The Experts below are selected from a list of 1296 Experts worldwide ranked by ideXlab platform
Pei Yee Tiew - One of the best experts on this subject based on the ideXlab platform.
-
a high risk airway Mycobiome is associated with frequent exacerbation and mortality in copd
European Respiratory Journal, 2021Co-Authors: Pei Yee Tiew, Alison Dicker, Holly R Keir, Mauern Poh, Sze Lei Pang, Mariko Siyue Koh, Micheal Mac Aogain, Jiunn Liang Tan, Augustine TeeAbstract:Introduction The COPD bacteriome associates with disease severity, exacerbations, and mortality. While COPD patients are susceptible to fungal sensitisation, the role of the fungal Mycobiome remains uncertain. Methods We report the largest multicenter evaluation of the COPD airway Mycobiome to date including participants from Asia (Singapore and Malaysia) and the United Kingdom (Scotland) when stable (n=337) and during exacerbations (n=66) as well as non-diseased controls (n=47). Longitudinal Mycobiome analyses performed during and following COPD exacerbations (n=34) were examined in terms of exacerbation frequency, two-year mortality, and the occurrence of serum specific-IgE against selected fungi. Results A distinct Mycobiome profile is observed in COPD compared to controls evidenced by increased alpha diversity (Shannon-index) (p Conclusion The airway Mycobiome in COPD is characterised by specific fungal genera associated with exacerbations and increased mortality.
-
a high risk airway Mycobiome characterises frequent copd exacerbators
European Respiratory Journal, 2020Co-Authors: Pei Yee Tiew, Alison Dicker, Holly R Keir, Mauern Poh, Sze Lei Pang, Sri Anusha Matta, Branden Qi Yu Chua, Mariko Siyue Koh, Augustine Tee, John AbisheganadenAbstract:Background: A lack of study on the COPD Mycobiome exists. Methods: We performed the largest multicenter evaluation of the COPD Mycobiome including patients from Asia (Singapore and Malaysia) and the UK (Scotland) (n=380). Non-diseased controls (n=47) were assessed and longitudinal analyses performed during and following exacerbations (n=34). COPD Mycobiomes were examined based on mortality and occurrence of serum specific-IgE against selected fungi. Results: A distinct Mycobiome profile in COPD evidenced by increased α-diversity (p Conclusion: Frequent COPD exacerbators are characterized by Aspergillus, Penicillium and Curvularia and illustrate poorer survival and systemic specific-IgE responses against these fungi allowing COPD risk stratification based on airway Mycobiomes. Funding: Singapore Ministry of Health’s National Medical Research Council under its Research Training Fellowship (NMRC/Fellowship/0049/2017) (P.Y.T) and Clinician-Scientist Individual Research Grant (MOH-000141) (S.H.C). The TARDIS study is funded by Glaxosmithkline & British Lung Foundation (Fellowship to JDC).
-
The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges
Mycopathologia, 2020Co-Authors: Pei Yee Tiew, Micheál Mac Aogain, Nur A’tikah Binte Mohamed Ali, Kai Xian Thng, Karlyn Goh, Kenny J. X. Lau, Sanjay H ChotirmallAbstract:Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘Mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging Mycobiome research into clinical practice.
-
optimisation and benchmarking of targeted amplicon sequencing for Mycobiome analysis of respiratory specimens
International Journal of Molecular Sciences, 2019Co-Authors: Nur Atikah Binte Mohamed Ali, Pei Yee Tiew, Micheal Mac Aogain, Raika Francesca Morales, Sanjay H ChotirmallAbstract:(1) Background: Firm consensus has yet to be established in relation to taxonomic classification and primer choice in targeted amplicon sequencing of the Mycobiome. While the nuclear ribosomal internal transcribed spacer (ITS) region are recognized as the formal fungal taxonomic barcode, appraisal of different ITS sub-regions and the influence of DNA extraction methods have not been comprehensively undertaken using human respiratory specimens. (2) Methods: We performed ITS analysis of respiratory (sputum) samples by assessing (a) the effect of alternate DNA extraction techniques and (b) an evaluation of four different ITS primer pairs (ITS1F and ITS2; ITS1-30F and ITS1-217R; gITS7ngs and ITS4ng; and Fseq and Rseq) on the Mycobiome profiles generated for mock fungal communities and their respective clinical (airway) specimens. (3) Results: Primer pairs varied in their resulting ITS Mycobiome profiles, suggesting that particular pairs may be more relevant for analysis of respiratory samples compared to others. Assessment of DNA extraction methods highlighted lower final DNA concentrations achieved by mechanical disruption compared to enzymatic lysis. However, despite lower yields, DNA liberated by mechanical lysis more readily yielded ITS bands with highest success in combination with the Fseq and Rseq primers. (4) Conclusion: Choice of extraction method, primers used, and sequencing approach are all important considerations in sequencing the Mycobiome and should be tailored to sample type. A standardization of approach to Mycobiome studies using respiratory specimens will permit more reliable comparisons between studies and improve our understanding of the role of fungi in the human airway.
