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Food Research International (Ottawa,... Oct 2023Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is...
Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is expected to play bio-functional activities. Due to limited studies, information on microbial community structure in jalebi is unknown. Hence, the present study is aimed to profile the microbial community in jalebi by shotgun metagenomics and also to predict putative probiotic and functional genes by metagenome-assembled genome (MAG). Bacteria were the most abundant domain (91.91%) under which Bacillota was the most abundant phylum (82%). The most abundant species was Lapidilactobacillus dextrinicus followed by several species of lactic acid bacteria, acetic acid bacteria including few yeasts. Lap. dextrinicus was also significantly abundant in jalebi when compared to similar fermented wheat-based sourdough. Additionally, Lap. bayanensis, Pediococcus stilesii, and yeast- Candida glabrata, Gluconobacter japonicus, Pichia kudriavzevii, Wickerhamomyces anomalus were only detected in jalebi, which are not detected in sourdough. Few viruses and archaea were detected with < 1 % abundance. In silico screening of genes from the abundant species was mined using both KEGG and EggNOG database for putative health beneficial attributes. Circular genomes of five high-quality MAGs, identified as Lapidilactobacillus dextrinicus, Enterococcus hirae, Pediococcus stilesii, Acetobacter indonesiensis and Acetobacter cibinongensis, were constructed separately and putative genes were mapped and annotated. The CRISPR/Cas gene clusters in the genomes of four MAGs except Acetobacter cibinongensis were detected. MAGs also showed several secondary metabolites. Since, the identified MAGs have different putative genes for bio-functional properties, this may pave the way to selectively culture the uncultivated putative microbes for jalebi production. We believe this is the first report on metagenomic and MAGs of jalebi.
Topics: Metagenome; Edible Grain; Metagenomics; India
PubMed: 37689895
DOI: 10.1016/j.foodres.2023.113130 -
The Journal of Small Animal Practice Jul 2023To culture Malassezia and other fungi from the duodenum of dogs with gastrointestinal signs undergoing routine endoscopic examination.
OBJECTIVES
To culture Malassezia and other fungi from the duodenum of dogs with gastrointestinal signs undergoing routine endoscopic examination.
MATERIALS AND METHODS
Quantitative microbial culture was performed on duodenal juice aspirated from dogs with suspected enteropathy during routine upper gastrointestinal endoscopy; samples were cultured on Sabouraud's dextrose agar (30, 32 and 37°C) and modified Dixon agar (32°C) for 14 days. Isolates were identified phenotypically and by matrix-assisted laser desorption ionisation-time of flight, and internal transcribed spacer sequencing. Yeast presence was also evaluated by cytological and histopathological examination of smears and biopsy specimens.
RESULTS
Forty-five dogs were recruited with chronic inflammatory enteropathy (n=38), granulomatous colitis (n=2), gastric adenocarcinoma (n=2), duodenal small cell lymphoma (n=1) and idiopathic severe gastrointestinal haemorrhage (n=2). Fungi were cultured from 14 dogs: Malassezia pachydermatis was isolated from eight [chronic inflammatory enteropathy (n=7) (along with Candida albicans n=1); granulomatous colitis (n=1)] and Malassezia sympodialis from another (gastric adenocarcinoma). Five dogs with chronic inflammatory enteropathy yielded other yeasts (C. albicans, Candida glabrata, Kazachstania slooffiae, Kazachstania telluris, Pichia kudriavzevii [syn. C. krusei]). Yeasts were never observed in histopathological specimens. Fluorescent microscopical examination of cytological specimens showed yeast in only one case, from which K. slooffiae was subsequently isolated.
CLINICAL SIGNIFICANCE
Based on a literature search, this is the first report of isolation of M. pachydermatis, M. sympodialis, K. slooffiae and K. telluris from the canine duodenum. Further studies are needed to determine whether these are resident or transient fungi in the canine duodenum and whether their presence has a pathogenic effect on the host.
