Special Issue "Recent Advances in Applied Microbiology"

A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (31 March 2020).

Special Issue Editor

Prof. Dr. Leticia M. Estevinho
E-Mail Website1 Website2
Guest Editor
Department of Biology and Biotechnology, School of Agriculture of the Polytechnic Institute of Bragança (ESA-IPB), Campus de Santa Apolónia, 5301-854 Bragança, Portugal
Interests: microbiology; food microbiology; food safety; healing; fenolic compounds; therapeutic properties; anti-inflammatory
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Special Issue Information

Dear Colleagues,

Microbiology is an important branch of life sciences that has grown exponentially since the establishment of genomics, transcriptomics, and proteomics, which have made it possible to unravel the biogeochemical processes that microorganisms facilitate, as well as their interactions with macroorganisms in both health and disease. Microorganisms that were, in the past, considered villains now play very important and beneficial roles in a wide variety of settings, including environmental, food, agricultural, veterinary, systematics, bioremediation, industrial, medical, and pharmaceutical—leading to the emergence of the term “applied microbiology”. Also, microbiology has evolved through the discovery of new species, the selection and improvement of known strains, and the introduction of non-native genes for acquiring new expression products or functional traits. The market analysis corroborates the importance of this branch of life sciences; indeed, applied microbiology was valued at around 24.3 billion USD in 2017, and is expected to exceed USD 675.2 billion by 2024.

This Special Issue, entitled “Recent Advances in Applied Microbiology”, calls for reviews as well as original research articles documenting the progress and current understanding of different aspects of the vast field of applied microbiology.

Prof. Dr. Leticia M. Estevinho
Guest Editor

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Editorial

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Open AccessEditorial
Recent Advances in Applied Microbiology: Editorial
Microorganisms 2020, 8(9), 1364; https://doi.org/10.3390/microorganisms8091364 - 07 Sep 2020
Viewed by 868
Abstract
The importance of microbiology has grown exponentially since the development of genomics, transcriptomics, and proteomics, making it possible to clarify microbial biogeochemical processes and their interactions with macroorganisms in both health and disease. Particular attention is being payed to applied microbiology, a discipline [...] Read more.
The importance of microbiology has grown exponentially since the development of genomics, transcriptomics, and proteomics, making it possible to clarify microbial biogeochemical processes and their interactions with macroorganisms in both health and disease. Particular attention is being payed to applied microbiology, a discipline that deals with the application of microorganisms to specific endeavors, whose economic value is expected to exceed USD 675.2 billion by 2024. In the Special Issue “Recent Advances in Applied Microbiology”, twenty-four papers were published (four reviews and twenty original research papers), covering a wide range of subjects within applied microbiology, including: microbial pathogenesis, the health-promoting properties of microorganisms and their by-products, food conservation, the production of alcoholic beverages, bioremediation and the application of microbiology to several industrial processes. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)

Research

Jump to: Editorial, Review

Open AccessArticle
Diversity, Chemical Constituents and Biological Activities of Endophytic Fungi Isolated from Schinus terebinthifolius Raddi
Microorganisms 2020, 8(6), 859; https://doi.org/10.3390/microorganisms8060859 - 07 Jun 2020
Cited by 3 | Viewed by 838
Abstract
Schinus terebinthifolius Raddi is a medicinal plant widely used for the treatment of various diseases. The secondary metabolites responsible for the pharmacological properties can be produced directly by the plant or by endophytic fungi. The objective of this study was to evaluate the [...] Read more.
Schinus terebinthifolius Raddi is a medicinal plant widely used for the treatment of various diseases. The secondary metabolites responsible for the pharmacological properties can be produced directly by the plant or by endophytic fungi. The objective of this study was to evaluate the diversity of endophytic fungi of different parts of S. terebinthifolius and to identify chemical compounds produced by endophytes and their antioxidant and antibacterial activities. For this, fruits, stem bark and roots were dried, ground and placed in fungal growth medium. The selected endophytes were grown and subjected to extraction with ethyl acetate. DPPH, FRAP, β-carotene bleaching and antimicrobial assays were performed. The phylogenetic tree was elaborated, encompassing 15 different species. The fungal extracts showed hydroxybenzoic acids and 1-dodecanol as predominant compounds. All fungal extracts exhibited antioxidant activity. The fungal extracts exhibited bactericidal and bacteriostatic activities against Gram-positive and Gram-negative bacterial ATCC strains and against methicillin-resistant nosocomial bacteria. Among the 10 endophytic fungi evaluated, the extract of the fungus Ochrocladosporium elatum showed higher phenolic content and exhibited higher antioxidant and antibacterial activities in all tests. Together, the results increase the known diversity of S. terebinthifolius endophytic fungi, secondary metabolites produced and their antioxidant and antibacterial activities. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Age and Species of Eucalyptus Plantations Affect Soil Microbial Biomass and Enzymatic Activities
Microorganisms 2020, 8(6), 811; https://doi.org/10.3390/microorganisms8060811 - 28 May 2020
Cited by 1 | Viewed by 588
Abstract
Soil microorganisms and extracellular enzymes play important roles in soil nutrient cycling. Currently, China has the second-largest area of eucalyptus plantations in the world. Information on the effects of eucalyptus age and species of trees on soil microbial biomass and enzyme activities, however, [...] Read more.
