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Teixeira M, Silva F, Ferreira RM, Pereira T, Figueiredo C, Oliveira HP. A review of machine learning methods for cancer characterization from microbiome data. NPJ Precis Oncol 2024; 8:123. [PMID: 38816569 PMCID: PMC11139966 DOI: 10.1038/s41698-024-00617-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Recent studies have shown that the microbiome can impact cancer development, progression, and response to therapies suggesting microbiome-based approaches for cancer characterization. As cancer-related signatures are complex and implicate many taxa, their discovery often requires Machine Learning approaches. This review discusses Machine Learning methods for cancer characterization from microbiome data. It focuses on the implications of choices undertaken during sample collection, feature selection and pre-processing. It also discusses ML model selection, guiding how to choose an ML model, and model validation. Finally, it enumerates current limitations and how these may be surpassed. Proposed methods, often based on Random Forests, show promising results, however insufficient for widespread clinical usage. Studies often report conflicting results mainly due to ML models with poor generalizability. We expect that evaluating models with expanded, hold-out datasets, removing technical artifacts, exploring representations of the microbiome other than taxonomical profiles, leveraging advances in deep learning, and developing ML models better adapted to the characteristics of microbiome data will improve the performance and generalizability of models and enable their usage in the clinic.
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Affiliation(s)
- Marco Teixeira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal.
- Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Francisco Silva
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
| | - Rui M Ferreira
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Ceu Figueiredo
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Hélder P Oliveira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
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2
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Grion BAR, Fonseca PLC, Kato RB, García GJY, Vaz ABM, Jiménez BN, Dambolenea AL, Garcia-Etxebarria K, Brenig B, Azevedo V, Bujanda L, Banales JM, Góes-Neto A. Identification of taxonomic changes in the fecal bacteriome associated with colorectal polyps and cancer: potential biomarkers for early diagnosis. Front Microbiol 2024; 14:1292490. [PMID: 38293554 PMCID: PMC10827328 DOI: 10.3389/fmicb.2023.1292490] [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: 09/11/2023] [Accepted: 12/26/2023] [Indexed: 02/01/2024] Open
Abstract
Colorectal cancer (CRC) commonly arises in individuals with premalignant colon lesions known as polyps, with both conditions being influenced by gut microbiota. Host-related factors and inherent characteristics of polyps and tumors may contribute to microbiome variability, potentially acting as confounding factors in the discovery of taxonomic biomarkers for both conditions. In this study we employed shotgun metagenomics to analyze the taxonomic diversity of bacteria present in fecal samples of 90 clinical subjects (comprising 30 CRC patients, 30 with polyps and 30 controls). Our findings revealed a decrease in taxonomic richness among individuals with polyps and CRC, with significant dissimilarities observed among the study groups. We identified significant alterations in the abundance of specific taxa associated with polyps (Streptococcaceae, Lachnoclostridium, and Ralstonia) and CRC (Lactobacillales, Clostridiaceae, Desulfovibrio, SFB, Ruminococcus, and Faecalibacterium). Clostridiaceae exhibited significantly lower abundance in the early stages of CRC. Additionally, our study revealed a positive co-occurrence among underrepresented genera in CRC, while demonstrating a negative co-occurrence between Faecalibacterium and Desulfovibrio, suggesting potential antagonistic relationships. Moreover, we observed variations in taxonomic richness and/or abundance within the polyp and CRC bacteriome linked to polyp size, tumor stage, dyslipidemia, diabetes with metformin use, sex, age, and family history of CRC. These findings provide potential new biomarkers to enhance early CRC diagnosis while also demonstrating how intrinsic host factors contribute to establishing a heterogeneous microbiome in patients with CRC and polyps.
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Affiliation(s)
- Beatriz Alessandra Rudi Grion
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Paula Luize Camargos Fonseca
- Integrative Biology Laboratory, Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Aline Bruna Martins Vaz
- Oswaldo Cruz Foundation (Fiocruz-MG), Minas Gerais, Brazil
- Medical School, Universidade José do Rosário Vellano (UNIFENAS), Belo Horizonte, Brazil
| | - Beatriz Nafría Jiménez
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, Ikerbasque, San Sebastian, Spain
| | - Ainhoa Lapitz Dambolenea
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, Ikerbasque, San Sebastian, Spain
| | - Koldo Garcia-Etxebarria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, Ikerbasque, San Sebastian, Spain
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, Ikerbasque, San Sebastian, Spain
| | - Jesus M. Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, Ikerbasque, San Sebastian, Spain
- CIBERehd, Madrid, Spain
- Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain
| | - Aristóteles Góes-Neto
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Brazil
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3
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Welham Z, Li J, Engel AF, Molloy MP. Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing. Cancers (Basel) 2023; 15:5045. [PMID: 37894412 PMCID: PMC10605900 DOI: 10.3390/cancers15205045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
Numerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial taxonomy, and this has led, in part, to inconsistent findings between studies. Here, we examined mucosal microbiota from patients who presented with one or more polyps, compared to patients with no polyps, at the time of colonoscopy. We evaluated the results obtained using both short-read and PacBio long-read 16S rRNA sequencing. Neither sequencing technology identified significant differences in microbial diversity measures between patients with or without bowel polyps. Differential abundance measures showed that amplicon sequence variants (ASVs) associated with Ruminococcus gnavus and Escherichia coli were elevated in mucosa from polyp patients, while ASVs associated with Parabacteroides merdae, Veillonella nakazawae, and Sutterella wadsworthensis were relatively decreased. Only R. gnavus was consistently identified using both sequencing technologies as being altered between patients with polyps compared to patients without polyps, suggesting differences in technologies and bioinformatics processing impact study findings. Several of the differentially abundant bacteria identified using either sequencing technology are associated with inflammatory bowel diseases despite these patients being excluded from the current study, which suggests that early bowel neoplasia may be associated with a local inflammatory niche.