PubMed: 37681754
DOI: 10.1111/jsap.13649 -
IMA Fungus Sep 2023Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region...
Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), is commonly used in clinical routine laboratories due to its simplicity, universality, efficacy, and affordability for fungal species identification. However, Sanger sequencing fails to identify mixed ITS sequences in the case of mixed infections. To overcome this limitation, different high-throughput sequencing technologies have been explored. The nanopore-based technology is now one of the most promising long-read sequencing technologies on the market as it has the potential to sequence the full-length ITS region in a single read. In this study, we established a workflow for species identification using the sequences of the entire ITS region generated by nanopore sequencing of both pure yeast isolates and mocked mixed species reads generated with different scenarios. The species used in this study included Candida albicans (n = 2), Candida tropicalis (n = 1), Nakaseomyces glabratus (formerly Candida glabrata) (n = 1), Trichosporon asahii (n = 2), Pichia kudriavzevii (formerly Candida krusei) (n = 1), and Cryptococcus neoformans (n = 1). Comparing various methods to generate the consensus sequence for fungal species identification, the results from this study indicate that read clustering using a modified version of the NanoCLUST pipeline is more sensitive than Canu or VSEARCH, as it classified species accurately with a lower abundance cluster of reads (3% abundance compared to 10% with VSEARCH). The modified NanoCLUST also reduced the number of classified clusters compared to VSEARCH, making the subsequent BLAST+ analysis faster. Subsampling of the datasets, which reduces the size of the datasets by approximately tenfold, did not significantly affect the identification results in terms of the identified species name, percent identity, query coverage, percentage of reads in the classified cluster, and the number of clusters. The ability of the method to distinguish mixed species within sub-populations of large datasets has the potential to aid computer analysis by reducing the required processing power. The herein presented new sequence analysis pipeline will facilitate better interpretation of fungal sequence data for species identification.
PubMed: 37674240
DOI: 10.1186/s43008-023-00125-6 -
Photodiagnosis and Photodynamic Therapy Dec 2023Candida krusei and Candida albicans present the ability to form communities of microorganisms called biofilms. Biofilms can be composed of a single species or more and...
Candida krusei and Candida albicans present the ability to form communities of microorganisms called biofilms. Biofilms can be composed of a single species or more and are an important virulence factor. The inhibition of C. albicans and C. krusei as well as of their dual-species biofilms by antimicrobial Photodynamic Therapy (aPDT) has been demonstrated. This study aimed to investigate the effect of aPDT, with TBO, on dual-species biofilms of C. albicans and C. krusei using different culture mediums, RPMI-1640 and Sabouraud-dextrose broth (SDB) to produce biofilms presenting different C. albicans/C. krusei ratio. Biofilms formed using RPMI-1640 presented a higher C. albicans/C. krusei ratio, however, biofilms formed using SDB presented a predominance of C. krusei. The metabolic activity of biofilms produced using RPMI-1640 was inhibited by aP (∼40%), while biofilms produced using SDB were not affected by aPDT. In addition, biofilm biomass was reduced in biofilms produced using RPMI-1640 and treated with aPDT (∼20%). The results demonstrated that aPDT reduces C. albicans development in dual-species biofilms with C. krusei. However, no effect could be observed on C. krusei, demonstrating that C. krusei, when present in the structure of dual-species biofilms can be resistant to aPDT.
Topics: Candida albicans; Photochemotherapy; Photosensitizing Agents; Anti-Infective Agents; Biofilms; Pichia
PubMed: 37673228
DOI: 10.1016/j.pdpdt.2023.103787 -
Letters in Applied Microbiology Sep 2023Film-forming yeasts are potential sources of defects in alcoholic beverages. The aim of this study is to assess the growth capacity of Pichia and Candida film-forming...
