Explore the vast range of titles available.

The yeast-26S rRNA libraries were constructed from two different fermented soybean foods, doenjang and kanjang. A total of 42 clones, containing the partial 26S rRNA sequences, 0.6 kb in length, were sequenced and subjected to an online similarity search. All doenjang yeast (DY) clones only appeared in the Saccharomycotina class. The 21 clones from the doenjang library were classified into five groups: Debaryomyces hansenii (DY I, 76.0 %), Zygosaccharomyces pseudorouxii (DY II, 9.6 %), Candida versatilis (DY III, 4.8 %), Candida etchellsii (DY IV, 4.8 %), and Debaryomyces castellii (DY V, 4.8 %). The 21 kanjang yeast (KY) clones were affiliated with the Saccharomycotina (52.4 %), Urediniomycetes (19.0 %), Ustilaginomycetes (23.8 %), and Hymenomycetes (4.8 %) classes and divided into six groups: D. hansenii (KY I, 38.0 %), Sterigmatomyces halophilus (KY II, 19.0 %), Malassezia restricta (KY III, 23.8 %), Cryptococcus magnus (KY V, 4.8 %), and Pichia triangularis (KY VI, 9.6 %). Yeast belonging to the Saccharomycotina class was predominant (76.2 %) in fermented soybean foods, doenjang and kanjang. These findings are of fundamental value for understanding the complexity of two different fermented soybean foods.

Investigations of the diversity of culturable yeasts at deep-sea hydrothermal sites have suggested possible interactions with endemic fauna. Samples were collected during various oceanographic cruises at the Mid-Atlantic Ridge, South Pacific Basins and East Pacific Rise. Cultures of 32 isolates, mostly associated with animals, were collected. Phylogenetic analyses of 26S rRNA gene sequences revealed that the yeasts belonged to Ascomycota and Basidiomycota phyla, with the identification of several genera: Rhodotorula, Rhodosporidium, Candida, Debaryomyces and Cryptococcus. Those genera are usually isolated from deep-sea environments. To our knowledge, this is the first report of yeasts associated with deep-sea hydrothermal animals.

Candida kefyr (Kluyveromyces marxianus) is a clinically important infectious yeast. It is found in nature, and is known to cause diseases in humans. No previous studies known have shown the detection of Candida kefyr in water sources of any country, and no studies have detected it anywhere in Lebanon. This present study is carried out to assess the quality of Lebanese water in terms of yeast pollution. The occurrence of Candida spp. (species) was inspected in 84 water samples that tested positive for containing Candida. Out of all isolates, 12 isolates were of C. kefyr and two were of P. kluyveri. The identification of Candida sp. was carried out by using HiCrome™ M1297A and M1297AR chromogenic media. Isolates identified were confirmed by MALDI-TOF MS and 26S rRNA sequencing. The isolates varied from sensitive to resistant to common antifungal agents, including Itraconazole, clotrimazole, fluconazole, miconazole, and nystatin, via disk diffusion assay. These results are the first to confirm the presence of C. kefyr in Lebanese water supplies and suggest that water consumed in Lebanon may be a potential transmission route for serious Candida-based infections.

About the Authors: Anuradha Chowdhary * E-mail: dranuradha@hotmail.com Affiliation: Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India ORCID http://orcid.org/0000-0002-2028-7462 Cheshta Sharma Affiliation: Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India Jacques F. Meis Affiliations Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands, Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, the Netherlands ORCID http://orcid.org/0000-0003-3253-6080Citation: Chowdhary A, Sharma C, Meis JF (2017) Candida auris: A rapidly emerging cause of hospital-acquired multidrug-resistant fungal infections globally. The species exhibits a close phylogenetic relationship to C. haemulonii and is differentiated based on sequence analysis of the D1/D2 domain of the large ribosomal subunit (LSU) of 26S rRNA gene and the internal transcribed spacer (ITS) regions of the nuclear rRNA gene operon [23]. [...]Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is considered a more rapid and robust diagnostic technique for C. auris identification [9, 10, 13, 16]. Worldwide reports of Candida auris along with their misidentification using commercial systems and frequency of antifungal resistance. https://doi.org/10.1371/journal.ppat.1006290.t001 Does genetic predisposition make C. auris virulent? A recently published draft genome of C. auris shows that it has a genome size of approximately 12.3 Mb [26, 27]. The emerging Candida auris: characterization of growth phenotype, virulence factors, antifungal activity, and effect of SCY-078, a novel glucan synthesis inhibitor, on growth morphology and biofilm formation. Identification and typing of the emerging pathogen Candida auris by matrix-assisted laser desorption ionisation time of flight mass spectrometry...

