The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network

Abstract

Although the nose, as a gateway for organism–environment interactions, may have a key role in asthmatic exacerbation, the rhinobiome of exacerbated children with asthma was widely neglected to date. The aim of this study is to understand the microbiome, the microbial immunology, and the proteome of exacerbated children and adolescents with wheeze and asthma. Considering that a certain proportion of wheezers may show a progression to asthma, the comparison of both groups provides important information regarding clinical and phenotype stratification. Thus, deep nasopharyngeal swab specimens, nasal epithelial spheroid (NAEsp) cultures, and blood samples of acute exacerbated wheezers (WH), asthmatics (AB), and healthy controls (HC) were used for culture (n = 146), 16 S-rRNA gene amplicon sequencing (n = 64), and proteomic and cytokine analyses. Interestingly, Proteobacteria were over-represented in WH, whereas Firmicutes and Bacteroidetes were associated with AB. In contrast, Actinobacteria commonly colonized HCs. Moreover, Staphylococcaceae, Enterobacteriaceae, Burkholderiaceae, Xanthobacteraceae, and Sphingomonadaceae were significantly more abundant in AB compared to WH and HC. The α-diversity analyses demonstrated an increase of bacterial abundance levels in atopic AB and a decrease in WH samples. Microbiome profiles of atopic WH differed significantly from atopic AB, whereby atopic samples of WH were more homogeneous than those of non-atopic subjects. The NAEsp bacterial exposure experiments provided a disrupted epithelial cell integrity, a cytokine release, and cohort-specific proteomic differences especially for Moraxella catarrhalis cultures. This comprehensive dataset contributes to a deeper insight into the poorly understood plasticity of the nasal microbiota, and, in particular, may enforce our understanding in the pathogenesis of asthma exacerbation in childhood.

Viral Infection and Respiratory Exacerbation in Children: Results from a Local German Pediatric Exacerbation Cohort

“…We tested for the presence of different bacteria in the pharyngeal and nasal microbiome profiles of our cohort. As also described before, the most frequent bacteria were Haemophilus parainfluenzae , Haemophilus influenzae, Staphylococcus aureus , Streptococcus pneumoniae , and Moraxella catarrhalis [ 57 ]. Out of 137 tested subjects, 115 (84.4%) were colonized by at least one bacterium, and 80 (58.4%) had virus–bacteria coinfections.…”

“…To determine to what extent the microbiome profile interacts with HRV or RSV, we compared our previously published microbiome dataset [ 57 ], reanalyzed with the current virus results. We tested for the presence of different bacteria in the pharyngeal and nasal microbiome profiles of our cohort.…”

“…Viral infections that have passed through may also have an impact on the composition of the microbiome [ 126 ]. In our previous work, we observed that the wheezer cohort showed more colonization with distinct bacteria, including Moraxella catarrhalis and Haemophilus (para-)influenzae , whereas asthmatics had an increased abundance of Staphylococcus and Streptococcus in the nasopharyngeal swabs [ 57 ]. Interestingly, Teo and colleagues showed that patients with a colonization of Streptococcus , Moraxella, and Haemophilus have an increased risk of infection with respiratory viruses, particularly when such patients with the combination of RSV and Moraxella suffered from severe symptoms [ 127 ].…”

“…Moreover, epidemiological and clinical parameters were recorded in order to perform correlation analyses. Among the biomaterials, nasopharyngeal swabs using Copan eSwabs TM versatile liquid Amies media were deep frozen at −80 °C upon collection for further analyses [ 52 , 57 ].…”

The Overlooked Microbiome—Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes

“…In order to perform 16S/18S-analyses via MinION Nanopore-sequencing (Oxford Nanopore Technologies (ONT), Oxford, UK), DNA was purified from nasopharyngeal swab specimens prior to PCR amplification and subsequent library preparation via PCR barcoding. We made use of the QIAamp ® DNA Mini Kit (Qiagen, Hilden, Germany) and the modified QIAamp ® tissue protocol according to manufacturer’s instructions (compare [ 40 ]). Purified DNA was quantified using the Promega Quantus fluorometer and the QuantiFluor dsDNA System (Promega, Madison, WI, USA) and, alternatively, using a Nanophotometer P330 (Implen NanoPhotometer ® , Westlake Village, CA, USA).…”