Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Electronic nicotine delivery system use and expectorated sputum microbiota in Lebanese adults: A Pilot Study

ABSTRACT: Electronic nicotine delivery systems (ENDS) are increasingly used worldwide, but their effects on respiratory microbial communities remain understudied. This pilot cross-sectional study compared the expectorated sputum microbiota of Lebanese adult ENDS users and non-ENDS users. Sputum samples were collected from 15 ENDS users and 15 non-ENDS users without chronic respiratory illness or recent antibiotic exposure. Samples were analyzed using 16S rRNA V3-V4 amplicon sequencing. Overall microbial richness, diversity, and evenness did not differ significantly between groups. In addition, presence/absence-based community composition showed no significant group-level separation. Both groups shared broadly similar dominant bacterial profiles with Bacillota, Pseudomonadota, and Bacteroidota among the most abundant phyla. Moreover, there was substantial overlap at the genus level. Despite these broad similarities, selective taxonomic differences were observed at finer resolutions including increased relative abundance of Nanosynbacter and decreased abundance of a putative Rothia species-level taxon among ENDS users after FDR correction. Actinomyces showed a nominal increase in ENDS users, but this did not remain significant after FDR correction. These findings suggest that ENDS use was not associated with broad sputum microbiota disruption in this cohort but may be associated with selective shifts in specific bacterial taxa.

ORGANISM(S): Homo sapiens

PROVIDER: GSE342083 | GEO | 2026/08/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	GSE342083_taxonomic_assignment_absolute_counts.csv.gz	Csv

Items per page:

1 - 2 of 2

Similar Datasets

The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation

Project description:In this paper, we first report that EC smoking significantly increases the odds of gingival inflammation. Then, we seek to identify and explain the mechanism that underlies the relationship between EC smoking and gingival inflammation via the oral microbiome. We performed mediation analyses to assess if EC smoking affects the oral microbiome, which in turn affects gingival inflammation. For this, we collected saliva and subgingival samples from EC users and non-users and profiled their microbial compositions via 16S rRNA amplicon sequencing. We then performed α-diversity, β-diversity, and taxonomic differential analyses to survey the disparity in microbial composition between EC users and non-users. We found significant increases in α-diversity in EC users and disparities in β-diversity between EC users and non-users.

2022-12-09 | GSE201949 | GEO

Transcriptomic responses in the blood and sputum of cigarette smokers compared to e-cigarette vapers

Project description:Objectives: To identify transcriptomic differences in the blood and sputum of e-cigarette users compared to conventional cigarettes smokers and healthy controls and describe biological pathways affected by these tobacco products. Methods: Cross-sectional analysis of whole blood and sputum RNA-sequencing data from 8 smokers, 9 e-cigarette users (e-cigs) and 4 controls. Weighted gene co-network analysis (WGCNA) identified gene module associations. Ingenuity Pathway Analysis (IPA) identified canonical pathways associated with tobacco products. Main Results: In blood, a three-group comparison showed 16 differentially expressed genes (DEGs); pair-wise comparison showed 7 DEGs between e-cigs and controls, 35 DEGs between smokers and controls, and 13 DEGs between smokers and e-cigs. In sputum, 438 DEGs were in the three-group comparison. In pair-wise comparisons, there were 2 DEGs between e-cigs and controls, 270 DEGs between smokers and controls, and 468 DEGs between smokers and e-cigs. Only 2 genes in the smokers vs. control comparison overlapped between blood and sputum. Most gene modules identified through WGCNA associated with tobacco product exposures also were associated with cotinine and exhaled CO levels. IPA showed multiple canonical pathways altered by conventional smoking but none by e-cigarette use. Conclusion: Cigarette smoking and e-cigarette use led to transcriptomic changes in both blood and sputum. However, conventional cigarettes induced much stronger transcriptomic responses in both compartments.

