed using 16S rRNA sequencing approaches. Results There were disparities in alpha and beta diversities that existed across the studies. Divergent results were found among various phyla, including Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Cyanobacteria, Fusobacteria, and Deinococcus-Thermus. Moreover, alteration in the gut microbiome diversity and abundance related to cancer treatment was associated with pelvic toxicities, specifically diarrhea. Following treatment, increases in the abundance of Bacteroides was associated with diarrhea and radiation enteritis. Conclusions Pelvic RT can disrupt the diversity and abundance of commensal gut microorganisms. A dysbiotic gut microbiome showed a promising association with radiation enteritis through alterations of the intestinal barrier function, innate immunity, and intestinal repair mechanisms; however, confounders, such as diet, were not thoroughly addressed.
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Affiliation(s)
- Jinbing Bai
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States.,Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Zahra A Barandouzi
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States
| | - Claire Rowcliffe
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Rebecca Meador
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States
| | - Despina Tsementzi
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Deborah Watkins Bruner
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States.,Winship Cancer Institute, Emory University, Atlanta, GA, United States
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González-Mercado VJ, Lim J, Marrero S, Pedro E, Saligan LN. Gut microbiota and fatigue in rectal cancer patients: a cross-sectional pilot study. Support Care Cancer 2021; 29:4615-4621. [PMID: 33495850 DOI: 10.1007/s00520-021-06013-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
CONTEXT Although microbial-mediated disturbance of intestinal mucosal homeostasis (dysbiosis) is believed to contribute to the pathogenesis of chemotherapy and radiotherapy (CRT)-related fatigue, potential differences in the gut microbial diversity and in the abundance of gut microbial taxa between fatigued and non-fatigued patients have not been adequately examined, particularly in the rectal cancer population. PURPOSE In this cross-sectional study, we aim to examine the differences in (a) gut microbial diversity and gut microbial abundances and (b) predicted functional pathways of the gut microbiome between rectal cancer participants with and without fatigue at the end of CRT. METHODS Rectal cancer patients (n = 50) provided stool samples for 16S rRNA gene sequencing and symptom ratings for fatigue at the end of CRT. Gut microbiome data were analyzed using QIIME2, LEfSe, and the R statistical package. RESULTS Fatigued (n = 35) participants showed enriched bacterial abundances of Eubacterium, Streptococcus, Adlercreutzia, and Actinomyces, as well as enriched abundances of the microbial sucrose degradation pathway, compared to non-fatigued patients at the end of CRT (n = 15). CONCLUSIONS Differentially abundant microbial taxa were identified in fatigued and non-fatigued rectal cancer participants at the end of CRT. However, the exact role of these taxa (and identification of species) in the biology of CRT-related fatigue remains to be examined.
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Affiliation(s)
| | - Jean Lim
- University of Miami, Miami, FL, USA
| | - Sara Marrero
- College of Arts and Sciences, University of South Florida, Tampa, FL, USA
| | - Elsa Pedro
- School of Pharmacy, Medical Science Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Leorey N Saligan
- Symptom Science Center, Principal Investigator, Symptom Biology Unit, Division of Intramural Research, NINR, NIH, DHHS, Bethesda, MD, USA
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Gut Microbiota and Depressive Symptoms at the End of CRT for Rectal Cancer: A Cross-Sectional Pilot Study. DEPRESSION RESEARCH AND TREATMENT 2021; 2021:7967552. [PMID: 35003805 PMCID: PMC8731300 DOI: 10.1155/2021/7967552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/24/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND The role of alterations in gut microbiota composition (termed dysbiosis) has been implicated in the pathobiology of depressive symptoms; however, evidence remains limited. This cross-sectional pilot study is aimed at exploring whether depressive symptom scores changed during neoadjuvant chemotherapy and radiation therapy to treat rectal cancer, and if gut microbial taxa abundances and predicted functional pathways correlate with depressive symptoms at the end of chemotherapy and radiation therapy. METHODS 40 newly diagnosed rectal cancer patients (ages 28-81; 23 males) were assessed for depressive symptoms using the Hamilton Rating Scale for Depression (HAM-D) and provided stool samples for 16S rRNA sequencing. Gut microbiome data were analyzed using QIIME2, and correlations and regression analyses were performed in R. RESULTS Participants had significantly higher depressive symptoms at the end as compared to before CRT. The relative abundances of Gemella, Bacillales Family XI, Actinomyces, Streptococcus, Lactococcus, Weissella, and Leuconostocaceae were positively correlated (Spearman's rho = 0.42 to 0.32), while Coprobacter, Intestinibacter, Intestimonas, Lachnospiraceae, Phascolarctobacterium, Ruminiclostridium, Ruminococcaceae (UCG-005 and uncultured), Tyzzerella, and Parasutterella (Spearman's rho = -0.43 to - 0.31) were negatively correlated with HAM-D scores. Of the 14 predicted MetaCyc pathways that correlated with depressive symptom scores at the end of CRT, 11 (79%) were associated with biosynthetic pathways. CONCLUSIONS Significant bacterial taxa and predicted functional pathways correlated with depressive symptoms at the end of chemotherapy and radiation therapy for rectal cancer which warrants further examination and replication of our findings.
