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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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Cavuoto KM, Galor A, Zhu AY. Role of the ocular surface microbiome in allergic eye diseases. Curr Opin Allergy Clin Immunol 2023; 23:376-382. [PMID: 37459276 DOI: 10.1097/aci.0000000000000930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an update on emerging literature on the role of the ocular surface microbiome (OSM) in allergic eye diseases. RECENT FINDINGS Findings in the literature suggest that the ocular surface microbiome plays a role in the pathophysiology and course of allergic disease of the ocular surface. SUMMARY Knowledge regarding the role of the ocular surface microbiome in allergic disease is important to guide development of targets for future therapeutic interventions.
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Affiliation(s)
- Kara M Cavuoto
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine
- Miami Veterans Administration Medical Center, Miami, Florida, USA
| | - Angela Y Zhu
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine
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Ramos-Tapia I, Reynaldos-Grandón KL, Pérez-Losada M, Castro-Nallar E. Characterization of the upper respiratory tract microbiota in Chilean asthmatic children reveals compositional, functional, and structural differences. FRONTIERS IN ALLERGY 2023; 4:1223306. [PMID: 37577334 PMCID: PMC10419220 DOI: 10.3389/falgy.2023.1223306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
Around 155 million people worldwide suffer from asthma. In Chile, the prevalence of this disease in children is around 15% and has a high impact in the health system. Studies suggest that asthma is caused by multiple factors, including host genetics, antibiotic use, and the development of the airway microbiota. Here, we used 16S rRNA high-throughput sequencing to characterize the nasal and oral mucosae of 63 asthmatic and 89 healthy children (152 samples) from Santiago, Chile. We found that the nasal mucosa was dominated by a high abundance of Moraxella, Dolosigranulum, Haemophilus, Corynebacterium, Streptococcus, and Staphylococcus. In turn, the oral mucosa was characterized by a high abundance of Streptococcus, Haemophilus, Gemella, Veillonella, Neisseria, and Porphyromonas. Our results showed significantly (P < 0.001) lower alpha diversity and an over-abundance of Streptococcus (P < 0.01) in nasal samples from asthmatics compared to samples from healthy subjects. Community structure, as revealed by co-occurrence networks, showed different microbial interactions in asthmatic and healthy subjects, particularly in the nasal microbiota. The networks revealed keystone genera in each body site, including Prevotella, Leptotrichia, and Porphyromonas in the nasal microbiota, and Streptococcus, Granulicatella, and Veillonella in the oral microbiota. We also detected 51 functional pathways differentially abundant on the nasal mucosa of asthmatic subjects, although only 13 pathways were overrepresented in the asthmatic subjects (P < 0.05). We did not find any significant differences in microbial taxonomic (composition and structure) and functional diversity between the oral mucosa of asthmatic and healthy subjects. This study explores for the first time the relationships between the upper respiratory airways bacteriome and asthma in Chile. It demonstrates that the nasal cavity of children from Santiago harbors unique bacterial communities and identifies potential taxonomic and functional biomarkers of pediatric asthma.
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Affiliation(s)
- Ignacio Ramos-Tapia
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, The George Washington University, Washington, DC, United States
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
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Pérez-Losada M, Castro-Nallar E, Laerte Boechat J, Delgado L, Azenha Rama T, Berrios-Farías V, Oliveira M. The oral bacteriomes of patients with allergic rhinitis and asthma differ from that of healthy controls. Front Microbiol 2023; 14:1197135. [PMID: 37440882 PMCID: PMC10335798 DOI: 10.3389/fmicb.2023.1197135] [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: 04/05/2023] [Accepted: 05/15/2023] [Indexed: 07/15/2023] Open
Abstract
Allergic rhinitis and asthma are two of the most common chronic respiratory diseases in developed countries and have become a major public health concern. Substantial evidence has suggested a strong link between respiratory allergy and upper airway dysbacteriosis, but the role of the oral bacteriota is still poorly understood. Here we used 16S rRNA massive parallel sequencing to characterize the oral bacteriome of 344 individuals with allergic rhinitis (AR), allergic rhinitis with asthma (ARAS), asthma (AS) and healthy controls (CT). Four of the most abundant (>2%) phyla (Actinobacteriota, Firmicutes, Fusobacteriota, and Proteobacteria) and 10 of the dominant genera (Actinomyces, Fusobacterium, Gemella, Haemophilus, Leptotrichia, Neisseria, Porphyromonas, Prevotella, Streptococcus, and Veillonella) in the oral cavity differed significantly (p ≤ 0.03) between AR, ARAS or AS and CT groups. The oral bacteriome of ARAS patients showed the highest intra-group diversity, while CT showed the lowest. All alpha-diversity indices of microbial richness and evenness varied significantly (p ≤ 0.022) in ARAS vs. CT and ARAS vs. AR, but they were not significantly different in AR vs. CT. All beta-diversity indices of microbial structure (Unifrac, Bray-Curtis, and Jaccard distances) differed significantly (p ≤ 0.049) between each respiratory disease group and controls. Bacteriomes of AR and ARAS patients showed 15 and 28 upregulated metabolic pathways (PICRUSt2) mainly related to degradation and biosynthesis (p < 0.05). A network analysis (SPIEC-EASI) of AR and ARAS bacteriomes depicted simpler webs of interactions among their members than those observed in the bacteriome of CT, suggesting chronic respiratory allergic diseases may disrupt bacterial connectivity in the oral cavity. This study, therefore, expands our understanding of the relationships between the oral bacteriome and allergy-related conditions. It demonstrates for the first time that the mouth harbors distinct bacteriotas during health and allergic rhinitis (with and without comorbid asthma) and identifies potential taxonomic and functional microbial biomarkers of chronic airway disease.
