Fungal Databases Research Articles

Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada.

In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015-2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real-time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land-use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early-warning system for farmers to detect and mitigate impending disease outbreaks.

CFPG: Creating a Common Fungal Pathogenic Genes Database through Data Mining

Fu ngal pathogenicity is one of the most vigorously tackled ecological and medicinal issues facing many scientists. Comparative genomics is an extremely important methodology and tool used to understand fungal pathogenicity, and it allows the development of early diagnostic tools for fungal-inflicted diseases across different host organisms. However, comparative genomics depends heavily on readily available fungal pathogenic gene databases to enable downstream genomics study and the development of new diagnosis and detection methods. Here, we have developed the Common Fungal Pathogenic Genes Database through comparative genomic analysis using 86 publicly available fungal genomic data against fungal pathogenicity-related databases, such as Pathogenic-Host Interaction Database (PHI-base), Carbohydrate-Active enZymes Database (CAZy), and Database of Fungal Virulence Factory (DFVF).

Ascomycota In the Shallow Ecoregion of Catarina, Caatinga, Brazil: Part 1

Objective: Inventories of fungi are essential, but they are rarely carried out, especially in areas of the Caatinga biome. It is therefore important to carry out surveys and mapping to make knowledge more accessible. In this context, the aim of this work was to organize and discuss the information and data related to the fungi of Raso da Catarina, cataloguing and presenting the first checklist of Ascomycota in an insufficiently researched locality, adding knowledge from scientific collections, publications, and field expeditions. Method: Literature searches were carried out on the Ascomycota of the Raso da Catarina Ecoregion; consultations of the Fungal Databases, U.S. National Fungus Collections, the EMBRAPA database (Fungi Reported on Plants in Brazil) and the Mycology Collections Portal; consultations of the speciesLink networks that integrate data from scientific collections; consultations of the Reflora Virtual Herbarium and the INCT-Herbário Virtual da Flora e dos Fungos. In addition to field expeditions in areas of the Raso da Catarina in the municipalities of Paulo Afonso, Jeremoabo and Glória. Results and conclusion: A total of 243 taxa comprising 75 asexual fungi, 85 lichenized sexual fungi and 73 non-lichenized sexual fungi, distributed in 148 genera, were catalogued. This work represents an initiative to systematize research carried out in Raso da Catarina, with the aim of adding knowledge to the estimate of Ascomycota species in the Caatinga. Originality/value: Work on fungi in areas of the Raso da Catarina is still incipient. Some data is scattered in a few publications and many taxa are in scientific collections without being published. This is therefore the first checklist of Ascomycota for the Ecoregion and provides relevant information.

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (-)-sandaracopimaradiene in the fungus Arthrinium sacchari.

Labdane-related diterpenoids (LRDs) in fungi are a pharmaceutically important, but underexplored family of natural products. In the biosynthesis of fungal LRDs, bifunctional terpene cyclases (TCs) consisting of αβγ domains are generally used to synthesize the polycyclic skeletones of LRDs. Herein, we conducted genome mining of LRDs in our fungal genome database and identified a unique pair of TCs, AsPS and AsCPS, in the fungus Arthrinium sacchari. AsPS consists of catalytically active α and inactive β domains, whereas AsCPS contains βγ domains and a truncated α domain. Heterologous expression in Aspergillus oryzae and biochemical characterization of recombinant proteins demonstrated that AsCPS synthesized copalyl diphosphate and that AsPS then converted it to (-)-sandaracopimaradiene. Since AsPS and AsCPS have distinct domain organizations from those of known fungal TCs and are likely generated through fusion or loss of catalytic domains, our findings provide insight into the evolution of TCs in fungi.

FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen.

Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans. The F. oxysporum Pangenome Database (FoPGDB) is a comprehensive resource integrating 35 high-quality FOSC genomes, coupled with robust analytical tools. FoPGDB allows for both gene-based and graph-based exploration of the F. oxysporum pangenome. It also curates a large repository of putative effector sequences, crucial for understanding the mechanisms of FOSC pathogenicity. With an assortment of functionalities including gene search, genomic variant exploration and tools for functional enrichment, FoPGDB provides a platform for in-depth investigations of the genetic diversity and adaptability of F. oxysporum. The modular and user-friendly interface ensures efficient data access and interpretation. FoPGDB promises to be a valuable resource for F. oxysporum research, contributing to our understanding of this pathogen's pangenomic landscape and aiding in the development of novel disease management strategies. Database URL: http://www.fopgdb.site.