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Hopper CP, De La Cruz LK, Lyles KV, Wareham LK, Gilbert JA, Eichenbaum Z, Magierowski M, Poole RK, Wollborn J, Wang B. Role of Carbon Monoxide in Host-Gut Microbiome Communication. Chem Rev 2020; 120:13273-13311. [PMID: 33089988 DOI: 10.1021/acs.chemrev.0c00586] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nature is full of examples of symbiotic relationships. The critical symbiotic relation between host and mutualistic bacteria is attracting increasing attention to the degree that the gut microbiome is proposed by some as a new organ system. The microbiome exerts its systemic effect through a diverse range of metabolites, which include gaseous molecules such as H2, CO2, NH3, CH4, NO, H2S, and CO. In turn, the human host can influence the microbiome through these gaseous molecules as well in a reciprocal manner. Among these gaseous molecules, NO, H2S, and CO occupy a special place because of their widely known physiological functions in the host and their overlap and similarity in both targets and functions. The roles that NO and H2S play have been extensively examined by others. Herein, the roles of CO in host-gut microbiome communication are examined through a discussion of (1) host production and function of CO, (2) available CO donors as research tools, (3) CO production from diet and bacterial sources, (4) effect of CO on bacteria including CO sensing, and (5) gut microbiome production of CO. There is a large amount of literature suggesting the "messenger" role of CO in host-gut microbiome communication. However, much more work is needed to begin achieving a systematic understanding of this issue.
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Affiliation(s)
- Christopher P Hopper
- Institute for Experimental Biomedicine, University Hospital Wuerzburg, Wuerzburg, Bavaria DE 97080, Germany.,Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, Florida 32611, United States
| | - Ladie Kimberly De La Cruz
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kristin V Lyles
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lauren K Wareham
- The Vanderbilt Eye Institute and Department of Ophthalmology & Visual Sciences, The Vanderbilt University Medical Center and School of Medicine, Nashville, Tennessee 37232, United States
| | - Jack A Gilbert
- Department of Pediatrics, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Zehava Eichenbaum
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Marcin Magierowski
- Cellular Engineering and Isotope Diagnostics Laboratory, Department of Physiology, Jagiellonian University Medical College, Cracow PL 31-531, Poland
| | - Robert K Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Sheffield S10 2TN, U.K
| | - Jakob Wollborn
- Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg DE 79085, Germany.,Department of Anesthesiology, Perioperative and Pain Management, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Binghe Wang
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
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Gonzalez-Mercado VJ, Marrero S, Marrero-Falcon MA, Saligan LN. Factors Affecting the Severity of Fatigue during Radiotherapy for Prostate Cancer; an Exploratory Study. UROLOGIC NURSING 2020; 40:129-138. [PMID: 34220179 PMCID: PMC8248518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Limited studies have examined potential risk factors associated with the fatigue experience of a sample of Puerto Rican men treated with radiotherapy for non-metastatic prostate cancer. Identifying these factors may provide initial information about targets for individualized interventions, leading to more effective management of fatigue in this population. PURPOSE To examine the relationship of age, body max index, depressive symptoms, physical activity, and sleep disturbance with fatigue during radiotherapy for prostate cancer. METHODS Twenty six participants completed five inventories: demographic intake, health form, the Functional Assessment of Cancer-Therapy-fatigue, Patient-Reported Outcome Measures Information System-Sleep disturbance, and the International Physical Activity Questionnaire-Short Form before, middle/days 19-21 and completion/days 38-42 of radiotherapy. The principal investigator rated the Hamilton depression scale. Descriptive statistics were performed. Interactions and influence of variables on fatigue were assessed using bivariate correlation and multiple linear regression, respectively. RESULTS At each study time point, sleep disturbance and depressive symptoms were strongly correlated with each other and fatigue. The linear combination of sleep disturbance and depressive symptoms was significantly related to fatigue. CONCLUSION Given the high association of sleep disturbance and depressive symptoms with fatigue, clinicians should assess and develop interventions to manage these symptoms altogether.
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Affiliation(s)
| | - Sara Marrero
- University of South Florida College of Arts and Sciences, Tampa, FL, United States
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