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Frontiers in Microbiology 2023The microbiological and metabolic outcomes of good cocoa fermentation practices can be standardized and influenced through the addition of starter culture mixtures...
The microbiological and metabolic outcomes of good cocoa fermentation practices can be standardized and influenced through the addition of starter culture mixtures composed of yeast and bacterial strains. The present study performed two spontaneous and 10 starter culture-initiated (SCI) cocoa fermentation processes (CFPs) in Costa Rica with local Trinitario cocoa. The yeast strains IMDO 050523, IMDO 020003, and IMDO 060005 were used to compose starter culture mixtures in combination with the lactic acid bacterium strain IMDO 0611222 and the acetic acid bacterium strain IMDO 0506386. The microbial community and metabolite dynamics of the cocoa pulp-bean mass fermentation, the metabolite dynamics of the drying cocoa beans, and the volatile organic compound (VOC) profiles of the chocolate production were assessed. An amplicon sequence variant approach based on full-length 16S rRNA gene sequencing instead of targeting the V4 region led to a highly accurate monitoring of the starter culture strains added, in particular the IMDO 0611222 strain. The latter strain always prevailed over the background lactic acid bacteria. A similar approach, based on the internal transcribed spacer (ITS1) region of the fungal rRNA transcribed unit, was used for yeast strain monitoring. The SCI CFPs evolved faster when compared to the spontaneous ones. Moreover, the yeast strains applied did have an impact. The presence of IMDO 050523 was necessary for successful fermentation of the cocoa pulp-bean mass, which was characterized by the production of higher alcohols and esters. In contrast, the inoculation of IMDO 020003 as the sole yeast strain led to underfermentation and a poor VOC profile, mainly due to its low competitiveness. The IMDO 060005 strain tested in the present study did not contribute to a richer VOC profile. Although differences in VOCs could be revealed in the cocoa liquors, no significant effect on the final chocolates could be obtained, mainly due to a great impact of cocoa liquor processing during chocolate-making. Hence, optimization of the starter culture mixture and cocoa liquor processing seem to be of pivotal importance.
PubMed: 37621398
DOI: 10.3389/fmicb.2023.1232323 -
Oral Oncology Nov 2023Head and neck cancer (HNC) impairs patient immunity and increases susceptibility to oral fungal infections (OFIs). Effectively treating such infections requires accurate...
OBJECTIVES
Head and neck cancer (HNC) impairs patient immunity and increases susceptibility to oral fungal infections (OFIs). Effectively treating such infections requires accurate identification of the causative pathogens. This study aimed to characterize the mycobiota profile of OFIs in HNC patients undergoing radiation treatment (RT).
MATERIALS AND METHODS
A 6-year retrospective analysis of oral mucosal samples from HNC patients with a history of RT and OFIs between 2014 and 2019 was conducted using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) profiling. Samples from the Clinical Microbiology Laboratory at Karolinska University Hospital were evaluated for mycobiota diversity and species co-occurrence patterns in the ongoing-RT and post-RT groups.
RESULTS
A total of 190 oral fungi (88% Candida, 5% Pichia) were isolated from 162 HNC patients receiving RT. In the ongoing-RT group, the emergent non-albicans Candida (NAC) species; F. solani and C. jadinii, were detected for the first time. The dominant pathogens in both ongoing and post-RT groups were C. albicans, C. glabrata, P. kudriavzevii, C. parapsilosis, and C. tropicalis, as shown by Venn analysis. Network analysis revealed greater fungi diversity and multi-species co-occurrence in the ongoing-RT group. C. albicans commonly co-occurred with C. glabrata in both ongoing-RT (21%) and post-RT groups (30%).
CONCLUSION
MALDI-TOF MS identified a wide range of oral fungal species in HNC patients receiving RT. While C. albicans remains the most prevalent OFIs pathogen, multi-species co-occurrence and novel NACs were noted. Understanding the ecological interactions among these causative pathogens could significantly advance the development of effective therapeutics for treating OFIs in HNC patients.
Topics: Humans; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Retrospective Studies; Candida; Mycoses; Head and Neck Neoplasms
PubMed: 37611433
DOI: 10.1016/j.oraloncology.2023.106556 -
3 Biotech Sep 2023This study aimed to isolate and characterize potential probiotic yeasts from Ethiopian injera sourdough and the study was conducted by collecting samples from Gondar and...
