Yeast Genera Research Articles

Global metagenomics analyses demonstrate metformin‐induced changes in the gut mycobiome in subjects with type 2 diabetes

The fungal component of the gut microbiota (mycobiome) has been less well studied than bacterial populations; however, emerging evidence suggests that the mycobiome might play an important role in metabolic disease. Intestinal fungi play an important role in modulating immune responses at mucosal and systemic sites, but the extent of host‐bacterial‐fungi interactions in disease pathogenesis remains unknown. Metabolic diseases such as obesity and type 2 diabetes are accompanied by an altered gut microbiome, known as dysbiosis, and recent work suggests that the gut mycobiome may also be perturbed in metabolic diseases. Correcting gut dysbiosis is hypothesized as a therapeutic target for obesity and some metabolic diseases, however, little data is available regarding the effects of medications on the gut mycobiome and associated host‐bacterial‐fungi interactions. Metformin is globally the most prescribed drug for type 2 diabetes mellitus (T2D), and its therapeutic effects cause decreased hepatic gluconeogenesis and consequently circulating blood glucose. Metformin treatment also impacts the gut microbiome composition, lowering circulating lipopolysaccharide and therefore reducing toll‐like‐receptor‐mediated inflammation. To date, the potential effects of metformin on the gut mycobiome are entirely unknown. Therefore, this study aims to address this knowledge gap by characterizing the impact of metformin on the gut mycobiome of healthy adults and adults with pre‐diabetes and T2D, defined by fasting plasma glucose values. We searched for published research articles with archived, publicly accessible shotgun metagenomics data and re‐processed the data with one uniform bioinformatics pipeline to identify fungal taxa and relative abundance. Our analysis involved a total of 4510 samples from 13 individual studies ranging from randomized clinical trials to cross‐sectional cohorts. We performed analyses on the compiled dataset to (1) characterize the impact of metformin treatment in healthy, pre‐diabetic, and T2D individuals on the gut mycobiome; and (2) correlate the changes in relative abundance of fungal taxa to available clinical covariates, such as body mass index and fasting blood glucose. Secondary analysis of a randomized controlled trial of 44 newly diagnosed, treatment‐naïve T2D patients who were prescribed metformin for three days demonstrated a significant effect of metformin on the gut mycobiome richness (Shannon and Simpson indices; t test p = 0.02 and p = 0.0061 respectively) and diversity (PERMANOVA p = 0.001). Additionally, the relative abundance of Saccharomyces,a well‐characterized yeast genus, was significantly higher after three days of metformin treatment (Wilcoxon p = 0.019). This study provides novel insight into the interactions between human hosts, the gut microbiome, and the gut mycobiome in response to metformin, a widely used drug to treat T2D. Furthermore, these analyses may provide greater understanding of the role of the mycobiome‐microbiome interaction in metabolic diseases.

Development of a Vector Set for High or Inducible Gene Expression and Protein Secretion in the Yeast Genus Blastobotrys.

Converting lignocellulosic biomass into value-added products is one of the challenges in developing a sustainable economy. Attempts to engineer fermenting yeasts to recover plant waste are underway. Although intensive metabolic engineering has been conducted to obtain Saccharomyces cerevisiae strains capable of metabolising pentose sugars mainly found in hemicellulose, enzymatic hydrolysis after pretreatment is still required. Blastobotrys raffinosifermentans, which naturally assimilates xylose and arabinose and displays numerous glycoside hydrolases, is a good candidate for direct and efficient conversion of renewable biomass. However, a greater diversity of tools for genetic engineering is needed. Here, we report the characterisation of four new promising promoters, a new dominant marker, and two vectors for the secretion of epitope tagged proteins along with a straightforward transformation protocol. The TDH3 promoter is a constitutive promoter stronger than TEF1, and whose activity is maintained at high temperature or in the presence of ethanol. The regulated promoters respond to high temperature for HSP26, gluconeogenic sources for PCK1 or presence of xylose oligomers for XYL1. Two expression/secretion vectors were designed based on pTEF1 and pTDH3, two endogenous signal peptides from an α-arabinanase and an α-glucuronidase, and two epitopes. A heterologous α-arabinoxylan hydrolase from Apiotrichum siamense was efficiently secreted using these two vectors.

Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats

The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.

Fecal Filobasidium Is Associated with Clinical Remission and Endoscopic Response following Fecal Microbiota Transplantation in Mild-to-Moderate Ulcerative Colitis.

Fecal microbiota transplantation (FMT) has the potential to restore (bacterial and fungal) microbial imbalance in ulcerative colitis (UC) patients and contribute to disease remission. Here, we aimed to identify fecal fungal species associated with the induction of clinical remission and endoscopic response to FMT for patients with mild-to-moderate ulcerative colitis. We analyzed the internal transcribed spacer 1 (ITS1)-based mycobiota composition in fecal samples from patients (n = 31) and donors (n = 7) that participated previously in a double-blinded randomized control trial evaluating the efficacy of two infusions of donor FMT compared with autologous FMT. The abundance of the yeast genus Filobasidium in fecal material used for transplantation was shown to correlate with clinical remission following FMT, irrespective of its presence in the material of donor or autologous fecal microbiota transfer. The amplified sequence variants within the genus Filobasidium most closely resembled Filobasidium magnum. Monocyte-derived macrophages and HT29 epithelial cells were stimulated with fungal species. Especially Filobasidium floriforme elicited an IL10 response in monocyte-derived macrophages, along with secretion of other cytokines following stimulation with other Filobasidium species. No effect of Filobasidium spp. was seen on epithelial wound healing in scratch assays. In conclusion, the enriched presence of Filobasidium spp. in donor feces is associated with the positive response to FMT for patients with UC and hence it may serve as a predictive fungal biomarker for successful FMT.

Anti-Candida Properties of Gossypium hirsutum L.: Enhancement of Fungal Growth, Biofilm Production and Antifungal Resistance.

(1) Background: Candida is a genus of yeasts with notable pathogenicity and significant ability to develop antimicrobial resistance. Gossypium hirsutum L., a medicinal plant that is traditionally used due to its antimicrobial properties, has demonstrated significant antifungal activity. Therefore, this study investigated the chemical composition and anti-Candida effects of aqueous (AELG) and hydroethanolic (HELG) extracts obtained from the leaves of this plant. (2) Methods: The extracts were chemically characterized by UPLC–QTOF-MS/MS, and their anti-Candida activities were investigated by analyzing cell viability, biofilm production, morphological transition, and enhancement of antifungal resistance. (3) Results: The UPLC–QTOF-MS/MS analysis revealed the presence of twenty-one compounds in both AELG and HELG, highlighting the predominance of flavonoids. The combination of the extracts with fluconazole significantly reduced its IC50 values against Candida albicans INCQS 40006, Candida tropicalis INCQS 40042, and C. tropicalis URM 4262 strains, indicating enhanced antifungal activity. About biofilm production, significant inhibition was observed only for the AELG-treated C. tropicalis URM 4262 strain in comparison with the untreated control. Accordingly, this extract showed more significant inhibitory effects on the morphological transition of the INCQS 40006 and URM 4387 strains of C. albicans (4) Conclusions: Gossypium hirsutum L. presents promising antifungal effects, that may be potentially linked to the combined activity of chemical constituents identified in its extracts.

Taxonomic Revision of the pulcherrima Clade of Metschnikowia (Fungi): Merger of Species

The type strains of 10 small-spored species of the ascomycetous yeast genus Metschnikowia usually form a compact group on the phylogenetic trees inferred from barcode sequences. Based on the name of the species, which was described first (Metschnikowia pulcherrima), the group is frequently referred to as the pulcherrima clade. All strains produce the iron-chelate pigment pulcherrimin and have antagonistic effects on many microorganisms. Recent results of molecular phylogenetic, genetic, and genomic research raised doubts about the taxonomic division of the clade. Those data—combined with results obtained in this study by comprehensive analysis of primary and secondary barcode sequences, physiological tests, and hybridisation experiments—demonstrate that the species cannot be distinguished from each other by the criteria of any of the phenotypic, phylogenetic, and biological species concepts. Therefore, I propose that the species of the pulcherrima clade be merged into one species under the oldest species name, M. pulcherrima.