Soil microorganisms and extracellular enzymes play important roles in soil nutrient cycling. Currently, China has the second-largest area of eucalyptus plantations in the world. Information on the effects of eucalyptus age and species of trees on soil microbial biomass and enzyme activities, however, is limited. In this paper, the soil microbial biomass and enzyme activities were studied in eucalyptus plantations with different ages (1 and 5+ years) and species of trees (E. urophylla×E. grandis, E. camaldulens and E. pellita) in South China. The results showed that both plantation age and eucalyptus species could affect the total microbial biomass and fungal biomass, whereas the bacterial biomass was affected only by plantation age. The fungal biomass and the fungi-to-bacteria ratio significantly increased along with increasing plantation age. Similarly, the plantation age and eucalyptus species significantly affected the enzyme activities associated with carbon cycling (β-xylosidase, β-d-glucuronidase, β-cellobiosidase and β-glucosidase). The activities of β-d-glucuronidase and β-glucosidase were significantly higher in the E. camaldulens plantation. The enzymes involved in nitrogen (N-acetyl-glucosamidase) and sulfur (sulfatase) cycling were only affected by the eucalyptus plantation age and species, respectively. The results highlight the importance of the age and species of eucalyptus plantations on soil microbial activities. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Investigation of Heterologously Expressed Glucose-6-Phosphate Dehydrogenase Genes in a Yeast zwf1 Deletion
Microorganisms 2020, 8(4), 546; https://doi.org/10.3390/microorganisms8040546 - 09 Apr 2020
Cited by 3 | Viewed by 916
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme of the oxidative part of the pentose phosphate pathway and serves as the major source of NADPH for metabolic reactions and oxidative stress response in pro- and eukaryotic cells. We here report on a strain of [...] Read more.
Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme of the oxidative part of the pentose phosphate pathway and serves as the major source of NADPH for metabolic reactions and oxidative stress response in pro- and eukaryotic cells. We here report on a strain of the model yeast Saccharomyces cerevisiae which lacks the G6PD-encoding ZWF1 gene and displays distinct growth retardation on rich and synthetic media, as well as a strongly reduced chronological lifespan. This strain was used as a recipient to introduce plasmid-encoded heterologous G6PD genes, synthesized in the yeast codon usage and expressed under the control of the native PFK2 promotor. Complementation of the hypersensitivity of the zwf1 mutant towards hydrogen peroxide to different degrees was observed for the genes from humans (HsG6PD1), the milk yeast Kluyveromyces lactis (KlZWF1), the bacteria Escherichia coli (EcZWF1) and Leuconostoc mesenteroides (LmZWF1), as well as the genes encoding three different plant G6PD isoforms from Arabidopsis thaliana (AtG6PD1, AtG6PD5, AtG6PD6). The plastidic AtG6PD1 isoform retained its redox-sensitive activity when produced in the yeast as a cytosolic enzyme, demonstrating the suitability of this host for determination of its physiological properties. Mutations precluding the formation of a disulfide bridge in AtG6PD1 abolished its redox-sensitivity but improved its capacity to complement the yeast zwf1 deletion. Given the importance of G6PD in human diseases and plant growth, this heterologous expression system offers a broad range of applications. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
A Novel Lactic Acid Bacteria Mixture: Macrophage-Targeted Prophylactic Intervention in Colorectal Cancer Management
Microorganisms 2020, 8(3), 387; https://doi.org/10.3390/microorganisms8030387 - 11 Mar 2020
Cited by 3 | Viewed by 1898
Abstract
Colorectal cancer (CRC) is one of the most common forms of cancer. Its onset from chronic inflammation is widely accepted. Moreover, dysbiosis plays an undeniable role, thus the use of probiotics in CRC has been suggested. They exhibit both anti- and pro-inflammatory properties [...] Read more.
Colorectal cancer (CRC) is one of the most common forms of cancer. Its onset from chronic inflammation is widely accepted. Moreover, dysbiosis plays an undeniable role, thus the use of probiotics in CRC has been suggested. They exhibit both anti- and pro-inflammatory properties and restore balance in the microbiota. The aim of this study was to investigate the immunomodulatory properties of six lactobacilli with probiotic features in an in vitro model of macrophage-like cells and to test these pooled probiotics for their anti-tumour properties in a chemically induced CRC model using Wistar male rats. Upon co-culture of M1- and M2-like macrophages with lactobacilli, cytokine release (TNF-α, IL-1β, IL-18, IL-23) and phagocytic activity using fluorescent-labelled bacteria were tested. The effects of orally administered probiotics on basic cancer and immune parameters and cytokine concentration (TNF-α, IL-1β, IL-18) in colon tumours were studied. Tested lactobacilli exhibited both pro- and anti-inflammatory properties in in vitro conditions. In vivo study showed that the administration of probiotics was able to decrease multiplicity, volume and total tumour numbers, restore colon length (p < 0.05) and increase IL-18 production (p < 0.05) in tumour tissue. These data indicate both an immunomodulatory effect of probiotics on distinct macrophage subsets and a protective effect against chemically-induced CRC. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Digestive Ability, Physiological Characteristics, and Rumen Bacterial Community of Holstein Finishing Steers in Response to Three Nutrient Density Diets as Fattening Phases Advanced
Microorganisms 2020, 8(3), 335; https://doi.org/10.3390/microorganisms8030335 - 27 Feb 2020
Cited by 9 | Viewed by 947
Abstract
The aim of this study is to track the dynamic alterations in nutrient intake and digestion, rumen fermentation and plasma metabolic characteristics, and rumen bacterial community of Holstein finishing steers in response to three nutrient density diets as fattening phases advanced. A total [...] Read more.