Film-forming yeasts are potential sources of defects in alcoholic beverages. The aim of this study is to assess the growth capacity of Pichia and Candida film-forming yeasts in cider and wine and the effects on their chemical composition. Cider, partially and fully fermented wine were inoculated with strains of C. californica, P. fermentans, P. kluyveri, P. kudriavzevii, P. manshurica, and P. membranifaciens to simulate a post-fermentative contamination. The former three species grew only in cider. Pichia manshurica and P. kudriavzevii displayed high viability in wine up to 13.18% (v v-1) ethanol. Significant changes in odour-active molecules from different chemical groups were observed in cider and wine in the inoculated samples, compared to the non-inoculated ones. Cider is more susceptible to contamination by all of the species tested, due to its low alcohol content, while P. membranifaciens, P. manshurica, and P. kudriavzevii are additionally potential spoilage agents of wine. This study highlights the risk of cider and wine contamination by film-forming yeasts. Their impact on aroma profiles depends on their ability to grow and their metabolism. This study contributes to an understanding of the possible physiological and metabolic mechanisms responsible for film formation and chemical changes in alcoholic beverages.
Topics: Wine; Fermentation; Pichia; Alcoholic Beverages; Candida
PubMed: 37656878
DOI: 10.1093/lambio/ovad099 -
Antonie Van Leeuwenhoek Nov 2023The use of yeasts as a feed supplement for cattle can promote animal development and performance. However, for the positive results to be consistent, strains with...
The use of yeasts as a feed supplement for cattle can promote animal development and performance. However, for the positive results to be consistent, strains with probiotic properties must be selected. The objective of this study was to isolate and identify yeasts present in the bovine feces and evaluate their probiotic potential together with strains previously isolated from the rumen (preliminary study). A total of 193 isolates were studied, including 139 isolates (19 species) from fecal samples from 11 different animals (Bos taurus and Bos indicus) and 54 strains previously isolated from rumen fluid (Bos taurus). The yeast population in the feces ranged from 3.51 to 4.99 log CFU/g, with Candida pararugosa being the most abundant (isolated from the feces of six samples analysed). Isolates were selected that had negative results in the safety tests (hemolytic activity, DNAse, and gelatinase) and had percentages greater than 35 and 70% for hydrophobicity and auto-aggregation, respectively. In addition, selected isolates had percentages greater than 77.7 and 74.7% for coaggregation with pathogenic strains of Escherichia coli and Clostridium perfringens, respectively. The isolates with percentage growth at 39 °C greater than 64.6% and viability greater than 96.7% were selected for survival testing under bovine gastrointestinal conditions. After the tests, the seven best isolates were selected, belonging to the species Candida pararugosa (L60, CCMA 928 and CCMA 930) and Pichia kudriavzevii (L97, L100, CCMA904, CCMA 907). The selected isolates were exopolysaccharide producers. Based on the results of the evaluated properties, the seven selected isolates were classified as potential probiotics for cattle.
Topics: Cattle; Animals; Saccharomyces cerevisiae; Gastrointestinal Tract; Feces; Escherichia coli; Probiotics
PubMed: 37650994
DOI: 10.1007/s10482-023-01865-6 -
Current Opinion in Critical Care Oct 2023The increasing incidence of drug-resistant Candida brings a new challenge to the treatment of invasive candidiasis. Although cross-resistance among azoles and... (Review)
Review
PURPOSE OF REVIEW
The increasing incidence of drug-resistant Candida brings a new challenge to the treatment of invasive candidiasis. Although cross-resistance among azoles and echinocandins was generally uncommon, reports of multidrug-resistant (MDR) Candida markedly increased in the last decade. The purpose of this review is to understand mechanisms and risk factors for resistance and how to tackle antifungal resistance.