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Affiliation(s)
- Zoe Welham
- Bowel Cancer and Biomarker Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia; (Z.W.); (J.L.)
| | - Jun Li
- Bowel Cancer and Biomarker Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia; (Z.W.); (J.L.)
| | - Alexander F. Engel
- Colorectal Surgical Unit, Royal North Shore Hospital, Sydney 2065, Australia;
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney 2050, Australia
| | - Mark P. Molloy
- Bowel Cancer and Biomarker Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, Australia; (Z.W.); (J.L.)
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Freitas P, Silva F, Sousa JV, Ferreira RM, Figueiredo C, Pereira T, Oliveira HP. Machine learning-based approaches for cancer prediction using microbiome data. Sci Rep 2023; 13:11821. [PMID: 37479864 PMCID: PMC10362018 DOI: 10.1038/s41598-023-38670-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023] Open
Abstract
Emerging evidence of the relationship between the microbiome composition and the development of numerous diseases, including cancer, has led to an increasing interest in the study of the human microbiome. Technological breakthroughs regarding DNA sequencing methods propelled microbiome studies with a large number of samples, which called for the necessity of more sophisticated data-analytical tools to analyze this complex relationship. The aim of this work was to develop a machine learning-based approach to distinguish the type of cancer based on the analysis of the tissue-specific microbial information, assessing the human microbiome as valuable predictive information for cancer identification. For this purpose, Random Forest algorithms were trained for the classification of five types of cancer-head and neck, esophageal, stomach, colon, and rectum cancers-with samples provided by The Cancer Microbiome Atlas database. One versus all and multi-class classification studies were conducted to evaluate the discriminative capability of the microbial data across increasing levels of cancer site specificity, with results showing a progressive rise in difficulty for accurate sample classification. Random Forest models achieved promising performances when predicting head and neck, stomach, and colon cancer cases, with the latter returning accuracy scores above 90% across the different studies conducted. However, there was also an increased difficulty when discriminating esophageal and rectum cancers, failing to differentiate with adequate results rectum from colon cancer cases, and esophageal from head and neck and stomach cancers. These results point to the fact that anatomically adjacent cancers can be more complex to identify due to microbial similarities. Despite the limitations, microbiome data analysis using machine learning may advance novel strategies to improve cancer detection and prevention, and decrease disease burden.
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Affiliation(s)
- Pedro Freitas
- INESC TEC - Institute for Systems and Computer Engineering, Technology and Science, 4200-465, Porto, Portugal.
- FEUP - Faculty of Engineering, University of Porto, 4200-465, Porto, Portugal.
| | - Francisco Silva
- INESC TEC - Institute for Systems and Computer Engineering, Technology and Science, 4200-465, Porto, Portugal
- FCUP -Faculty of Science, University of Porto, 4150-177, Porto, Portugal
| | - Joana Vale Sousa
- INESC TEC - Institute for Systems and Computer Engineering, Technology and Science, 4200-465, Porto, Portugal
- FEUP - Faculty of Engineering, University of Porto, 4200-465, Porto, Portugal
| | - Rui M Ferreira
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135, Porto, Portugal
| | - Céu Figueiredo
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135, Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135, Porto, Portugal
- FMUP - Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Tania Pereira
- INESC TEC - Institute for Systems and Computer Engineering, Technology and Science, 4200-465, Porto, Portugal
| | - Hélder P Oliveira
- INESC TEC - Institute for Systems and Computer Engineering, Technology and Science, 4200-465, Porto, Portugal
- FCUP -Faculty of Science, University of Porto, 4150-177, Porto, Portugal
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Alharfi S, Furey N, Al-Shakhshir H, Ghannoum M, Cooper GS. Fecal Microbiome Associated with Both Colon Adenomas and Lifetime Colorectal Cancer Risk. Dig Dis Sci 2023; 68:1492-1499. [PMID: 35986796 DOI: 10.1007/s10620-022-07673-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/12/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Increasing data indicates the gut flora including bacteria and fungi combined with environmental factors are important in the pathogenesis of colorectal cancer (CRC). Understanding differences in the microbiome in patients with colon neoplasia will foster the development of biomarkers for early detection. AIMS Determine the association of microbiome with presence of adenomas and predicted CRC risk. METHODS In subjects referred for colonoscopy, the NCI CRC risk assessment tool was completed and stool for microbiome analysis as well as fecal immunochemical test (FIT) were collected. We calculated the microbiome alpha diversity using the Shannon index as well as individual bacterial and fungal species. RESULTS Among 34 patients, we identified 10 with one or more adenomas. Only 2 patients were FIT positive. The median predicted lifetime CRC risk was 2.75% and the prevalence of adenoma was higher in the fourth quartile (P < 0.001). The measured alpha diversity was somewhat higher in patients with adenomas (P = 0.07). We identified 4 bacterial species with an increased relative abundance among patients with adenomas [P < 0.5]. Lifetime CRC risk was associated with 2 specific bacterial species, P. distasonis & E. hermannii [P = 0.05 & 0.09, respectively]. No associations were seen with fungal species and adenoma prevalence or lifetime CRC risk. CONCLUSIONS In addition to a strong correlation of predicted CRC risk and adenoma prevalence, we also found important differences in specific bacterial species and both adenoma prevalence and CRC risk. Larger trials are needed to potentially implement further data in the clinical setting.
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Affiliation(s)
- Sarah Alharfi
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nancy Furey
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Division of Gastroenterology, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106-5066, USA
| | - Hilmi Al-Shakhshir
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Mahmoud Ghannoum
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- The Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Gregory S Cooper
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- The Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Division of Gastroenterology, University Hospitals Cleveland Medical Center, Cleveland, OH, 44106-5066, USA.
