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Yeast (Chichester, England) Dec 2023A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses...
A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446 (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
Topics: Pichia; Phylogeny; Soil; DNA, Fungal; Mycological Typing Techniques; Yeasts; Carbon; Nitrogen; Sequence Analysis, DNA
PubMed: 37921542
DOI: 10.1002/yea.3905 -
Microorganisms Sep 2022The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, has been the most common and widely... (Review)
Review
The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, has been the most common and widely used microorganism in the food industry. However, species have also been used as an adjuvant in cheese production or as starters for coffee, cocoa, vegetable, meat, beer, and wine fermentations. A thorough screening of candidate is sometimes performed to obtain the best performing strains to enhance specific features. Some commonly selected species include (teleomorph ) (wine), (teleomorph ) (coffee), (teleomorph ) (cheese), and (teleomorph ) and (teleomorph ) (cocoa). These species are associated with the production of key metabolites (food aroma formation) and different enzymes. However, safety-associated selection criteria are often neglected. It is widely known that some species are opportunistic human pathogens, with important clinical relevance. Here, the physiology and metabolism of species are addressed, initially emphasizing their clinical aspects and potential pathogenicity. Then, species used in food fermentations and their functional roles are reported. We recommended that not be used as food cultures if safety assessments are not performed. Some safety features are highlighted to help researchers choose methods and selection criteria.
PubMed: 36144457
DOI: 10.3390/microorganisms10091855 -
FEBS Letters Apr 2022Flavohaemoglobins (FlavoHbs) function as nitric oxide dioxygenases, oxidizing nitric oxide with nitrite and shuttling electrons from NAD(P)H via FAD and O . Here, using...
Flavohaemoglobins (FlavoHbs) function as nitric oxide dioxygenases, oxidizing nitric oxide with nitrite and shuttling electrons from NAD(P)H via FAD and O . Here, using pulse radiolysis, we investigate intramolecular electron transfer between FAD and haem b in FlavoHbs. We found that reduction of FlavoHb with hydrated electrons proceeded via two phases: an initial fast phase and a second slower process. Absorbance measured at 600 nm revealed fast flavin reduction followed by a slower decrease corresponding to reoxidation of FAD. The slower process was partially lost in FlavoHbs lacking FAD. These results suggest that the slower phase is attributable to intramolecular electron transfer from FAD to the haem iron. The rate constant in the absence of azole compound (3.3 × 10 s ) was accelerated ~ 10-fold (2.7 × 10 s ) by the binding of econazole, reflecting a conformational change in the open-to-closed transition.
Topics: Anti-Bacterial Agents; Azoles; Candida; Electron Transport; Electrons; Flavin-Adenine Dinucleotide; Heme; Kinetics; NAD; Nitric Oxide; Oxidation-Reduction; Pichia
PubMed: 35253217
DOI: 10.1002/1873-3468.14327 -
Foods (Basel, Switzerland) Oct 2021Yeast can be isolated from tofu wastewater and the cell wall in the form of β-glucan can act as a natural decontaminant agent. This study aimed to isolate and...
Yeast can be isolated from tofu wastewater and the cell wall in the form of β-glucan can act as a natural decontaminant agent. This study aimed to isolate and characterize native yeast from tofu wastewater, which can be extracted to obtain β-glucan and then identify the yeast and its β-glucan activity regarding antifungal ability against and aflatoxin-reducing activity towards aflatoxin B1 (AFB1) and B2 (AFB2). Tofu wastewater native yeast was molecularly identified, and the growth observed based on optical density for 96 h and the pH also measured. β-glucan was extracted from native yeast cell walls with the acid-base method and then the inhibition activity towards was tested using the well diffusion method and microscopic observation. AFB1 and AFB2 reduction were identified using HPLC LC-MS/MS. The results showed that the native yeast isolated was with a β-glucan yield of 6.59%. and its β-glucan showed an inhibition zone against of 11.33 ± 4.93 and 7.33 ± 3.51 mm, respectively. Total aflatoxin-reducing activity was also shown by of 26.85 ± 2.87%, and β-glucan of 27.30 ± 1.49%, while AFB1- and AFB2-reducing activity by was 36.97 ± 3.07% and 27.13 ± 1.69%, and β-glucan was 27.13 ± 1.69% and 32.59 ± 4.20%, respectively.
PubMed: 34828900
DOI: 10.3390/foods10112619 -
Infection and Drug Resistance 2021To investigate the colonization and susceptibility to antifungal drugs of oral yeasts in head and neck cancer patients in Hainan, China.
PURPOSE
To investigate the colonization and susceptibility to antifungal drugs of oral yeasts in head and neck cancer patients in Hainan, China.
METHODS
Oral mucosa samples from 211 head and neck cancer patients were collected. Oral yeasts were isolated and identified to species by rDNA ITS sequencing. The susceptibilities of all yeasts to amphotericin B, fluconazole, fluorocytosine, itraconazole, and ketoconazole were determined.