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Affiliation(s)
- Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Talca, Chile
| | - José Laerte Boechat
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS@RISE), Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Luís Delgado
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS@RISE), Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Serviço de Imunoalergologia, Centro Hospitalar Universitário São João (CHUSJ), Porto, Portugal
| | - Tiago Azenha Rama
- Serviço de Imunologia Básica e Clínica, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- Serviço de Imunoalergologia, Centro Hospitalar Universitário São João (CHUSJ), Porto, Portugal
| | - Valentín Berrios-Farías
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Talca, Chile
| | - Manuela Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
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Striz I, Golebski K, Strizova Z, Loukides S, Bakakos P, Hanania N, Jesenak M, Diamant Z. New insights into the pathophysiology and therapeutic targets of asthma and comorbid chronic rhinosinusitis with or without nasal polyposis. Clin Sci (Lond) 2023; 137:727-753. [PMID: 37199256 PMCID: PMC10195992 DOI: 10.1042/cs20190281] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023]
Abstract
Asthma and chronic rhinosinusitis with nasal polyps (CRSwNP) or without (CRSsNP) are chronic respiratory diseases. These two disorders often co-exist based on common anatomical, immunological, histopathological, and pathophysiological basis. Usually, asthma with comorbid CRSwNP is driven by type 2 (T2) inflammation which predisposes to more severe, often intractable, disease. In the past two decades, innovative technologies and detection techniques in combination with newly introduced targeted therapies helped shape our understanding of the immunological pathways underlying inflammatory airway diseases and to further identify several distinct clinical and inflammatory subsets to enhance the development of more effective personalized treatments. Presently, a number of targeted biologics has shown clinical efficacy in patients with refractory T2 airway inflammation, including anti-IgE (omalizumab), anti-IL-5 (mepolizumab, reslizumab)/anti-IL5R (benralizumab), anti-IL-4R-α (anti-IL-4/IL-13, dupilumab), and anti-TSLP (tezepelumab). In non-type-2 endotypes, no targeted biologics have consistently shown clinical efficacy so far. Presently, multiple therapeutical targets are being explored including cytokines, membrane molecules and intracellular signalling pathways to further expand current treatment options for severe asthma with and without comorbid CRSwNP. In this review, we discuss existing biologics, those under development and share some views on new horizons.
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Affiliation(s)
- Ilja Striz
- Department of Clinical and Transplant Immunology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Subdivision of Allergology and Clinical Immunology, Institute for Postgraduate Education in Medicine, Prague, Czech Republic
| | - Kornel Golebski
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, University of Amsterdam, the Netherlands
| | - Zuzana Strizova
- Institute of Immunology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Stelios Loukides
- Department of Respiratory Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Petros Bakakos
- First Respiratory Medicine Department, National and Kapodistrian University of Athens, Athens, Greece
| | - Nicola A. Hanania
- Section of Pulmonary and Critical Care Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Milos Jesenak
- Department of Pulmonology and Phthisiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, University Hospital in Martin, Slovakia
- Department of Pediatrics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, University Hospital in Martin, Slovakia
- Department of Clinical Immunology and Allergology, University Hospital in Martin, Slovakia
| | - Zuzana Diamant
- Department of Microbiology Immunology and Transplantation, KU Leuven, Catholic University of Leuven, Belgium
- Department of Respiratory Medicine and Allergology, Institute for Clinical Science, Skane University Hospital, Lund University, Lund, Sweden
- Department of Respiratory Medicine, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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