Biology subjects

Gschwendtner, S.

Publications and source records attributed to Gschwendtner, S..

4 recordsLinked to original sources

bioRxiv2026

Fragmented gut-airway microbial networks and airway Moraxella clusters in preschool wheeze

Early-life wheezing in children has been associated with microbial alterations along the gut-airway axis, yet studies simultaneously investigating bacterial communities in both compartments remain scarce. The aim of this cross-sectional exploratory pilot study (n=25) was to characterize and compare nasal and stool bacterial communities in preschool children aged 1-4 years with recurrent wheezing and healthy controls using 16S rRNA gene metabarcoding. Across participants, nasal and stool bacteriomes were highly individualized and taxonomically diverse. Overall richness, evenness, and community composition did not differ significantly between healthy children and wheezers in either compartment. However, wheezers displayed markedly higher within-group variability, particularly in nasal communities. Stratification based on microbiome similarity to healthy samples revealed increased Moraxella and reduced commensal genera including Prevotella spp. and Veillonella, along with lower richness and evenness (all p<0.001) in nasal samples with divergent bacterial communities. Stool alterations were more subtle but included trends toward reduced Bacteroides, Faecalibacterium, and Alistipes in wheezers more divergent from healthy controls. Community assembly in both compartments was largely governed by stochastic processes but accompanied by less complex and more fragmented bacterial interaction networks in wheezing children. Cross-compartment correlations were also altered, most prominently involving stool Lactococcus showing stronger and more numerous correlations with nasal taxa in wheezers than in healthy controls. Divergent wheezers exhibited distinct modular network structure and cross-compartment profiles, consistent with a differentiated microbial organization. Together, these findings suggest compartment-specific differences in microbial interaction patterns across the gut-airway axis in early-life wheezing, despite limited differences in overall community diversity. Take home messagePreschool wheezers showed fragmented gut-airway microbial networks and Moraxella-associated airway community stratification despite limited differences in overall diversity.

microbiology↗

bioRxiv2026

Longitudinal Dynamics and Site-Specific Recovery of the Human Respiratory Microbiome Following Smoking Cessation

BackgroundThe human respiratory tract harbours diverse microbial communities crucial for health, but their dynamics during environmental perturbations like smoking remain poorly understood. While smoking is a major risk factor for various diseases, its compartment-specific effects on the respiratory microbiome and potential recovery following cessation have not been fully elucidated. Here, we present a longitudinal, multi-site study of respiratory microbiome dynamics in smokers undergoing cessation, benchmarked against healthy never-smokers. MethodsUsing standardized sampling of the anterior nares, oropharynx, and bronchoalveolar lavage (BAL), combined with 16S rRNA gene amplicon sequencing and rigorous contamination controls, we characterized community composition, diversity, personalization, and microbial interactions across airway compartments. ResultsSmokers exhibited pronounced microbiome alterations: nasal richness increased, while lung richness and core taxa were reduced. Smoking-induced changes were compartment-specific and most pronounced in nose and lung. The degree of individuum-specific differences in community structure was elevated in smokers and correlated with smoking intensity and duration. Short-term cessation (6 weeks) led to minor shifts in taxa abundance but increased similarity between oropharyngeal and lung communities, whereas long-term cessation (1 year) resulted in partial restoration, particularly in lung and nasal microbiomes. Some taxa, including Haemophilus and Prevotella_7, showed persistent alterations, highlighting lasting smoking effects. Network analyses revealed that smoking disrupted microbial co-occurrence and reduced community connectivity, whereas cessation partially restored interaction networks, with dynamics differing between oropharynx and lung, reflecting different underlying ecological assembly processes. Recovery trajectories were highly individualized, with lung microbiomes influenced by deterministic processes and upper airway microbiomes shaped by stochastic factors, explaining site-specific responses and the persistence of personalized microbial signatures. ConclusionThese results provide the first time-resolved, multi-compartment characterization of respiratory microbiome recovery after smoking cessation, revealing that smoking leaves long-lasting, site-specific imprints on airway microbial communities and interactions. Our findings underscore the need for individual and compartment-specific approaches when designing microbiome-based interventions to support respiratory health.

microbiology↗

bioRxiv2025

Comparison of Pairwise Samples of Endotracheal Aspirate and Bronchoalveolar Lavage for Microbial Analysis in Critically ill Patients

IntroductionBronchoalveolar lavage (BAL) is considered as gold-standard for the characterization of the lung microbiome. The aim of this study was to elucidate the applicability of less-invasive sampling by endotracheal aspirate (ETA) compared with BAL for the analysis of respiratory microorganisms in critically ill patients who required mechanical ventilation. MethodsPairwise samples of ETA and BAL obtained from mechanically ventilated patients at our intensive care units were collected anonymously for testing the accuracy of ETA compared to BAL. Bacterial community structure was assessed by a metabarcoding approach based on 16S rRNA gene sequencing in ETA and BAL samples. ResultsIn total, 13 samples of each, BAL and ETA, were collected from 13 critically ill patients. No differences between BAL and ETA were found for alpha diversity based on species richness (p=0.77), Shannon diversity (p = 0.41), Simpson index (p = 0.85) and evenness (p = 0.98). Overall, BAL and ETA samples demonstrated strong taxonomic concordance at the levels of bacterial phyla and genera but differed distinctly at the amplicon sequence variants (ASV) level. ConclusionIn an unselected cohort of mechanically ventilated patients, BAL and ETA samples exhibited profound resemblance at higher taxonomic ranks, with increasing divergence observed at finer taxonomic resolutions. Our findings may facilitate guidance towards the reliability of non-invasive ETA as a valuable approach for clinical studies investigating the lung microbiome.

microbiology↗

bioRxiv2025

Skin but not gut microbial communities in Antarctic fur seals vary with social density

Comparative studies of microbial communities occupying different body sites in wild vertebrates are scarce, but they are crucial for advancing our understanding of the ecological and evolutionary factors shaping animal microbiomes. We therefore used a "natural experiment" comprising mother-offspring pairs from two adjacent Antarctic fur seal breeding colonies that differ in social density to investigate differences between skin and gut microbial communities in relation to host-specific and environmental factors. Using 16S rRNA amplicon sequencing, we uncovered a strong influence of colony on the diversity and composition of skin but not gut microbial communities. Specifically, we observed a suppressive effect of high social density on skin microbial alpha diversity as well as an overabundance of phyla associated with diseases and bite wounds in the high-density colony. Our findings suggest that skin microbial communities may be more sensitive to external factors, whereas gut communities are more tightly regulated by the host. Overall, this study highlights the importance of considering multiple body sites and their distinct microbial communities to develop a more comprehensive understanding of the factors shaping microbial diversity and composition in marine mammals.

microbiology↗