Applied Microbiology

Research

14 pages, 2737 KiB

Open AccessArticle

Comparative Analysis of Ligninolytic Potential among Pleurotus ostreatus and Fusarium sp. with a Special Focus on Versatile Peroxidase

by Manisha Parmar, Sayeed A. H. Patel, Urmila Gupta Phutela and Manish Dhawan

Appl. Microbiol. 2024, 4(3), 1348-1361; https://doi.org/10.3390/applmicrobiol4030093 - 18 Sep 2024

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Abstract

Lignocellulosic biomass is contemplated to be an inexpensive and copious feedstock that can be used for numerous industrial applications. However, lignin forms the lignin sheath and provides a physical barrier to enzymatic hydrolysis. In addition, lignin physically blocks cellulase, preventing it from being [...] Read more.

Lignocellulosic biomass is contemplated to be an inexpensive and copious feedstock that can be used for numerous industrial applications. However, lignin forms the lignin sheath and provides a physical barrier to enzymatic hydrolysis. In addition, lignin physically blocks cellulase, preventing it from being combined with the substrate in a process known as non-productive binding. Therefore, the depletion of lignin is a crucial method for obtaining fermentable sugars from the lignocellulosic biomass. Different white-rot fungi secrete different sets of lignin-mineralizing enzymes and each fungus secretes one or more of the three enzymes essential for lignin degradation. Among efficient redox enzymes, versatile peroxidase is extensively studied for its ability to degrade aromatics without the need for a mediator or polyvalent catalytic site. However, the presence of versatile peroxidase in F. spp. has not been studied. This study was planned with the objective of screening and comparing the production of versatile peroxidase enzymes from F. spp. and a standard culture of Pleurotus ostreatus MTCC-142. These fungal strains were first screened on solid media containing tannic acid, malachite green, or bromocresol green. The potency index for the tannic acid, malachite green, and bromocresol green on the 16th day of incubation was reported to be 1.28, 1.07, 1.09, and 1.10, respectively. Versatile peroxidase production patterns were investigated under solid state fermentation conditions for a period of 25 days at different temperatures ranging from 10 to 35 °C. The highest versatile peroxidase activity (592 UL⁻¹) in F. sp. was observed at 30 °C after the 7th day of incubation. The molecular confirmation showed the presence of the vp gene in F. sp. along with Pleurotus ostreatus MTCC-142. The results determined that F. sp. possesses a versatile peroxidase enzyme and is able to degrade lignin efficiently, and thus it could be utilized as an alternative to other ligninolytic enzyme-producing fungi. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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20 pages, 3520 KiB

Open AccessArticle

Unraveling Microbial Endosymbiosis Dynamics in Plant-Parasitic Nematodes with a Genome Skimming Strategy

by Sulochana K. Wasala, Cedar Hesse, Catherine L. Wram, Dana K. Howe, Inga A. Zasada and Dee R. Denver

Appl. Microbiol. 2023, 3(4), 1229-1248; https://doi.org/10.3390/applmicrobiol3040085 - 20 Oct 2023

Cited by 2 | Viewed by 1870

Abstract

Bacterial endosymbionts, in genera Wolbachia and Cardinium, infect various arthropods and some nematode groups. Manipulating these microbial symbionts presents a promising biocontrol strategy for managing disease-causing parasites. However, the diversity of Wolbachia and Cardinium in nematodes remains unclear. This study employed a [...] Read more.

Bacterial endosymbionts, in genera Wolbachia and Cardinium, infect various arthropods and some nematode groups. Manipulating these microbial symbionts presents a promising biocontrol strategy for managing disease-causing parasites. However, the diversity of Wolbachia and Cardinium in nematodes remains unclear. This study employed a genome skimming strategy to uncover their occurrence in plant-parasitic nematodes, analyzing 52 populations of 12 species. A metagenome analysis revealed varying endosymbiont genome content, leading to the categorization of strong, weak, and no evidence for endosymbiont genomes. Strong evidence for Wolbachia was found in five populations, and for Cardinium in one population, suggesting a limited occurrence. Strong Wolbachia evidence was noted in Pratylenchus penetrans and Radopholus similis from North/South America and Africa. Heterodera glycines from North America showed strong Cardinium evidence. Weak genomic evidence for Wolbachia was observed in Globodera pallida, Meloidogyne incognita, Rotylenchus reniformis, Pratylechus coffeae, Pratylenchus neglectus, and Pratylenchus thornei; for Cardinium was found in G. pallida, R. reniformis and P. neglectus; 27/52 populations exhibited no endosymbiont evidence. Wolbachia and Cardinium presence varied within nematode species, suggesting non-obligate mutualism. Wolbachia and Cardinium genomes differed among nematode species, indicating potential species-specific functionality. This study advances knowledge of plant-parasitic nematode–bacteria symbiosis, providing insights for downstream eco-friendly biocontrol strategies. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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10 pages, 561 KiB

Open AccessArticle

Better COVID-19 Outcomes in Children with Good Asthma Control

by Jasna Rodman Berlot, Malena Aldeco, Dušanka Lepej, Marina Praprotnik, Saša Šetina Šmid, Aleksandra Zver and Uroš Krivec

Appl. Microbiol. 2023, 3(4), 1204-1213; https://doi.org/10.3390/applmicrobiol3040083 - 17 Oct 2023

Cited by 1 | Viewed by 1644

Abstract

Factors associated with COVID-19 presentation in children with asthma are poorly defined. Our study aimed to assess the clinical course of COVID-19 in children with asthma, with particular attention to possible risk factors for severe disease and long-term sequelae in this group of [...] Read more.

