Methodology for Biomarker Discovery with Reproducibility in Microbiome Data using Machine Learning DOI Creative Commons
David Rojas-Velázquez, Sarah Kidwai, Aletta D. Kraneveld

et al.

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 6, 2023

Abstract Background: In recent years, human microbiome studies have receivedincreasing attention as this field is considered a potential source for clinicalapplications. With the advancements in omics technologies and AI, researchfocused on discovery biomarkers microbime usingmachine learning tools has produced positive outcomes. Despite promisingresults, several issues can still be found these such datasets withsmall number of samples, inconsistent results, lack uniform processing andmethodologies, other additional factors lead to reproducibility inbiomedical research. work, we propose methodology that combines theDADA2 pipeline 16s rRNA sequences Recursive EnsembleFeature Selection (REFS) multiple increase andobtain robust reliable results biomedical Results: Three experiments were performed analysing data frompatients/cases Inflammatory Bowel Disease (IBD), Autism Spectrum Disorder(ASD), Type 2 Diabetes (T2D). each experiment, biomarkersignature one dataset applied further validation. Theeffectiveness proposed was compared with featureselection methods K-Best F-score random selection baseline. The Area Under Curve (AUC) employed measure diagnosticaccuracy used metric comparing proposedmethodology feature methods. Conclusions: We developed reproducible biomarker discoveryfor sequence analysis, addressing related withdata dimensionality, validation across independentdatasets. findings from three experiments, 9 different datasets,show achieved higher accuracy toother This first approach increasereproducibility, provide results.

Language: Английский

New insights into the pathophysiology and therapeutic targets of asthma and comorbid chronic rhinosinusitis with or without nasal polyposis DOI Creative Commons
Ilja Střı́ž, Korneliusz Golebski, Zuzana Střížová

et al.

Clinical Science, Journal Year: 2023, Volume and Issue: 137(9), P. 727 - 753

Published: May 1, 2023

Abstract Asthma and chronic rhinosinusitis with nasal polyps (CRSwNP) or without (CRSsNP) are respiratory diseases. These two disorders often co-exist based on common anatomical, immunological, histopathological, pathophysiological basis. Usually, asthma comorbid CRSwNP is driven by type 2 (T2) inflammation which predisposes to more severe, intractable, disease. In the past decades, innovative technologies detection techniques in combination newly introduced targeted therapies helped shape our understanding of immunological pathways underlying inflammatory airway diseases further identify several distinct clinical subsets enhance development effective personalized treatments. Presently, a number biologics has shown efficacy patients refractory T2 inflammation, including anti-IgE (omalizumab), anti-IL-5 (mepolizumab, reslizumab)/anti-IL5R (benralizumab), anti-IL-4R-α (anti-IL-4/IL-13, dupilumab), anti-TSLP (tezepelumab). non-type-2 endotypes, no have consistently so far. multiple therapeutical targets being explored cytokines, membrane molecules intracellular signalling expand current treatment options for severe CRSwNP. this review, we discuss existing biologics, those under share some views new horizons.

Language: Английский

Citations

33
Methodology for biomarker discovery with reproducibility in microbiome data using machine learning DOI Creative Commons
David Rojas-Velázquez, Sarah Kidwai, Aletta D. Kraneveld

et al.

BMC Bioinformatics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 15, 2024

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 discovery biomarkers using machine learning tools has produced positive outcomes. Despite promising results, several issues can still be found these such datasets with small number of samples, inconsistent lack uniform processing methodologies, other additional factors lead to reproducibility biomedical research. work, we propose methodology that combines DADA2 pipeline 16s rRNA sequences Recursive Ensemble Feature Selection (REFS) multiple increase obtain robust reliable results Results Three experiments were performed analyzing data from patients/cases Inflammatory Bowel Disease (IBD), Autism Spectrum Disorder (ASD), Type 2 Diabetes (T2D). each experiment, biomarker signature one dataset applied further validation. The effectiveness proposed was compared feature selection methods K-Best F-score random base line. Area Under Curve (AUC) employed measure diagnostic accuracy used metric comparing methods. Additionally, use Matthews Correlation Coefficient (MCC) evaluate performance well comparison Conclusions We developed reproducible sequence analysis, addressing related dimensionality, validation across independent datasets. findings three experiments, 9 different datasets, show achieved higher This first approach reproducibility, provide results.