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6
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Schlechte J, Zucoloto AZ, Yu IL, Doig CJ, Dunbar MJ, McCoy KD, McDonald B. Dysbiosis of a microbiota-immune metasystem in critical illness is associated with nosocomial infections. Nat Med 2023; 29:1017-1027. [PMID: 36894652 PMCID: PMC10115642 DOI: 10.1038/s41591-023-02243-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
Critically ill patients in intensive care units experience profound alterations of their gut microbiota that have been linked to a high risk of hospital-acquired (nosocomial) infections and adverse outcomes through unclear mechanisms. Abundant mouse and limited human data suggest that the gut microbiota can contribute to maintenance of systemic immune homeostasis, and that intestinal dysbiosis may lead to defects in immune defense against infections. Here we use integrated systems-level analyses of fecal microbiota dynamics in rectal swabs and single-cell profiling of systemic immune and inflammatory responses in a prospective longitudinal cohort study of critically ill patients to show that the gut microbiota and systemic immunity function as an integrated metasystem, where intestinal dysbiosis is coupled to impaired host defense and increased frequency of nosocomial infections. Longitudinal microbiota analysis by 16s rRNA gene sequencing of rectal swabs and single-cell profiling of blood using mass cytometry revealed that microbiota and immune dynamics during acute critical illness were highly interconnected and dominated by Enterobacteriaceae enrichment, dysregulated myeloid cell responses and amplified systemic inflammation, with a lesser impact on adaptive mechanisms of host defense. Intestinal Enterobacteriaceae enrichment was coupled with impaired innate antimicrobial effector responses, including hypofunctional and immature neutrophils and was associated with an increased risk of infections by various bacterial and fungal pathogens. Collectively, our findings suggest that dysbiosis of an interconnected metasystem between the gut microbiota and systemic immune response may drive impaired host defense and susceptibility to nosocomial infections in critical illness.
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Affiliation(s)
- Jared Schlechte
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Amanda Z Zucoloto
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ian-Ling Yu
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Christopher J Doig
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mary J Dunbar
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kathy D McCoy
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Braedon McDonald
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
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Khannous-Lleiffe O, Willis JR, Saus E, Moreno V, Castellví-Bel S, Gabaldón T. Microbiome Profiling from Fecal Immunochemical Test Reveals Microbial Signatures with Potential for Colorectal Cancer Screening. Cancers (Basel) 2022; 15:cancers15010120. [PMID: 36612118 PMCID: PMC9817783 DOI: 10.3390/cancers15010120] [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: 11/09/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer deaths worldwide. Early diagnosis of CRC, which saves lives and enables better outcomes, is generally implemented through a two-step population screening approach based on the use of Fecal Immunochemical Test (FIT) followed by colonoscopy if the test is positive. However, the FIT step has a high false positive rate, and there is a need for new predictive biomarkers to better prioritize cases for colonoscopy. Here we used 16S rRNA metabarcoding from FIT positive samples to uncover microbial taxa, taxon co-occurrence and metabolic features significantly associated with different colonoscopy outcomes, underscoring a predictive potential and revealing changes along the path from healthy tissue to carcinoma. Finally, we used machine learning to develop a two-phase classifier which reduces the current false positive rate while maximizing the inclusion of CRC and clinically relevant samples.
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Affiliation(s)
- Olfat Khannous-Lleiffe
- Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jesse R. Willis
- Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Av. de Monforte de Lemos, 3–5, 28029 Madrid, Spain
- Gastroenterology Department, University of Barcelona, 08036 Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, University of Barcelona, 08036 Barcelona, Spain
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, 08036 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Center (BSC-CNS), Carrer de Jordi Girona, 29, 31, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Centro Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), 08028 Barcelona, Spain
- Correspondence:
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Loganathan T, Priya Doss C G. The influence of machine learning technologies in gut microbiome research and cancer studies - A review. Life Sci 2022; 311:121118. [DOI: 10.1016/j.lfs.2022.121118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022]
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9
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Zhang H, Wu J, Ji D, Liu Y, Lu S, Lin Z, Chen T, Ao L. Microbiome analysis reveals universal diagnostic biomarkers for colorectal cancer across populations and technologies. Front Microbiol 2022; 13:1005201. [PMID: 36406447 PMCID: PMC9668862 DOI: 10.3389/fmicb.2022.1005201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/05/2022] [Indexed: 01/19/2024] Open
Abstract
The gut microbial dysbiosis is a risk of colorectal cancer (CRC) and some bacteria have been reported as potential markers for CRC diagnosis. However, heterogeneity among studies with different populations and technologies lead to inconsistent results. Here, we investigated six metagenomic profiles of stool samples from healthy controls (HC), colorectal adenoma (CA) and CRC, and six and four genera were consistently altered between CRC and HC or CA across populations, respectively. In FengQ cohort, which composed with 61 HC, 47 CA, and 46 CRC samples, a random forest (RF) model composed of the six genera, denoted as signature-HC, distinguished CRC from HC with an area under the curve (AUC) of 0.84. Similarly, another RF model composed of the four universal genera, denoted as signature-CA, discriminated CRC from CA with an AUC of 0.73. These signatures were further validated in five metagenomic sequencing cohorts and six independent 16S rRNA gene sequencing cohorts. Interestingly, three genera overlapped in the two models (Porphyromonas, Parvimonas and Peptostreptococcus) were with very low abundance in HC and CA, but sharply increased in CRC. A concise RF model on the three genera distinguished CRC from HC or CA with AUC of 0.87 and 0.67, respectively. Functional gene family analysis revealed that Kyoto Encyclopedia of Genes and Genomes Orthogroups categories which were significantly correlated with markers in signature-HC and signature-CA were mapped into pathways related to lipopolysaccharide and sulfur metabolism, which might be vital risk factors of CRC development. Conclusively, our study identified universal bacterial markers across populations and technologies as potential aids in non-invasive diagnosis of CRC.