Factors associated with COVID-19 presentation in children with asthma are poorly defined. Our study aimed to assess the clinical course of COVID-19 in children with asthma, with particular attention to possible risk factors for severe disease and long-term sequelae in this group of patients. We assessed the occurrence of SARS-CoV-2 infection in children with asthma six months before their regular outpatient visit to the asthma clinic. Characteristics of patients presenting with signs of SARS-CoV-2 upper (URTI) or lower respiratory tract infection (LRTI) were compared. We focused on factors previously associated with COVID-19 severity. Twenty-seven percent of patients (57/210) reported exposure to SARS-CoV-2 infection. In the symptomatic group, 36% (15/42) reported symptoms of LRTI and 64% (27/42) of URTI. Poorer asthma control was observed in patients with LRTI compared to URTI (80% vs. 7%, p < 0.001). In addition, children with poorer asthma control had a higher risk of presenting with SARS-CoV-2 LRTI in a multiple logistic regression analysis. COVID-19 disease course was not associated with regular ICS use and asthma severity. However, patients on regular ICS had better asthma control (p = 0.026). We found no PFT deterioration post-COVID-19 in either group of patients. Our results suggest good asthma control and treatment adherence prior to infection are associated with better COVID-19 outcomes in children with asthma. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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19 pages, 3754 KiB

Open AccessArticle

Bacillus velezensis and Paenibacillus peoriae Strains Effective as Biocontrol Agents against Xanthomonas Bacterial Spot

by Snizhana Olishevska, Arvin Nickzad, Concetta Restieri, Fadi Dagher, Yan Luo, Jie Zheng and Eric Déziel

Appl. Microbiol. 2023, 3(3), 1101-1119; https://doi.org/10.3390/applmicrobiol3030076 - 14 Sep 2023

Cited by 2 | Viewed by 2470

Abstract

Gram-negative bacteria belonging to the Xanthomonas genus include plant pathogens representing a major challenge in the field of agriculture for a wide variety of economically important crops, such as tomato, pepper, and lettuce. Due to the massive usage of agrochemicals, Xanthomonas spp. are [...] Read more.

Gram-negative bacteria belonging to the Xanthomonas genus include plant pathogens representing a major challenge in the field of agriculture for a wide variety of economically important crops, such as tomato, pepper, and lettuce. Due to the massive usage of agrochemicals, Xanthomonas spp. are developing resistance to copper pesticides typically used to control microbial infections. An interesting alternative approach to control bacterial phytopathogens consists of using eco-friendly biocontrol agents, often beneficial microorganisms. Here, following the targeted, broad-spectrum screening of thousands of microorganisms isolated from different environmental locations, we isolated Bacillus velezensis strain 71 and Paenibacillus peoriae strain To99 displaying potent antagonistic activity against Xanthomonas spp. We found that oxydifficidin and polymyxin A secreted by B. velezensis 71 and P. peoriae To99, respectively, are mainly responsible for the anti-Xanthomonas activity. We further evaluated the performance of cell suspensions and cell-free supernatants of these isolates in controlling tomato bacterial spot disease in growth chamber and greenhouse conditions to validate the in vitro results. The overall results demonstrate the potential of treatments based on the secondary metabolites from both isolates and their cells as an alternative to copper-based chemicals to control leaf spot diseases caused by Xanthomonas spp. phytopathogens. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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14 pages, 10214 KiB

Open AccessArticle

Safety and Effects of Intravaginal Administration of Lacticaseibacillus rhamnosus CRL1332 Immobilized on Nanofibers in a Murine Experimental Model

by Jessica Alejandra Silva, Priscilla Romina De Gregorio and María Elena Fátima Nader-Macías

Appl. Microbiol. 2023, 3(3), 1013-1026; https://doi.org/10.3390/applmicrobiol3030069 - 24 Aug 2023

Cited by 1 | Viewed by 1550

Abstract

The design of probiotic hygiene products for daily use is considered an adequate alternative for the restoration of the vaginal microbiome, maintaining health, and/or preventing infections of the female urogenital tract. Most of these probiotic products are available on the world market, but [...] Read more.