2023-05-24 | GSE223736 | GEO

The impact of vaping on adolescent lung function and nasal epithelial gene expression [RNA-seq]

Project description:Electronic cigarette use (vaping) among adolescents is a pressing public health issue. We aimed to investigate the impact of vape use on lung function and nasal epithelial gene expression in adolescents. We hypothesized that vaping results in abnormal lung function and differential expression of inflammatory genes in the nasal epithelium of adolescent vape users in comparison to non-vape users. We assessed airflow obstruction with impulse oscillometry (IOS) and collected nasal epithelial brush samples for genome-wide gene expression and targeted DNA methylation analyses in middle and high school students in Colorado. Written informed consent was obtained from participants and Institutional Review Board approval was obtained. Vape users [mean age (standard deviation): 14.8 (1.4) years] reported vaping within the past 6 months while non-vape users [14.8 (1.4)] years did not report any vape use in the past 6 months. Mean airway resistance identified by the IOS R5 measure revealed that vape users (n=13) had higher values than non-vape users (n=37) [p=0.026]. Of 16,860 nasal epithelial genes tested, 7,136 were significantly differentially expressed between vape and non-vape users (false discovery rate (FDR) <0.05), after covariate adjustment. Enrichment analyses identified overexpression of inflammatory response genes and underexpression of ciliogenesis genes in vape users compared to non-vape users. DNA methylation analysis revealed that REXO1 (FDR=0.01) and CERK (FDR=0.06) were differentially methylated among vape users compared to non-vape users. Vaping during adolescence may increase airway resistance and dysresgulation of nasal epithelial genes, including genes involved in airway inflammation and ciliary function.

2024-07-05 | GSE238235 | GEO

A draft map of the human sputum proteome

Project description:Chronic respiratory diseases are a growing burden, and potentially life-threatening condition if left untreated. It is an urgent medical concern that requires proper diagnosis, treatment, and management to prevent serious complications. Analyzing induced sputum is a non-invasive approach for investigating the mechanisms and progression of respiratory diseases. It allows for the collection of sputum samples without disrupting the patient's normal life. By analyzing the proteins and other molecular substances present in the sputum, it can provide valuable insights into the pathological changes and evaluate the effectiveness of treatments for respiratory diseases. In this study, we carried out proteomic analysis of three types of sputum collected from patients with chronic respiratory diseases using three different digestion methods. In comparison, FASP method was found to be more efficient than In-gel digestion and in-solution digestions, yielding the highest number of unique protein identifications. Integrate the proteomic and phosphoproteomic profiling of three types of sputum, it was observed that raw sputum samples exhibited a higher number of unique protein and phosphoprotein identifications. Our study provides valuable insights into the application of proteomics to the analysis of sputum samples, and serves as a useful resource for understanding the potential of this approach in the study of respiratory diseases.

2023-01-28 | PXD039725 |

An API for dynamic estimation of reference intervals for functional abundances of gut microbiota

Project description:This study demonstrates the usefulness of the API by generating a baseline gut microbiota profile of a healthy population and estimating reference intervals for the functional abundance of manually selected KEGG pathways. API facilitates microbiome research by providing dynamic and customizable tools for estimating reference intervals for gut microbiota functional abundances. Through the API, researchers can rapidly generate gut microbiota functional profiles of healthy populations to use as a baseline for comparison. The API also allows users to manually select specific KEGG pathways and estimate reference intervals for the functional abundance of those pathways. By generating these customized reference intervals, researchers can better understand the expected range of gut microbiota functions in healthy individuals. API enables microbiome studies to go beyond simple taxonomic profiling and delve deeper into the functional potential of gut microbiome communities. In summary, API represents a valuable tool for microbiome researchers that enhances the ability to elucidate connections between gut microbial functions and human health.

2023-10-20 | GSE228552 | GEO

Nasopharyngeal microbiota, host transcriptome and disease severity in children with respiratory syncytial virus infection

Project description:Rationale: Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and hospitalizations in infants worldwide. Known risk factors, however, incompletely explain the variability of RSV disease severity among children. We postulate that severity of RSV infection is influenced in part by modulation of the host immune response by the local microbial ecosystem at the time of infection. Objectives: To define whether different nasopharyngeal microbiota profiles are associated with distinct host transcriptome profiles and severity in children with RSV infection. Methods: We analyzed the nasopharyngeal microbiota profiles of young children with mild and severe RSV disease and healthy matched controls by 16S-rRNA sequencing. In parallel, we analyzed whole blood gene expression profiles to study the relationship between microbial community composition, the RSV-induced host transcriptional response and clinical disease severity. Measurements and Main results: We identified five nasopharyngeal microbiota profiles characterized by enrichment of H. influenzae, Streptococcus, Corynebacterium, Moraxella or S. aureus. RSV infection and RSV hospitalization were positively associated with H. influenzae and Streptococcus, and negatively associated with S. aureus abundance, independent of age. The host response to RSV was defined by overexpression of interferon-related genes, and this was independent of the microbiota composition. On the other hand, transcriptome profiles of RSV infected children with H. influenzae and Streptococcus-dominated microbiota were characterized by greater overexpression of genes linked to toll-like receptor-signaling and neutrophil activation and were more frequently hospitalized Conclusions: Our data suggest an immunomodulatory role for the resident nasopharyngeal microbial community early in RSV infection, potentially affecting RSV disease severity.