RESULTS
Yeasts were isolated from 124 of the 211 oral swabs. The 124 yeast isolates were classified into following 10 species, from the most frequent to the least frequent, (53.2%), (22.6%), (6.5%), (5.6%), (4.8%), (2.4%), (1.6%), (1.6%), (0.8%), and (0.8%). The overall frequencies of resistance among the yeasts to amphotericin B, fluconazole, flucytosine, itraconazole, and ketoconazole were 4.8%, 8.1%, 16.1%, 9.7%, and 9.7%, respectively. One strain and one strain were tolerant/resistant to all five drugs.
CONCLUSION
Given the high prevalence of oral yeast colonization in head and neck cancer patients and the observed resistance of certain yeast isolates to the five antifungal drugs, our results suggest that rapid identification and susceptibility testing should be implemented before antifungal treatment is applied among patients with head and neck cancer in Hainan.
PubMed: 34168468
DOI: 10.2147/IDR.S316368 -
Medical Mycology Oct 2020Antifungal susceptibility profiles of rare Saccharomycotina yeasts remain missing, even though an increase in prevalence of such rare Candida species was reported in...
Antifungal susceptibility profiles of rare Saccharomycotina yeasts remain missing, even though an increase in prevalence of such rare Candida species was reported in candidemia. Majority of these rare yeast species carry intrinsic resistances against at least one antifungal compound. Some species are known to be cross-resistant (against multiple drugs of the same drug class) or even multi-drug resistant (against multiple drugs of different drug classes). We performed antifungal susceptibility testing (AFST) according to EUCAST broth microdilution for 14 rare species (Clavispora lusitaniae, Candida intermedia, Candida auris, Diutina rugosa, Wickerhamiella pararugosa, Yarrowia lipolytica, Pichia norvegensis, Candida nivariensis, Kluyveromyces marxianus, Wickerhamomyces anomalus, Candida palmioleophila, Meyerozyma guilliermondii, Meyerozyma caribbica, and Debaryomyces hansenii) known to cause candidemia. In total, 234 isolates were tested for amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, micafungin, and caspofungin. Amphothericin B had the broadest efficiency against the 14 tested rare yeast species, while high minimum inhibitory concentrations (MICs) against azole drugs and echinocandins were common. Voriconazole was the most efficient azole drug. Multidrug resistance was observed for the species C. auris and K. marxianus. Multidrug resistant individual isolates were found for Y. lipolytica and M. caribbica. In conclusion, the observed high MIC values of the rare Saccharomycotina species tested limit antifungal treatment options, complicating the management of such infections.
Topics: Antifungal Agents; Candidemia; Drug Resistance, Fungal; Fluconazole; Humans; Microbial Sensitivity Tests; Saccharomyces; Voriconazole
PubMed: 32043147
DOI: 10.1093/mmy/myaa005 -
Food Research International (Ottawa,... Feb 2020Guangxi Suansun (Guangxi SS) and Guangxi Suancai (Guangxi SC) are two kinds of traditionally fermented vegetables consumed as cooking ingredients in Guangxi Province,... (Comparative Study)
Comparative Study
Guangxi Suansun (Guangxi SS) and Guangxi Suancai (Guangxi SC) are two kinds of traditionally fermented vegetables consumed as cooking ingredients in Guangxi Province, China, for thousands of years. However, little is known about their microbial communities as well as the differences between them. Thus, this study was aimed to investigate and compare the physicochemical indexes as well as the bacterial and fungal profiles of Guangxi SS and Guangxi SC. Results showed that the titratable acidity, lactic acid and acetic acid content in SS were significantly higher than those in SC, while the salinity of SS was significantly lower than that in SC, and the nitrite contents in all samples were are far lower than the limit of nitrite contents in fermented vegetables. Firmicutes, Proteobacteria, Ascomycota and Basidiomycota were the main phyla observed in both SS and SC samples. Lactobacillus, Serratia, Stenotrophomonas and Lactococcus were the major bacterial genera in both SS and SC samples, the predominant fungal genera in SS group were Kazachstania, Debaryomyces and Pichia, while the major genera in SC group were Kazachstania, Debaryomyces and Nakaseomyces. At the species level, Lactobacillus acetotolerans, Pichia kudriavzevii, Debaryomyces hansenii, Pichia norvegensis, Kazachstania exigua and Kazachstania humilis were the major species observed in SS, while L. delbrueckii, L. fermentum, L. aviarius, and Pichia kudriavzevii and Debaryomyces hansenii were the predominant species in SC. Salinity was found to be more strongly correlated to the bacterial and fungal communities of both SS and SC than other physicochemical factors (pH, the titratable acidity, lactic acid and acetic acid content). This study provided detailed insight into the microbial communities of Guangxi SS and Guangxi SC, and the findings may help understand the microbial structures of Chinese traditional fermented vegetables.