The design of probiotic hygiene products for daily use is considered an adequate alternative for the restoration of the vaginal microbiome, maintaining health, and/or preventing infections of the female urogenital tract. Most of these probiotic products are available on the world market, but their efficacy and safety are not sufficiently documented. One of the requirements to transfer novel probiotic formulas/products to the productive sector is to demonstrate their innocuity and the absence of adverse or collateral effects on the host, mainly assayed in experimental models. The inclusion of beneficial lactobacilli in nanofibers by electrospinning technique has shown promising application possibilities, and the immobilization of Lacticaseibacillus rhamnosus CRL1332 in nanofibers with and without bioprotective substances and their characterization were previously performed by our research group. In this work, the safety of the intravaginal (i.va.) administration of these functional nanofibers in a murine experimental model was evaluated. L. rhamnosus CRL1332 immobilized in different nanofibers was intravaginally inoculated into mice (seven daily doses). Vaginal washes were taken for microbiological (cultivable lactobacilli) and cytological techniques, and the vagina was used for histological and morphological-ultrastructural evaluation. Our results demonstrated that the intravaginal administration of L. rhamnosus CRL1332 immobilized in nanofibers is safe in murine models, given the absence of an inflammatory response at the cytological and histological levels, with minor modifications at the ultrastructural level, and also related to the normal cultivable vaginal microbiota. On the other hand, the number of cultivable lactobacilli increased in the vagina of mice receiving L. rhamnosus CRL1332 nanofibers. The results indicate the safety of lactobacilli-functional nanofibers and support their inclusion in the design of vaginal probiotic products to prevent/treat urogenital infections and reconstitute the women’s vaginal microbiota. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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9 pages, 1480 KiB

Open AccessCommunication

Comparative Efficacy of Systemic and Combination Fungicides for the Control of Alternaria Leaf Spot of Cabbage

by Patience U. Ishieze, Chinedu F. Amuji, Kevin I. Ugwuoke, Paul K. Baiyeri and Michael O. Eze

Appl. Microbiol. 2023, 3(3), 906-914; https://doi.org/10.3390/applmicrobiol3030062 - 12 Aug 2023

Cited by 2 | Viewed by 2977

Abstract

Alternaria leaf spot of cabbage, caused by the Alternaria brassicicola, affects leaves of cabbages and often results in head rots causing severe decline in yield. In this work, the effects of systemic and combination fungicides on A. brassicicola mycelia growth in vitro [...] Read more.

Alternaria leaf spot of cabbage, caused by the Alternaria brassicicola, affects leaves of cabbages and often results in head rots causing severe decline in yield. In this work, the effects of systemic and combination fungicides on A. brassicicola mycelia growth in vitro and disease severity in field trials were investigated. The results of in vitro evaluation revealed that both fungicides significantly inhibited (p < 0.05) the growth of A. brassicicola under in vitro conditions. However, metalaxyl-M 6% was less effective with 100 μg/mL having only 30 ± 3.5% inhibition. On the other hand, 100 μg/mL of mancozeb 63% + carbendazim 12% had 94 ± 3.5% growth inhibition of A. brassicicola, respectively, under the same conditions. Dose-response analysis of the efficacy of the two fungicides showed that the LC₅₀ of metalaxyl-M 6% and mancozeb 63% + carbendazim 12% were 125.52 ppm and 57.22 ppm, respectively, indicating the superiority of combination fungicide over systemic fungicide alone. Field studies showed that while manure type significantly impacted on biomass production (p < 0.001), it did not significantly affect disease severity. On the other hand, the frequency of fungicide application impacted on disease severity, with biweekly application leading to a significant reduction in disease severity after 10 weeks. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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15 pages, 1144 KiB

Open AccessArticle

The Basis for Variations in the Biofilm Formation by Different Salmonella Species and Subspecies: An In Vitro and In Silico Scoping Study

by Amreeta Sarjit, Yi Cheah and Gary A. Dykes

Appl. Microbiol. 2023, 3(3), 841-855; https://doi.org/10.3390/applmicrobiol3030058 - 3 Aug 2023

Viewed by 1452

Abstract

This study examined whether the presence/absence of biofilm-associated genes may indicate the potential for differences in the biofilm formation among the Salmonella species/subspecies. We conducted an in vitro study on the biofilm formation by eighteen Salmonella strains of different species/subspecies. Strains belonging to [...] Read more.

