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Rojas-Velazquez D, Kidwai S, Kraneveld AD, Tonda A, Oberski D, Garssen J, Lopez-Rincon A. Methodology for biomarker discovery with reproducibility in microbiome data using machine learning. BMC Bioinformatics 2024; 25:26. [PMID: 38225565 PMCID: PMC10789030 DOI: 10.1186/s12859-024-05639-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND In recent years, human microbiome studies have received increasing attention as this field is considered a potential source for clinical applications. With the advancements in omics technologies and AI, research focused on the discovery for potential biomarkers in the human microbiome using machine learning tools has produced positive outcomes. Despite the promising results, several issues can still be found in these studies such as datasets with small number of samples, inconsistent results, lack of uniform processing and methodologies, and other additional factors lead to lack of reproducibility in biomedical research. In this work, we propose a methodology that combines the DADA2 pipeline for 16s rRNA sequences processing and the Recursive Ensemble Feature Selection (REFS) in multiple datasets to increase reproducibility and obtain robust and reliable results in biomedical research. RESULTS Three experiments were performed analyzing microbiome data from patients/cases in Inflammatory Bowel Disease (IBD), Autism Spectrum Disorder (ASD), and Type 2 Diabetes (T2D). In each experiment, we found a biomarker signature in one dataset and applied to 2 other as further validation. The effectiveness of the proposed methodology was compared with other feature selection methods such as K-Best with F-score and random selection as a base line. The Area Under the Curve (AUC) was employed as a measure of diagnostic accuracy and used as a metric for comparing the results of the proposed methodology with other feature selection methods. Additionally, we use the Matthews Correlation Coefficient (MCC) as a metric to evaluate the performance of the methodology as well as for comparison with other feature selection methods. CONCLUSIONS We developed a methodology for reproducible biomarker discovery for 16s rRNA microbiome sequence analysis, addressing the issues related with data dimensionality, inconsistent results and validation across independent datasets. The findings from the three experiments, across 9 different datasets, show that the proposed methodology achieved higher accuracy compared to other feature selection methods. This methodology is a first approach to increase reproducibility, to provide robust and reliable results.
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Affiliation(s)
- David Rojas-Velazquez
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands.
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Sarah Kidwai
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Department of Neuroscience, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alberto Tonda
- UMR 518 MIA - PS, INRAE, Institut des Systèmes Complexes de Paris, Île - de - France (ISC-PIF) - UAR 3611 CNRS, Université Paris-Saclay, Paris, France
| | - Daniel Oberski
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Global Centre of Excellence Immunology, Danone Nutricia Research, Utrecht, The Netherlands
| | - Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Utrecht, The Netherlands
- Department of Data Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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Teramoto Y, Akagawa S, Hori SI, Tsuji S, Higasa K, Kaneko K. Dysbiosis of the gut microbiota as a susceptibility factor for Kawasaki disease. Front Immunol 2023; 14:1268453. [PMID: 38022552 PMCID: PMC10644744 DOI: 10.3389/fimmu.2023.1268453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Gut microbial imbalance (dysbiosis) has been reported in patients with acute Kawasaki disease (KD). However, no studies have analyzed the gut microbiota while focusing on susceptibility to KD. This study aimed to evaluate whether dysbiosis elevates susceptibility to KD by assessing children with a history of KD. Methods Fecal DNA was extracted from 26 children with a history of KD approximately 1 year prior (KD group, 12 boys; median age, 32.5 months; median time from onset, 11.5 months) and 57 age-matched healthy controls (HC group, 35 boys; median age, 36.0 months). 16S rRNA gene analysis was conducted with the Illumina Miseq instrument. Sequence reads were analyzed using QIIME2. Results For alpha diversity, Faith's phylogenetic diversity was significantly higher in the KD group. Regarding beta diversity, the two groups formed significantly different clusters based on Bray-Curtis dissimilarity. Comparing microbial composition at the genus level, the KD and HC groups were significantly different in the abundance of two genera with abundance over 1% after Benjamini-Hochberg false discovery rate correction for multiple comparisons. Compared with the HC group, the KD group had higher relative abundance of Ruminococcus gnavus group and lower relative abundance of Blautia. Discussion and conclusion Ruminococcus gnavus group reportedly includes pro-inflammatory bacteria. In contrast, Blautia suppresses inflammation via butyrate production. In the predictive functional analysis, the proportion of gut microbiota involved in several pathways was lower in the KD group. Therefore, dysbiosis characterized by distinct microbial diversity and decreased abundance of Blautia in parallel with increased abundance of Ruminococcus gnavus group might be a susceptibility factor for KD.