Chloe E Huseyin - One of the best experts on this subject based on the ideXlab platform.
-
the fungal frontier a comparative analysis of methods used in the study of the human gut Mycobiome
Frontiers in Microbiology, 2017Co-Authors: Chloe E Huseyin, Raul Cabrera Rubio, Orla Osullivan, Paul D Cotter, Pauline D ScanlanAbstract:The human gut is host to a diverse range of fungal species, collectively referred to as the gut “Mycobiome”. The gut Mycobiome is emerging as an area of considerable research interest due to the potential roles of these fungi in human health and disease. However, there is no consensus as to what the best or most suitable methodologies available are with respect to characterising the human gut Mycobiome. The aim of this study is to provide a comparative analysis of several previously published Mycobiome-specific culture-dependent and -independent methodologies, including choice of culture media, incubation conditions (aerobic versus anaerobic), DNA extraction method, primer set and freezing of faecal samples to assess their relative merits and suitability for gut Mycobiome analysis. There was no significant effect of media type or aeration on culture-dependent results. However, freezing was found to have a significant effect on fungal viability, with significantly lower fungal numbers recovered from frozen samples. DNA extraction method had a significant effect on DNA yield and quality. However, freezing and extraction method did not have any impact on either α or β diversity. There was also considerable variation in the ability of different fungal-specific primer sets to generate PCR products for subsequent sequence analysis. Through this investigation two DNA extraction methods and one primer set was identified which facilitated the analysis of the Mycobiome for all samples in this study. Ultimately, a diverse range of fungal species were recovered using both approaches, with Candida and Saccharomyces identified as the most common fungal species recovered using culture-dependent and culture-independent methods, respectively. As has been apparent from ecological surveys of the bacterial fraction of the gut microbiota, the use of different methodologies can ultimately impact on our understanding of gut Mycobiome composition and therefore requires careful consideration. Future research into the gut Mycobiome needs to adopt a common strategy to minimize potentially confounding effects of methodological choice and to facilitate comparative analysis of datasets.
-
forgotten fungi the gut Mycobiome in human health and disease
Fems Microbiology Reviews, 2017Co-Authors: Paul W Otoole, Chloe E Huseyin, Paul D Cotter, Pauline D ScanlanAbstract:The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our 'Mycobiome'. Although research into the Mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut Mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
Nezar Noor Alhebshi - One of the best experts on this subject based on the ideXlab platform.
-
supragingival Mycobiome and inter kingdom interactions in dental caries
Journal of Oral Microbiology, 2020Co-Authors: Divyashri Baraniya, Tsute Chen, Anubhav Nahar, Fadhl M Alakwaa, Jennifer Hill, Marisol Tellez, Amid I Ismail, Sumant Puri, Nezar Noor AlhebshiAbstract:Background: Recent studies have reveled the presence of a complex fungal community (Mycobiome) in the oral cavity. However, the role of oral Mycobiome in dental caries and its interaction with cari...
-
the bacteriome and Mycobiome associated with oral squamous cell carcinoma metagenomic analysis of samples from yemeni and sri lankan cohorts
Journal of Oral Microbiology, 2017Co-Authors: Nezar Noor Alhebshi, Akram Thabet Nasher, Mohamed Maryoud, Husham Homeida, Manosha Perera, Irosha Perera, Deepak S Ipe, Glen C Ulett, David Speicher, Ali Mohamed IdrisAbstract:ABSTRACTThere is increasing interest in the possible role of the oral microbiome in oral squamous cell carcinoma (OSSC). However, studies on the possible association between the oral bacteriome and OSCC remain inconclusive, while the potential role of the “Mycobiome” in oral carcinogenesis has never been explored. I hereby present results from our recent studies on the bacteriome and Mycobiome associated with OSCC based on analysis of samples from Yemeni and Sri Lankan cohorts. Tissue biopsies were obtained from the cases while deep buccal swabs or fibro-epithelial polyps were collected from the controls. Sequencing of the bacterial V1-V3 region of the 16S rRNA gene and the fungal ITS2 region using Illumina’s 2x300 bp chemistry was employed to study the bacteriome and Mycobiome, respectively. Merged reads were classified to species level using a BLASTN-algorithm. Downstream analyses were performed using QIIME, PICRUSt, and LEfSe. Fusobacterium nucleatum subsp. polymorphum, Pseudomonas aeruginosa, Prevotel...