Language: Английский

Citations

6
The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19 DOI Creative Commons

Benita Martín-Castaño,

Patricia Diez‐Echave, Jorge García-García

et al.

eLife, Journal Year: 2025, Volume and Issue: 13

Published: Feb. 18, 2025

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play key role the infection, progression, outcome of disease. SARS-CoV-2 infection has associated nasopharyngeal gut dysbiosis higher abundance opportunistic pathogens. To identify new prognostic markers for disease, multicentre prospective observational cohort study was carried out COVID-19 patients divided into three cohorts based on symptomatology: mild (n = 24), moderate 51), severe/critical 31). Faecal samples were taken, analysed. Linear discriminant analysis identified Mycoplasma salivarium , Prevotella dentalis Haemophilus parainfluenzae as biomarkers microbiota, while bivia timonensis defined faecal microbiota. Additionally, connection between identified, significant ratio P. (faeces) M. (nasopharyngeal) abundances found critically ill patients. This serve novel tool identifying cases.

Language: Английский

Citations

0
The oral bacteriomes of patients with allergic rhinitis and asthma differ from that of healthy controls DOI Creative Commons
Marcos Pérez‐Losada, Eduardo Castro‐Nallar, José Laerte Boechat

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: June 7, 2023

Allergic rhinitis and asthma are two of the most common chronic respiratory diseases in developed countries have become a major public health concern. Substantial evidence has suggested strong link between allergy upper airway dysbacteriosis, but role oral bacteriota is still poorly understood. Here we used 16S rRNA massive parallel sequencing to characterize bacteriome 344 individuals with allergic (AR), (ARAS), (AS) healthy controls (CT). Four abundant (>2%) phyla (Actinobacteriota, Firmicutes, Fusobacteriota, Proteobacteria) 10 dominant genera ( Actinomyces, Fusobacterium, Gemella, Haemophilus, Leptotrichia, Neisseria, Porphyromonas, Prevotella, Streptococcus, Veillonella ) cavity differed significantly p ≤ 0.03) AR, ARAS or AS CT groups. The patients showed highest intra-group diversity, while lowest. All alpha-diversity indices microbial richness evenness varied 0.022) vs. they were not different AR CT. beta-diversity structure (Unifrac, Bray-Curtis, Jaccard distances) 0.049) each disease group controls. Bacteriomes 15 28 upregulated metabolic pathways (PICRUSt2) mainly related degradation biosynthesis < 0.05). A network analysis (SPIEC-EASI) bacteriomes depicted simpler webs interactions among their members than those observed CT, suggesting may disrupt bacterial connectivity cavity. This study, therefore, expands our understanding relationships allergy-related conditions. It demonstrates for first time that mouth harbors distinct bacteriotas during (with without comorbid asthma) identifies potential taxonomic functional biomarkers disease.

Language: Английский

Citations

10
Innate players in Th2 and non-Th2 asthma - emerging roles for the epithelial cell, mast cell and monocyte/macrophage network DOI
Johanna Kotrba,

Ilka Müller,

Alexander Pausder

et al.

AJP Cell Physiology, Journal Year: 2024, Volume and Issue: 327(6), P. C1373 - C1383

Published: Oct. 14, 2024

Asthma is one of the most common chronic respiratory diseases and characterized by airway inflammation, increased mucus production, structural changes in airways. Recently, there increasing evidence that disease much more heterogeneous than expected, with several distinct asthma endotypes. Based on specificity T cells as best-known driving force bronchial categorized into helper cell 2 (Th2) non-Th2 asthma. The studied effector Th2 include eosinophils. In contrast to asthma, less known about pathophysiology which often associated treatment resistance. Besides cells, interaction myeloid such monocytes/macrophages mast epithelium significantly contributes pathogenesis However, underlying molecular regulation particularly specific relevance this cellular network certain endotypes remain be understood. review, we summarize recent findings complex interplay between epithelial “nonclassical” innate ultimate goal providing rationale for future research targeted therapy regimens.

Language: Английский

Citations

3
Microbiome-Mucosal Immunity Nexus: Driving Forces in Respiratory Disease Progression DOI

Young Chae Park,

Soo Yeon Choi,

Y.-H. Cha

et al.

The Journal of Microbiology, Journal Year: 2024, Volume and Issue: 62(9), P. 709 - 725

Published: Sept. 1, 2024

Language: Английский

Citations

2
Role of the ocular surface microbiome in allergic eye diseases DOI
Kara M. Cavuoto, Anat Galor, Angela Y. Zhu

et al.