FGCD: a database of fungal gene clusters related to secondary metabolism.

Fungal secondary metabolites are not necessary for growth, but they are important for fungal metabolism and ecology because they provide selective advantages for competition, survival and interactions with the environment. These various metabolites are widely used as medicinal precursors and insecticides. Secondary metabolism genes are commonly arranged in clusters along chromosomes, which allow for the coordinate control of complete pathways. In this study, we created the Fungal Gene Cluster Database to store, retrieve, and visualize secondary metabolite gene cluster information across fungal species. The database was created by merging data from RNA sequencing, Basic Local Alignment Search Tool, genome browser, enrichment analysis and the R Shiny web framework to visualize and query putative gene clusters. This database facilitated the rapid and thorough examination of significant gene clusters across fungal species by detecting, defining and graphically displaying the architecture, organization and expression patterns of secondary metabolite gene clusters. In general, this genomic resource makes use of the tremendous chemical variety of the products of these ecologically and biotechnologically significant gene clusters to our further understanding of fungal secondary metabolism. Database URL: https://www.hebaubioinformatics.cn/FungalGeneCluster/.

Analysis of climate change impacts on the biogeographical patterns of species-specific productivity of socioeconomically important edible fungi in Mediterranean forest ecosystems

In Mediterranean forests, many species of fungi produce fruiting bodies every autumn, some of which are of great social and economic interest as NTFPs. In addition, these fungi are an essential part of the biodiversity network that ensures the proper functioning of natural ecosystems and that is currently in check due to global change. Therefore, understanding the biogeographic patterns of species-specific fungal productivity is fundamental to anticipate possible changes in the socioeconomic value of our forests and to understand the role they play in the functioning of ecosystems in terms of mitigation and adaptation to climate change. In this study we estimate the future impact of climate change (in Catalonia region, between 2023 and 2100) on five fungal species with high socioeconomic interest in a broad bioclimatic gradient representative of the Mediterranean basin using high resolution at the landscape scale. To achieve this, we use predictive models based on machine learning algorithms and a fungal database resulting from the sampling of more than 100 permanent sampling plots over 20 years. We estimate that current and future productivity patterns differ among species, under different climate change scenarios and bioclimatic regions. Our results suggest that optimal productivity areas may be shifted to higher elevations, making those species with higher productivity at higher elevations the most affected by climate change. This would mean that some species with high socioeconomic value, such as Lactarius deliciosus and Boletus edulis, could be negatively affected in their total productivity in the study area. This study highlights the need to anticipate the potential effects of climate change on fungal productivity and in particular on high socioeconomic value species and to develop management policies oriented to maintain the important role of fungi in natural ecosystems.

Current trends, limitations and future research in the fungi?

The field of mycology has grown from an underappreciated subset of botany, to a valuable, modern scientific discipline. As this field of study has grown, there have been significant contributions to science, technology, and industry, highlighting the value of fungi in the modern era. This paper looks at the current research, along with the existing limitations, and suggests future areas where scientists can focus their efforts, in the field mycology. We show how fungi have become important emerging diseases in medical mycology. We discuss current trends and the potential of fungi in drug and novel compound discovery. We explore the current trends in phylogenomics, its potential, and outcomes and address the question of how phylogenomics can be applied in fungal ecology. In addition, the trends in functional genomics studies of fungi are discussed with their importance in unravelling the intricate mechanisms underlying fungal behaviour, interactions, and adaptations, paving the way for a comprehensive understanding of fungal biology. We look at the current research in building materials, how they can be used as carbon sinks, and how fungi can be used in biocircular economies. The numbers of fungi have always been of great interest and have often been written about and estimates have varied greatly. Thus, we discuss current trends and future research needs in order to obtain more reliable estimates. We address the aspects of machine learning (AI) and how it can be used in mycological research. Plant pathogens are affecting food production systems on a global scale, and as such, we look at the current trends and future research needed in this area, particularly in disease detection. We look at the latest data from High Throughput Sequencing studies and question if we are still gaining new knowledge at the same rate as before. A review of current trends in nanotechnology is provided and its future potential is addressed. The importance of Arbuscular Mycorrhizal Fungi is addressed and future trends are acknowledged. Fungal databases are becoming more and more important, and we therefore provide a review of the current major databases. Edible and medicinal fungi have a huge potential as food and medicines, especially in Asia and their prospects are discussed. Lifestyle changes in fungi (e.g., from endophytes, to pathogens, and/or saprobes) are also extremely important and a current research trend and are therefore addressed in this special issue of Fungal Diversity.