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Affiliation(s)
- Huarong Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Junling Wu
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Daihan Ji
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Yijuan Liu
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
- Department of Gastroenterology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Shuting Lu
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Zeman Lin
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Ting Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lu Ao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
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10
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The crosstalk of the human microbiome in breast and colon cancer: A metabolomics analysis. Crit Rev Oncol Hematol 2022; 176:103757. [PMID: 35809795 DOI: 10.1016/j.critrevonc.2022.103757] [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: 05/27/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
The human microbiome's role in colon and breast cancer is described in this review. Understanding how the human microbiome and metabolomics interact with breast and colon cancer is the chief area of this study. First, the role of the gut and distal microbiome in breast and colon cancer is investigated, and the direct relationship between microbial dysbiosis and breast and colon cancer is highlighted. This work also focuses on the many metabolomic techniques used to locate prospective biomarkers, make an accurate diagnosis, and research new therapeutic targets for cancer treatment. This review clarifies the influence of anti-tumor medications on the microbiota and the proactive measures that can be taken to treat cancer using a variety of therapies, including radiotherapy, chemotherapy, next-generation biotherapeutics, gene-based therapy, integrated omics technology, and machine learning.
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11
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Luo Y, Cui X, Cheruba E, Chua YK, Ng C, Tan RZ, Tan KK, Cheow LF. SAMBA: A Multicolor Digital Melting PCR Platform for Rapid Microbiome Profiling. SMALL METHODS 2022; 6:e2200185. [PMID: 35652511 DOI: 10.1002/smtd.202200185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/27/2022] [Indexed: 06/15/2023]
Abstract
During the past decade, breakthroughs in sequencing technology have provided the basis for studies of the myriad ways in which microbial communities in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and quantitative profiling of the microbiota for use in diagnostic and therapeutic applications. However, the current next-generation sequencing approach for microbiome profiling is costly, requires laborious library preparation, and is challenging to scale up for routine diagnostics. Split, Amplify, and Melt analysis of BActeria-community (SAMBA), a novel multicolor digital melting polymerase chain reaction platform with unprecedented multiplexing capability is presented, and the capability to distinguish and quantify 16 bacteria species in mixtures is demonstrated. Subsequently, SAMBA is applied to measure the compositions of bacteria in the gut microbiome to identify microbial dysbiosis related to colorectal cancer. This rapid, low cost, and high-throughput approach will enable the implementation of microbiome diagnostics in clinical laboratories and routine medical practice.
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Affiliation(s)
- Yongqiang Luo
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Xu Cui
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Yong Kang Chua
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Charmaine Ng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Rui Zhen Tan
- Engineering Cluster, Singapore Institute of Technology, Singapore, 138683, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Division of Colorectal Surgery, National University Hospital, Singapore, 119074, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
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12
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Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R. Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Bioessays 2022; 44:e2100252. [PMID: 35253252 PMCID: PMC10506734 DOI: 10.1002/bies.202100252] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022]
Abstract
The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome-the metagenome-are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host-centric methods. Furthermore, the discoveries of intracellular and intra-metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non-human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs.
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Affiliation(s)
| | - Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Lucie Laplane
- Institut d’histoire et de philosophie des sciences et des techniques (UMR8590), CNRS & Panthéon-Sorbonne University, 75006 Paris, France
- Hematopoietic stem cells and the development of myeloid malignancies (UMR1287), Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Thomas Pradeu
- ImmunoConcept (UMR5164), CNRS & University of Bordeaux, 33076 Bordeaux Cedex, France
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
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13
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Liang JQ, Zeng Y, Kwok G, Cheung CP, Suen BY, Ching JYL, To KF, Yu J, Chan FKL, Ng SC. Novel microbiome signatures for non-invasive diagnosis of adenoma recurrence after colonoscopic polypectomy. Aliment Pharmacol Ther 2022; 55:847-855. [PMID: 35224756 PMCID: PMC9303256 DOI: 10.1111/apt.16799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/14/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND We previously reported a panel of novel faecal microbiome gene markers for diagnosis of colorectal adenoma and cancer. AIM To evaluate whether these markers are useful in detecting adenoma recurrence after polypectomy. METHODS Subjects were enrolled in a polyp surveillance study from 2009 to 2019. Stool samples were collected before bowel preparation of index colonoscopy (baseline) and surveillance colonoscopy (follow-up). Fusobacterium nucleatum (Fn), Lachnoclostridium marker (m3), Clostridium hathewayi (Ch) and Bacteroides clarus were quantified in baseline and follow-up samples by quantitative polymerase chain reaction (qPCR) to correlate with adenoma recurrence. Recurrence was defined as new adenomas detected >6 months after polypectomy. Faecal immunochemical test (FIT) was performed for comparison. RESULTS A total of 161 baseline and 104 follow-up samples were analysed. Among patients with adenoma recurrence, Fn and m3 increased (both P < 0.05) while Ch were unchanged in follow-up versus baseline samples. Among patients without recurrence, Fn and m3 were unchanged while Ch decreased (P < 0.05) in follow-up versus baseline samples. Logistic regression that included changes of m3, Fn and Ch at follow-up compared with baseline achieved an area under receiver operating characteristic curve (AUROC) of 0.95 (95%CI: 0.84-0.99) with 90.0% sensitivity and 87.0% specificity for detecting recurrent adenoma. Combination of m3, Fn and Ch at follow-up sample achieved AUROC of 0.74 (95%CI: 0.65-0.82) with 81.3% sensitivity and 55.4% specificity for detecting recurrent adenoma. FIT showed limited sensitivity (8.3%) in detecting recurrent adenomas. CONCLUSION Our combinations of faecal microbiome gene markers can be potentially useful non-invasive tools for detecting adenoma recurrence.
