Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus

TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads

Telomeres are eukaryotic chromosome end structures that guard against sequence loss and aberrant chromosome fusions. Telomeric repeat motifs (TRMs), the minimal repeating unit of a telomere, vary from species to species, with some evolutionary clades experiencing a rapid sequence divergence. To explore the full scope of this evolutionary divergence, many bioinformatic tools have been developed to infer novel TRMs using repetitive sequence search on short sequencing reads. However, novel telomeric motifs remain unidentified in up to half of the sequencing libraries assayed with these tools. A possible reason may be that short reads, derived from extensively sheared DNA, preserve little to no positional context of the repetitive sequences assayed. On the other hand, if a sequencing read is sufficiently long, telomeric sequences must appear at either end rather than in the middle. The TeloSearchLR algorithm relies on this to help identify novel TRMs on long reads, in many cases where short-read search tools have failed. In addition, we demonstrate that TeloSearchLR can reveal unusually long telomeric motifs not maintained by telomerase, and it can also be used to anchor terminal scaffolds in new genome assemblies.

A Case of Pulmonary Infection Due to Magnusiomyces capitatus in a Non-Immunocompromised Patient with Cerebral Palsy

Background

Magnusiomyces capitatus (M. capitatus) is a dimorphic opportunistic fungus that is a rare yeast and rarely reported in Asia. Owing to the absence of established clinical breakpoints, the treatment of this fungus poses challenges.

Case Presentation

We report a rare case of a young, non-immunocompromised man with cerebral palsy, spinal deformity, and pulmonary M. capitatus infection. The patient's condition improved after treatment with voriconazole and became stable.

Conclusion

M. capitatus infection is commonly associated with hematologic tumors and compromised immunity. Reports of M. capitatus infection in patients with non-immunocompromised host are uncommon. Insufficient understanding of these fungi may lead to underdiagnosis of fungal infection and clinical misdiagnosis, potentially resulting in delayed treatment and increased mortality.

Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework

Yeasts in the subphylum Saccharomycotina are found across the globe in disparate ecosystems. A major aim of yeast research is to understand the diversity and evolution of ecological traits, such as carbon metabolic breadth, insect association, and cactophily. This includes studying aspects of ecological traits like genetic architecture or association with other phenotypic traits. Genomic resources in the Saccharomycotina have grown rapidly. Ecological data, however, are still limited for many species, especially those only known from species descriptions where usually only a limited number of strains are studied. Moreover, ecological information is recorded in natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework for the analysis of yeast ecology. A total of 1,088 yeast strains were added to the Ontology of Yeast Environments (OYE) and analyzed in a machine-learning framework to connect genotype to ecology. This framework is flexible and can be extended to additional isolates, species, or environmental sequencing data. Widespread adoption of OYE would greatly aid the study of macroecology in the Saccharomycotina subphylum.

Draft genome sequence of Magnusiomyces sp. LA-1 isolated from a C6-C8 acid-producing bioreactor

Here, we report the draft genome of Magnusiomyces sp. LA-1, which was isolated from a C6-C8 carboxylic acid-producing bioreactor. The draft genome of Magnusiomyces sp. LA-1 is 19,829,165 bp in length, is divided into six contigs that comprise 6,557 CDS regions, and has a GC content of 34.5%.

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

Taxonomic revision of Geotrichum and Magnusiomyces, with the descriptions of five new Geotrichum species from China

The arthroconidial yeast-like species currently classified in the asexual genera Geotrichum and Saprochaete and the sexual genera Dipodascus, Galactomyces and Magnusiomyces are frequently associated with dairy and cosmetics production, fruit rot and human infection. However, the taxonomic system of these fungi has not been updated to accommodate the new nomenclature code adopting the "one fungus, one name" principle. Here, we performed phylogenetic analyses of these yeast-like species based on the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit of the rRNA gene. Two monophyletic groups were recognised from these species. One group contained Dipodascus, Galactomyces, and Geotrichum species and the other Magnusiomyces and Saprochaete species. We thus assigned the species in each group into one genus and selected the genus name Geotrichum for the first group and Magnusiomyces for the second one based on the principle of priority of publication. Five new Geotrichum species were identified from arthroconidial yeast strains recently isolated from various sources in China. The new species are described as Ge. dehoogii sp. nov., Ge. fujianense sp. nov., Ge. maricola sp. nov., Ge. smithiae sp. nov., and Ge. sinensis sp. nov.

Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing

In Streptomyces species, the cell cycle involves a switch from an early and vegetative state to a later phase where secondary products including antibiotics are synthesized, aerial hyphae form and sporulation occurs. AdpA, which has two domains, activates the expression of numerous genes involved in the switch from the vegetative growth phase. The adpA mRNA of many Streptomyces species has a UUA codon in a linker region between 5' sequence encoding one domain and 3' sequence encoding its other and C-terminal domain. UUA codons are exceptionally rare in Streptomyces, and its functional cognate tRNA is not present in a fully modified and acylated form, in the early and vegetative phase of the cell cycle though it is aminoacylated later. Here, we report candidate recoding signals that may influence decoding of the linker region UUA. Additionally, a short ORF 5' of the main ORF has been identified with a GUG at, or near, its 5' end and an in-frame UUA near its 3' end. The latter is commonly 5 nucleotides 5' of the main ORF start. Ribosome profiling data show translation of that 5' region. Ten years ago, UUA-mediated translational bypassing was proposed as a sensor by a Streptomyces phage of its host's cell cycle stage and an effector of its lytic/lysogeny switch. We provide the first experimental evidence supportive of this proposal.

