The pulmonary mycobiome—A study of subjects with and without chronic obstructive pulmonary disease

Martinsen, Einar Marius Hjellestad; Eagan, Tomas Mikal; Leiten, Elise Orvedal; Haaland, Ingvild; Husebø, Gunnar Reksten; Knudsen, Kristel Svalland; Drengenes, Christine; Sanseverino, Walter; Paytuví-Gallart, Andreu; Nielsen, Rune

doi:10.1371/journal.pone.0248967

Cited by 23 publications

(28 citation statements)

References 42 publications

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“…The remaining ASVs assigned as Fungi at kingdom level only, or with unidentified phylum were manually assessed using the program BLASTN in NCBI (Zhang et al, 2000). The ASVs with non-fungal BLASTN results were discarded and the remaining were repeatedly assigned to new taxonomic assignments using different UNITE databases threshold levels (Abarenkov et al, 2020a,b,c) and taxonomy classification methods (q2-feature-classifier classify-sklearn and classify-consensus-blast) in QIIME2, as described previously (Martinsen et al, 2021). The data was imported into R using the R package "qiime2R" (version 0.99.13) and additional filtering was performed using "phyloseq" (version 1.30.0) to remove singletons and samples with less than 1,000 reads (McMurdie and Holmes, 2013;Bisanz, 2018;Depner et al, 2020).…”

Section: Bioinformatics and Statistical Analysismentioning

confidence: 99%

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries

et al. 2021

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The human oral cavity harbors one of the most diverse microbial communities with different oral microenvironments allowing the colonization of unique microbial species. This study aimed to determine which of two commonly used sampling sites (dental plaque vs. oral swab) would provide a better prediction model for caries-free vs. severe early childhood caries (S-ECC) using next generation sequencing and machine learning (ML). In this cross-sectional study, a total of 80 children (40 S-ECC and 40 caries-free) < 72 months of age were recruited. Supragingival plaque and oral swab samples were used for the amplicon sequencing of the V4-16S rRNA and ITS1 rRNA genes. The results showed significant differences in alpha and beta diversity between dental plaque and oral swab bacterial and fungal microbiomes. Differential abundance analyses showed that, among others, the cariogenic species Streptococcus mutans was enriched in the dental plaque, compared to oral swabs, of children with S-ECC. The fungal species Candida dubliniensis and C. tropicalis were more abundant in the oral swab samples of children with S-ECC compared to caries-free controls. They were also among the top 20 most important features for the classification of S-ECC vs. caries-free in oral swabs and for the classification of dental plaque vs. oral swab in the S-ECC group. ML approaches revealed the possibility of classifying samples according to both caries status and sampling sites. The tested site of sample collection did not change the predictability of the disease. However, the species considered to be important for the classification of disease in each sampling site were slightly different. Being able to determine the origin of the samples could be very useful during the design of oral microbiome studies. This study provides important insights into the differences between the dental plaque and oral swab bacteriome and mycobiome of children with S-ECC and those caries-free.

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Section: Bioinformatics and Statistical Analysismentioning

confidence: 99%

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries

et al. 2021

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“…This was considered appropriate due to small observed differences in taxonomies from the participant categories. Additionally, in a previous paper, we reported few differences between the healthy and COPD mycobiomes in the MicroCOPD study [ 13 ]. Distance matrices used in beta diversity (i.e.…”

Section: Discussionmentioning

confidence: 84%

“…Second, possible batch effects occur when multiple sequencing runs are included. Batch effects have been considered on the whole MicroCOPD mycobiome data set, suggesting some effect on beta diversity and Sarocladium abundance [ 13 ]. Third, despite being a large study, some analyses suffer from low statistical power.…”

Section: Discussionmentioning

confidence: 99%

“…Samples were collected from both the upper and the lower airways, the latter providing particular attention to contamination by using a sterile inner catheter in the working channel of a bronchoscope. We have previously published analyses on the oral and pulmonary mycobiome, in addition to comparisons between the healthy and the COPD oral and pulmonary mycobiomes using data from the MicroCOPD study [ 13 ]. In the current paper, we report on the stability of the oral and pulmonary mycobiomes in participants with and without COPD who underwent bronchoscopies at two different time points, and the potential effects on the mycobiomes from intercurrent antibiotic use.…”

Section: Introductionmentioning

confidence: 99%

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A longitudinal study of the pulmonary mycobiome in subjects with and without chronic obstructive pulmonary disease

et al. 2022

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Background Few studies have examined the stability of the pulmonary mycobiome. We report longitudinal changes in the oral and pulmonary mycobiome of participants with and without COPD in a large-scale bronchoscopy study (MicroCOPD). Methods Repeated sampling was performed in 30 participants with and 21 without COPD. We collected an oral wash (OW) and a bronchoalveolar lavage (BAL) sample from each participant at two time points. The internal transcribed spacer 1 region of the ribosomal RNA gene cluster was PCR amplified and sequenced on an Illumina HiSeq sequencer. Differences in taxonomy, alpha diversity, and beta diversity between the two time points were compared, and we examined the effect of intercurrent antibiotic use. Results Sample pairs were dominated by Candida. We observed less stability in the pulmonary taxonomy compared to the oral taxonomy, additionally emphasised by a higher Yue-Clayton measure in BAL compared to OW (0.69 vs 0.22). No apparent effect was visually seen on taxonomy from intercurrent antibiotic use or participant category. We found no systematic variation in alpha diversity by time either in BAL (p-value 0.16) or in OW (p-value 0.97), and no obvious clusters on bronchoscopy number in PCoA plots. Pairwise distance analyses showed that OW samples from repeated sampling appeared more stable compared to BAL samples using the Bray-Curtis distance metric (p-value 0.0012), but not for Jaccard. Conclusion Results from the current study propose that the pulmonary mycobiome is less stable than the oral mycobiome, and neither COPD diagnosis nor intercurrent antibiotic use seemed to influence the stability.

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“…A predominance of Pneumocystis spp. is described in COPD with co-existing HIV while Candida , Malassezia , and Sarocladium ( Figure 1 ) have been detected in stable COPD using BAL [ 27 , 106 ]. The dominant fungal organisms remain similar between oral, sputum, and BAL specimens; however, variations are noted in the taxonomic composition.…”

Section: The Pulmonary Mycobiome In Health Copd and Bronchiectasismentioning

confidence: 99%

Clinical Aspergillus Signatures in COPD and Bronchiectasis

Tiew

Thng

Chotirmall

2022

JoF

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Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.

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The pulmonary mycobiome—A study of subjects with and without chronic obstructive pulmonary disease

Cited by 23 publications

References 42 publications

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries

A longitudinal study of the pulmonary mycobiome in subjects with and without chronic obstructive pulmonary disease

Clinical Aspergillus Signatures in COPD and Bronchiectasis

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