A preliminary evaluation of yeast fermented palm wine sourced from Imo State in Nigeria was carried out to establish compounds that contribute to the distinct flavor of the beverage and to determine if the product abundance is affected when the drink is supplemented with Sacoglottis gabonensis. Palm wine samples from two different trees Elaeis sp. and Raphia sp. (pH less than 5) that contain Saccharomyces cerevisiae and other yeast species identified by sequencing the D1/D2 domain of the 26S rRNA genes were used. Evaluation was carried out using high performance liquid chromatography (HPLC), atmospheric pressure chemical ionization-mass spectrometry (APCI-MS) and gas chromatography-mass spectrometry (GC-MS). Samples contained 5.9–11.6, 2.2–7.1, 4.2–43.0, and 4.4–43.7 g/L of acetic acid, lactic acid, ethanol and glucose, respectively. Ethyl acetate, acetic acid and ethanol had the most aroma intensity and an assessment on the yeast metabolome database showed that 23 out of the 31 products detected were present in the database. Addition of Sacoglottis gabonensis supplement to a Raphia sp. palm wine sample showed lower abundance of acetoin, acetic acid, methylpropyl lactate, ethyl octanoate and propyl acetate. We conclude that Sacoglottis gabonensis supplementation could suppress specific compounds during palm wine fermentation. This knowledge could be applied in new product development for the beverage.

Shangri-La is a wine region that has the highest altitude vineyards in China. This is the first study investigated the biodiversity of non-Saccharomyces yeasts associated with spontaneous fermentation of Cabernet Sauvignon wines produced from two sub-regions (Lancang River and Jinsha River) of Shangri-La. The culturable yeasts were preliminarily classified based on their colonial morphology on the Wallerstein Laboratory nutrient agar plates. Yeast species were identified by the sequencing of the 26S rRNA D1/D2 region and the 5.8S rRNA ITS region. Twenty-five non-Saccharomyces yeast species belonging to sixteen genera were isolated and identified in Shangri-La wine region. Candida, Hanseniaspora, Pichia, and Starmerella were found in both sub-regions, but the Lancang River showed more diverse yeast species than the Jinsha River. Shangri-La not only exhibited high diversity of non-Saccharomyces yeasts, and furthermore, seven species of non-Saccharomyces yeasts were exclusively found in this region, including B. bruxellensis, D. hansenii, M. guilliermondii, S. vini, S. diversa, T. delbrueckii and W. anomalus, which might play an important role in distinctive regional wine characteristics. This study provide a relatively comprehensive analysis of indigenous non-Saccharomyces yeasts associated with Cabernet Sauvignon from Shangri-La, and has significance for exploring ‘microbial terroir’ of wine regions in China.

Abstract Sequencing of the complete 26S rRNA genes of all Dekkera/Brettanomyces species colonizing different beverages revealed the potential for a specific primer and probe design to support diagnostic PCR approaches and FISH. By analysis of the complete 26S rRNA genes of all five currently known Dekkera/Brettanomyces species (Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. nanus and B. naardenensis), several regions with high nucleotide sequence variability yet distinct from the D1/D2 domains were identified. FISH species-;specific probes targeting the 26S rRNA gene's most variable regions were designed. Accessibility of probe targets for hybridization was facilitated by the construction of partially complementary ‘side’-;labeled probes, based on secondary structure models of the rRNA sequences. The specificity and routine applicability of the FISH-;based method for yeast identification were tested by analyzing different wine isolates. Investigation of the prevalence of Dekkera/Brettanomyces yeasts in the German viticultural regions Wonnegau, Nierstein and Bingen (Rhinehesse, Rhineland-;Palatinate) resulted in the isolation of 37 D. bruxellensis strains from 291 wine samples.

