Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species

Abstract During 2017, the Westerdijk Fungal Biodiversity Institute (WI) and the Utrecht University Museum launched a Citizen Science project. Dutch school children collected soil samples from gardens at different localities in the Netherlands, and submitted them to the WI where they were analysed in order to find new fungal species. Around 3000 fungal isolates, including filamentous fungi and yeasts, were cultured, preserved and submitted for DNA sequencing. Through analysis of the ITS and LSU sequences from the obtained isolates, several plectosphaerellaceous fungi were identified for further study. Based on morphological characters and the combined analysis of the ITS and TEF1-α sequences, some isolates were found to represent new species in the genera Phialoparvum, i.e. Ph. maaspleinense and Ph. rietveltiae, and Plectosphaerella, i.e. Pl. hanneae and Pl. verschoorii, which are described and illustrated here.

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Modified culture method detects a high diversity of fungal species in cystic fibrosis patients

Medical Mycology ◽

10.3109/13693786.2013.792438 ◽

2013 ◽

pp. 1-8 ◽

Cited By ~ 12

Author(s):

Lilian Masoud-Landgraf ◽

Alexandra Badura ◽

Ernst Eber ◽

Gebhard Feierl ◽

Egon Marth ◽

...

Keyword(s):

Cystic Fibrosis ◽

Culture Method ◽

Fungal Species ◽

High Diversity

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Presence of Fungal Species in Sputum of Adult Patients with Cystic Fibrosis Is Associated with Pseudomonas Spp. Colonization, Frequent Exacerbations, Inhaled Antibiotic and Steroid Use Single Center Experience

10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2115 ◽

2020 ◽

Author(s):

L. Zhang ◽

L. Borish ◽

D.P. Albon

Keyword(s):

Cystic Fibrosis ◽

Fungal Species ◽

Adult Patients ◽

Single Center ◽

Steroid Use ◽

Pseudomonas Spp ◽

Single Center Experience

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Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

Journal of Clinical Microbiology ◽

10.1128/jcm.01094-15 ◽

2015 ◽

Vol 53 (9) ◽

pp. 2900-2907 ◽

Cited By ~ 35

Author(s):

Rolf Kramer ◽

Annette Sauer-Heilborn ◽

Tobias Welte ◽

Carlos A. Guzman ◽

Wolf-Rainer Abraham ◽

...

Keyword(s):

Cystic Fibrosis ◽

Fungal Spores ◽

Rare Event ◽

Single Strand Conformation Polymorphism ◽

Fungal Species ◽

Fungal Communities ◽

Fungal Colonization ◽

Molecular Fingerprinting ◽

High Exposure ◽

Entire Cohort

The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF.

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Coinfection with Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis

European Respiratory Review ◽

10.1183/16000617.0011-2020 ◽

2020 ◽

Vol 29 (158) ◽

pp. 200011

Author(s):

Karen Keown ◽

Alastair Reid ◽

John E. Moore ◽

Clifford C. Taggart ◽

Damian G. Downey

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Aspergillus Fumigatus ◽

Lung Disease ◽

Disease Progression ◽

Expert Knowledge ◽

Fungal Species ◽

Interspecies Interactions ◽

Cross Sectional ◽

Infection And Inflammation

ObjectivesCystic fibrosis (CF) lung disease is characterised by mucus stasis, chronic infection and inflammation, causing progressive structural lung disease and eventual respiratory failure. CF airways are inhabited by an ecologically diverse polymicrobial environment with vast potential for interspecies interactions, which may be a contributing factor to disease progression. Pseudomonas aeruginosa and Aspergillus fumigatus are the most common bacterial and fungal species present in CF airways respectively and coinfection results in a worse disease phenotype.MethodsIn this review we examine existing expert knowledge of chronic co-infection with P. aeruginosa and A. fumigatus in CF patients. We summarise the mechanisms of interaction and evaluate the clinical and inflammatory impacts of this co-infection.ResultsP. aeruginosa inhibits A. fumigatus through multiple mechanisms: phenazine secretion, iron competition, quorum sensing and through diffusible small molecules. A. fumigatus reciprocates inhibition through gliotoxin release and phenotypic adaptations enabling evasion of P. aeruginosa inhibition. Volatile organic compounds secreted by P. aeruginosa stimulate A. fumigatus growth, while A. fumigatus stimulates P. aeruginosa production of cytotoxic elastase.ConclusionA complex bi-directional relationship exists between P. aeruginosa and A. fumigatus, exhibiting both mutually antagonistic and cooperative facets. Cross-sectional data indicate a worsened disease state in coinfected patients; however, robust longitudinal studies are required to derive causality and to determine whether interspecies interaction contributes to disease progression.

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Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition

Microbiome ◽

10.1186/s40168-018-0592-3 ◽

2018 ◽

Vol 6 (1) ◽

Cited By ~ 19

Author(s):

Jesse R. Willis ◽

Pedro González-Torres ◽

Alexandros A. Pittis ◽

Luis A. Bejarano ◽

Luca Cozzuto ◽

...

Keyword(s):

Drinking Water ◽

Citizen Science ◽

Oral Microbiome ◽

Water Composition

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Characterization of Oral Microbiota in Cats: Novel Insights on the Potential Role of Fungi in Feline Chronic Gingivostomatitis

Pathogens ◽

10.3390/pathogens10070904 ◽

2021 ◽

Vol 10 (7) ◽

pp. 904

Author(s):

Janina A. Krumbeck ◽

Alexander M. Reiter ◽

James C. Pohl ◽

Shuiquan Tang ◽

Young J. Kim ◽

...

Keyword(s):

Oral Health ◽

Health Assessment ◽

Fungal Species ◽

Oral Microbiome ◽

Oral Microbiota ◽

Biological Interactions ◽

Potential Biomarker ◽

Microbial Infections ◽

Bacteria And Fungi

Previous studies have suggested the involvement of viral and bacterial components in the initiation and progression of feline chronic gingivostomatitis (FCGS), but the role of fungi remains entirely unknown. This pilot study aimed to investigate the bacteriome and mycobiome in feline oral health and disease. Physical exams, including oral health assessment, of privately owned, clinically healthy (CH) cats (n = 14) and cats affected by FCGS (n = 14) were performed. Using a sterile swab, oral tissue surfaces of CH and FCGS cats were sampled and submitted for 16S rRNA and ITS-2 next-generation DNA sequencing. A high number of fungal species (n = 186) was detected, with Malassezia restricta, Malassezia arunalokei, Cladosporium penidielloides/salinae, and Aspergillaceae sp. being significantly enriched in FCGS samples, and Saccharomyces cerevisiae in CH samples. The bacteriome was significantly distinct between groups, and significant inter-kingdom interactions were documented. Bergeyella zoohelcum was identified as a potential biomarker of a healthy feline oral microbiome. These data suggest that fungi might play a role in the etiology and pathogenesis of FCGS, and that oral health should not simply be regarded as the absence of microbial infections. Instead, it may be viewed as the biological interactions between bacterial and fungal populations that coexist to preserve a complex equilibrium in the microenvironment of the mouth. Additional investigations are needed to improve our understanding of the feline oral ecosystem and the potential interactions between viruses, bacteria, and fungi in FCGS.

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