This study examined whether the presence/absence of biofilm-associated genes may indicate the potential for differences in the biofilm formation among the Salmonella species/subspecies. We conducted an in vitro study on the biofilm formation by eighteen Salmonella strains of different species/subspecies. Strains belonging to subspecies enterica were generally poorer biofilm formers than strains belonging to species bongori and subspecies arizonae, diarizonae, and indica. A broader in silico study was subsequently conducted. The presence/absence of 57 biofilm-associated genes was further investigated among 323 Salmonella whole genomes of various species/subspecies. The lpfE gene was present in in 88.2% of subspecies enterica but was absent in ~90.2–100% of other subspecies. The sirA gene was present in 11.8% of subspecies enterica and 2.9% of S. diarizonae genomes while absent in other species/subspecies. The lpfe gene and sirA gene in subspecies enterica negatively correlated with environmental biofilm formation. The csrB gene was present in 71.4% of the S. arizonae and 94.3% of S. diarizonae genomes but absent in other species/subspecies. The absence of csrB in subspecies enterica positively correlated with weaker environmental biofilm formation. This may contribute to subspecies arizonae and diarizonae being better biofilm formers. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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15 pages, 10768 KiB

Open AccessArticle

Conversion of Unsaturated Short- to Medium-Chain Fatty Acids by Unspecific Peroxygenases (UPOs)

by Alexander Karich, Fabian Salzsieder, Martin Kluge, Miguel Alcalde, René Ullrich and Martin Hofrichter

Appl. Microbiol. 2023, 3(3), 826-840; https://doi.org/10.3390/applmicrobiol3030057 - 19 Jul 2023

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Abstract

Eighteen short- to medium-chain monounsaturated fatty acids were screened for hydroxylation and epoxidation using eleven different peroxygenase preparations. Most of these unspecific peroxygenases (UPOs) are secreted by fungal species of the dark-spored basidiomycetous families Psathyrellaceae and Strophariaceae, two belonged to the white-spored [...] Read more.

Eighteen short- to medium-chain monounsaturated fatty acids were screened for hydroxylation and epoxidation using eleven different peroxygenase preparations. Most of these unspecific peroxygenases (UPOs) are secreted by fungal species of the dark-spored basidiomycetous families Psathyrellaceae and Strophariaceae, two belonged to the white-spored genus Marasmius (Marasmiaceae), and one belonged to the ascomycetous family Chaetomiaceae. The fatty acids (FAs) studied were categorized into three groups based on the position of the double bond: (i) terminal unsaturated FAs (between ω and ω-1), (ii) α-β-unsaturated FAs (between C2 and C3), and (iii) β-γ-unsaturated FAs (between C3 and C4). Their chain lengths ranged from three to nine carbon atoms. FAs with a terminal double bond were significantly oxidized by only two UPOs, namely CglUPO and CraUPO (peroxygenases from Chaetomium globosum and Coprinellus radians, respectively), producing different products. FAs with internal double bonds were converted by all tested UPOs. While epoxides were observed as products in the case of α-β-unsaturated fatty acids, only CglUPO formed β-γ-epoxides from the corresponding FAs. The product pattern of the other UPOs for β-γ-unsaturated FAs was quite similar. On the other hand, the product pattern for oxidized α-β-unsaturated FAs was more variable and, in some cases, specific to a particular UPO. For example, in the reaction with trans-2-nonenoic acid, the enzymes clustered into six groups based on the formed products. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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13 pages, 1794 KiB

Open AccessArticle

Sugar-Induced Cell Death in the Yeast S. cerevisiae Is Accompanied by the Release of Octanoic Acid, Which Does Not Originate from the Fatty Acid Synthesis Type II Mitochondrial System

by Alexander Avtukh, Boris Baskunov, Varlam Keshelava and Airat Valiakhmetov

Appl. Microbiol. 2023, 3(3), 722-734; https://doi.org/10.3390/applmicrobiol3030050 - 12 Jul 2023

Viewed by 1694

Abstract

Incubation of the yeast S. cerevisiae with glucose, in the absence of other nutrients, leads to Sugar-Induced Cell Death (SICD), accompanied by the accumulation of Reactive Oxygen Species (ROS). Yeast acidifies the environment during glucose metabolism not only as a result of the [...] Read more.

Incubation of the yeast S. cerevisiae with glucose, in the absence of other nutrients, leads to Sugar-Induced Cell Death (SICD), accompanied by the accumulation of Reactive Oxygen Species (ROS). Yeast acidifies the environment during glucose metabolism not only as a result of the activity of the H⁺-ATPase of the plasma membrane but also due to the release of carboxylic acids. Acetic acid is known to induce apoptosis in growing yeast. We analyzed the composition of the incubation medium and found octanoic acid (OA) but no other carboxylic acids. Its concentration (0.675 µM) was significantly lower than the one at which OA had a toxic effect on the cell. However, the theoretically calculated concentration of OA inside the cell (about 200 μM) was found to be high enough to lead to cell necrosis. To test the hypothesis that OA might cause SICD, we used a ΔACP1 strain incapable of synthesizing OA in the yeast mitochondrial Fatty Acid Synthesis type II system (FAS-II). The deletion of the ACP1 gene did not affect the OA content in the medium. But, on the other hand, OA is a precursor of lipoic acid, which has antioxidant properties. However, strains with deleted genes for lipoic acid biosynthesis from OA (ΔPPT2, ΔLIP2, ΔLIP5, and ΔSGV3) showed no change in ROS and SICD levels. Thus, lipoic acid synthesized in FAS-II does not protect cells from ROS accumulated during SICD. We conclude that OA synthesized in the mitochondrial FAS-II system and its derivative lipoic acid are not involved in SICD in yeast S. cerevisiae. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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13 pages, 1612 KiB