Ribosome biogenesis is a multistep process, during which mistakes can occur at any step of pre-rRNA processing, modification, and ribosome assembly. Misprocessed rRNAs are usually detected and degraded by surveillance machineries. Recently, we identified a class of antisense ribosomal siRNAs (risiRNAs) that down-regulate pre-rRNAs through the nuclear RNAi pathway. To further understand the biological roles of risiRNAs, we conducted both forward and reverse genetic screens to search formore suppressor of siRNA (susi) mutants. We isolated a number of genes that are broadly conserved from yeast to humans and are involved in pre-rRNA modification and processing. Among them, SUSI-2(ceRRP8) is homologous to human RRP8 and engages in m1A methylation of the 26S rRNA. C27F2.4(ceBUD23) is an m7G-methyltransferase of the 18S rRNA. E02H1.1(ceDIMT1L) is a predicted m6(2)Am6(2)A-methyltransferase of the 18S rRNA. Mutation of these genes led to a deficiency in modification of rRNAs and elicited accumulation of risiRNAs, which further triggered the cytoplasmic-to-nuclear and cytoplasmic-to-nucleolar translocations of the Argonaute protein NRDE-3. The rRNA processing deficiency also resulted in accumulation of risiRNAs. We also isolated SUSI-3(RIOK-1), which is similar to human RIOK1, that cleaves the 20S rRNA to 18S. We further utilized RNAi and CRISPR-Cas9 technologies to perform candidate-based reverse genetic screens and identified additional pre-rRNA processing factors that suppressed risiRNA production. Therefore, we concluded that erroneous rRNAs can trigger risiRNA generation and subsequently, turn on the nuclear RNAi-mediated gene silencing pathway to inhibit pre-rRNA expression, which may provide a quality control mechanism to maintain homeostasis of rRNAs.

Ribosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from a thermophilic fungus in two rotational states, which due to increased 80S stability provide a number of mechanistic details of eukaryotic translation. We identify a universally conserved ‘nested base-triple knot’ in the 26S rRNA at the polypeptide tunnel exit with a bulged-out nucleotide that likely serves as an adaptable element for nascent chain containment and handover. We visualize the structure and dynamics of the ribosome protective factor Stm1 upon ribosomal 40S head swiveling. We describe the structural impact of a unique and essential m 1 acp 3 Ψ 18S rRNA hyper-modification embracing the anticodon wobble-position for eukaryotic tRNA and mRNA translocation. We complete the eEF2-GTPase switch cycle describing the GDP-bound post-hydrolysis state. Taken together, our data and their integration into the structural landscape of 80S ribosomes furthers our understanding of protein biogenesis. High-resolution cryo-EM structures of a thermophilic 80S ribosome in two rotational states in complex with the protective factor Stm1, eEF2, and nascent chains are presented, providing insights into rRNA modifications and eukaryotic translation.

Feed security, feed quality and issues surrounding the safety of raw materials are always of interest to all livestock farmers, feed manufacturers and competent authorities. These concerns are even more important when alternative feed ingredients, new product developments and innovative feeding trends, like insect-meals, are considered. The black soldier fly (Hermetia illucens) is considered a good candidate to be used as feed ingredient for aquaculture and other farm animals, mainly as an alternative protein source. Data on transfer of contaminants from different substrates to the insects, as well as the possible occurrence of toxin-producing fungi in the gut of non-processed insects are very limited. Accordingly, we investigated the impact of the substrate/diet on the intestinal mycobiota of H. illucens larvae using culture-dependent approaches (microbiological analyses, molecular identification through the typing of isolates and the sequencing of the 26S rRNA D1/D2 domain) and amplicon-based next-generation sequencing (454 pyrosequencing). We fed five groups of H. illucens larvae at the third growing stage on two substrates: chicken feed and/or vegetable waste, provided at different timings. The obtained results indicated that Pichia was the most abundant genus associated with the larvae fed on vegetable waste, whereas Trichosporon, Rhodotorula and Geotrichum were the most abundant genera in the larvae fed on chicken feed only. Differences in the fungal communities were highlighted, suggesting that the type of substrate selects diverse yeast and mold genera, in particular vegetable waste is associated with a greater diversity of fungal species compared to chicken feed only. A further confirmation of the significant influence of diet on the mycobiota is the fact that no operational taxonomic unit common to all groups of larvae was detected. Finally, the killer phenotype of isolated yeasts was tested, showing the inhibitory activity of just one species against sensitive strains, out of the 11 tested species.