First report of Gymnotelium blasdaleanum causing Saskatoon serviceberry rust in Canada.

Saskatoon serviceberry (Amelanchier alnifolia) is a tall shrub native to the western regions of North America. In British Columbia, serviceberries are a resource for Indigenous communities, used in cooking and for medicinal purposes (Turner et al. 1990). The Saskatoon serviceberry is popular for ornamental and food purposes, with increasing demand for commercial production in British Columbia. (FLNR, 2003). In June 2023 leaf and fruit samples displaying signs of a rust fungus were collected from three ornamental Saskatoon serviceberry shrubs on the University of British Columbia's campus in Vancouver, BC (49°15'35.0"N 123°15'05.6"W). Morphological characteristics were taken from six leaves and berries. Infected leaf tissue was misshapen due to the development of aecia on the abaxial side of the leaves. Approximately 80% of the berries were enveloped in aecia, while infected leaf tissue constituted only around 5% across all three shrubs. Aecia were aecidioid (aecidium type) 0.25 to 0.35mm in diameter, hypophylous and, fructicolous. Peridial cells had a rhomboid shape measuring 21-29 × 18-23 μm (average dimension 25 × 20 μm, n = 30). Aeciospores were globoid with yellowish walls, verrucose and the dimensions ranged from 16-24 × 12-15 μm, (average dimensions 19 ×15 μm, n = 30) (Fig. x). These morphological features fit well with description of Gymnotelium blasdaleanum (Dietel & Holw.) Arthur (= Gymnosporangium libocedri (Henn.) F. Kern) (Arthur 1934). Judging from U.S. National Fungal Databases (https://fungi.ars.usda.gov/) G. blasdaleanum has never been reported in Canada, thus this discovery represents the first report of G. blasdaleanum in the country, specifically in the province of British Columbia. G. blasdaleanum is a hetero-demicyclic rust fungus with a broad aecial host range which includes several Rosaceous genera such as Amelanchier, Crataegus, Cydonia, Malus, Pyrus, and Sorbus (Farr & Rossman 2019). The telial host range is limited to California incense cedar (Calocedrus decurrens) and was not observed on nearby trees, some located within one kilometer of the serviceberries. To confirm morphological identification, DNA was extracted from infected leaves and fruits from all three plants using a modified protocol (Russell et al., 2010). The D1/D2 region was amplified using primers LR6 and 2Rust1R (Beenken, et al., 2012). A BLASTn search of all three sequences revealed 99.52 to 99.62% identity to available sequence in GenBank from Gymnotelium blasdaleanum (AF522168). Newly generated sequences were submitted to the GenBank under accession numbers OR567878, OR568568, and OR654105. Specimens from three Saskatoon serviceberry plants were provided to the UBC herbarium (Beaty Biodiversity Museum) and deposited in their fungarium (F35820). Infected fruits undergo deformation and premature dropping, posing a significant threat to ornamental and fruit production varieties of serviceberries (EPPO, 2006). The spread and establishment of the G. blasdaleanum is highly dependent on the presence of C. decurrens because of its limited range. However, California incense cedar is planted outside its natural range in suitable environments for G. blasdaleanum to thrive such as southern BC allowing the rust pathogen to spread to Canada. To prevent potential spread into other agricultural industries, particularly the 256-acre pear cultivation, continued planting of C. decurrens in British Columbia should be closely monitored. (BC MFLNRO, 2003).