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Affiliation(s)
- Jessie Qiaoyi Liang
- Department of Microbiology, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Yao Zeng
- Department of Microbiology, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Grace Kwok
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina
| | - Chun Pan Cheung
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Bing Yee Suen
- Department of SurgeryThe Chinese University of Hong KongHong KongChina
| | - Jessica Y. L. Ching
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Ka Fai To
- Department of Anatomy Chemical PathologyThe Chinese University of Hong KongHong KongChina
| | - Jun Yu
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina
| | - Francis K. L. Chan
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Siew Chien Ng
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
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14
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Comparing Published Gut Microbiome Taxonomic Data Across Multinational Studies. Nurs Res 2022; 71:43-53. [PMID: 34985847 PMCID: PMC8740627 DOI: 10.1097/nnr.0000000000000557] [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: 01/03/2023]
Abstract
BACKGROUND Nurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design and hypothesis generation. OBJECTIVES This article aims to present and define important analysis considerations in microbiome study planning and to identify genera shared across studies despite methodological differences. This methods article will highlight a workflow that the nurse scientist can use to combine and evaluate taxonomy tables for microbiome study or research proposal planning. METHODS We compiled taxonomy tables from 13 published gut microbiome studies that had used Ion Torrent sequencing technology. We searched for studies that had amplified multiple hypervariable (V) regions of the 16S rRNA gene when sequencing the bacteria from healthy gut samples. RESULTS We obtained 15 taxonomy tables from the 13 studies, comprised of samples from four continents and eight V regions. Methodology among studies was highly variable, including differences in V regions amplified, geographic location, and population demographics. Nevertheless, of the 354 total genera identified from the 15 data sets, 25 were shared in all V regions and the four continents. When relative abundance differences across the V regions were compared, Dorea and Roseburia were statistically different. Taxonomy tables from Asian subjects had increased average abundances of Prevotella and lowered abundances of Bacteroides compared with the European, North American, and South American study subjects. DISCUSSION Evaluating taxonomy tables from previously published literature is essential for study planning. The genera found from different V regions and continents highlight geography and V region as important variables to consider in microbiome study design. The 25 shared genera across the various studies may represent genera commonly found in healthy gut microbiomes. Understanding the factors that may affect the results from a variety of microbiome studies will allow nurse scientists to plan research proposals in an informed manner. This work presents a valuable framework for future cross-study comparisons conducted across the globe.
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15
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Chen H, Lu B, Dai M. Colorectal Cancer Screening in China: Status, Challenges, and Prospects — China, 2022. China CDC Wkly 2022; 4:322-328. [PMID: 35548454 PMCID: PMC9081894 DOI: 10.46234/ccdcw2022.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/10/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hongda Chen
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Lu
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Dai
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Min Dai,
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16
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Wan XH. Artificial intelligence reveals roles of gut microbiota in driving human colorectal cancer evolution. Artif Intell Cancer 2021; 2:69-78. [DOI: 10.35713/aic.v2.i5.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
With the rapid development of high-throughput sequencing and artificial intelligence (AI) techniques, gut mucosal microbiota begins to be recognized as critical drivers of human colorectal cancer (CRC). Various AI approaches have been designed to obtain effective information from enormous numbers of microbial cells residing in gut mucosal as well as cancer cells. These mainly include detection of microbial markers for early clinical diagnosis of stage-specific CRC, characterization of pathogenic bacterial activities via genomic and transcriptomic analyses, and prediction of interplay between bacterial drivers and host immune systems. Here I review the current progresses of AI applications in profiling gut microbiomes linked to CRC initiation and development. I further look forward to future AI research for improving our understanding of the roles of gut microbiota in CRC evolution.
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Affiliation(s)
- Xue-Hua Wan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
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17
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Shamsaddini A, Gillevet PM, Acharya C, Fagan A, Gavis E, Sikaroodi M, McGeorge S, Khoruts A, Albhaisi S, Fuchs M, Sterling RK, Bajaj JS. Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis. Gastroenterology 2021; 161:508-521.e7. [PMID: 33857456 PMCID: PMC9069394 DOI: 10.1053/j.gastro.2021.04.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes. METHODS In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning. RESULTS A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs. CONCLUSIONS Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.
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Affiliation(s)
| | | | - Chathur Acharya
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Andrew Fagan
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Edith Gavis
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | | | - Sara McGeorge
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Alexander Khoruts
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Somaya Albhaisi
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Michael Fuchs
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Richard K. Sterling
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
| | - Jasmohan S. Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia
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18
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Sin RWY, Foo DCC, Iyer DN, Fan MSY, Li X, Lo OSH, Law WL, Ng L. A Pilot Study Investigating the Expression Levels of Pluripotency-Associated Genes in Rectal Swab Samples for Colorectal Polyp and Cancer Diagnosis and Prognosis. Stem Cells Int 2021; 2021:4139528. [PMID: 34335790 PMCID: PMC8324395 DOI: 10.1155/2021/4139528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 12/11/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Change in gene expression is inevitable in cancer development. With more studies demonstrating the contributions of cancer stem cells (CSCs) in colorectal cancer (CRC) development, this study is aimed at investigating whether rectal swab specimen serves as a tool for detection of dysregulation of CSC or stem cell (SC) markers and at evaluating its potential as a new promising screening method for high-risk patients. Expression levels of 15 pluripotency-associated genes were assessed by quantitative PCR in 53 rectal swab specimens referred for endoscopic screening. Dysregulated genes and joint panels based on such genes were examined for their diagnostic potentials for both polyp and CRC. Out of 15 genes, Oct4, CD26, c-MYC, and CXCR4 showed significantly differential expression among normal, polyp, and CRC patients. A panel of Oct4 and CD26 showed an AUC value of 0.80 (p = 0.003) in identifying CRC patients from polyp/normal subjects, with sensitivity and specificity of 84.6% and 69.2%. A panel of c-MYC and CXCR4 achieved CRC/polyp identification with an AUC value of 0.79 (p = 0.002), with a sensitivity of 82.8% and specificity of 80.0%. The sensitivity for polyp and CRC was 80.0% and 85.7%, respectively. Further analysis showed that higher c-MYC and CXCR4 level was detected in normal subjects who developed polyps after 5-6 years, in comparison with subjects with no lesion developed, and the AUC of the c-MYC and CXCR4 panel increased to 0.88 (p < 0.001), with sensitivity and specificity of 84.4% and 92.3%, respectively, when these patients were included in the polyp group. This study suggests that the Oct4 and CD26 panel is a promising biomarker for distinguishing CRC from normal and polyp patients, whereas the c-MYC and CXCR4 panel may identify polyp and CRC from normal individuals.