-
a dysbiotic Mycobiome dominated by candida albicans is identified within oral squamous cell carcinomas
2017Co-Authors: Manosha Perera, Nezar Noor Alhebshi, Irosha Perera, Deepak S Ipe, Glen C Ulett, David Speicher, Tsute Chen, Newell W JohnsonAbstract:ABSTRACTThe aim of this study was to characterize the Mycobiome associated with oral squamous-cell carcinoma (OSCC). DNA was extracted from 52 tissue biopsies (cases: 25 OSCC; controls: 27 intra-oral fibro-epithelial polyps [FEP]) and sequenced for the fungal internal transcribed spacer 2 region using Illumina™ 2 x300bp chemistry. Merged reads were classified to species level using a BLASTN-algorithm with UNITE’s named species sequences as reference. Downstream analyses were performed using QIIME™ and linear discriminant analysis effect size. A total of 364 species representing 160 genera and two phyla (Ascomycota and Basidiomycota) were identified, with Candida and Malassezia making up 48% and 11% of the average Mycobiome, respectively. However, only five species and four genera were detected in ≥50% of the samples. The species richness and diversity were significantly lower in OSCC. Genera Candida, Hannaella, and Gibberella were overrepresented in OSCC; Alternaria and Trametes were more abundant in FEP....
Martin Unterseher - One of the best experts on this subject based on the ideXlab platform.
-
the needle Mycobiome of picea glauca a dynamic system reflecting surrounding environment and tree phenological traits
Fungal Ecology, 2019Co-Authors: David G Wurth, Mathilde Borg Dahl, Martin Unterseher, Martin Wilmking, Mario Trouillier, Markus Scholler, Soren J Sorensen, Martin Steen Mortensen, Martin SchnittlerAbstract:Abstract Fungi play a crucial role in terrestrial Arctic ecosystems as symbionts of vascular plants and nutrient recyclers in soil, with many species persistently or temporarily inhabiting the phyllosphere of the vegetation. In this study we apply high-throughput sequencing to investigate the Mycobiome of 172 samples of fresh (current year) and aged (3 year old) needles of Picea glauca from three sites over a distance of 500 km in Alaska (USA). We analysed Illumina-generated ITS2 sequences to relate Mycobiome data with phenotypic tree traits, measures of genetic variation and climate variables obtained from long-term monitoring of the sites. Alpha-diversity declined with increasing environmental stress/climate harshness. Fungal communities differed in richness and taxonomic composition between sites, with a pronounced difference in the relative abundance of OTUs assigned to species of the rust genus Chrysomyxa , plant pathogens which seem to have been in an outbreak at two sites at the time of sampling. Beside climate parameters, needle age was the second strongest explanatory variable of the Mycobiome composition, whereas we found no effect of tree genetic variation, indicating that environmental and tree trait specific variables mainly determined individual white spruce Mycobiomes at Alaska's treelines.
-
Mycobiomes of sympatric amorphophallus albispathus araceae and camellia sinensis theaceae a case study reveals clear tissue preferences and differences in diversity and composition
Mycological Progress, 2018Co-Authors: Martin Unterseher, Mathilde Borg Dahl, Henrik R Nilsson, Samantha C Karunarathna, Garcia Roberto Cruz, Nikki Heherson A Dagamac, Serena E Dool, Michelle Galla, Lina Herbst, Sebastien J PuechmailleAbstract:Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic Mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The Mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α- and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the Mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The Mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while Mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.
-
habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle Mycobiome picea glauca system at an arctic treeline ecotone
New Phytologist, 2016Co-Authors: Pascal Eusemann, Mathilde Borg Dahl, Martin Schnittler, Henrik R Nilsson, Ari Jumpponen, David G Wurth, Allan Buras, Martin Wilmking, Martin UnterseherAbstract:- Plant-associated Mycobiomes in extreme habitats are understudied and poorly understood. - We analysed Illumina-generated ITS1 sequences from the needle Mycobiome of white spruce (Picea glauca) at the northern treeline in Alaska (USA). Sequences were obtained from the same DNA that was used for tree genotyping. In the present study, fungal metabarcoding and tree microsatellite data were compared for the first time. - In general, neighbouring trees shared more fungal taxa with each other than trees growing in further distance. Mycobiomes correlated strongly with phenological host traits and local habitat characteristics contrasting a dense forest stand with an open treeline site. Genetic similarity between trees did not influence fungal composition and no significant correlation existed between needle Mycobiome and tree genotype. - Our results suggest the pronounced influence of local habitat conditions and phenotypic tree traits on needle-inhabiting fungi. By contrast, the tree genetic identity cannot be benchmarked as a dominant driver for needle-inhabiting Mycobiomes, at least not for white spruce in this extreme environment.