The aim of this study is to track the dynamic alterations in nutrient intake and digestion, rumen fermentation and plasma metabolic characteristics, and rumen bacterial community of Holstein finishing steers in response to three nutrient density diets as fattening phases advanced. A total of eighteen Holstein steers were randomly allocated into three nutrient density groups and steers in each group were fed under a three-phase fattening strategy, with nutrient density increased in each group when fattening phase advanced. Results showed that both fattening phase and dietary nutrient density significantly influenced the nutrient digestion, most of the rumen fermentation parameters, and part of bacteria at phylum and genus levels. Individually, dietary nutrient density affected the concentrations of plasma alanine aminotransferase and urea N, bacterial richness and evenness. All determined nutrient intake and plasma biochemical parameters, except for alanine aminotransferase and triglyceride, differed among fattening phases. Spearman correlation analysis revealed strong correlations between fiber intake and bacterial richness and evenness, rumen fermentation characteristics and certain bacteria. Moreover, Patescibacteria abundance was positively correlated with ambient temperature and plasma total protein. These results indicate that rumen fermentation and nutrient digestion were influenced by both dietary nutrient density and fattening phase, and these influences were regulated by certain rumen bacterial community and ruminal bacteria may be affected simultaneously by ambient temperature. This study may provide insights into diet optimization and potentially adaptive mechanism of rumen bacterial community in response to fattening phases and gradually climatic change. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
High-Level Production of Bacteriotoxic Phospholipase A1 in Bacterial Host Pseudomonas fluorescens via ABC Transporter-Mediated Secretion and Inducible Expression
Microorganisms 2020, 8(2), 239; https://doi.org/10.3390/microorganisms8020239 - 11 Feb 2020
Cited by 2 | Viewed by 1179
Abstract
Bacterial phospholipase A1 (PLA1) is used in various industrial fields because it can catalyze the hydrolysis, esterification, and transesterification of phospholipids to their functional derivatives. It also has a role in the degumming process of crude plant oils. However, bacterial expression of the [...] Read more.
Bacterial phospholipase A1 (PLA1) is used in various industrial fields because it can catalyze the hydrolysis, esterification, and transesterification of phospholipids to their functional derivatives. It also has a role in the degumming process of crude plant oils. However, bacterial expression of the foreign PLA1-encoding gene was generally hampered because intracellularly expressed PLA1 is inherently toxic and damages the phospholipid membrane. In this study, we report that secretion-based production of recombinant PlaA, a bacterial PLA1 gene, or co-expression of PlaS, an accessory gene, minimizes this harmful effect. We were able to achieve high-level PlaA production via secretion-based protein production. Here, TliD/TliE/TliF, an ABC transporter complex of Pseudomonas fluorescens SIK-W1, was used to secrete recombinant proteins to the extracellular medium. In order to control the protein expression with induction, a new strain of P. fluorescens, which had the lac operon repressor gene lacI, was constructed and named ZYAI strain. The bacteriotoxic PlaA protein was successfully produced in a bacterial host, with help from ABC transporter-mediated secretion, induction-controlled protein expression, and fermentation. The final protein product is capable of degumming oil efficiently, signifying its application potential. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Macroalgae Derived Fungi Have High Abilities to Degrade Algal Polymers
Microorganisms 2020, 8(1), 52; https://doi.org/10.3390/microorganisms8010052 - 26 Dec 2019
Cited by 5 | Viewed by 1406
Abstract
Marine fungi associated with macroalgae are an ecologically important group that have a strong potential for industrial applications. In this study, twenty-two marine fungi isolated from the brown seaweed Fucus sp. were examined for their abilities to produce algal and plant biomass degrading [...] Read more.
Marine fungi associated with macroalgae are an ecologically important group that have a strong potential for industrial applications. In this study, twenty-two marine fungi isolated from the brown seaweed Fucus sp. were examined for their abilities to produce algal and plant biomass degrading enzymes. Growth of these isolates on brown and green algal biomass revealed a good growth, but no preference for any specific algae. Based on the analysis of enzymatic activities, macroalgae derived fungi were able to produce algae specific and (hemi-)cellulose degrading enzymes both on algal and plant biomass. However, the production of algae specific activities was lower than the production of cellulases and xylanases. These data revealed the presence of different enzymatic approaches for the degradation of algal biomass by macroalgae derived fungi. In addition, the results of the present study indicate our poor understanding of the enzymes involved in algal biomass degradation and the mechanisms of algal carbon source utilization by marine derived fungi. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Molecular Biomarkers and Influential Factors of Denitrification in a Full-Scale Biological Nitrogen Removal Plant
Microorganisms 2020, 8(1), 11; https://doi.org/10.3390/microorganisms8010011 - 19 Dec 2019
Cited by 1 | Viewed by 601
Abstract
Three denitrifying bacteria, Paracoccus spp., Thauera spp., Pseudomonas-like spp., and two functional genes, nitrate reductase (narG and napA), were studied as potential biomarkers for total nitrogen removal. These bacterial genera and the functional genes showed significant negative correlations with [...] Read more.