This study aimed to isolate and characterize potential probiotic yeasts from Ethiopian injera sourdough and the study was conducted by collecting samples from Gondar and Bahir Dar cities, Ethiopia. The potential yeasts were isolated and identified using morphological, physiological, biochemical and molecular based analysis. Promising isolates were selected to further investigate their in vitro probiotic properties, including survival at different temperatures (25, 30, 37, and 42 °C), acidic pH (2, 3, 4 and 5), bile salt (0.1, 0.3, and 0.5%), and osmotolerance (20, 30, 40, and 50% glucose concentration), antimicrobial activities, proteolytic and lipolytic activities as well as resistance to four antibiotics. From 20 samples, 38 isolates were obtained. Among these, 10 produced low or non-hydrogen sulfide and were selected for further work. Further screening tests revealed that five isolates (G1N1, G2N4, G3N1, G8N1, and B6N3) were able tolerate and grow at 37 °C, with harsh conditions of the human digestive tract like low pH, bile salt, and higher osmotic effect. The maximum growth OD values were recorded at 37 °C by isolate G4N1 (OD value (0.6667), while G3N1 exhibited a maximum growth OD value of 0.4227 at pH 2. On the other hand, G2N4 gave a maximum OD value of 0.8800 at 0.3% bile salt concentration. The promising isolates were sequenced and identified to species level. Based on phylogenetic tree analysis, all the five probiotic yeast isolates had one common ancestor and belonging to (G1N1 and G2N4), (G3N1 and B6N3), and (G8N1). This study revealed that Ethiopian injera sourdough could be potential source of different probiotic yeast strains. Strong emphasis should be given about the use of probiotic yeasts that are isolated from Ethiopian fermented foods.
PubMed: 37581092
DOI: 10.1007/s13205-023-03729-2 -
Food Science & Nutrition Aug 2023Soybean paste was a traditional fermented product in northeast China, mainly fermented by molds, yeast, , and lactic acid bacteria. In this study, the safety and...
Soybean paste was a traditional fermented product in northeast China, mainly fermented by molds, yeast, , and lactic acid bacteria. In this study, the safety and fermentation ability of lactic acid bacteria and yeast strains isolated from traditional soybean paste in northeast China were evaluated, and the dynamic changes of biogenic amines, aflatoxin, total acids, amino acid nitrogen, and volatile compounds were investigated during the fermentation of the traditional soybean paste. Among the tested strains, DPUL-J8 could decompose putrescine by 100%, and no biogenic amine was produced by DPUY-J8. DPUL-J8 and DPUY-J8 with strong biogenic amine degrading capacities were inoculated into the soybean paste. After 30 days of fermentation, the content of biogenic amines and aflatoxin in the fermented soybean paste declined by more than 60% and 50%, respectively. At the same time, compared with the control group without inoculation, the contents of total acid (1.29 ± 0.05 g/100 g), amino acid nitrogen (0.82 ± 0.01 g/100 g), and volatile compounds in soybean paste fermented by DPUL-J8 and DPUY-J8 were significantly increased, which had a good flavor. These results indicated that the use of DPUL-J8 and DPUY-J8 as starter cultures for soybean paste might be a good strategy to improve the safety and flavor of traditional Chinese soybean paste.
PubMed: 37576040
DOI: 10.1002/fsn3.3372 -
Archives of Microbiology Aug 2023Recently, there has been growing interest in the characterization of native yeasts for their use in production of wines with regional characteristics. This study aimed...
Recently, there has been growing interest in the characterization of native yeasts for their use in production of wines with regional characteristics. This study aimed to investigate Saccharomyces and non-Saccharomyces yeasts present in the spontaneous fermentation of Tannat and Marselan grape musts collected from Concordia (Entre Ríos, Argentina) over 2019, 2020, and 2021 vintages. The evolution of these fermentative processes was carried out by measuring total soluble solids, total acidity, volatile acidity, pH, ethanol concentration, and total carbon content. Isolated Saccharomyces and non-Saccharomyces yeasts were identified based on colony morphology in WL medium, 5.8S-ITS-RFLP analysis, and 26S rDNA D1/D2 gene sequencing. Two hundred and ten yeast colonies were isolated and identified as Pichia kudriavzevii, Saccharomyces cerevisiae, Hanseniaspora uvarum, Metschnikowia pulcherrima, Candida albicans, Candida parapsilosis, Pichia occidentalis, Pichia bruneiensis, Hanseniaspora opuntiae, Issatchenkia terricola, and Hanseniaspora vineae. P. kudriavzevii isolated from all vintages was associated with the spontaneous fermentation of grape musts from the Concordia region.
