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

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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Bio-stimulation by seed priming with Bacillus subtilis for suppressing seed-borne fungal pathogens of vegetables in Bangladesh

Journal of the Bangladesh Agricultural University ◽

10.3329/jbau.v14i2.32692 ◽

2017 ◽

Vol 14 (2) ◽

pp. 177-184

Author(s):

FH Tumpa ◽

A Sultana ◽

MZ Alam ◽

MAR Khokon

Keyword(s):

Bacillus Subtilis ◽

Fungal Pathogens ◽

Culture Method ◽

Seed Priming ◽

Macrophomina Phaseolina ◽

Fungal Species ◽

Dual Culture ◽

Control Seed ◽

Rhizopus Sp ◽

Wax Gourd

Aqueous formulation of rhizopheric beneficial bacteria viz. Bacillus subtilis, an exotic strain collected from Russia was assayed for its performance to suppress the growth of various seed-borne fungi of vegetable. The performance of the bio-agent was appraised based on growth suppression by dual culture method and reduction of seed-borne fungi in the bio-agent treated seeds. Ten seed samples comprise of summer and winter vegetables were examined collected from different local farmers. A total of fourteen fungal species belongs to twelve genera viz. Fusarium moniliforme, Botrytis cinerea, Aspergillus flavus, F. oxysporum, Botryodiplodia theobromae, Macrophomina phaseolina, A.niger, Cercospora sp., Phoma exigua, Rhizopus sp., Colletotrichum sp., Phytophthora sp., Penicillium sp., and Curvularia sp. were recorded from different untreated seeds. Vegetables seeds were treated in a concentration (10-3) of aqueous formulation of B. subtilis for two hours followed by air drying for 30 minutes. In general, the incidences of all fungal species of all kinds of vegetables seeds were reduced. But, selectively the best performances were observed in tomato, brinjal, cucumber, wax gourd and okra where most of the fungal species were completely suppressed by seed treatment with Bacillus subtilis. The growth of seed-borne fungi was inhibited highest in wax gourd (100%). The growth inhibition was also at satisfactory level in cucumber (95%), tomato (95%), brinjal (92%) and okra (86%) seeds. The findings of this research indicate the possibility of utilizing B. subtilis as seed treating agents instead of chemical fungicides to control seed-borne diseases of vegetables.J. Bangladesh Agril. Univ. 14(2): 177-184, December 2016

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Isolation and potential biocontrol of the fungus causing anthracnose in longan in Vietnam

Science and Technology Development Journal ◽

10.32508/stdj.v24i1.2500 ◽

2021 ◽

Vol 24 (1) ◽

pp. 1889-1896

Author(s):

Phan Thi Huyen ◽

Vo Thi Xuan Huong ◽

Do Thanh Nhan

Keyword(s):

Human Health ◽

Economic Value ◽

Culture Method ◽

Fungal Species ◽

Yield And Quality ◽

Wide Range ◽

Microbial Community Structures ◽

Increasing Demand ◽

First Time

Introduction: Longan is a crop plant of very high economic value, and both its fruit and flower are beneficial for human health. Longan has been increasingly cultivated in Vietnam due to the increasing demand for domestic consumption as well as export of its fruit. However, the widespread emergence and spread of anthracnose, a group of fungal disease affecting a wide range of plant species, in longan has seriously affected both the longan fruit yield and quality in Vietnam. Current methods for the prevention of anthracnose in longan depend mainly on the use of fungicides which are very harmful to human health as well as disruptive to microbial community structures in different ecosystems. In order to obtain an environmentally friendly method of control for this disease, the agent causing anthracnose in longan must first be identified. Therefore, the aim of this study was to isolate and identify the causal anthracnose agent in longan in Vietnam. Methods: Experiments were first carried out with pieces of anthracnose longan leaves pressed onto the surface of potato-dextrose agar (PDA) and incubated for days at 30◦C. Colonies, varying in appearance, were repeatedly isolated and purified on PDA agar, and the anthracnose-causing agent was initially recognized on the basis of colony characteristics and cell morphology. The suspected isolate was then tested for its ability to decompose healthy longan leaf in vitro, and its rDNA region was cloned and sequenced to determine its taxonomy. Antifungal activity testing was performed using the co-culture method. Results: We obtained a fungal isolate with septate hyphae, ovoid appressoria, and conidia (which were cylindrical in shape with rounded ends). This isolate showed a clear ability to decompose healthy longan leaves. At the molecular level, the isolate was determined to be a fungal species belonging to genus Colletotrichum, and therefore named Colletotrichum sp. strain BKHCM. We also found that its growth was inhibited when co-cultured with Streptomyces flaveus, an actinomycete originating from soil. Conclusion: For the first time, we isolated a fungal species belonging to genus Colletotrichum from anthracnose-infected longan leaves in Vietnam. We also showed that the growth of this fungus could potentially be biocontrolled.

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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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Real time polymerase chain reaction versus conventional culture method to detect respiratory pathogens in subjects with non-cystic fibrosis bronchiectasis

10.1183/13993003.congress-2019.pa2166 ◽

2019 ◽

Author(s):

Boitumelo Pitso ◽

Robin Green ◽

Refiloe Masekela ◽

Goga Ameena

Keyword(s):

Cystic Fibrosis ◽

Polymerase Chain Reaction ◽

Real Time ◽

Culture Method ◽

Respiratory Pathogens ◽

Chain Reaction ◽

Conventional Culture ◽

Polymerase Chain ◽

Conventional Culture Method

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Evaluation of Various Culture Media for Detection of Rapidly Growing Mycobacteria from Patients with Cystic Fibrosis

Journal of Clinical Microbiology ◽

10.1128/jcm.00471-16 ◽

2016 ◽

Vol 54 (7) ◽

pp. 1797-1803 ◽

Cited By ~ 14

Author(s):

Clair L. Preece ◽

Thomas A. Wichelhaus ◽

Audrey Perry ◽

Amanda L. Jones ◽

Stephen P. Cummings ◽

...