Three denitrifying bacteria, Paracoccus spp., Thauera spp., Pseudomonas-like spp., and two functional genes, nitrate reductase (narG and napA), were studied as potential biomarkers for total nitrogen removal. These bacterial genera and the functional genes showed significant negative correlations with total nitrogen in the effluent (TNeff). Thauera spp. had the highest correlation (r = −0.793, p < 0.001) with TNeff, and narG-like and napA genes also showed significant correlations (r = −0.663 and −0.643, respectively), suggesting functional genes have equal validity to 16S rRNA genes in monitoring denitrification performance. The most explanatory variables were a combination of constituents, with temperature emerging as the most important in Pearson’s correlation and redundancy analysis. Thauera spp. had the highest correlation with temperature (r = 0.739) followed closely by Paracoccus spp. (r = 0.705). Denitrification was also significantly affected by pH (r = 0.369), solids retention time (r = −0.377), total nitrogenin (r = 0.635), and organic matter in the influent (biochemical oxygen demand and chemical oxygen demand; r = 0.320 and 0.522, respectively). Our data verified that major denitrifiers’ 16S rRNA genes and nitrate reductase genes were better biomarkers than the biomass concentration, and any of the biomarkers could track denitrification in real time. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessCommunication
Enhanced Production of Fatty Acid Ethyl Ester with Engineered fabHDG Operon in Escherichia coli
Microorganisms 2019, 7(11), 552; https://doi.org/10.3390/microorganisms7110552 - 11 Nov 2019
Cited by 3 | Viewed by 957
Abstract
Biodiesel, or fatty acid ethyl ester (FAEE), is an environmentally safe, next-generation biofuel. Conventionally, FAEE is produced by the conversion of oil/fats, obtained from plants, animals, and microorganisms, by transesterification. Recently, metabolic engineering of bacteria for ready-to-use biodiesel was developed. In Escherichia coli [...] Read more.
Biodiesel, or fatty acid ethyl ester (FAEE), is an environmentally safe, next-generation biofuel. Conventionally, FAEE is produced by the conversion of oil/fats, obtained from plants, animals, and microorganisms, by transesterification. Recently, metabolic engineering of bacteria for ready-to-use biodiesel was developed. In Escherichia coli, it is produced by fatty acyl-carrier proteins and ethanol, with the help of thioesterase (TesB) and wax synthase (WS) enzymes. One of the foremost barriers in microbial FAEE production is the feedback inhibition of the fatty acid (FA) operon (fabHDG). Here, we studied the effect of biodiesel biosynthesis in E. coli with an engineered fabHDG operon. With a basic FAEE producing BD1 strain harboring tes and ws genes, biodiesel of 32 mg/L were produced. Optimal FAEE biosynthesis was achieved in the BD2 strain that carries an overexpressed operon (fabH, fabD, and fabG genes) and achieved up to 1291 mg/L of biodiesel, a 40-fold rise compared to the BD1 strain. The composition of FAEE obtained from the BD2 strain was 65% (C10:C2, decanoic acid ethyl ester) and 35% (C12:C2, dodecanoic acid ethyl ester). Our findings indicate that overexpression of the native FA operon, along with FAEE biosynthesis enzymes, improved biodiesel biosynthesis in E. coli. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Characterizing the Potential of the Non-Conventional Yeast Saccharomycodes ludwigii UTAD17 in Winemaking
Microorganisms 2019, 7(11), 478; https://doi.org/10.3390/microorganisms7110478 - 23 Oct 2019
Cited by 5 | Viewed by 1126
Abstract
Non-Saccharomyces yeasts have received increased attention by researchers and winemakers, due to their particular contributions to the characteristics of wine. In this group, Saccharomycodes ludwigii is one of the less studied species. In the present study, a native S. ludwigii strain, UTAD17 [...] Read more.
Non-Saccharomyces yeasts have received increased attention by researchers and winemakers, due to their particular contributions to the characteristics of wine. In this group, Saccharomycodes ludwigii is one of the less studied species. In the present study, a native S. ludwigii strain, UTAD17 isolated from the Douro wine region was characterized for relevant oenological traits. The genome of UTAD17 was recently sequenced. Its potential use in winemaking was further evaluated by conducting grape-juice fermentations, either in single or in mixed-cultures, with Saccharomyces cerevisiae, following two inoculation strategies (simultaneous and sequential). In a pure culture, S. ludwigii UTAD17 was able to ferment all sugars in a reasonable time without impairing the wine quality, producing low levels of acetic acid and ethyl acetate. The overall effects of S. ludwigii UTAD17 in a mixed-culture fermentation were highly dependent on the inoculation strategy which dictated the dominance of each yeast strain. Wines whose fermentation was governed by S. ludwigii UTAD17 presented low levels of secondary aroma compounds and were chemically distinct from those fermented by S. cerevisiae. Based on these results, a future use of this non-Saccharomyces yeast either in monoculture fermentations or as a co-starter culture with S. cerevisiae for the production of wines with greater expression of the grape varietal character and with flavor diversity could be foreseen. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Transposition of Insertion Sequences was Triggered by Oxidative Stress in Radiation-Resistant Bacterium Deinococcus geothermalis
Microorganisms 2019, 7(10), 446; https://doi.org/10.3390/microorganisms7100446 - 12 Oct 2019
Cited by 3 | Viewed by 801
Abstract
During an oxidative stress-response assay on a putative Dps-like gene-disrupted Δdgeo_0257 mutant strain of radiation-resistant bacterium Deinococcus geothermalis, a non-pigmented colony was observed among the normal reddish color colonies. This non-pigmented mutant cell subsequently displayed higher sensitivity to H2 [...] Read more.