Topics: Vitis; Fermentation; Yeasts; Wine; Saccharomyces cerevisiae; DNA, Ribosomal
PubMed: 37550458
DOI: 10.1007/s00203-023-03646-1 -
Mycoses Nov 2023Rapid and accurate yeasts species identification in clinical laboratories is important for appropriate and timely antifungal treatment. We evaluate the performance of...
Rapid and accurate yeasts species identification in clinical laboratories is important for appropriate and timely antifungal treatment. We evaluate the performance of the new medium CHROMagar™ Candida Plus for presumptive identification of yeasts species and MALDI-TOF identification. We identify 303 strains belonging to 60 clinically relevant yeasts species by using the new medium. Presumptive identification was correct at the Candida albicans complex, Candida tropicalis and Pichia kudriavzevii (Candida krusei) species. However, although this medium was able to identify all Candida auris and Candida glabrata strains, other species were misidentified as C. auris or C. glabrata. A total of 215 strains were identified by using MALDI-TOF and evaluated two incubation temperatures (30°C and 37°C) and two incubation times (24 h and 72 h). Most strains (94%; 202/215) were correctly identified at the species (n:190) or complex level (n:12) at both temperatures and incubation times. However, we observed that the time of incubation (24 h vs. 72 h) affects the score values when yeasts are incubated at 37°C, but does not affect score values when yeasts are incubated at 30°C. In conclusion, the new medium has a good performance in the presumptive identification of the C. albicans complex, C. tropicalis and P. kudriavzevii (C. krusei). In addition, this medium is useful for the screening of C. auris and C. glabrata isolates, but identification should be confirmed by other more specific techniques, like MALDI-TOF.
Topics: Humans; Candida; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Culture Media; Yeasts; Candida albicans; Candida glabrata; Candida tropicalis
PubMed: 37518770
DOI: 10.1111/myc.13633 -
Yeast (Chichester, England) Sep 2023During wet fermentation, mucilage layers in coffee cherries must be removed completely. To explain mucilage degradation, several controversial hypotheses have been...
During wet fermentation, mucilage layers in coffee cherries must be removed completely. To explain mucilage degradation, several controversial hypotheses have been proposed. The aim of this work was to improve our understanding of the kinetics of mucilage breakdown. Pulped coffee beans were wet fermented with seven different treatments for 36 h. Endogenous bacteria and yeasts are selectively suppressed, and pectinases or lactic acid are added. They also involve maintaining the beans at pH 7 throughout fermentation and using spontaneous fermentation without additives as a control. During spontaneous fermentation, yeast and lactic acid bacteria were detected and significantly increased to 5.5 log colony-forming units (CFU)/mL and 5.2 log CFU/mL, respectively. In the first 12 h of fermentation, there was a significant degree of endogenous pectinolytic activity, which resulted in partly destroyed beans in the absence of microorganisms. By adding pectinase and lactic acid to the fermentation mass, the breakdown process was accelerated in less than 8 h. When yeast was present throughout the fermentation, complete degradation was achieved. Bacteria played no critical role in the degradation. Klebsiella pneumoniae and Erwinia soli were found in a lower population and showed weaker pectinolytic activities compared to Hanseniaspora uvarum and Pichia kudriavzevii. During wet fermentation, mucilage degradation appears to be mediated by endogenous enzymes at the early stage, whereas microbial contributions, mainly yeasts, occur subsequently. H. uvarum and P. kudriavzevii may be promising candidates to be tested in future studies as coffee starter cultures to better control the mucilage degradation process.
Topics: Fermentation; Coffea; Yeasts; Bacteria; Polysaccharides; Lactic Acid
PubMed: 37464909
DOI: 10.1002/yea.3888 -
l-Lactic Acid Production via Sustainable Neutralizer-Free Route by Engineering Acid-Tolerant Yeast .Journal of Agricultural and Food... Jul 2023l-Lactic acid (l-LA) is a platform chemical obtained via microbial fermentation at a near-neutral pH value. Large amounts of neutralizers are required during this...