Open AccessArticle

The Effect of Antibiotic Treatment and Gene Expression of Mex B Efflux Transporters on the Resistance in Pseudomonas Aeruginosa Biofilms

by Evan Kello, Rochelle Greenberg, Weiqi Li, Shaya Polansky, Roberto Maldonado, Yakov Peter and Paramita Basu

Appl. Microbiol. 2023, 3(3), 709-721; https://doi.org/10.3390/applmicrobiol3030049 - 6 Jul 2023

Viewed by 2540

Abstract

Pseudomonas aeruginosa, a Gram-negative, rod-shaped bacterium, holds a prominent position as an antibiotic-resistant priority pathogen, according to the World Health Organization. Particularly prevalent in healthcare settings, this bacterium acts as an opportunistic pathogen, causing nosocomial infections. The significant antibiotic resistance observed in [...] Read more.

Pseudomonas aeruginosa, a Gram-negative, rod-shaped bacterium, holds a prominent position as an antibiotic-resistant priority pathogen, according to the World Health Organization. Particularly prevalent in healthcare settings, this bacterium acts as an opportunistic pathogen, causing nosocomial infections. The significant antibiotic resistance observed in P. aeruginosa is multifactorial, encompassing intrinsic, acquired, and adaptive resistance mechanisms. The present study aims to explore specific RND-type efflux pump genes implicated in the acquisition of antibiotic resistances during the transition of P. aeruginosa PAO1 from its planktonic state to the more formidable and resistant biofilm form. This investigation is centered on MexB, a prominent RND-type efflux pump in P. aeruginosa. Our research is focused on MexB, a highly significant component characterized by its broad substrate specificity, primary function as the primary efflux pump, substantial expression levels, and notable clinical implications. Considering MexB’s critical role in expelling various clinically relevant antimicrobial agents and its significant contribution to multidrug resistance, our study aims to evaluate the comparative efficacy of three distinct antibiotic categories, namely, Ofloxacin (OFX), Tobramycin (TOB), and Ceftazidime (CAZ), in regulating the expression levels of identified multidrug efflux pump genes associated with the biofilm’s ability to remove antibiotics from bacterial cells. Expression analysis of efflux transporter genes in P. aeruginosa was performed by isolating total RNA from both planktonic and biofilm samples, both untreated and treated with Tobramycin (TOB), Ofloxacin (OFX), and Ceftazidime (CAZ). Real-time quantitative reverse transcriptase PCR was employed to investigate changes in the expression levels of MexA, MexB, MexX, MexY, OprM, and RPSL genes in the collected samples. In the absence of antibiotic treatment, the MexB efflux pump gene exhibited higher expression compared to other efflux pump genes in the biofilm’s state, supporting its involvement in multidrug resistance when active. To further explore the role of the MexB gene in antibiotic resistance, P. aeruginosa was cultured in both planktonic and biofilm forms while simultaneously treating them with TOB, OFX, and CAZ. Among the three antibiotics employed, OFX demonstrated superior efficacy in inhibiting the growth of biofilms by downregulating the expression of the Mex B efflux pump gene in P. aeruginosa, thereby enhancing its susceptibility to OFX. TOB yielded comparable outcomes to OFX, albeit with a slightly lesser extent of Mex B expression reduction. Conversely, CAZ exhibited ineffectiveness in reducing MexB gene expression in both biofilm and planktonic forms of the organism, rendering it incapable of eradicating the pathogen. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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11 pages, 1573 KiB

Open AccessArticle

Translation Enhancement by a Short Nucleotide Insertion at 5′UTR: Application to an In Vitro Cell-Free System and a Photosynthetic Bacterium

by Tomo Kondo and Takayuki Shimizu

Appl. Microbiol. 2023, 3(3), 687-697; https://doi.org/10.3390/applmicrobiol3030047 - 2 Jul 2023

Cited by 2 | Viewed by 2235

Abstract

We previously showed that insertion of Dictyostelium gene sequences, such as mlcR, upstream of the Shine–Dalgarno sequence, positively impacts downstream gene expression in Escherichia coli. However, the mechanism by which protein production is facilitated and its applicability to other bacteria remains [...] Read more.