Clinical characteristics of allergic bronchopulmonary mycosis caused by Schizophyllum commune.

Allergic bronchopulmonary mycosis (ABPM) is an allergic disease caused by type I and type III hypersensitivity to environmental fungi. Schizophyllum commune, a basidiomycete fungus, is one of the most common fungi that causes non-Aspergillus ABPM. Herein, we attempted to clarify the clinical characteristics of ABPM caused by S. commune (ABPM-Sc) compared with those of allergic bronchopulmonary aspergillosis (ABPA). Patients with ABPM-Sc or ABPA were recruited from a nationwide survey in Japan, a multicenter cohort, and a fungal database at the Medical Mycology Research Center of Chiba University. The definition of culture-positive ABPM-Sc/ABPA is as follows: (1) fulfills five or more of the 10 diagnostic criteria for ABPM proposed by Asano etal., and (2) positive culture of S. commune/Aspergillus spp. in sputum, bronchial lavage fluid, or mucus plugs in the bronchi. Thirty patients with ABPM-Sc and 46 with ABPA were recruited. Patients with ABPM-Sc exhibited less severe asthma and presented with better pulmonary function than those with ABPA (p=0.008-0.03). Central bronchiectasis was more common in ABPM-Sc than that in ABPA, whereas peripheral lung lesions, including infiltrates/ground-glass opacities or fibrotic/cystic changes, were less frequent in ABPM-Sc. Aspergillus fumigatus-specific immunoglobulin (Ig)E was negative in 10 patients (34%) with ABPM-Sc, who demonstrated a lower prevalence of asthma and levels of total serum IgE than those with ABPM-Sc positive for A. fumigatus-specific IgE or ABPA. Clinical characteristics of ABPM-Sc, especially those negative for A. fumigatus-specific IgE, differed from those of ABPA.

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients

BackgroundThe accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities.ResultsWe found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging.ConclusionTogether, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome.1fa3y2hSmo38JAQk6TMPiwVideo

TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization.

The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens. TheiaEuk was designed using containerized components and written in the workflow description language (WDL) to facilitate deployment on the cloud-based open bioinformatics platform Terra. This species-agnostic workflow enables the analysis of fungal genomes without requiring coding, thereby reducing the entry barrier for laboratory scientists. To demonstrate the usefulness of this pipeline, an ongoing outbreak of C. auris in southern Nevada was investigated. We performed whole-genome sequence analysis of 752 new C. auris isolates from this outbreak. Furthermore, TheiaEuk was utilized to observe the accumulation of mutations in the FKS1 gene over the course of the outbreak, highlighting the utility of TheiaEuk as a monitor of emerging public health threats when combined with whole-genome sequencing surveillance of fungal pathogens. A primary result of this work is a curated fungal database containing 5,667 unique genomes representing 245 species. TheiaEuk also incorporates taxon-specific submodules for specific species, including clade-typing for Candida auris (C. auris). In addition, for several fungal species, it performs dynamic reference genome selection and variant calling, reporting mutations found in genes currently associated with antifungal resistance (FKS1, ERG11, FUR1). Using genome assemblies from the ATCC Mycology collection, the taxonomic identification module used by TheiaEuk correctly assigned genomes to the species level in 126/135 (93.3%) instances and to the genus level in 131/135 (97%) of instances, and provided zero false calls. Application of TheiaEuk to actual specimens obtained in the course of work at a local public health laboratory resulted in 13/15 (86.7%) correct calls at the species level, with 2/15 called at the genus level. It made zero incorrect calls. TheiaEuk accurately assessed clade type of Candida auris in 297/302 (98.3%) of instances. TheiaEuk demonstrated effectiveness in identifying fungal species from whole genome sequence. It further showed accuracy in both clade-typing of C. auris and in the identification of mutations known to associate with drug resistance in that organism.

A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification.