When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships

DNA barcoding is based on the premise that the barcode sequences can distinguish individuals (strains) of different species because their sequence variation between species exceeds that within species. The primary barcodes used in fungal and yeast taxonomy are the ITS segments and the LSU (large subunit) D1/D2 domain of the homogenized multicopy rDNA repeats. The secondary barcodes are conserved segments of protein‐encoding genes, which usually have single copies in haploid genomes. This study shows that the analysis of barcode sequences fails to reconstruct accurate species trees and differentiate species when the organisms have chimeric genomes composed of admixed mosaics of different origins. It is shown that the type strains of 10 species of the pulcherrima clade of the ascomycetous yeast genus Metschnikowia cannot be differentiated with standard barcodes because their intragenomic diversity is comparable to or even higher than the interstrain diversity. The analysis of a large group of genes of the sequenced genomes of the clade and the viability and segregation of the hybrids of ex‐type strains indicate that the high intragenomic barcode differences can be attributed to admixed genome structures. Because of the mosaic structures of the genomes, the rDNA repeats do not form continuous arrays and thus cannot be homogenized. Since the highly diverse ITS and D1/D2 sequences of the type strains form a continuous pool including pseudogenes, the evolution of their rDNA appears to involve reticulation. The secondary barcode sequences and the nonbarcode genes included in the analysis show incongruent phylogenetic relationships among the type strains, which can also be attributed to differences in the phylogenetic histories of the genes.

A species by any other name would sound as sweet.

David Smith argues against the prevalent practice of naming newly discovered species after human beings.

Melanodevriesia, a New Genus of Endolichenic Oleaginous Black Yeast Recovered from the Inner Mongolia Region of China

Black yeasts are a phylogenetically diverse group of ascomycetous fungi that may exist in both unicellular and mycelial morphs. This group of fungi contains numerous commercially significant species as well as others whose precise roles are unknown, such as endolichenic species. There is currently a paucity of data about endolichenic black yeast species. To bridge this gap, we surveyed China's Inner Mongolia Autonomous Region in July 2019. Several fungal species associated with diverse lichens were isolated during this survey. Among these were two isolates of a previously unknown species of oleaginous black yeast fromMycosphaerellales. Analyses of morphological and molecular data revealed that these two isolates were closely related toXenodevriesia strelitziicola(Xenodevriesiaceae), although with significant differences. As a result, we established the genusMelanodevriesia gen. nov.to describe this previously unknown species,Melanodevriesia melanelixiae sp. nov.In addition, we used Transmission Electron Microscopy to visualise the intracellular oil bodies metabolised by this fungus in its unicellular state. The black yeast species identified in this study may have a wide range of commercial applications. More research is needed to determine the chemical composition of the microbial oil synthesized by this fungus and whether it has commercial value.

Flood induced changes in the diversity of yeasts from the mangroves of Valanthakadu, Kerala, India