During an oxidative stress-response assay on a putative Dps-like gene-disrupted Δdgeo_0257 mutant strain of radiation-resistant bacterium Deinococcus geothermalis, a non-pigmented colony was observed among the normal reddish color colonies. This non-pigmented mutant cell subsequently displayed higher sensitivity to H2O2. While carotenoid has a role in protecting as scavenger of reactive oxygen species the reddish wild-type strain from radiation and oxidative stresses, it is hypothesized that the carotenoid biosynthesis pathway has been disrupted in the mutant D. geothermalis cell. Here, we show that, in the non-pigmented mutant cell of interest, phytoene desaturase (Dgeo_0524, crtI), a key enzyme in carotenoid biosynthesis, was interrupted by transposition of an ISDge7 family member insertion sequence (IS) element. RNA-Seq analysis between wild-type and Δdgeo_0257 mutant strains revealed that the expression level of ISDge5 family transposases, but not ISDge7 family members, were substantially up-regulated in the Δdgeo_0257 mutant strain. We revealed that the non-pigmented strain resulted from the genomic integration of ISDge7 family member IS elements, which were also highly up-regulated, particularly following oxidative stress. The transposition path for both transposases is a replicative mode. When exposed to oxidative stress in the absence of the putative DNA binding protein Dgeo_0257, a reddish D. geothermalis strain became non-pigmented. This transformation was facilitated by transposition of an ISDge7 family IS element into a gene encoding a key enzyme of carotenoid biosynthesis. Further, we present evidence of additional active transposition by the ISDge5 family IS elements, a gene that was up-regulated during the stationary phase regardless of the presence of oxidative stress. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis
Microorganisms 2019, 7(10), 412; https://doi.org/10.3390/microorganisms7100412 - 01 Oct 2019
Cited by 5 | Viewed by 796
Abstract
In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several [...] Read more.
In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Temporal Dynamics in Rumen Bacterial Community Composition of Finishing Steers during an Adaptation Period of Three Months
Microorganisms 2019, 7(10), 410; https://doi.org/10.3390/microorganisms7100410 - 01 Oct 2019
Cited by 15 | Viewed by 992
Abstract
The objective of this study was to explore whether collecting rumen samples of finishing steers at monthly intervals differed, and whether this difference or similarity varied with diets. For these purposes, 12 Chinese Holstein steers were equally divided into two groups. The dietary [...] Read more.
The objective of this study was to explore whether collecting rumen samples of finishing steers at monthly intervals differed, and whether this difference or similarity varied with diets. For these purposes, 12 Chinese Holstein steers were equally divided into two groups. The dietary treatments were either standard energy and standard protein (C) or low energy and low protein (L). Rumen samples were obtained on day 30, day 60 and day 90 from both dietary treatments and were analyzed by using 16S rRNA gene sequencing. The results showed that monthly intervals had no effect on the richness and evenness of the rumen bacterial community in the two diets. However, taxonomic difference analysis (relative abundance >0.5%) revealed that the relative abundance of three phyla (Proteobacteria, Fibrobacteres and Cyanobacteria) and six genera (Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Fibrobacter, Eubacterium_coprostanoligenes_group, Ruminococcaceae_UCG-010 and Ruminobacter) were significantly different between monthly sampling intervals, and the difference was prominent between sampling in the first month and the subsequent two months. Moreover, the differences in abundances of phyla and genera between monthly sampling intervals were affected by diets. Analysis of similarity (ANOSIM) showed no significant differences between monthly sampling intervals in the C diet. However, ANOSIM results revealed that significant differences between the first month and second month and between the first month and third month were present in the L diet. These results indicated that temporal dynamics in rumen bacterial community composition did occur even after an adaptation period of three months. This study tracked the changes in rumen bacterial populations of finishing cattle after a shift in diet with the passage of time. This study may provide insight into bacterial adaptation time to dietary transition in finishing steers. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Volatile Composition and Sensory Properties of Mead
Microorganisms 2019, 7(10), 404; https://doi.org/10.3390/microorganisms7100404 - 29 Sep 2019
Cited by 7 | Viewed by 940
Abstract
Mead is a traditional beverage that results from the alcoholic fermentation of diluted honey performed by yeasts. Although the process of mead production has been optimized in recent years, studies focused on its sensory properties are still scarce. Therefore, the aim of this [...] Read more.
Mead is a traditional beverage that results from the alcoholic fermentation of diluted honey performed by yeasts. Although the process of mead production has been optimized in recent years, studies focused on its sensory properties are still scarce. Therefore, the aim of this work was to analyse the sensory attributes of mead produced with free or immobilized cells of the Saccharomyces cerevisiae strains QA23 and ICV D47, and to establish potential correlations with its volatile composition. In the volatile composition of mead, the effect of yeast condition was more important than the strain. In respect to sensory analysis, the most pleasant aroma descriptors were correlated with mead obtained with free yeast cells, independently of the strain. Both sensory analysis and volatile composition indicates that the most pleasant mead was produced by free yeast cells. Although this study has provided a significant contribution, further research on the sensory quality of mead is still needed. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
A Discovery of Relevant Hepatoprotective Effects and Underlying Mechanisms of Dietary Clostridium butyricum Against Corticosterone-Induced Liver Injury in Pekin Ducks
Microorganisms 2019, 7(9), 358; https://doi.org/10.3390/microorganisms7090358 - 16 Sep 2019
Cited by 3 | Viewed by 1053
Abstract
Clostridium butyricum (C. butyricum) can attenuate oxidative stress, inflammation, and hepatic fatty deposition in poultry, however, the underlying mechanisms for this in Pekin ducks remain unclear. This study evaluated these hepatoprotective effects and the underlying mechanisms in a corticosterone (CORT)-induced liver [...] Read more.