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Affiliation(s)
- Yoshiki Teramoto
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Shohei Akagawa
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Shin-ichiro Hori
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Shoji Tsuji
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka, Japan
| | - Kazunari Kaneko
- Department of Pediatrics, Kansai Medical University, Hirakata, Osaka, Japan
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Aldriwesh MG, Al-Mutairi AM, Alharbi AS, Aljohani HY, Alzahrani NA, Ajina R, Alanazi AM. Paediatric Asthma and the Microbiome: A Systematic Review. Microorganisms 2023; 11:microorganisms11040939. [PMID: 37110362 PMCID: PMC10142236 DOI: 10.3390/microorganisms11040939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Evidence from the literature suggests an association between the microbiome and asthma development. Here, we aimed to identify the current evidence for the association between asthma and the upper airway, lower airway and/or the gut microbiome. An electronic systemic search of PubMed, EBSCO, Science Direct and Web of Science was conducted until February 2022 to identify the eligible studies. The Newcastle–Ottawa Scale and the Systematic Review Centre for Laboratory Animal Experimentation risk of the bias tools were used to assess quality of included studies. Twenty-five studies met the inclusion criteria. Proteobacteria and Firmicutes were identified as being significantly higher in the asthmatic children compared with the healthy controls. The high relative abundance of Veillonella, Prevotella and Haemophilus in the microbiome of the upper airway in early infancy was associated with a higher risk of asthma development later in life. The gut microbiome analyses indicated that a high relative abundance of Clostridium in early childhood might be associated with asthma development later in life. The findings reported here serve as potential microbiome signatures associated with the increased risk of asthma development. There is a need for large longitudinal studies to further identify high-risk infants, which will help in design strategies and prevention mechanisms to avoid asthma early in life.
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Affiliation(s)
- Marwh G. Aldriwesh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
| | - Abrar M. Al-Mutairi
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
- Research Unit, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Azzah S. Alharbi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Jeddah 21362, Saudi Arabia
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Hassan Y. Aljohani
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
- Department of Respiratory Therapy, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Nabeel A. Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
| | - Reham Ajina
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
| | - Abdullah M. Alanazi
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Ministry of the National Guard-Health Affairs, Riyadh 11426, Saudi Arabia
- Department of Respiratory Therapy, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
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DuPont HL, Jiang ZD, Alexander AS, DuPont AW, Brown EL. Intestinal IgA-Coated Bacteria in Healthy- and Altered-Microbiomes (Dysbiosis) and Predictive Value in Successful Fecal Microbiota Transplantation. Microorganisms 2022; 11:microorganisms11010093. [PMID: 36677385 PMCID: PMC9862469 DOI: 10.3390/microorganisms11010093] [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: 11/21/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
IgA-coated bacteria in the gut (IgA-biome) provide a homeostatic function in healthy people through inhibition of microbial invaders and by protecting the epithelial monolayer of the gut. The laboratory methods used to detect this group of bacteria require flow cytometry and DNA sequencing (IgA-Seq). With dysbiosis (reduced diversity of the microbiome), the IgA-biome also is impaired. In the presence of enteric infection, oral vaccines, or an intestinal inflammatory disorder, the IgA-biome focuses on the pathogenic bacteria or foreign antigens, while in other chronic diseases associated with dysbiosis, the IgA-biome is reduced in capacity. Fecal microbiota transplantation (FMT), the use of fecal product from well-screened, healthy donors administered to patients with dysbiosis, has been successful in engrafting the intestine with healthy microbiota and metabolites leading to improve health. Through FMT, IgA-coated bacteria have been transferred to recipients retaining their immune coating. The IgA-biome should be evaluated in FMT studies as these mucosal-associated bacteria are more likely to be associated with successful transplantation than free luminal organisms. Studies of the microbiome pre- and post-FMT should employ metagenomic methods that identify bacteria at least at the species level to better identify organisms of interest while allowing comparisons of microbiota data between studies.