-
diversity and composition of the leaf Mycobiome of beech fagus sylvatica are affected by local habitat conditions and leaf biochemistry
PLOS ONE, 2016Co-Authors: Martin Unterseher, Abu Bakar Siddique, Andreas Brachmann, Derek PeršohAbstract:Comparative investigations of plant-associated fungal communities (Mycobiomes) in distinct habitats and under distinct climate regimes have been rarely conducted in the past. Nowadays, high-throughput sequencing allows routine examination of Mycobiome responses to environmental changes and results at an unprecedented level of detail. In the present study, we analysed Illumina-generated fungal ITS1 sequences from European beech (Fagus sylvatica) originating from natural habitats at two different altitudes in the German Alps and from a managed tree nursery in northern Germany. In general, leaf-inhabiting Mycobiome diversity and composition correlated significantly with the origin of the trees. Under natural condition the Mycobiome was more diverse at lower than at higher elevation, whereas fungal diversity was lowest in the artificial habitat of the tree nursery. We further identified significant correlation of leaf chlorophylls and flavonoids with both habitat parameters and Mycobiome biodiversity. The present results clearly point towards a pronounced importance of local stand conditions for the structure of beech leaf Mycobiomes and for a close interrelation of phyllosphere fungi and leaf physiology.
Alison Morris - One of the best experts on this subject based on the ideXlab platform.
-
diversity of the lung Mycobiome is associated with severity of disease in acute respiratory distress syndrome
European Respiratory Journal, 2020Co-Authors: Noel Britton, Adam Fitch, Georgios D Kitsios, Barbara Methe, Bryan J Mcverry, Alison MorrisAbstract:Background: Research into the lung microbiome has focused on bacteria. Research into the fungal communities (Mycobiome) has been limited, in part due to technical limitations. Given that the lung Mycobiome may represent a potential source of infection as well as driver of immune and inflammatory pathway activation, we sought to describe the diversity of the lung Mycobiome in patients with acute respiratory distress syndrome (ARDS). Methods: We enrolled mechanically-ventilated patients with and at risk for ARDS and collected endotracheal aspirates (ETA) within 48hrs of intubation. We used extracted DNA from ETAs to perform fungal (internal transcribed spacer) rRNA gene sequencing on the Illumina MiSeq platform. Results: Of the 202 patients enrolled, 21% had a diagnosis of ARDS (mean age 50.2 years; 61% females). Fungal alpha diversity was lower in ARDS compared to airway controls (p Conclusion: Next-generation sequencing analysis identifies differences in the diversity of the Mycobiome of patients with ARDS. Lower fungal alpha diversity in ARDS and increased severity of disease suggests a relationship between the lung Mycobiome and the inflammatory cascade associated with ARDS.
-
the lung Mycobiome in the next generation sequencing era
Virulence, 2017Co-Authors: Laura Tipton, Elodie Ghedin, Alison MorrisAbstract:The fungi that reside in the human lungs represent an understudied, but medically relevant comm-unity. From the few studies published on the lung Mycobiome, we find that there are fungi in both the healthy and diseased respiratory tract, that these fungi vary widely between individuals, and that there is a trend toward lower fungal diversity among individuals with disease. This review discusses the few studies of the lung Mycobiome and details the challenges that accompany lung Mycobiome studies. These challenges include sample collection and processing, sequence amplification and processing, and a history of multiple names for species. Some challenges may never be solved, but others can be solved with more data and additional studies of the lung Mycobiome.
-
The human Mycobiome in health and disease
Genome Medicine, 2013Co-Authors: Lijia Cui, Alison Morris, Elodie GhedinAbstract:The Mycobiome, referring primarily to the fungal biota in an environment, is an important component of the human microbiome. Despite its importance, it has remained understudied. New culture-independent approaches to determine microbial diversity, such as next-generation sequencing methods, are greatly broadening our view of fungal importance. An integrative analysis of current studies shows that different body sites harbor specific fungal populations, and that diverse Mycobiome patterns are associated with various diseases. By interfacing with other biomes, as well as with the host, the Mycobiome probably contributes to the progression of fungus-associated diseases and plays an important role in health and disease.