Clostridium butyricum (C. butyricum) can attenuate oxidative stress, inflammation, and hepatic fatty deposition in poultry, however, the underlying mechanisms for this in Pekin ducks remain unclear. This study evaluated these hepatoprotective effects and the underlying mechanisms in a corticosterone (CORT)-induced liver injury model in Pekin ducks fed a C. butyricum intervention diet. A total of 500 Pekin ducks were randomly divided into five groups: one group (CON group) was only provided with a basal diet, three groups were provided a basal diet with 200 mg/kg (LCB group), 400 mg/kg (MCB group), or 600 mg/kg (HCB group) C. butyricum, respectively, and one group was provided a basal diet with 150 mg/kg aureomycin (ANT group) for 42 d. At 37 days-old, all ducks received daily intraperitoneal injections of CORT for five days to establish a liver injury model. C. butyricum intervention alleviated liver injury by decreasing the liver organ indices, hepatic steatosis and hepatocyte necrosis, and improving liver function, antioxidant capacity, and inflammatory factors. Hepatic RNA-seq revealed 365 differentially expressed genes (DEGs) between the MCB and CON groups, with 229 up- and 136 down-regulated DEGs in the MCB group. Between the MCB and ANT groups, 407 DEGs were identified, including 299 up- and 108 down-regulated genes in MCB group. Some DEGs in the MCB group related to oxidative stress and inflammatory responses such as Sod3, Tlr2a/b, and Il10, which were up-regulated, while Apoa1, Cyp7a1, Acsl1/5, Fasn, Ppar-γ, and Scd, which are involved in lipid metabolism, were down-regulated, indicating that these genes were responsive to dietary C. butyricum for the alleviation of corticosterone-induced hepatic injury. Toll-like receptor signaling, PI3K-Akt signaling pathway, cytokine-cytokine receptor interaction, peroxisome proliferator-activated receptor (PPAR) signaling pathway, adipocytokine and glycerophospholipid metabolism signaling pathway were significantly enriched in the MCB group. These findings indicate that C. butyricum intervention can protect Pekin ducks from corticosterone-induced liver injury by the modulation of immunoregulatory- and lipid metabolism-related genes and pathways. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Analysis of Factors Influencing the Transmembrane Voltage Induced in Filamentous Fungi by Pulsed Electric Fields
Microorganisms 2019, 7(9), 307; https://doi.org/10.3390/microorganisms7090307 - 01 Sep 2019
Cited by 3 | Viewed by 827
Abstract
This article studies the sterilization effects of high-voltage pulsed electric field (PEF) of technology on filamentous fungi. A cell dielectric model was proposed based on the physical structure of filamentous fungi. Basic theories of the electromagnetic field were comprehensively applied, and the multiphysics [...] Read more.
This article studies the sterilization effects of high-voltage pulsed electric field (PEF) of technology on filamentous fungi. A cell dielectric model was proposed based on the physical structure of filamentous fungi. Basic theories of the electromagnetic field were comprehensively applied, and the multiphysics field simulation software COMSOL Multiphysics was used for more detailed study. The effects of PEF treatment parameters and microbial characteristic parameters on the resulting cell membrane and nuclear membrane changes were simulated and analyzed. The results showed significant effects on the transmembrane voltage of the cell membrane and nuclear membrane from the electric field intensity, pulse duration, cell membrane thickness, superposition effect of the pulses. However, the amount of hyphae had little effect, and the number of cell nuclei and the thickness of the cell walls had almost no effect on the transmembrane voltage of the cell membranes and the nuclear membranes. The results provide theoretical support for applying high-voltage PEFs to kill fungi in practical applications. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Heterologous Hyaluronic Acid Production in Kluyveromyces lactis
Microorganisms 2019, 7(9), 294; https://doi.org/10.3390/microorganisms7090294 - 28 Aug 2019
Cited by 5 | Viewed by 1470
Abstract
Hyaluronic Acid (HA) is a biopolymer composed by the monomers Glucuronic Acid (GlcUA) and N-Acetyl Glucosamine (GlcNAc). It has a broad range of applications in the field of medicine, being marketed between USD 1000–5000/kg. Its primary sources include extraction of animal tissue and [...] Read more.
Hyaluronic Acid (HA) is a biopolymer composed by the monomers Glucuronic Acid (GlcUA) and N-Acetyl Glucosamine (GlcNAc). It has a broad range of applications in the field of medicine, being marketed between USD 1000–5000/kg. Its primary sources include extraction of animal tissue and fermentation using pathogenic bacteria. However, in both cases, extensive purification protocols are required to prevent toxin contamination. In this study, aiming at creating a safe HA producing microorganism, the generally regarded as safe (GRAS) yeast Kluyveroymyces lactis is utilized. Initially, the hasB (UDP-Glucose dehydrogenase) gene from Xenopus laevis (xlhasB) is inserted. After that, four strains are constructed harboring different hasA (HA Synthase) genes, three of humans (hshasA1, hshasA2, and hshasA3) and one with the bacteria Pasteurella multocida (pmhasA). Transcript values analysis confirms the presence of hasA genes only in three strains. HA production is verified by scanning electron microscopy in the strain containing the pmHAS isoform. The pmHAS strain is grown in a 1.3 l bioreactor operating in a batch mode, the maximum HA levels are 1.89 g/L with a molecular weight of 2.097 MDa. This is the first study that reports HA production in K. lactis and it has the highest HA titers reported among yeast. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Evaluation of Physiological Effects Induced by Manuka Honey Upon Staphylococcus aureus and Escherichia coli
Microorganisms 2019, 7(8), 258; https://doi.org/10.3390/microorganisms7080258 - 13 Aug 2019
Cited by 5 | Viewed by 1548
Abstract
Several studies have explored the antimicrobial properties of manuka honey (MkH). However, the data available regarding antibacterial action mechanisms are scarcer. The aim of this study was to scrutinize and characterize primary effects of manuka honey (MkH) upon the physiological status of Staphylococcus [...] Read more.