This is the first report on the influence of the devastating August 2018 floods of Kerala on yeast communities associated with the mangrove ecosystem of Valanthakadu, 'Kochi’s oxygen parlour’. Samples were collected for the study from six stations in Valanthakadu during three different periods with regard to floods i.e. April – May 2018: Pre flood (PRF), September – October 2018: Just after floods (JAF), and March 2019: Post floods (POF) and plated onto Malt-yeast-glucose-peptone agar for isolation and enumeration. Morphologically distinct colonies were picked, clustered on biochemical basis, representative strains identified on molecular basis or using API 20 C AUX strip. On enumeration, the average colony counts of yeasts in the sediments were found to be greater than in water samples. Out of 89 morphologically distinct yeast strains isolated, the majority were non-pigmented (73 %) and belonged to the phyla Ascomycetes (58 %). Six different yeast genera: Candida spp., Cryptococcus spp., Hortaea sp., Rhodotorula spp., Rhodosporidiobolus sp., and Trichosporon sp. were recorded in this study. C. tropicalis was noted to be not only the predominant species but also resilient to the effect of floods. Flood was found to influence the diversity of yeasts, with the introduction of certain genera (Hortaea wernekii (first report)) and the loss of certain others (C. gatti). Analysis of diversity indices evidently revealed the influence of floods, with an increase in yeast diversity just after floods (1.62) when compared to other periods of sampling. A change in the hydrolytic profile of isolates was also noticed in relation to floods. This study clearly indicated that floods do affect the diversity of yeast communities and their function in the ecosystems, at least temporarily. Nevertheless, the long-term impacts remain unknown and deserve further studies.

Diversity of fermentative yeasts with probiotic potential isolated from Thai fermented food products.

This research aimed to evaluate the diversity of yeasts recovered from fermented foods gathered from some areas of Northeastern Thailand. The fermented food items included Pla-som, Nham-pla, Kem-buknud, Isan-sausage, Pla-ra, Mhum-neu, Mhum-Khai-pla, Nham-neu, Nham-mu, Kung-joom, Som-pla-noi, and Poo-dong. Their probiotic characteristics were also investigated. A total of 103 yeast isolates of nine genera were identified using 28S rDNA sequencing. The yeast genera were Candida (20.3%), Diutina (2.9%), Filobasidium (1.0%), Kazachstania (33.0%), Pichia (3.9%), Saccharomyces (1.0%), Starmerella (28.2%), Torulaspora (2.9%), and Yarrowia (6.8%). Based on probiotic characteristic analysis of ten selected yeast strains, Kazachstania bulderi KKKS4-1 showed the strongest probiotic characteristics in terms of hemolytic activity, antimicrobial activity against pathogenic bacteria, tolerance to low pH and bile salt and hydrophobicity. Isolated yeasts with probiotic characteristics may be useful in fermented food and animal feed production to improve their nutritional values.

Analysis of yeast conservative nucleotide sequences by genomic bioinformatic methods

The purpose of the present study was the bioinformatic analysis of conservative nucleotide sequences, their variability between different yeast species and genus. The results obtained in the study can facilitate the selection of yeast phylogenetic biomarkers and promote the establishment of yeast sequences database.

Nonconventional yeasts to produce aroma compounds by using agri-food waste materials.

Nowadays, biotechnological applications are emphasized to ensure sustainable development by reutilizing waste materials to prevent ecological problems and to produce or recover compounds that may have positive effects on health. Yeasts are fascinating microorganisms that play a key role in several traditional and innovative processes. Although Saccharomyces is the most important genus of yeasts, and they are major producers of biotechnological products worldwide, a variety of other yeast genera and species than Saccharomyces that are called 'non-Saccharomyces' or 'nonconventional' yeasts also have important potential for use in biotechnological applications. Some of the nonconventional yeast strains offer a unique potential for biotechnological applications to produce valuable secondary metabolites due to their characteristics of surviving and growing in such extreme conditions, e.g. wide substrate range, rapid growth, thermotolerance, etc. In this review, we aimed to summarize potential biotechnological applications of some nonconventional yeasts (Kluyveromyces spp., Yarrowia spp., Pichia spp., Candida spp., etc.) to produce industrially important aroma compounds (phenylethyl alcohol, phenylethyl acetate, isobutyl acetate, diacetyl, etc.) by reutilizing agri-food waste materials in order to prevent ecological problems and to produce or recover compounds that may have positive effects on health.