We previously showed that insertion of Dictyostelium gene sequences, such as mlcR, upstream of the Shine–Dalgarno sequence, positively impacts downstream gene expression in Escherichia coli. However, the mechanism by which protein production is facilitated and its applicability to other bacteria remains unknown. In this study, a translation-enhancing effect, associated with this system, on the mRNA amount and property as well as the versatility of the method has been demonstrated. The insertion of mlcR-terminal 25 bp (mlcR25) stabilized the mRNAs and led to increased mRNA levels in E. coli. In the in vitro translation system, a four-fold enhancement was observed when DNA was used as the template, and a three-fold enhancement was observed when mRNA was used as the template. This suggests that mlcR25 has an effect on the facilitation of the interaction between mRNA and ribosome. Furthermore, when this enhancement system was adapted to the photosynthetic bacterium Rhodobacter capsulatus, a more than six-fold increase in translation was observed. Thus, we propose that enhanced translation by mlcR25 is mediated by mechanisms that help the translation machinery to work efficiently, and the system can be applied to bacteria other than E. coli. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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9 pages, 1917 KiB

Open AccessCommunication

Pterostilbene, a Natural Methoxylated Analog of Resveratrol, Exhibits Antifungal Activity Induced by Reactive Oxygen Species Production and Plasma Membrane Injury

by Naoko Mizuhara, Moe Inoue, Hideki Kurotaki, Kazuyori Matsumoto, Akira Ogita and Ken-Ichi Fujita

Appl. Microbiol. 2023, 3(3), 666-674; https://doi.org/10.3390/applmicrobiol3030045 - 28 Jun 2023

Cited by 1 | Viewed by 1344

Abstract

Pterostilbene has been shown to exhibit antifungal activities. However, the detailed action mechanism is unknown. Here, we analyzed the antifungal mechanism of pterostilbene against Saccharomyces cerevisiae. The minimum growth inhibitory and fungicidal concentrations of pterostilbene were 120 and 240 µM in a [...] Read more.

Pterostilbene has been shown to exhibit antifungal activities. However, the detailed action mechanism is unknown. Here, we analyzed the antifungal mechanism of pterostilbene against Saccharomyces cerevisiae. The minimum growth inhibitory and fungicidal concentrations of pterostilbene were 120 and 240 µM in a YPD medium, respectively. Although pterostilbene produced reactive oxygen species (ROS), resveratrol did not. This effect was maximized at 120 µM. Furthermore, α-tocopherol acetate inhibited ROS production and reversed pterostilbene-induced growth inhibition. At 240 µM, pterostilbene showed fungicidal effects accompanied by the leakage of intracellular potassium ions, suggesting the involvement of membrane injury in addition to oxidative stress in fungicidal action. Nevertheless, the antioxidants gradually reversed the decrease in cell viability caused by pterostilbene, suggesting that ROS production mainly contributed to the lethal effect. As Pterocarpus marsupium extract, mainly containing pterostilbene, is used as a traditional medicine, pterostilbene has great potential for development as a preservative with fewer adverse effects. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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18 pages, 1086 KiB

Open AccessArticle

Antioxidant, Antimicrobial and Cosmeceutical Potential of Wild Mushroom Extracts

by Tânia Martins, Liliana Machado-Carvalho, Alfredo Aires, Maria José Saavedra and Guilhermina Marques

Appl. Microbiol. 2023, 3(2), 562-579; https://doi.org/10.3390/applmicrobiol3020040 - 15 Jun 2023

Cited by 2 | Viewed by 2318

Abstract

Macrofungi have been previously studied for their nutritional value and medicinal properties. However, despite wild mushrooms being a great source of beneficial bioactive compounds, the literature exploring their biotechnological application as nutraceuticals, cosmeceuticals and nutricosmetics is scarce. In this work, the species Butyriboletus [...] Read more.

Macrofungi have been previously studied for their nutritional value and medicinal properties. However, despite wild mushrooms being a great source of beneficial bioactive compounds, the literature exploring their biotechnological application as nutraceuticals, cosmeceuticals and nutricosmetics is scarce. In this work, the species Butyriboletus regius, Ganoderma lucidum, Inonotus hispidus, Lanmaoa fragrans, Pisolithus tinctorius, Suillellus luridus, Suillellus mendax and Xerocomus subtomentosus were characterized according to their phenolic composition, antioxidant capacity, antimicrobial activity and cosmeceutical potential. For that purpose, dried and ground mushrooms were extracted with ethanol (40% v/v) using ultrasound-assisted extraction. Of the eight mushrooms analyzed, I. hispidus and P. tinctorius stood out for their high content of phenolic compounds, high antioxidant capacity and anti-hyaluronidase activity. Regarding antimicrobial activity, both mushrooms showed good inhibition of bacterial growth and bactericidal activity, especially on Gram-positive bacteria; however, L. fragans obtained the best results. Cream formulations with I. hispidus and P. tinctorius extracts in their composition improved their antioxidant activity. These results indicate that I. hispidus and P. tinctorius can be proposed as a new potential source of natural compounds with application in the cosmetic industry. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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17 pages, 3978 KiB

Open AccessArticle

Probiotic Lactic Acid Bacteria for Vaginal Application. Optimization of Biomass Production and Freeze-Drying Conditions

by Antonella Marchesi and María Elena Fátima Nader-Macías

Appl. Microbiol. 2023, 3(2), 519-535; https://doi.org/10.3390/applmicrobiol3020037 - 2 Jun 2023

Cited by 1 | Viewed by 2377

Abstract

Probiotic formula for the vaginal tract must contain high numbers of viable beneficial bacteria that maintain their characteristics during the production and further storage, in order to exert the claimed probiotic effect. Four probiotic strains—Lactobacillus gasseri CRL1320, Limosilactobacillus reuteri CRL1324, Ligilactobacillus salivarius [...] Read more.