Several studies have explored the antimicrobial properties of manuka honey (MkH). However, the data available regarding antibacterial action mechanisms are scarcer. The aim of this study was to scrutinize and characterize primary effects of manuka honey (MkH) upon the physiological status of Staphylococcus aureus and Escherichia coli (as Gram-positive and Gram-negative bacteria models, respectively), using flow cytometry (FC) to reveal its antibacterial action mechanisms. Effects of MkH on membrane potential, membrane integrity and metabolic activity were assessed using different fluorochromes in a 180 min time course assay. Time-kill experiments were carried out under the same conditions. Additionally, MkH effect on efflux pumps was also studied in an E. coli strain with an over-expression of several efflux pumps. Exposure of bacteria to MkH resulted in physiological changes related to membrane potential and membrane integrity; these effects displayed slight differences among bacteria. MkH induced a remarkable metabolic disruption as primary physiological effect upon S. aureus and was able to block efflux pump activity in a dose-dependent fashion in the E. coli strain. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Encapsulated Bdellovibrio Powder as a Potential Bio-Disinfectant against Whiteleg Shrimp-Pathogenic Vibrios
Microorganisms 2019, 7(8), 244; https://doi.org/10.3390/microorganisms7080244 - 07 Aug 2019
Cited by 8 | Viewed by 1315
Abstract
Liquid preparations of bdellovibrios are currently commercialized as water quality improvers to control bacterial pathogens in whiteleg shrimp Penaeus vannamei. However, the efficacy of these liquid preparations is significantly impaired due to a dramatic loss of viable cells during long-term room temperature [...] Read more.
Liquid preparations of bdellovibrios are currently commercialized as water quality improvers to control bacterial pathogens in whiteleg shrimp Penaeus vannamei. However, the efficacy of these liquid preparations is significantly impaired due to a dramatic loss of viable cells during long-term room temperature storage. Thus, new formulations of bdellovibrios are greatly needed for high-stablility room-temperature storage. In the present study, the encapsulated powder of Bdellovibrio sp. strain F16 was prepared using spray drying with 20 g L−1 gelatin as the coating material under a spray flow of 750 L h−1, a feed rate of 12 mL min−1, and an air inlet temperature of 140 °C. It was found to have a cell density of 5.4 × 107 PFU g−1 and to have spherical microparticles with a wrinkled surface and a diameter of 3 μm to 12 μm. In addition, the encapsulated Bdellovibrio powder presented good storage stability with its cell density still remaining at 3.5 × 107 PFU g−1 after 120 days of room-temperature storage; it was safe for freshwater-farmed whiteleg shrimp with an LD50 over 1200 mg L−1, and it exhibited significant antibacterial and protective effects at 0.8 mg L−1 against shrimp-pathogenic vibrios. To our knowledge, this is the first report on a promising Bdellovibrio powder against shrimp vibrios with high stable room-temperature storage. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessArticle
Oxidative Stress Response of Aspergillus oryzae Induced by Hydrogen Peroxide and Menadione Sodium Bisulfite
Microorganisms 2019, 7(8), 225; https://doi.org/10.3390/microorganisms7080225 - 30 Jul 2019
Cited by 4 | Viewed by 1504
Abstract
Oxidative stress response protects organisms from deleterious effects of reactive oxygen species (ROS), which can damage cellular components and cause disturbance of the cellular homeostasis. Although the defensive biochemical mechanisms have been extensively studied in yeast and other filamentous fungi, little information is [...] Read more.
Oxidative stress response protects organisms from deleterious effects of reactive oxygen species (ROS), which can damage cellular components and cause disturbance of the cellular homeostasis. Although the defensive biochemical mechanisms have been extensively studied in yeast and other filamentous fungi, little information is available about Aspergillus oryzae. We investigated the effect of two oxidant agents (menadione sodium bisulfite, MSB, and hydrogen peroxide, H2O2) on cellular growth and antioxidant enzyme induction in A. oryzae. Results indicated severe inhibition of biomass and conidia production when high concentration of oxidants was used. Transcriptomic analysis showed an up-regulated expression of genes involved in oxidoreduction, such as catalase, glutathione peroxidase, and superoxide dismutase. In addition, it was observed that oxidative stress stimuli enhanced the expression of Yap1 and Skn7 transcription factors. Further, metabolomic analysis showed that glutathione content was increased in the oxidative treatments when compared with the control. Moreover, the content of unsaturated fatty acid decreased with oxidative treatment accompanying with the down-regulated expression of genes involved in linoleic acid biosynthesis. This study provided a global transcriptome characterization of oxidative stress response in A. oryzae, and can offer multiple target genes for oxidative tolerance improvement via genetic engineering. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Review

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Open AccessReview
Advances in Molecular Tools and In Vivo Models for the Study of Human Fungal Pathogenesis
Microorganisms 2020, 8(6), 803; https://doi.org/10.3390/microorganisms8060803 - 26 May 2020
Cited by 6 | Viewed by 1393
Abstract
Pathogenic fungi represent an increasing infectious disease threat to humans, especially with an increasing challenge of antifungal drug resistance. Over the decades, numerous tools have been developed to expedite the study of pathogenicity, initiation of disease, drug resistance and host-pathogen interactions. In this [...] Read more.