DNA barcoding approaches provide powerful tools for characterizing fungal diversity. However, DNA barcoding is limited by poor representation of species-level diversity in fungal sequence databases. Can the development of custom, regionally focused DNA reference libraries improve species-level identification rates for lichen-forming fungi? To explore this question, we created a regional ITS database for lichen-forming fungi (LFF) in the Intermountain West of the United States. The custom database comprised over 4800 sequences and represented over 600 formally described and provisional species. Lichen communities were sampled at 11 sites throughout the Intermountain West, and LFF diversity was characterized using high-throughput ITS2 amplicon sequencing. We compared the species-level identification success rates from our bulk community samples using our regional ITS database and the widely used UNITE database. The custom regional database resulted in significantly higher species-level assignments (72.3%) of candidate species than the UNITE database (28.3-34.2%). Within each site, identification of candidate species ranged from 72.3-82.1% using the custom database; and 31.5-55.4% using the UNITE database. These results highlight that developing regional databases may accelerate a wide range of LFF research by improving our ability to characterize species-level diversity using DNA barcoding.

Inclusion of database outgroups reduces false positives in fungal metabarcoding taxonomic assignments

ABSTRACT Metabarcoding studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other nonfungal environmental sequences that are amplified during polymerase chain reaction (PCR) are inherently assigned taxonomy by these same databases, possibly leading to ambiguous nonfungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including nonfungal outgroups in a fungal taxonomic database to aid in detecting and removing these nontarget amplicons. We processed 15 publicly available fungal metabarcode data sets and discovered that roughly 40% of the reads from these studies were not fungal, although they were assigned as Fungus sp. when using a database without nonfungal outgroups. We discuss implications for metabarcoding studies and recommend assigning taxonomy using a database with outgroups to better detect these nonfungal amplicons.

MP27-07 PENILE PROSTHESES UNIVERSALLY HARBOR BIOFILMS, AND COMPOSITION DIFFERS BY DEVICE TYPE, BUT NOT COMPONENT OR INFECTION STATUS

You have accessJournal of UrologyCME1 Apr 2023MP27-07 PENILE PROSTHESES UNIVERSALLY HARBOR BIOFILMS, AND COMPOSITION DIFFERS BY DEVICE TYPE, BUT NOT COMPONENT OR INFECTION STATUS Glenn Werneburg, Ava Adler, Prajit Khooblall, Hadley Wood, Bradley Gill, Sarah Vij, Kenneth Angermeier, Scott Lundy, Aaron Miller, and Petar Bajic Glenn WerneburgGlenn Werneburg More articles by this author , Ava AdlerAva Adler More articles by this author , Prajit KhooblallPrajit Khooblall More articles by this author , Hadley WoodHadley Wood More articles by this author , Bradley GillBradley Gill More articles by this author , Sarah VijSarah Vij More articles by this author , Kenneth AngermeierKenneth Angermeier More articles by this author , Scott LundyScott Lundy More articles by this author , Aaron MillerAaron Miller More articles by this author , and Petar BajicPetar Bajic More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003255.07AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: To characterize microbial biofilms of indwelling penile prostheses by device component, manufacturer and infection status. Understanding biofilms in the presence and absence of infection will guide development of novel materials and coatings resistant to pathogenic biofilm formation – improving strategies for the prevention and treatment of device infection. METHODS: Penile prosthetic devices were removed in 20 patients having mechanical failure, pain, or infection. Device components were subjected to sonication, DNA extraction, next generation sequencing, shotgun metagenomics, and culture-based approaches. Curated reads were compared to known bacterial, viral, fungal, and protozoal databases, then mapped to KEGG and antibiotic resistance gene databases. RESULTS: Biofilms were detected in all 102 prosthetic components. 65% of species were prokaryotic, 15% viral, 15% protozoan, and 0% fungal in origin. Beta-diversity of prokaryotes and viruses did not differ by infection status or device component, but differed by device type (p<0.05) (Figure 1). The most abundant bacterial phyla were Proteobacteria and Actinobacteria. Mobiluncus curtisii was enriched in Manufacturer A (M.A.) device biofilms relative to Manufacturer B (M.B.). Bordetella bronchialis and Methylomicrobium alcaliphilum were enriched in M.B. relative to M.A. devices. The most abundant viruses across device components were the bean 58058 virus and cotesia congregate virus. The angelica virus and magnaporthe oryzae chrisovirus were enriched in M.B. relative to M.A. devices. CONCLUSIONS: Penile prostheses harbored biofilms regardless of device component and infection status (Figure 2). The significance of biofilm differences based on device type remains unknown. Stable, non-pathogenic biofilms may inhibit pathogenic infection and further investigation is needed into prevention of the transition to a state of dysbiosis. Source of Funding: This study was funded by the 2020 Sexual Medicine Society of North America Young Clinicians Research Grant © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e364 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Glenn Werneburg More articles by this author Ava Adler More articles by this author Prajit Khooblall More articles by this author Hadley Wood More articles by this author Bradley Gill More articles by this author Sarah Vij More articles by this author Kenneth Angermeier More articles by this author Scott Lundy More articles by this author Aaron Miller More articles by this author Petar Bajic More articles by this author Expand All Advertisement PDF downloadLoading ...