Mutational Effects of Mobile Introns on the Mitochondrial Genomes of Metschnikowia Yeasts

It has been argued that DNA repair by homologous recombination in the context of endonuclease-mediated cleavage can cause mutations. To better understand this phenomenon, we examined homologous recombination following endonuclease cleavage in a native genomic context: the movement of self-splicing introns in the mitochondrial genomes of Metschnikowia yeasts. Self-splicing mitochondrial introns are mobile elements, which can copy and paste themselves at specific insertion sites in mitochondrial DNA using a homing endonuclease in conjunction with homologous recombination. Here, we explore the mutational effects of self-splicing introns by comparing sequence variation within the intron-rich cox1 and cob genes from 71 strains (belonging to 40 species) from the yeast genus Metschnikowia. We observed a higher density of single nucleotide polymorphisms around self-splicing-intron insertion sites. Given what is currently known about the movement of organelle introns, it is likely that their mutational effects result from the high binding affinity of endonucleases and their interference with repair machinery during homologous recombination (or, alternatively, via gene conversion occurring during the intron insertion process). These findings suggest that there are fitness costs to harbouring self-splicing, mobile introns and will help us better understand the risks associated with modern biotechnologies that use endonuclease-mediated homologous recombination, such as CRISPR-Cas9 gene editing.

Efficacy of Tea Tree, Sesame, and Cumin Extracts against Oral Candida Species – An in Vitro Study

Background and Objective: Oral cavity ports have diverse, abundant, and complex microbial communities. Candida is (a genus of yeast) and is the most common cause of oral fungal infection. The standard treatment of oral candidiasis is the use of antifungal agents, which cause different adverse effects. To combat this, herbal drugs can be considered as an alternative to allopathic drugs. The literature has reported that these herbal products are a rich source of antimicrobial agents. The present study determined the antifungal efficacy of tea tree, sesame, and cumin extracts against oral candidiasis in comparison to clotrimazole. Material and Methods: An in vitro study was carried out on 30 patients, wherein saliva and swab samples were collected and subjected to culture on chromagar and incubated at 37°C for 24 to 48 hours. The cultured Candida species were subjected to an antifungal susceptibility test. Clotrimazole (Group I: positive control), tea tree extracts (Group II–Group VI), sesame extracts (Group VII–Group XI), and cumin extracts (Group XII–Group XVI) were inoculated in wells and incubated. Zones of inhibitions were measured and subjected to statistical analysis. Results: Antifungal efficacy of tea tree (Group II–VI), sesame (Group VII–IX), cumin (Group XII–XIV), and clotrimazole (Group I) were compared and proven to be statistically significant with a P value < 0.05. Conclusion: Clotrimazole had a higher antimicrobial activity compared to medicinal plants. The extracts of tea tree, sesame, and cumin had significant antimicrobial activity and they might prove to be promising alternatives as a therapeutic agent for oral candidiasis.

Identification and characterization of Nramp transporter AoNramp1 in Aspergillus oryzae.

The online version contains supplementary material available at 10.1007/s13205-021-02998-z.

Effect of freeze-dried kombucha culture on microbial composition and assessment of metabolic dynamics during fermentation

Kombucha is a traditional fermented beverage gaining popularity around the world. So far, few studies have investigated its microbiome using next-generation DNA sequencing, whereas the correlation between the microbial community and metabolites evolution along fermentation is still unclear. In this study, we explore this correlation in a traditionally produced kombucha by evaluating its microbial community and the main metabolites produced. We also investigated the effects of starter cultures processed in three different ways (control, starter culture without liquid suspension (CSC), and a freeze-dried starter culture (FDSC)) to evaluate changes in kombucha composition, such as antioxidant activity and sensory analysis. We identified seven genera of bacteria, including Komagataeibacter, Gluconacetobacter, Gluconobacter, Acetobacter, Liquorilactobacillus, Ligilactobacillus, and Zymomonas, and three genera of yeasts, Dekkera/Brettanomyces, Hanseniaspora, and Saccharomyces. Although there were no statistically significant differences in the acceptance test in sensory analysis, different starter cultures resulted in products showing different microbial and biochemical compositions. FDSC decreased Zymomonas and Acetobacter populations, allowing for Gluconobacter predominance, whereas in the control and CSC kombuchas the first two were the predominant genera. Results suggest that the freeze-drying cultures could be implemented to standardize the process and, despite it changes the microbial community, a lower alcohol content could be obtained.