Pathogenic fungi represent an increasing infectious disease threat to humans, especially with an increasing challenge of antifungal drug resistance. Over the decades, numerous tools have been developed to expedite the study of pathogenicity, initiation of disease, drug resistance and host-pathogen interactions. In this review, we highlight advances that have been made in the use of molecular tools using CRISPR technologies, RNA interference and transposon targeted mutagenesis. We also discuss the use of animal models in modelling disease of human fungal pathogens, focusing on zebrafish, the silkworm, Galleria mellonella and the murine model. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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Open AccessReview
d-Amino Acids and Lactic Acid Bacteria
Microorganisms 2019, 7(12), 690; https://doi.org/10.3390/microorganisms7120690 - 12 Dec 2019
Cited by 5 | Viewed by 1125
Abstract
Proteins are composed of l-amino acids except for glycine, which bears no asymmetric carbon atom. Accordingly, researchers have studied the function and metabolism of l-amino acids in living organisms but have paid less attention to the presence and roles of their [...] Read more.
Proteins are composed of l-amino acids except for glycine, which bears no asymmetric carbon atom. Accordingly, researchers have studied the function and metabolism of l-amino acids in living organisms but have paid less attention to the presence and roles of their d-enantiomers. However, with the recent developments in analytical techniques, the presence of various d-amino acids in the cells of various organisms and the importance of their roles have been revealed. For example, d-serine (d-Ser) and d-aspartate (d-Asp) act as neurotransmitters and hormone-like substances, respectively, in humans, whereas some kinds of d-amino acids act as a biofilm disassembly factor in bacteria. Interestingly, lactic acid bacteria produce various kinds of d-amino acids during fermentation, and many d-amino acids taste sweet, compared with the corresponding l-enantiomers. The influence of d-amino acids on human health and beauty has been reported in recent years. These facts suggest that the d-amino acids produced by lactic acid bacteria are important in terms of the taste and function of lactic-acid-fermented foods. Against this background, unique d-amino-acid-metabolizing enzymes have been searched for and observed in lactic acid bacteria. This review summarizes and introduces the importance of various d-amino acids in this regard. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
Open AccessReview
Fungal Laccase Production from Lignocellulosic Agricultural Wastes by Solid-State Fermentation: A Review
Microorganisms 2019, 7(12), 665; https://doi.org/10.3390/microorganisms7120665 - 09 Dec 2019
Cited by 18 | Viewed by 1570
Abstract
Laccases are copper-containing oxidase enzymes found in many fungi. They have received increasing research attention because of their broad substrate specificity and applicability in industrial processes, such as pulp delignification, textile bleaching, phenolic removal, and biosensors. In comparison with traditional submerged fermentation (SF), [...] Read more.
Laccases are copper-containing oxidase enzymes found in many fungi. They have received increasing research attention because of their broad substrate specificity and applicability in industrial processes, such as pulp delignification, textile bleaching, phenolic removal, and biosensors. In comparison with traditional submerged fermentation (SF), solid-state fermentation (SSF) is a simpler technique for laccase production and has many advantages, including higher productivity, efficiency, and enzyme stability as well as reduced production costs and environmental pollution. Here, we review recent advances in laccase production technology, with focus on the following areas: (i) Characteristics and advantages of lignocellulosic agricultural wastes used as SSF substrates of laccase production, including detailed suggestions for the selection of lignocellulosic agricultural wastes; (ii) Comparison of fungal laccase production from lignocellulosic substrates by either SSF or SF; (iii) Fungal performance and strain screening in laccase production from lignocellulosic agricultural wastes by SSF; (iv) Applications of laccase production under SSF; and (v) Suggestions and avenues for future studies of laccase production by fungal SSF with lignocellulosic materials and its applications. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
Open AccessReview
Trends in Diatom Research Since 1991 Based on Topic Modeling
Microorganisms 2019, 7(8), 213; https://doi.org/10.3390/microorganisms7080213 - 24 Jul 2019
Cited by 8 | Viewed by 1334
Abstract
Diatoms are fundamental carbon sources in a wide range of aquatic food webs and have the potential for wide application in addressing environmental change. Understanding the evolution of topics in diatom research will provide a clear and needed guide to strengthen research on [...] Read more.
Diatoms are fundamental carbon sources in a wide range of aquatic food webs and have the potential for wide application in addressing environmental change. Understanding the evolution of topics in diatom research will provide a clear and needed guide to strengthen research on diatoms. However, such an overview remains unavailable. In this study, we used Latent Dirichlet Allocation (LDA), a generative model, to identify topics and determine their trends (i.e., cold and hot topics) by analyzing the abstracts of 19,000 publications from the Web of Science that were related to diatoms during 1991–2018. A total of 116 topics were identified from a Bayesian model selection. The hot topics (diversity, environmental indicator, climate change, land use, and water quality) that were identified by LDA indicated that diatoms are increasingly used as indicators to assess water quality and identify modern climate change impacts due to intensive anthropogenic activities. In terms of cold topics (growth rate, culture growth, cell life history, copepod feeding, grazing by microzooplankton, zooplankton predation, and primary productivity) and hot topics (spatial-temporal distribution, morphology, molecular identification, gene expression, and review), we determined that basic studies on diatoms have decreased and that studies tend to be more comprehensive. This study notes that future directions in diatom research will be closely associated with the application of diatoms in environmental management and climate change to cope with environmental challenges, and more comprehensive issues related to diatoms should be considered. Full article
(This article belongs to the Special Issue Recent Advances in Applied Microbiology)
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