Probiotic formula for the vaginal tract must contain high numbers of viable beneficial bacteria that maintain their characteristics during the production and further storage, in order to exert the claimed probiotic effect. Four probiotic strains—Lactobacillus gasseri CRL1320, Limosilactobacillus reuteri CRL1324, Ligilactobacillus salivarius CRL1328 and Lacticaseibacillus rhamnosus CRL1332—originally isolated from vagina of healthy women exhibiting beneficial properties were evaluated. Therefore, the optimization of growth parameters and dry biomass production with high viability while preserving probiotic features of strains is a great challenge. Different growth conditions in MRS medium were set up in a laboratory bioreactor; two initial pH and agitation were recorded speeds during static or controlled fermentations. Production conditions of 37 °C with controlled pH 6.5 and 5.5-MRS with 150 and 75 rpm stirring speeds were used for CRL1329 and CRL1332 strains, respectively, while static and free pH MRS for CRL1324 and CRL1328 probiotics allowed us to obtain maximal cell viability counts. However, during 12 h of fermentation, biomass yields of 19.3, 16.2 and 15.2 g/L were achieved when CRL1329, CRL1328 and CRL1324 probiotic strains were grown in static and free pH MRS. The highest biomass yield for CRL1332 strain was produced under controlled MRS-initial pH 6.5 and 75 rpm fermentation conditions. To preserve probiotic high biomass viability, freeze-drying was carried out in the presence of different cryoprotective agents. Thus, the highest viable numbers (10.9–11.8 log CFU/g) with survival rates between 91.3 and 95.6% were attained in the presence of 10% trehalose (L. reuteri and L. salivarius), lactose (L. rhammosus) and lactose + trehalose + sucrose mix (L. gasseri). When stability during post-freeze-drying storage was evaluated, probiotic strains showed a remarkably higher viability recovery when stored at 4 °C than at 25 °C for 12 and 3 months, respectively. In addition, surface characteristics of vaginal probiotics were affected to different extents during storage depending on the strain, protective agent and storage time/temperature. Critical factors for growth conditions, drying process and storage stability of probiotic lactobacilli strains were optimized in view to preserve cell high viability and surface features for the design of vaginal probiotic formula. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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15 pages, 2167 KiB

Open AccessArticle

Spatial Variation of Tetracycline-Resistant E. coli and Relationships with Water Quality Variables in Irrigation Water: A Pilot Study

by Matthew Stocker, Jaclyn Smith and Yakov Pachepsky

Appl. Microbiol. 2023, 3(2), 504-518; https://doi.org/10.3390/applmicrobiol3020036 - 30 May 2023

Cited by 3 | Viewed by 1838

Abstract

Irrigation waters may facilitate the spread of antibiotic-resistant bacteria or genes to humans and animals. Monitoring of resistance in irrigated waters has become common; however, many studies do not incorporate a spatial component into sampling designs. The objective of this work was to [...] Read more.

Irrigation waters may facilitate the spread of antibiotic-resistant bacteria or genes to humans and animals. Monitoring of resistance in irrigated waters has become common; however, many studies do not incorporate a spatial component into sampling designs. The objective of this work was to assess spatiotemporal variations in tetracycline-resistant E. coli in an irrigation pond. Water samples were collected at 10 locations and two different water depths, and in situ and laboratory water quality measurements were performed. The percentage of E. coli resistant to the low (4 μg mL⁻¹) and high (16 μg mL⁻¹) tetracycline doses varied by date and location but were observed to be as high as 12.7% and 6.3% of the total population throughout the study, respectively. While significant differences were not observed between resistance levels measured at different depths, on one date resistant E. coli were only detected in samples collected at depth. Nitrate, fluorescent dissolved organic matter, and dissolved oxygen concentrations were found to be the leading control variables for the percentage of resistant E. coli. This work demonstrates that there may be substantial spatial variability in concentrations of antibiotic-resistant E. coli in irrigation ponds which should be accounted for in the design of monitoring programs. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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8 pages, 1756 KiB

Open AccessCommunication

Skin Microbiota of Salmonids: A Procedure to Examine Active Bacterial Populations Using an RNA-Based Approach

by Alda Pardo, Alejandro Villasante and Jaime Romero

Appl. Microbiol. 2023, 3(2), 485-492; https://doi.org/10.3390/applmicrobiol3020034 - 18 May 2023

Cited by 1 | Viewed by 1678

Abstract

Fish microbiota studies have mostly addressed intestinal bacterial communities because of their role in fish physiology; however, the skin microbiota has been studied less despite its role as the first pathogen barrier in the host. DNA-based molecular techniques have contributed to improving our [...] Read more.