Selection of Yeast and Lactic Acid Bacteria Strains, Isolated from Spontaneous Raw Milk Fermentation, for the Production of a Potential Probiotic Fermented Milk

Probiotic milk is a class of fermented milk that possesses health-promoting effects, not only due to the lactic acid bacteria (LAB) presence but potentially also to yeast activity. Hence, the aim of this work was to isolate and select yeasts from spontaneous milk fermentations to be used as inoculum, together with LAB, for manufacturing a potentially probiotic acidic low-alcohol fermented milk. Six yeast species were detected from the spontaneous milk fermentation. A screening of 13 yeast strains and 14 previously isolated LAB strains, based on the resistance to bile salts and to acidic conditions, was carried out. The best performing strains were successively tested for in vitro gastrointestinal tolerance. A strain of Kluyveromyces marxianus and a strain of Lactococcus lactis were selected for the manufacturing of two different fermented milk. The values of the main technological and microbiological parameters (pH, organic acids, ethanol, and microbial concentrations) of the experimental milk were in the range of those reported for this category of products. The evaluation of microorganism survival in fermented milk samples subjected to simulated gastrointestinal conditions highlighted a high resistance of both strains. In conclusion, the selected microbial starter culture enabled the setting up of potential probiotic fermented milk.

Unexpected Diversity of Yeast Species in Esophageal Mycosis of Waterfowls

This study was performed to evaluate the diversity and prevalence of yeasts associated with esophageal mycosis in domestic ducks and geese. Fungi were isolated from esophageal lesions of dead animals sent for microbiologic laboratory diagnosis. Species identification using a culture-dependent method was carried out by sequencing of the internal transcribed spacer (ITS)1-5.8S rRNA-ITS2 region. The most frequently isolated yeast was Candida albicans (43.1%) followed by Saccharomyces cerevisiae (17.6%), Candida kefyr (11.7%), Kazachstania bovina (11.7%), Candida lambica (3.9%), and single isolates (1.9%) representing Candida inconspicua, Candida rugosa, Candida pelliculosa, Candida krusei, Magnusiomyces capitatus, and Trichosporon asahii. Our results indicate that a number of potentially pathogenic yeast species can be isolated from esophageal mycosis of waterfowls, but additional studies are needed to make conclusions regarding their possible etiologic role in disease.

Development and Analysis of qPCR for the Identification of Arthroconidial Yeasts of the Genus Magnusiomyces

The arthroconidial yeasts Magnusiomyces capitatus and M. clavatus are emerging opportunistic pulmonary pathogens. They are closely related and difficult to distinguish based on morphological and physiological traits. We applied an SYBR^® green-based quantitative PCR (qPCR) assay to identify the species. We analyzed 30 reference strains originating from clinical and environmental sources by targeting the Rpb2 gene encoding the second largest subunit of RNA polymerase II. The qPCR assays were tested by direct identification of M. capitatus and M. clavatus in spiked sputum and household dishwasher swabs, respectively, as models for clinical and environmental samples. The assays were proved to be reliable for species-level identification of both species, with 100% sensitivity and 100% specificity, lowest inter-assay deviations (RSDr ≤ 1.65%, R² values >0.99), detection limit of 10 theoretical copy number of target DNA, and detection cell limit of ≥5000 yeast cells from spiked sputum samples. The developed qPCR assay is a practical molecular approach for the detection of M. capitatus and M. clavatus that can be used as a stand-alone assay or in conjunction with culture-dependent approaches.

Genome Sequence of the Yeast Saprochaete ingens CBS 517.90

Chromosome-scale genome assembly of the yeast Saprochaete ingens CBS 517.90 was determined by a combination of technologies producing short (HiSeq X; Illumina) and long (MinION; Oxford Nanopore Technologies) reads. The 21.2-Mbp genome sequence has a GC content of 36.9% and codes for 6,475 predicted proteins.

Chromosome-scale genome assembly of the yeast Saprochaete ingens CBS 517.90 was determined by a combination of technologies producing short (HiSeq X; Illumina) and long (MinION; Oxford Nanopore Technologies) reads. The 21.2-Mbp genome sequence has a GC content of 36.9% and codes for 6,475 predicted proteins.

Bioinformatics of nanopore sequencing

Nanopore sequencing is one of the most exciting new technologies that undergo dynamic development. With its development, a growing number of analytical tools are becoming available for researchers. To help them better navigate this ever changing field, we discuss a range of software available to analyze sequences obtained using nanopore technology.

Genome Sequence of an Arthroconidial Yeast, Saprochaete fungicola CBS 625.85

Saprochaete fungicola is an arthroconidial yeast classified in the Magnusiomyces/Saprochaete clade of the subphylum Saccharomycotina. Here, we report the genome sequence of holotype strain CBS 625.85, assembled to five putative chromosomes. The genome sequence is 20.2 Mbp long and codes for 6,138 predicted proteins.

Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-17571

Saprochaete suaveolens is an ascomycetous yeast that produces a range of fruity flavors and fragrances. Here, we report the high-contiguity genome sequence of the ex-holotype strain, NRRL Y-17571 (CBS 152.25). The nuclear genome sequence contains 24.4 Mbp and codes for 8,119 predicted proteins.