Current Opinion in Allergy and Clinical Immunology, Journal Year: 2023, Volume and Issue: 23(5), P. 376 - 382

Published: July 17, 2023

The purpose of this review is to provide an update on emerging literature the role ocular surface microbiome (OSM) in allergic eye diseases.Findings suggest that plays a pathophysiology and course disease surface.Knowledge regarding important guide development targets for future therapeutic interventions.

Language: Английский

Citations

4
Granule Dendrobii suppresses chronic atrophic gastritis induced by N-methyl-N'-nitro-N-nitrosoguanidine by modulating the gastrointestinal bacteria in rats DOI Creative Commons

Caicai Xi,

Kang Feng,

Xuan Chen

et al.

Cellular and Molecular Biology, Journal Year: 2023, Volume and Issue: 69(7), P. 205 - 211

Published: July 31, 2023

Chronic atrophic gastritis (CAG) is an important stage in the transformation of normal gastric mucosa into cancer. Granule Dendrobii (GD), a proprietary Chinese medicine, has proven clinical efficacy treating CAG. GD might promote reversal precancerous lesions by improving them CAG patients. However, mechanism treatment relatively less understood. Here, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced rats were treated with and its was evaluated observing changes rats' weight pathology tissues. The potential effect on bacteria predicted verified large small intestines stomachs using amplicon sequencing RT-qPCR. results showed that could ameliorate symptoms body loss rats. Hematoxylin-Eosin (HE) Alcian Blue (AB) staining significantly improved pathological state relative abundance (RA) Lactobacillus Turicibacter decreased after intervention compared model group (P < 0.05), indicating improve regulating RA Turicibacter. These findings revealed as agents associated gastritis, have to inhibit cancer, especially maybe another pathogen besides Helicobacter pylori (HP), which worthy further study. Meanwhile, provided new ideas materials for research development drugs.

Language: Английский

Citations

4
The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19 DOI Creative Commons

Benita Martín-Castaño,

Patricia Diez‐Echave, Jorge García-García

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 13, 2024

ABSTRACT Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play key role the infection, progression, outcome of disease. SARS-CoV-2 infection has associated nasopharyngeal gut dysbiosis higher abundance opportunistic pathogens. To identify new prognostic markers for disease, multicenter prospective observational cohort study was carried out COVID-19 patients divided into three cohorts based on symptomatology: mild (n=24), moderate (n=51), severe/critical (n=31). Faecal samples were taken, analyzed. Linear discriminant analysis identified M. salivarium , P. dentalis H. parainfluenzae as biomarkers microbiota, while bivia timonensis defined faecal microbiota. Additionally, connection between identified, significant ratio (faeces) (nasopharyngeal) abundances found critically ill patients. This serve novel tool identifying cases.

Language: Английский

Citations

1
Characterization of the upper respiratory tract microbiota in Chilean asthmatic children reveals compositional, functional, and structural differences DOI Creative Commons
Ignacio Ramos-Tapia, Katiuska Reynaldos-Grandón, Marcos Pérez‐Losada

et al.

Frontiers in Allergy, Journal Year: 2023, Volume and Issue: 4

Published: July 28, 2023

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 health system. Studies suggest that asthma caused by multiple factors, including host genetics, antibiotic use, development airway microbiota. Here, we used 16S rRNA high-throughput sequencing to characterize nasal oral mucosae 63 asthmatic 89 healthy (152 samples) Santiago, Chile. We found mucosa was dominated abundance Moraxella, Dolosigranulum, Haemophilus, Corynebacterium, Streptococcus, Staphylococcus. turn, characterized Gemella, Veillonella, Neisseria, Porphyromonas. Our results showed significantly (P < 0.001) lower alpha diversity an over-abundance Streptococcus 0.01) samples asthmatics compared subjects. Community structure, as revealed co-occurrence networks, different microbial interactions subjects, particularly The networks keystone genera each body site, Prevotella, Leptotrichia, Porphyromonas microbiota, Granulicatella, Veillonella also detected 51 functional pathways differentially abundant on although only 13 were overrepresented subjects 0.05). did not find any significant differences taxonomic (composition structure) between This study explores for first time relationships upper respiratory airways bacteriome It demonstrates cavity Santiago harbors unique bacterial communities identifies potential biomarkers pediatric

Language: Английский

Citations

3