Topics: Debaryomyces; Fermentation; Fermented Foods; Food Microbiology; Lactobacillus; Microbiota; Pichia; Saccharomycetales; Salinity; Vegetables; Zygosaccharomyces
PubMed: 31955789
DOI: 10.1016/j.foodres.2019.108755 -
The Journal of Antimicrobial... Sep 2019To generate antifungal susceptibility patterns for Trichomonascus ciferrii (Candida ciferrii), Candida inconspicua (Torulopsis inconspicua) and Diutina rugosa species...
OBJECTIVES
To generate antifungal susceptibility patterns for Trichomonascus ciferrii (Candida ciferrii), Candida inconspicua (Torulopsis inconspicua) and Diutina rugosa species complex (Candida rugosa species complex), and to provide key parameters such as MIC50, MIC90 and tentative epidemiological cut-off values (TECOFFs).
METHODS
Our strain set included isolates of clinical origin: C. inconspicua (n = 168), D. rugosa species complex (n = 90) [Candida pararugosa (n = 60), D. rugosa (n = 26) and Candida mesorugosa (n = 4)], Pichia norvegensis (Candida norvegensis) (n = 15) and T. ciferrii (n = 8). Identification was performed by MALDI-TOF MS or internal transcribed spacer sequencing. Antifungal susceptibility patterns were generated for azoles, echinocandins and amphotericin B using commercial Etest and the EUCAST broth microdilution method v7.3.1. Essential agreement (EA) was calculated for Etest and EUCAST.
RESULTS
C. inconspicua, C. pararugosa and P. norvegensis showed elevated azole MICs (MIC50 ≥0.06 mg/L), and D. rugosa and C. pararugosa elevated echinocandin MICs (MIC50 ≥0.06 mg/L). EA between methods was generally low (<90%); EA averaged 77.45%. TECOFFs were suggested for C. inconspicua and D. rugosa species complex.
CONCLUSIONS
Rare yeast species tested shared high fluconazole MICs. D. rugosa species complex displayed high echinocandin MICs, while C. inconspicua and P. norvegensis were found to have high azole MICs. Overall, the agreement between EUCAST and Etest was poor and therefore MIC values generated with Etest cannot be directly compared with EUCAST results.
Topics: Antifungal Agents; Ascomycota; Humans; Microbial Sensitivity Tests; Mycoses; Sensitivity and Specificity
PubMed: 31203366
DOI: 10.1093/jac/dkz231 -
BMC Infectious Diseases Feb 2015Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms...
BACKGROUND
Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.
METHODS
We selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.
RESULTS
Among 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.
CONCLUSIONS
Molecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.
Topics: Candida; Candidiasis, Invasive; Communicable Diseases, Emerging; Cross Infection; DNA Mutational Analysis; DNA, Ribosomal Spacer; Genetic Variation; Humans; Phylogeny; Polymorphism, Genetic
PubMed: 25887032
DOI: 10.1186/s12879-015-0793-3 -
Journal of Clinical Microbiology May 2015Candida inconspicua and Candida (Pichia) norvegensis are two emerging pathogenic species that exhibit reduced susceptibility to azole derivatives. Conventional...
Candida inconspicua and Candida (Pichia) norvegensis are two emerging pathogenic species that exhibit reduced susceptibility to azole derivatives. Conventional (biochemical) approaches do not readily differentiate between the two species. The first aim of this work was to analyze the performance of biochemical, proteomic (matrix-assisted laser desorption ionization-time of flight [MALDI-TOF]), and molecular approaches in the precise identification of these species. These results then led us to sequence 3 genomic loci, i.e., the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), the D1/D2 domain of the 28S rDNA, and the elongation factor 1α (EF-1α) gene, either directly or following cloning, of 13 clinical isolates and 9 reference strains belonging to the 5 species included in the Pichia cactophila clade, namely, Pichia cactophila, Pichia insulana, C. inconspicua, C. norvegensis, and P. pseudocactophila. Finally, isolates of C. inconspicua were challenged for sexual reproduction on the appropriate medium. Our results show that EF-1α sequencing and proteic profiling by MALDI-TOF are the two most efficient approaches to distinguish between C. norvegensis and C. inconspicua. As a characteristic of the P. cactophila clade, we found multiple alleles of the rDNA regions in certain strains belonging to the tested species, making ITS or D1/D2 sequencing not appropriate for identification. Whatever the method of identification, including MALDI-TOF and EF-1α sequencing, none could differentiate C. inconspicua from P. cactophila. The results of phylogenetic analysis and the generation of asci from pure cultures of all C. inconspicua strains both support the identification of P. cactophila as the teleomorph of C. inconspicua.
Topics: Candida; Candidiasis; Cluster Analysis; Crosses, Genetic; DNA, Fungal; DNA, Ribosomal; DNA, Ribosomal Spacer; Gene Order; Humans; Molecular Sequence Data; Mycological Typing Techniques; Peptide Elongation Factor 1; Phylogeny; Proteome; RNA, Ribosomal, 28S; Sequence Analysis, DNA; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 25762773
DOI: 10.1128/JCM.02913-14