l-Lactic acid (l-LA) is a platform chemical obtained via microbial fermentation at a near-neutral pH value. Large amounts of neutralizers are required during this process, which increases the production costs in downstream processing as well as environmental burden. To address this challenge, an acid-tolerant yeast E1 was isolated and metabolically engineered to produce l-LA without neutralizers. The genome of strain E1 was sequenced and a CRISPR-Cas9 system was developed in this newly isolated strain. Subsequently, the gene encoding pyruvate decarboxylase () was knocked out to subdue ethanol formation. Furthermore, the l-lactate dehydrogenase gene from 2-6 and the codon-optimized gene from were introduced into E1 chromosome to redirect the ethanol fermentation pathway to l-LA production. Deletion of the () gene further increased the optical purity of l-LA. After optimizing fermentation conditions, the maximum titer of l-LA in the 5 L fermenter reached 74.57 g/L without any neutralizers, with an optical purity of 100% and a maximum yield of 0.93 g/g glucose. This is the first report of optically pure l-LA production without neutralizers and the engineered acid-tolerant yeast paves the way for the sustainable production of l-LA via a green route.
Topics: Animals; Cattle; Saccharomyces cerevisiae; Lactic Acid; Acids; Pichia; Fermentation; Ethanol
PubMed: 37439413
DOI: 10.1021/acs.jafc.3c03163 -
F1000Research 2022is a non-albicans species with a high prevalence, which causes candidaemia. Current treatment guidelines include fluconazole as a primary therapeutic option for the...
is a non-albicans species with a high prevalence, which causes candidaemia. Current treatment guidelines include fluconazole as a primary therapeutic option for the treatment of these infections; however, it is only a fungistatic against ., and both inherent and acquired resistance to fluconazole have been reported. . species is also reported as the only . which has an intrinsic resistance factor to fluconazole. Therefore, in dealing with antifungal resistance, it is necessary to develop new antifungal agents that are efficient in the treatment of fungal infections, especially those caused by . The purpose of this study was to investigate the genome of clinical isolates and correlate the resistant phenotypes with mutations in resistance genes. A total of 16 samples of from clinical samples from hospitals in Jakarta were used in the experiment. All colonies were extracted using the QIAamp DNA Mini Kit. The library was prepared using the Illumina DNA Prep Kit. The sequencing process was carried out on the Illumina MiSeq Platform using a 2x301 paired-end configuration. FASTQ raw files are available under the BioProject Accession Number PRJNA819536 and Sequence Read Archive Accession Numbers SRR18739949 and SRR18739964.
Topics: Humans; Fluconazole; Indonesia; Microbial Sensitivity Tests; Candida albicans; Whole Genome Sequencing; Faculty
PubMed: 37416067
DOI: 10.12688/f1000research.121402.2 -
Probiotics and Antimicrobial Proteins Jun 2023Potential probiotic yeast strains isolated from fermented food need to meet safe and beneficial conditions for the host's health. The Pichia kudriavzevii YGM091 strain...
Potential probiotic yeast strains isolated from fermented food need to meet safe and beneficial conditions for the host's health. The Pichia kudriavzevii YGM091 strain isolated from fermented goat milk has outstanding probiotic characteristics, including: the high survival percentage in digestive system conditions (reaching up 247.13 ± 0.12 and 145.03 ± 0.06% at pH 3.0 and bile salt 0.5%, respectively); good tolerance to temperature, salt, phenol, ethanol; good surface properties such as high hydrophobicity percentage (> 60%), the high auto-aggregation percentage rate (66.56 ± 1.45% after 45 min of incubation) and the high co-aggregation percentage rate with pathogenic bacteria in a short time (> 40% after 2 h of incubation); biofilm forming after 24 h of incubation on abiotic surfaces; antioxidant activity reached excellent level after only 24 h of incubation (The percentage free radical scavenging and the Trolox equivalent reaching up 79.86 ± 0.70% and 92.09 ± 0.75 µg/mL after 72 h of incubation); extracellular enzymes production protease and cellulase with high activity, amylase and pectinase with moderate activity and non-lipase activity. Simultaneously, the YGM091 strain is the in vitro safety yeast: insensitive to antibiotics and fluconazole, negative for gelatinase, phospholipase, coagulase, and non-hemolysis activities. Furthermore, this strain is in vivo safety yeast with the dosages below 10 CFU/larva in the Galleria mellonella model with over 90% survival larvae and the yeast density reduced to just 10-10 CFU/larva after 72 h post-injection. Research results have demonstrated that the Pichia kudriavzevii YGM091 strain is a safe potential probiotic yeast and could become a candidate probiotic food to be used in the future.
PubMed: 37368223
DOI: 10.1007/s12602-023-10114-1