Deciphering the Shifts in Microbial Community Diversity From Material Pretreatment to Saccharification Process of Fuyu-Flavor Baijiu.

The microbiota of the pretreatment phase is crucial to the assembly of the microbial community in the saccharification of fuyu-flavor baijiu. This study investigates the shifts in microbial community diversity from the pretreatment of raw materials to the end of saccharification. High-throughput sequencing reveals that Lactobacillus, Weissella, and Bacillus in the bacterial community and Rhizopus, Candida, Pichia, and Aspergillus in the fungal community are predominant during raw material pretreatment and saccharification processes. Also, 11 bacterial genera, including Bacillus, Lactobacillus, Leuconostoc, Weissella, Lactococcus, and Acetobacter, and eight yeast genera, including Candida, Pichia, Saccharomyces, and Wickerhamomyces, were isolated from the initial saccharification stage by culture-dependent approaches. Sourcetracker analysis indicates that the cooling grains and rice husks were the main contributors to the bacterial community composition of the saccharification process, and Qu was the main contributor to the shaping of the fungal community structure during the saccharification process. Abundance variation of the predictive functional profiles of microbial communities encoding for key enzymes involved in pyruvate metabolism, starch and sucrose metabolism, and glycolysis/gluconeogenesis during the pretreatment and saccharification phases were inferred by PICRUSt2 analysis. The results of this study will be utilized to produce consistently high-quality fuyu-flavor baijiu via better controlling the shaping of microbial community structures during the pretreatment and fermentation processes.

Study on the dynamic changes of potato microbes in soil affected by environmental pollution using high-throughput sequencing

To analyse the dynamic changes of the microbial community and biodiversity in potato liquor, this experiment uses potato and corn as raw materials and uses solid fermentation method to obtain potato liquor to brew liquor. The fermentation of the 1st, 3rd, 5th, 7th, 9th, 11th, 13th and 15th days of wine samples and sent for inspection. The results show that potato liquor brews wine in the fermentation process, the bacterial community is more than fungi, and in the end of fermentation is mainly played by bacteria. Lactobacillus and Weissella accounted for the largest proportion of lactobacillus and Weissella, and found that the number of Lactobacillus (Lactobacillus) increased as fermentation progressed, but the number of Weissella continued to decrease. In the fungal community, the abnormal Wickerham yeast and the false silk yeast genus (Candida) account edged the largest proportion of the entire fermentation process. Aspergillus, on the other hand, plays a role in the early fermentation phase.

Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America.

Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of the fermenting tea and represents an interphase environment, where embedded microbes gain access to oxygen as well as nutrients in the tea. To date, various yeast and bacteria have been reported to exist within the SCOBY, with little consensus as to which species are essential and which are incidental to Kombucha production. In this study, we used high-throughput sequencing approaches to evaluate spatial homogeneity within a single commercial SCOBY and taxonomic diversity across a large number (n = 103) of SCOBY used by Kombucha brewers, predominantly in North America. Our results show that the most prevalent and abundant SCOBY taxa were the yeast genus Brettanomyces and the bacterial genus Komagataeibacter, through careful sampling of upper and lower SCOBY layers. This sampling procedure is critical to avoid over-representation of lactic acid bacteria. K-means clustering was used on metabarcoding data of all 103 SCOBY, delineating four SCOBY archetypes based upon differences in their microbial community structures. Fungal genera Zygosaccharomyces, Lachancea and Starmerella were identified as the major compensatory taxa for SCOBY with lower relative abundance of Brettanomyces. Interestingly, while Lactobacillacae was the major compensatory taxa where Komagataeibacter abundance was lower, phylogenic heat-tree analysis infers a possible antagonistic relationship between Starmerella and the acetic acid bacterium. Our results provide the basis for further investigation of how SCOBY archetype affects Kombucha fermentation, and fundamental studies of microbial community assembly in an interphase environment.