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Affiliation(s)
- Herbert L. DuPont
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA
- Kelsey Research Foundation, Houston, TX 77005, USA
- Correspondence: ; Tel.: +1-713-500-9366
| | - Zhi-Dong Jiang
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
| | | | - Andrew W. DuPont
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Eric L. Brown
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
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Forno E, Brandenburg DD, Castro-Rodriguez JA, Celis-Preciado CA, Holguin F, Licskai C, Lovinsky-Desir S, Pizzichini M, Teper A, Yang C, Celedón JC. Asthma in the Americas: An Update: A Joint Perspective from the Brazilian Thoracic Society, Canadian Thoracic Society, Latin American Thoracic Society, and American Thoracic Society. Ann Am Thorac Soc 2022; 19:525-535. [PMID: 35030062 PMCID: PMC8996271 DOI: 10.1513/annalsats.202109-1068cme] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/14/2022] [Indexed: 11/20/2022] Open
Abstract
Asthma affects a large number of people living in the Americas, a vast and diverse geographic region comprising 35 nations in the Caribbean and North, Central, and South America. The marked variability in the prevalence, morbidity, and mortality from asthma across and within nations in the Americas offers a unique opportunity to improve our understanding of the risk factors and management of asthma phenotypes and endotypes in children and adults. Moreover, a better assessment of the causes and treatment of asthma in less economically developed regions in the Americas would help diagnose and treat individuals migrating from those areas to Canada and the United States. In this focused review, we first assess the epidemiology of asthma, review known and potential risk factors, and examine commonalities and differences in asthma management across the Americas. We then discuss future directions in research and health policies to improve the prevention, diagnosis, and management of pediatric and adult asthma in the Americas, including standardized and periodic assessment of asthma burden across the region; large-scale longitudinal studies including omics and comprehensive environmental data on racially and ethnically diverse populations; and dissemination and implementation of guidelines for asthma management across the spectrum of disease severity. New initiatives should recognize differences in socioeconomic development and health care systems across the region while paying particular attention to novel or more impactful risk factors for asthma in the Americas, including indoor pollutants such as biomass fuel, tobacco use, infectious agents and the microbiome, and psychosocial stressor and chronic stress.
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Affiliation(s)
- Erick Forno
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine and Pediatric Asthma Center, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Diego D. Brandenburg
- Department of Pediatrics, Pediatric Pulmonology Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Jose A. Castro-Rodriguez
- Department of Pediatric Pulmonology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos A. Celis-Preciado
- Pulmonary Unit, Internal Medicine Department, Hospital Universitario San Ignacio and Faculty of Medicine, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care, University of Colorado Denver, Denver, Colorado
| | - Christopher Licskai
- Department of Medicine, Western University Canada, Schulich School of Medicine and Dentistry, London Health Sciences Centre, London, Ontario, Canada
| | - Stephanie Lovinsky-Desir
- Division of Pediatric Pulmonary Medicine, Columbia University Irving Medical Center, New York, New York
| | - Marcia Pizzichini
- Post-Graduate Program of Medical Sciences, Federal University of Santa Catarina, Florianopolis, Santa Catarina, Brazil
| | - Alejandro Teper
- Respiratory Center, Hospital de Niños Dr. Ricardo Gutiérrez, Ciudad Autónoma de Buenos Aires, Argentina; and
| | - Connie Yang
- Division of Respiratory Medicine, University of British Columbia, British Columbia Children’s Hospital, Vancouver, British Columbia, Canada
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine and Pediatric Asthma Center, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
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