Comprehensive investigation of long non-coding RNAs in an endophytic fungus Calcarisporium arbuscula NRRL 3705.

Long non-coding RNAs (lncRNAs) play an important role in eukaryotic cells. However, there is no report of lncRNAs in endophytic fungi Calcarisporium arbuscula. Here, in Calcarisporium arbuscula NRRL 3705, an endophytic fungus predominantly producing mycotoxins aurovertins, the genome-wide identification of lncRNAs was carried out based on RNA-Seq. Totally, 1332 lncRNAs were identified, including 1082 long intergenic noncoding RNAs, 64 long intronic noncoding RNAs and 186 long noncoding natural antisense transcripts. The average length of lncRNA and mRNA were 254 and 1102bp, respectively. LncRNAs were shorter, with fewer exons and lower expression levels. Moreover, there were 39 up-regulated lncRNAs and 10 down-regulated lncRNAs in the ΔaurA mutant, which lacks the aurovertin biosynthetic enzyme AurA. Interestingly, expression of genes related to the metabolism of linoleic acid and methane were significantly down regulated in the ΔaurA mutant. This study enriches the endophytic fungal lncRNA database and provide a basis for further research.

Genome Sequence Resource for Colletotrichum gloeosporioides, an Important Pathogenic Fungus Causing Anthracnose of Dioscorea alata.

Anthracose disease is one of the most important diseases of Dioscorea alata and many other food yams, which is caused by Colletotrichum gloeosporioides fugus from the Glomerellaceae family of the Sordariomycetes class. In the present study, a C. gloeosporioides starin named CgDa01 was isolated from D. alata, and its genome was sequenced based on Oxford Nanopore technology (ONT) and the Illumina sequencing platform. The high-quality genome of CgDa01 was assembled with a 62.78 Mb genome size and 15,845 predicted protein-coding genes. The proteins of predicted genes were annotated using multiple public databases, including the nonredundant protein database, the InterProScan databases, and Kyoto Encyclopedia of Genes and Genomes. Among the annotated protein-coding genes, 55 were predicted as potential virulence genes by the fungal virulence factor database. The C. gloeosporioides CgDa01 genome assembly described in this study can serve as a resource for better understanding the pathogenic mechanism of C. gloeosporioides on yam hosts.

Porcine fungal mock community analyses: Implications for mycobiome investigations.

The gut microbiome is an integral partner in host health and plays a role in immune development, altered nutrition, and pathogen prevention. The mycobiome (fungal microbiome) is considered part of the rare biosphere but is still a critical component in health. Next generation sequencing has improved our understanding of fungi in the gut, but methodological challenges remain. Biases are introduced during DNA isolation, primer design and choice, polymerase selection, sequencing platform selection, and data analyses, as fungal reference databases are often incomplete or contain erroneous sequences. Here, we compared the accuracy of taxonomic identifications and abundances from mycobiome analyses which vary among three commonly selected target gene regions (18S, ITS1, or ITS2) and the reference database (UNITE - ITS1, ITS2 and SILVA - 18S). We analyze multiple communities including individual fungal isolates, a mixed mock community created from five common fungal isolates found in weanling piglet feces, a purchased commercial fungal mock community, and piglet fecal samples. In addition, we calculated gene copy numbers for the 18S, ITS1, and ITS2 regions of each of the five isolates from the piglet fecal mock community to determine whether copy number affects abundance estimates. Finally, we determined the abundance of taxa from several iterations of our in-house fecal community to assess the effects of community composition on taxon abundance. Overall, no marker-database combination consistently outperformed the others. Internal transcribed space markers were slightly superior to 18S in the identification of species in tested communities, but Lichtheimia corymbifera, a common member of piglet gut communities, was not amplified by ITS1 and ITS2 primers. Thus, ITS based abundance estimates of taxa in piglet mock communities were skewed while 18S marker profiles were more accurate. Kazachstania slooffiae displayed the most stable copy numbers (83-85) while L. corymbifera displayed significant variability (90-144) across gene regions. This study underscores the importance of preliminary studies to assess primer combinations and database choice for the mycobiome sample of interest and raises questions regarding the validity of fungal abundance estimates.