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Affiliation(s)
- Ryan Wai-Yan Sin
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Dominic Chi-Chung Foo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Deepak Narayanan Iyer
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - May Sau-Yee Fan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xue Li
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Oswens Siu-Hung Lo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wai-Lun Law
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lui Ng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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19
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Genomic, Microbial and Immunological Microenvironment of Colorectal Polyps. Cancers (Basel) 2021; 13:cancers13143382. [PMID: 34298598 PMCID: PMC8303543 DOI: 10.3390/cancers13143382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Colorectal cancers (CRC) initiate from small cell clusters known as polyps. Colonoscopic surveillance and removal of polyps is an important strategy to prevent CRC progression. Recent advances in sequencing technologies have highlighted genetic mutations in polyps that potentially contribute to CRC development. However, CRC might be considered more than a genetic disease, as emerging evidence describes early changes to immune surveillance and gut microbiota in people with polyps. Here, we review the molecular landscape of colorectal polyps, considering their genomic, microbial and immunological features, and discuss the potential clinical utility of these data. Abstract Colorectal cancer (CRC) develops from pre-cancerous cellular lesions in the gut epithelium, known as polyps. Polyps themselves arise through the accumulation of mutations that disrupt the function of key tumour suppressor genes, activate proto-oncogenes and allow proliferation in an environment where immune control has been compromised. Consequently, colonoscopic surveillance and polypectomy are central pillars of cancer control strategies. Recent advances in genomic sequencing technologies have enhanced our knowledge of key driver mutations in polyp lesions that likely contribute to CRC. In accordance with the prognostic significance of Immunoscores for CRC survival, there is also a likely role for early immunological changes in polyps, including an increase in regulatory T cells and a decrease in mature dendritic cell numbers. Gut microbiotas are under increasing research interest for their potential contribution to CRC evolution, and changes in the gut microbiome have been reported from analyses of adenomas. Given that early changes to molecular components of bowel polyps may have a direct impact on cancer development and/or act as indicators of early disease, we review the molecular landscape of colorectal polyps, with an emphasis on immunological and microbial alterations occurring in the gut and propose the potential clinical utility of these data.
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20
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Illescas O, Rodríguez-Sosa M, Gariboldi M. Mediterranean Diet to Prevent the Development of Colon Diseases: A Meta-Analysis of Gut Microbiota Studies. Nutrients 2021; 13:nu13072234. [PMID: 34209683 PMCID: PMC8308215 DOI: 10.3390/nu13072234] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota dysbiosis is a common feature in colorectal cancer (CRC) and inflammatory bowel diseases (IBD). Adoption of the Mediterranean diet (MD) has been proposed as a therapeutic approach for the prevention of multiple diseases, and one of its mechanisms of action is the modulation of the microbiota. We aimed to determine whether MD can be used as a preventive measure against cancer and inflammation-related diseases of the gut, based on its capacity to modulate the local microbiota. A joint meta-analysis of publicly available 16S data derived from subjects following MD or other diets and from patients with CRC, IBD, or other gut-related diseases was conducted. We observed that the microbiota associated with MD was enriched in bacteria that promote an anti-inflammatory environment but low in taxa with pro-inflammatory properties capable of altering intestinal barrier functions. We found an opposite trend in patients with intestinal diseases, including cancer. Some of these differences were maintained even when MD was compared to healthy controls without a defined diet. Our findings highlight the unique effects of MD on the gut microbiota and suggest that integrating MD principles into a person’s lifestyle may serve as a preventive method against cancer and other gut-related diseases.
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Affiliation(s)
- Oscar Illescas
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy;
| | - Miriam Rodríguez-Sosa
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), Tlalnepantla C.P. 54090, MEX, Mexico;
| | - Manuela Gariboldi
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy;
- Correspondence: ; Tel.: +39-2-23902042
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21
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Cao B, Zhang KC, Wei B, Chen L. Status quo and future prospects of artificial neural network from the perspective of gastroenterologists. World J Gastroenterol 2021; 27:2681-2709. [PMID: 34135549 PMCID: PMC8173384 DOI: 10.3748/wjg.v27.i21.2681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/29/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Artificial neural networks (ANNs) are one of the primary types of artificial intelligence and have been rapidly developed and used in many fields. In recent years, there has been a sharp increase in research concerning ANNs in gastrointestinal (GI) diseases. This state-of-the-art technique exhibits excellent performance in diagnosis, prognostic prediction, and treatment. Competitions between ANNs and GI experts suggest that efficiency and accuracy might be compatible in virtue of technique advancements. However, the shortcomings of ANNs are not negligible and may induce alterations in many aspects of medical practice. In this review, we introduce basic knowledge about ANNs and summarize the current achievements of ANNs in GI diseases from the perspective of gastroenterologists. Existing limitations and future directions are also proposed to optimize ANN’s clinical potential. In consideration of barriers to interdisciplinary knowledge, sophisticated concepts are discussed using plain words and metaphors to make this review more easily understood by medical practitioners and the general public.