2016-05-09 | GSE77087 | GEO

Gut Microbiota Profiling of Lebanese Patients with Ulcerative Colitis and Healthy Controls: A Pilot Study

Project description:Ulcerative colitis (UC) is a chronic inflammatory disease of the colon, associated with gut microbiota dysbiosis. While global studies have explored this link, region-specific microbial profiles remain underreported. This pilot study aimed to characterize and compare, for the first time, the gut microbiota of Lebanese UC patients and healthy controls using 16S rRNA gene sequencing (V3–V4 region). Fecal samples from 11 UC patients and 11 healthy individuals were analyzed. Alpha and beta diversity metrics were computed, and gut microbial composition was assessed across taxonomic levels. Statistical comparisons used Mann-Whitney and Fisher’s exact tests. UC patients showed significantly reduced microbial diversity based on Faith’s Phylogenetic Diversity and Shannon index (p < 0.05), though evenness was unaffected. Beta diversity also revealed significant group-level dissimilarities (p < 0.05). At the phylum level, Bacteroidota was elevated in UC, while Bacillota and Actinomycetota were reduced. Genera such as Ruminococcus, Fusicatenibacter, Mediterraneibacter, Eubacterium, and Coprococcus were depleted in UC. Faecalibacterium, commonly reduced in UC, showed no significant difference. This first analysis of gut microbiota in Lebanese UC patients reveals a distinct microbial signature that partially diverges from global trends, supporting the need for region-specific microbiome studies and personalized microbiota-targeted therapies.

2025-11-27 | GSE303706 | GEO

Comparison of the inflammatory niches of CF and COPD and the differences to healthy controls

Project description:This study aimed to compare – at a multi-omics level, inflammation, protease abundance and activity, microbiome, and proteome in sputum samples from patients with cystic fibrosis (CF, n=38) or chronic obstructive pulmonary disease (COPD, n=18) and healthy controls (n=10) to identify shared and unique pathways between these respiratory conditions. Sputum analysis revealed elevated inflammatory cell counts in both CF and COPD patients, with neutrophils being the dominant cell type. Key inflammatory markers, including IL-1β, TNF-α, TGF-β1, IL-8, and LTB4, were increased in both disease groups, with the highest levels observed in CF. Conversely, COPD patients exhibited higher levels of IL-5, IL-6, and IL-10. Microbiome analysis showed distinct clusters for each group, with CF patients often characterized by a preponderance of Pseudomonas. Hierarchical clustering unveiled robust interdependencies between microbiome parameters and inflammation, a richer and more diverse microbiome was associated with a healthier microbial community. This study uncovered significant disparities in inflammation, microbiome composition, and proteome profiles among CF, COPD, and healthy control cohorts. Neutrophilic inflammation and protease activity emerged as common factors in both diseases highlighting proteases as good targets for both indications, while distinct microbial signatures were identified. These findings offer valuable insights into the underlying mechanisms of CF and COPD and may inform future clinical strategies.

2025-09-08 | PXD048388 | Pride

HuMiChip analysis of Saliva microbiota

Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults.

2013-08-15 | E-GEOD-49875 | biostudies-arrayexpress

Microbial RNAseq analysis of cecal and fecal samples collected from mice colonized with the microbiota of human twins discordant for obesity

Project description:Microbial RNAseq analysis of cecal and fecal samples collected from mice colonized with the microbiota of human twins discordant for obesity. Samples were colleted at the time of sacrifice, or 15 days after colonization from mice gavaged with uncultured or cultured fecal microbiota from the lean twins or their obese co-twins. Samples were sequenced using Illumina HiSeq technology, with 101 paired end chemistry. Comparisson of microbial gene expression between the microbiota of lean and obese twins fed a Low fat, rich in plant polysaccharide diet.

2013-10-01 | E-GEOD-48861 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data