DIFFERENTIAL ABUNDANCE OF THE FUNGAL MYCOBIOME IN PATIENTS WITH ULCERATIVE COLITIS

Abstract BACKGROUND The fungal mycobiome has been increasingly implicated in the pathogenesis of inflammatory bowel disease (IBD). Circulating antibodies to Saccharomyces antibodies are detected in 60-70% of Crohn’s disease and in 10-15% of patients with ulcerative colitis (UC). Specific fungal species, including Candida albicans, are increased in active IBD compared to healthy controls. Recently, UC patients with high fecal Candida prior to fecal microbial transplantation (FMT) were more likely to demonstrate robust treatment responses to transplant, with low Candida levels post-FMT predicting ameliorated inflammation in the recipient. Despite the accumulation of findings supporting the role of fungi in IBD, the mycobiome remains poorly characterized in UC. Few studies have examined changes in the UC mycobiome with respect to validated endoscopic indices or histologic parameters; furthermore, the effects of treatment exposure, including biologic medications, on fungal communities in UC are unknown. AIMS In this study, we aim to characterize the fungal mycobiome in UC patients with varying levels of endoscopic activity, endo-histologic activity, and treatment exposure. METHODS We performed a secondary analysis using the data extracted from the Crohn’s and Colitis Foundation’s Study of a Prospective Adult Research Cohort with IBD, which contains clinical, endoscopic, histologic, and metagenomic data. Using Internal Transcribed Spacer based deep sequencing of fungal rDNA from fecal samples, we classified sequences utilizing the UNITE fungal database and a fitted classifier. The R package DESeq2 was used to calculate the log-2 fold change of differential abundance. RESULTS We identified 504 unique fungal amplicon sequence variants across the cohort of 98 patients, belonging to phylum Ascomycota (71.5%), Basidiomycota (11%), Mucoromycota (0.16%), or unidentified (17.2%). Compared to endoscopic remission, patients with endoscopic activity (n=25) were enriched with Saccharomyces (4.31, p&amp;lt; 5 x 10-5) and Candida (2.53, p&amp;lt; 1 x 10-3). Similarly, compared to endo-histologic remission, patients with endo-histologic activity (n=19) were also enriched for Saccharomyces (2.71, p&amp;lt;0.05) and Candida (2.07, p=0.05). Biologic exposure favored the growth of Candida (p-adj &amp;lt; 1 x10-4). After adjusting for age, gender, and biologic exposure among patients with endoscopic activity, Saccharomyces (p-adj &amp;lt; 5 x 10-12) and Candida (p-adj&amp;lt; 1 x 10-8) remained enriched. CONCLUSION These data demonstrate that endoscopic and histologic inflammation in UC is associated with expansion of Saccharomyces and Candida compared to remission, even after controlling for exposure to biologic exposure. These findings are recapitulated during endo-histologic activity. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in UC should be evaluated.

First Report of Powdery Mildew Caused by Podosphaera xanthii on Glandularia tenera in China.