RECENT FINDINGS
The paper describes the action of the three main classes of antifungals - azoles, echinocandins and polyenes - and Candida's mechanisms of resistance. The current evolution from cross-resistance to multiresistance among Candida explains the modern glossary - multidrug-resistant (MDR), extensively drug-resistant (XDR), and pandrug-resistant (PDR) - imported from bacteria. MDR Candida most commonly involves acquired resistance in species with intrinsic resistance, therefore it mostly involves C. glabrata, C. parapsilosis, C. krusei, C guilliermondii or C. auris , which is intrinsically multidrug resistant. Finally, strategies to tackle antifungal resistance became clearer, ideally implemented through antifungal stewardship.
SUMMARY
Avoiding antifungal's overuse and selecting the best drug, dose and duration, when they are needed, is fundamental. Knowledge of risk factors for resistance, microbiological diagnosis to the species, use of susceptibility test supported by antifungal stewardship programs help attaining effective therapy and sustaining the effectiveness of the current antifungal armamentarium.
Topics: Humans; Candida; Antifungal Agents; Candidiasis, Invasive; Echinocandins; Azoles
PubMed: 37641511
DOI: 10.1097/MCC.0000000000001077 -
Foods (Basel, Switzerland) Aug 2023The responses of various microbial populations to modifications in the physicochemical properties of a food matrix, as well as interactions between these populations...
The responses of various microbial populations to modifications in the physicochemical properties of a food matrix, as well as interactions between these populations already present, are the main factors that shape microbial dynamics in that matrix. This work focused on the study of microbial dynamics during labneh Ambaris production, a traditional Lebanese concentrated fermented goat milk made in jars during 3 months. This was assessed in two earthenware jars at a production facility. DNA metabarcoding of the ITS2 region as well as the V3-V4 region of the 16S rRNA gene was used to characterize the fungal and bacterial communities, respectively. Viable bacterial isolates were also identified by Sanger sequencing of the V1-V4 region of the 16S rRNA gene. Our results showed that the dominant microorganisms identified within labneh Ambaris (, , , , and sp.) settle early in the product and remain until the end of maturation with varying abundances throughout fermentation. Microbial counts increased during early fermentation stage, and remained stable during mid-fermentation, then declined during maturation. While microbial compositions were globally comparable between the two jars during mid-fermentation and maturation stages, differences between the two jars were mainly detected during early fermentation stage (D0 until D10). No significant sensorial differences were observed between the final products made in the two jars. Neither coliforms nor were detected in their viable state, starting D7 in both jars, suggesting the antimicrobial properties of the product.
PubMed: 37628130
DOI: 10.3390/foods12163131 -
Applied Biochemistry and Biotechnology Jun 2024Deoxynivalenol (DON) is a mycotoxin that significantly threatens the food and feed industry. Corn steep liquor (CSL) is an acidic byproduct of the corn starch industry,...
Deoxynivalenol (DON) is a mycotoxin that significantly threatens the food and feed industry. Corn steep liquor (CSL) is an acidic byproduct of the corn starch industry, and DON is concentrated in CSL once the material is contaminated. In this work, a Pichia kudriavzevii strain that could remove DON from CSL was isolated and characterized. The strain P. kudriavzevii E4-205 showed detoxifying activity in a pH range of 4.0~7.0 and temperature of 25~42 °C, and 39.4% DON was reduced by incubating this strain in CSL supernatant diluted by 2-fold (5 μg/mL DON) for 48 h at pH 5.0 and 30 °C. Further mechanism studies showed that P. kudriavzevii E4-205 could adsorb DON by the cell wall and degrade DON by intracellular enzymes with NADH as a cofactor. The degradation product was identified as 3,7,8,15-tetrahydroxyscirpene by liquid chromatography-tandem mass spectrometry. DON adsorption by inactivated cells was characterized, and the adsorption followed pseudo first-order kinetics. This study revealed a novel mechanism by which microbes degrade DON and might serve as a guide for the development of DON biological detoxification methods.
Topics: Trichothecenes; Pichia; Cell Wall; Adsorption; Hydrogen-Ion Concentration; Zea mays; Temperature; Kinetics
PubMed: 37624506
DOI: 10.1007/s12010-023-04712-6 -
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