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Affiliation(s)
- Bo Cao
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Ke-Cheng Zhang
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Bo Wei
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
| | - Lin Chen
- Department of General Surgery & Institute of General Surgery, Chinese People’s Liberation Army General Hospital, Beijing 100853, China
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22
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Wu Y, Jiao N, Zhu R, Zhang Y, Wu D, Wang AJ, Fang S, Tao L, Li Y, Cheng S, He X, Lan P, Tian C, Liu NN, Zhu L. Identification of microbial markers across populations in early detection of colorectal cancer. Nat Commun 2021; 12:3063. [PMID: 34031391 PMCID: PMC8144394 DOI: 10.1038/s41467-021-23265-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
Associations between gut microbiota and colorectal cancer (CRC) have been widely investigated. However, the replicable markers for early-stage adenoma diagnosis across multiple populations remain elusive. Here, we perform an integrated analysis on 1056 public fecal samples, to identify adenoma-associated microbial markers for early detection of CRC. After adjusting for potential confounders, Random Forest classifiers are constructed with 11 markers to discriminate adenoma from control (area under the ROC curve (AUC) = 0.80), and 26 markers to discriminate adenoma from CRC (AUC = 0.89), respectively. Moreover, we validate the classifiers in two independent cohorts achieving AUCs of 0.78 and 0.84, respectively. Functional analysis reveals that the altered microbiome is characterized with increased ADP-L-glycero-beta-D-manno-heptose biosynthesis in adenoma and elevated menaquinone-10 biosynthesis in CRC. These findings are validated in a newly-collected cohort of 43 samples using quantitative real-time PCR. This work proves the validity of adenoma-specific markers across multi-populations, which would contribute to the early diagnosis and treatment of CRC.
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Affiliation(s)
- Yuanqi Wu
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Na Jiao
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ruixin Zhu
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Dingfeng Wu
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - An-Jun Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Sa Fang
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Liwen Tao
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Yichen Li
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Sijing Cheng
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Medicine, Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiaosheng He
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ping Lan
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Medicine, Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Chuan Tian
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.
| | - Ning-Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
| | - Lixin Zhu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.
- Genome, Environment and Microbiome Community of Excellence, The State University of New York at Buffalo, Buffalo, NY, USA.
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23
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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.
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24
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Shamsaddini A, Dadkhah K, Gillevet PM. BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline. PLoS One 2020; 15:e0234860. [PMID: 32555605 PMCID: PMC7302521 DOI: 10.1371/journal.pone.0234860] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Current microbiome applications require substantial bioinformatics expertise to execute. As microbiome clinical diagnostics are being developed, there is a critical need to implement computational tools and applications that are user-friendly for the medical community to understand microbiome correlation with the health. To address this need, we have developed BiomMiner (pronounced as “biominer”), an automated pipeline that provides a comprehensive analysis of microbiome data. The pipeline finds taxonomic signatures of microbiome data and compiles actionable clinical report that allows clinicians and biomedical scientists to efficiently perform statistical analysis and data mining on the large microbiome datasets. BiomMiner generates web-enabled visualization of the analysis results and is specifically designed to facilitate the use of microbiome datasets in clinical applications.
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Affiliation(s)
- Amirhossein Shamsaddini
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, United States of America
- * E-mail:
| | - Kimia Dadkhah
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, United States of America
| | - Patrick M. Gillevet
- Microbiome Analysis Center, George Mason University, Manassas, Virginia, United States of America
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25
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Topçuoğlu BD, Lesniak NA, Ruffin MT, Wiens J, Schloss PD. A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems. mBio 2020; 11:e00434-20. [PMID: 32518182 PMCID: PMC7373189 DOI: 10.1128/mbio.00434-20] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made toward developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs) (n = 490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1- and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, a decision tree, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an area under the receiver operating characteristic curve (AUROC) of 0.695 (interquartile range [IQR], 0.651 to 0.739) but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 (IQR, 0.625 to 0.735), trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability.IMPORTANCE Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.
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Affiliation(s)
- Begüm D Topçuoğlu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas A Lesniak
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mack T Ruffin
- Department of Family Medicine and Community Medicine, Penn State Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Jenna Wiens
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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26
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Seneviratne CJ, Balan P, Suriyanarayanan T, Lakshmanan M, Lee DY, Rho M, Jakubovics N, Brandt B, Crielaard W, Zaura E. Oral microbiome-systemic link studies: perspectives on current limitations and future artificial intelligence-based approaches. Crit Rev Microbiol 2020; 46:288-299. [PMID: 32434436 DOI: 10.1080/1040841x.2020.1766414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In the past decade, there has been a tremendous increase in studies on the link between oral microbiome and systemic diseases. However, variations in study design and confounding variables across studies often lead to inconsistent observations. In this narrative review, we have discussed the potential influence of study design and confounding variables on the current sequencing-based oral microbiome-systemic disease link studies. The current limitations of oral microbiome-systemic link studies on type 2 diabetes mellitus, rheumatoid arthritis, pregnancy, atherosclerosis, and pancreatic cancer are discussed in this review, followed by our perspective on how artificial intelligence (AI), particularly machine learning and deep learning approaches, can be employed for predicting systemic disease and host metadata from the oral microbiome. The application of AI for predicting systemic disease as well as host metadata requires the establishment of a global database repository with microbiome sequences and annotated host metadata. However, this task requires collective efforts from researchers working in the field of oral microbiome to establish more comprehensive datasets with appropriate host metadata. Development of AI-based models by incorporating consistent host metadata will allow prediction of systemic diseases with higher accuracies, bringing considerable clinical benefits.