Keyword(s):

Cystic Fibrosis ◽

Burkholderia Cepacia ◽

Nontuberculous Mycobacteria ◽

Culture Media ◽

Culture Method ◽

Content Type ◽

Selective Media ◽

Rapidly Growing Mycobacteria ◽

Selective Agar ◽

Bacteria And Fungi

Isolation of nontuberculous mycobacteria (NTM) from the sputum of patients with cystic fibrosis (CF) is challenging due to overgrowth by rapidly growing species that colonize the lungs of patients with CF. Extended incubation onBurkholderia cepaciaselective agar (BCSA) has been recommended as an expedient culture method for the isolation of rapidly growing NTM in this setting. The aim of this study was to assess five selective media designed for the isolation ofBurkholderia cepaciacomplex, along with two media designed for the isolation of mycobacteria (rapidly growing mycobacteria [RGM] medium and Middlebrook 7H11 agar), for their abilities to isolate NTM. All seven media were challenged with 147 isolates of rapidly growing mycobacteria and 185 isolates belonging to other species. RGM medium was then compared with the most selective brand of BCSA for the isolation of NTM from 224 sputum samples from patients with CF. Different agars designed for the isolation ofB. cepaciacomplex varied considerably in their inhibition of other bacteria and fungi. RGM medium supported the growth of all isolates of mycobacteria and was more selective than any other medium. NTM were recovered from 17 of 224 sputum samples using RGM medium, compared with only 7 samples using the most selective brand of BCSA (P= 0.023). RGM medium offers a superior option, compared to other selective agars, for the isolation of rapidly growing mycobacteria from the sputum of patients with CF. Furthermore, the convenience of using RGM medium enables routine screening for rapidly growing NTM in all submitted sputum samples from patients with CF.

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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

Journal of Oral Microbiology ◽

10.1080/20002297.2021.1897328 ◽

2021 ◽

Vol 13 (1) ◽

pp. 1897328

Author(s):

Jesse R. Willis ◽

Ester Saus ◽

Susana Iraola-Guzmán ◽

Elena Cabello-Yeves ◽

Ewa Ksiezopolska ◽

...

Keyword(s):

Cystic Fibrosis ◽

Citizen Science ◽

Fungal Species ◽

Oral Microbiome

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A highly diverse fungal community associated with leaves of the mangrove plant Acanthus ilicifolius var. xiamenensis revealed by isolation and metabarcoding analyses

PeerJ ◽

10.7717/peerj.7293 ◽

2019 ◽

Vol 7 ◽

pp. e7293 ◽

Cited By ~ 3

Author(s):

Wei-Chiung Chi ◽

Weiling Chen ◽

Chih-Chiao He ◽

Sheng-Yu Guo ◽

Hyo-Jung Cha ◽

...

Keyword(s):

Endophytic Fungi ◽

Plant Pathogens ◽

Fungal Species ◽

Corynespora Cassiicola ◽

Mangrove Plant ◽

Operational Taxonomic Units ◽

The Core ◽

Acanthus Ilicifolius ◽

Read Abundance ◽

High Diversity

A high diversity of culturable foliar endophytic fungi is known from various mangrove plants, and the core taxa include species from Colletotrichum, Pestalotiopsis, Phoma, Phomopsis, Sporomiella, among others. Since a small fraction of fungi is able to grow in culture, this study investigated the diversity of fungi associated with leaves of Acanthus ilicifolius var. xiamenensis using both isolation and metabarcoding approaches. A total of 203 isolates were cultured from surface-sterilized leaves, representing 47 different fungal species: 30 species from the winter samples (104 isolates), and 26 species from the summer samples (99 isolates). Ascomycota was dominant in both types of leaf samples, while Basidiomycota was isolated only from the summer samples. Drechslera dematioidea (10.58%, percentage of occurrence), Colletotrichum sp. 3 (7.69%) and Alternaria sp. (7.69%) were dominant in the winter samples; Fusarium oxysporum (13.13%), Diaporthe endophytica (10.10%) and Colletotrichum sp. 1 (9.09%) in the summer samples. Overall, Corynespora cassiicola (6.90%), F. oxysporum (6.40%) and Guignardia sp. (6.40%) had the highest overall percentage of occurrence. In the metabarcoding analysis, a total of 111 operational taxonomic units (OTUs) were identified from 17 leaf samples: 96 OTUs from the winter and 70 OTUs from the summer samples. Sequences belonging to Ascomycota and Basidiomycota were detected in both samples but the former phylum was dominant over the latter. Based on read abundance, taxa having the highest percentage of occurrence included Alternaria sp. (3.46%), Cladosporium delicatulum (2.56%) and Pyrenochaetopsis leptospora (1.41%) in the winter leaves, and Aureobasidium sp. (10.72%), Cladosporium sp. (7.90%), C. delicatulum (3.45%) and Hortaea werneckii (3.21%) in the summer leaves. These latter four species also had the highest overall percentage of occurrence. Combining the results from both methods, a high diversity of fungi (at least 110 species) was found associated with leaves of A. ilicifolius var. xiamenensis. Many of the fungi identified were plant pathogens and may eventually cause diseases in the host.

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