Glandularia tenera (syn. Verbena tenera) is an herbaceous perennial ornamental plant used in gardens as an edging plant with beautiful white, red, or purple flowers. In autumn 2020 and 2021, severe powdery mildew infection was observed on G. tenera cultivar Xianghe in Renming Botanical garden in Shangqiu, Henan province, China (34.4568° N, 115.6640° E). Approximately 80% of leaves on each plant were symptomatic, and about 90% of the plants were infected. Powdery mildew colonies appeared as white spots on the adaxial surface of the leaves and stems of the plants in the initial infection stage. Later, mycelial growth was amphigenous, thick, forming irregular white patches, and effused to cover the whole leaf surface. Finally, leaves turned yellow and senescence occurred. Samples of symptomatic leaves were stained with trypan blue and examined under a Leica DM2500 microscope. Microscopic observations showed that conidia on infected leaves were hyaline and ellipsoid to oval with fibrosin bodies, measured 25 to 37 × 14 to 23 μm with a length/width ratio of 1.4 to 2.0. Conidiophores were unbranched, straight, 80 to 210× 10 to 14 µm in size, and produced two to five immature conidia in chains. Foot cells of conidiophores were cylindrical with slight constrictions at basal septa, and followed by one to three short cells. Fungal hyphae were septate, branched, and flexuous to straight and 4 to 7µm wide with indistinct to slightly nipple-shaped appressoria. Chasmothecia were not observed. These morphological characteristics were identical with the previous description of Podosphaera xanthii (Castagne) U. Braun & Shishkoff (Braun and Cook 2012). To confirm the identification, the sequence of ITS1-5.8s-ITS2 region of rDNA for the isolate SQVT was amplified from conidia collected from infected leaves with universal primers ITS1 and ITS4, sequenced and analyzed using the BLASTn search of GenBank. Amplicon was 565 bp (OM293967) and showed 99.82% similarity with sequence of P. xanthii from Eclipta prostrate (MT260063) in China (Xu et al. 2020), from Youngia denticulate (AB040351) in Japan (Hirata et al. 2000), and 99.65% with sequence of P. xanthii from V. brasiliensis in Korea (Cho et al. 2014). The domains D1 and D2 of the 28S rDNA for the isolate SQVTPX-1 was amplified with primer NL1/NL4. Amplicon was 613 bp (ON259308) and showed 100% similarity with sequence of P. xanthii from V. brasiliensis (AB936277) (Meeboon and Takamatsu, 2015). Pathogenicity tests were conducted by gently pressing the infected leaves onto leaves of five healthy G. tenera cultivar Xianghe plants. Five non-inoculated plants served as controls. Plants were maintained in a greenhouse at 25 ± 2°C. Eight days after inoculation, symptoms similar to those observed under natural conditions developed on the inoculated leaves of G. tenera plants, whereas the control plants remained symptomless. The fungus on inoculated leaves was morphologically identical to that first observed in the field. P. xanthii is a cosmopolitan powdery mildew fungus, parasitic on numerous plant species, especially Cucurbitaceae and Compositae plants. The pathogen has been reported infecting V. bonariensis (Hong et al. 2021), V. × hybrida in China (Zhuang 2005), and V. brasiliensis in Korea (Cho et al. 2014). Interestingly, G. tenera plants infected by P. xanthii were adjacent with V. × hybrida plants infected by P. xanthii in Renming Botanical garden. Incidence of P. xanthii on G. tenera add information on pathogen's host range and help us develop comprehensive survey and effective management of the disease. To our knowledge, this is the first report of P. xanthii on G. tenera in China (Farr and Rossman 2021). Braun, U., and Cook, R. T. A. 2012. Taxonomic Manual of the Erysiphales (Powdery Mildews). CBS Biodiversity Series No. 11. CBS, Utrecht, the Netherlands. Cho, S. E., et al. 2014. Plant Dis. 98: 1159. Farr, D. F., and Rossman, A. Y. 2021. Fungal Databases, Syst. Mycol. Microbiol. Lab., ARS, USDA. Hong, Q. Q., et al. 2021. Plant Dis. 105: 3297. Hirata, T., et al. 2000. Can. J. Bot. 78: 1521-1530. Meeboon, J. and Takamatsu, S. 2015. Mycoscience . 56: 243-251. Xu, D. D., et al. 2020. Plant Dis. 104: 3263. Zhuang, W. Y. 2005. Fungi of northwestern China. Mycotaxon, Ltd., Ithaca, NY.