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Affiliation(s)
- Chaminda Jayampath Seneviratne
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre Singapore, Duke NUS Medical School, Singapore, Singapore
| | - Preethi Balan
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre Singapore, Duke NUS Medical School, Singapore, Singapore
| | - Tanujaa Suriyanarayanan
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre Singapore, Duke NUS Medical School, Singapore, Singapore
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute (BTI), ASTAR - Agency for Science, Technology and Research, Singapore, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute (BTI), ASTAR - Agency for Science, Technology and Research, Singapore, Singapore.,School of Chemical Engineering, Sungkyunkwan University, Jongno-gu, Republic of Korea
| | - Mina Rho
- Departments of Computer Science and Engineering & Biomedical Informatics, Hanyang University, Seoul, Korea
| | - Nicholas Jakubovics
- Oral Biology, School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bernd Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wim Crielaard
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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27
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Elsalem L, Jum'ah AA, Alfaqih MA, Aloudat O. The Bacterial Microbiota of Gastrointestinal Cancers: Role in Cancer Pathogenesis and Therapeutic Perspectives. Clin Exp Gastroenterol 2020; 13:151-185. [PMID: 32440192 PMCID: PMC7211962 DOI: 10.2147/ceg.s243337] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
The microbiota has an essential role in the pathogenesis of many gastrointestinal diseases including cancer. This effect is mediated through different mechanisms such as damaging DNA, activation of oncogenic pathways, production of carcinogenic metabolites, stimulation of chronic inflammation, and inhibition of antitumor immunity. Recently, the concept of "pharmacomicrobiomics" has emerged as a new field concerned with exploring the interplay between drugs and microbes. Mounting evidence indicates that the microbiota and their metabolites have a major impact on the pharmacodynamics and therapeutic responses toward anticancer drugs including conventional chemotherapy and molecular-targeted therapeutics. In addition, microbiota appears as an attractive target for cancer prevention and treatment. In this review, we discuss the role of bacterial microbiota in the pathogenesis of different cancer types affecting the gastrointestinal tract system. We also scrutinize the evidence regarding the role of microbiota in anticancer drug responses. Further, we discuss the use of probiotics, fecal microbiota transplantation, and antibiotics, either alone or in combination with anticancer drugs for prevention and treatment of gastrointestinal tract cancers.
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Affiliation(s)
- Lina Elsalem
- Department of Pharmacology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Ahmad A Jum'ah
- Department of Conservative Dentistry, Faculty of Dentistry, Jordan University of Science and Technology, Irbid, Jordan
| | - Mahmoud A Alfaqih
- Department of Physiology and Biochemistry, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Osama Aloudat
- Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
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28
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Song M, Chan AT, Sun J. Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer. Gastroenterology 2020; 158:322-340. [PMID: 31586566 PMCID: PMC6957737 DOI: 10.1053/j.gastro.2019.06.048] [Citation(s) in RCA: 410] [Impact Index Per Article: 102.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/11/2019] [Accepted: 06/16/2019] [Indexed: 02/07/2023]
Abstract
Researchers have discovered associations between elements of the intestinal microbiome (including specific microbes, signaling pathways, and microbiota-related metabolites) and risk of colorectal cancer (CRC). However, it is unclear whether changes in the intestinal microbiome contribute to the development of sporadic CRC or result from it. Changes in the intestinal microbiome can mediate or modify the effects of environmental factors on risk of CRC. Factors that affect risk of CRC also affect the intestinal microbiome, including overweight and obesity; physical activity; and dietary intake of fiber, whole grains, and red and processed meat. These factors alter microbiome structure and function, along with the metabolic and immune pathways that mediate CRC development. We review epidemiologic and laboratory evidence for the influence of the microbiome, diet, and environmental factors on CRC incidence and outcomes. Based on these data, features of the intestinal microbiome might be used for CRC screening and modified for chemoprevention and treatment. Integrated prospective studies are urgently needed to investigate these strategies.
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Affiliation(s)
- Mingyang Song
- Departments of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Medicine, Microbiology/Immunology, UIC Cancer Center, University of Illinois at Chicago, Illinois.
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29
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Sakowski E, Uritskiy G, Cooper R, Gomes M, McLaren MR, Meisel JS, Mickol RL, Mintz CD, Mongodin EF, Pop M, Rahman MA, Sanchez A, Timp W, Vela JD, Wolz CM, Zackular JP, Chopyk J, Commichaux S, Davis M, Dluzen D, Ganesan SM, Haruna M, Nasko D, Regan MJ, Sarria S, Shah N, Stacy B, Taylor D, DiRuggiero J, Preheim SP. Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019. mSystems 2019; 4:e00392-19. [PMID: 31594828 PMCID: PMC6787564 DOI: 10.1128/msystems.00392-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.
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Affiliation(s)
- Eric Sakowski
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gherman Uritskiy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rachel Cooper
- Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya Gomes
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
| | - Jacquelyn S Meisel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - C David Mintz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, Maryland, USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven Connecticut, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Howard University, Washington, DC, USA
| | - Carly Muletz Wolz
- Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, USA
| | - Joseph P Zackular
- Department of Pathology and Laboratory Medicine, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jessica Chopyk
- School of Public Health, University of Maryland, College Park, Maryland, USA
| | - Seth Commichaux
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Meghan Davis
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Douglas Dluzen
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
| | - Sukirth M Ganesan
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Muyideen Haruna
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
| | - Dan Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Mary J Regan
- University of Maryland School of Nursing, Baltimore, Maryland, USA
| | - Saul Sarria
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Nidhi Shah
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Brook Stacy
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Dylan Taylor
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - Sarah P Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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