Fish microbiota studies have mostly addressed intestinal bacterial communities because of their role in fish physiology; however, the skin microbiota has been studied less despite its role as the first pathogen barrier in the host. DNA-based molecular techniques have contributed to improving our understanding of the skin microbiota, but this approach faces challenges, such as the low count of bacteria in healthy fish skin. To overcome this limitation, an RNA-based approach was developed to study the skin microbiota in salmonids, including tissue sampling, RNA extraction, and downstream procedures to obtain PCR amplicons for next-generation sequencing. The protocol originated in this work overcomes the limitations of low bacterial counts and is useful for describing active microbiota in fish skin. The application of the protocol to salmonids reared in both an experimental setting and on a farm revealed that the trout skin microbiota was dominated by bacteria from the phylum Proteobacteria (>65%). At the genus level, Piscirickettsia (46%) was highlighted as the most abundant in the experimental unit samples; in contrast, Pseudoalteromonas (26%), followed by Escherichia_Shigella (~25%), was the most abundant in farmed trout. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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17 pages, 2254 KiB

Open AccessArticle

Limnospira indica PCC8005 and Lacticaseibacillus rhamnosus GG Mixed Dietary Combination Reduces Pelvic Irradiation-Induced Symptoms in Mice

by Sarah-Renée Gholam, Charlotte Segers, Mohamed Mysara, Amelie Coolkens, Sarah Baatout, Natalie Leys and Felice Mastroleo

Appl. Microbiol. 2023, 3(2), 448-464; https://doi.org/10.3390/applmicrobiol3020031 - 11 May 2023

Cited by 1 | Viewed by 1743

Abstract

Throughout their cancer treatments, around half of all patients will undergo irradiation that is accompanied by several side effects reducing their quality of life and leading to the interruption or extension of their treatment course. Pelvic irradiation leads to the triggering of mucositis [...] Read more.

Throughout their cancer treatments, around half of all patients will undergo irradiation that is accompanied by several side effects reducing their quality of life and leading to the interruption or extension of their treatment course. Pelvic irradiation leads to the triggering of mucositis and dysbiosis, further impairing the daily life of the patients. In this work, we address the ability of Limnospira indica strain PCC 8005 and Lacticaseibacillus rhamnosus GG ATCC 53103 in alleviating the above-mentioned side effects triggered by the local pelvic irradiation of 12 Gy in a mouse model. We found that the combinatorial administration of these food supplements was able to confer partial tight junction protection while the bacterial translocation towards the mesenteric lymph nodes was found to be identical between the saline sham-irradiated and supplemented irradiated group. Furthermore, the supplemented group did not present a significant shift in microbial composition following pelvic irradiation, indicating that the bacterial formulation was able to mitigate the dysbiosis induced by the latter treatment, as observed in the saline irradiated group. These very promising results will be further completed by investigating the mode of action and/or active molecules mediating the beneficial effects of both L. indica PCC 8005 and L. rhamnosus GG. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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12 pages, 2424 KiB

Open AccessArticle

Survival Time, Mortality Rate, and Feeding Damage of Adult Myllocerus undecimpustulatus undatus (Coleoptera: Curculionidae) Exposed to Biopesticides in Laboratory Bioassays

by Anita S. Neal, Pasco B. Avery and Ronald D. Cave

Appl. Microbiol. 2023, 3(2), 388-399; https://doi.org/10.3390/applmicrobiol3020027 - 25 Apr 2023

Viewed by 1781

Abstract

Survival time, percentage mortality, and feeding behavior were evaluated for adults of the weevil Myllocerus undecimpustulatus undatus Marshall (Coleoptera: Curculionidae) exposed to biopesticides by using a Petri dish plant-based bioassay system. Treatments consisted of three registered entomopathogenic fungal formulations (BotaniGard ES, PFR-97 20% [...] Read more.

Survival time, percentage mortality, and feeding behavior were evaluated for adults of the weevil Myllocerus undecimpustulatus undatus Marshall (Coleoptera: Curculionidae) exposed to biopesticides by using a Petri dish plant-based bioassay system. Treatments consisted of three registered entomopathogenic fungal formulations (BotaniGard ES, PFR-97 20% WDG, and Met52 EC) and three biochemical formulations (AzaMax, Entrust, and PyGanic EC); a synthetic chemical insecticide (Sevin SL) and distilled water served as control treatments. Thirty adult M. undecimpustulatus undatus (ten per bioassay cage replicate, three replicates per treatment) were given cocoplum leaves sprayed to the point of runoff with a treatment. Survivorship of weevils was checked daily for 15 days. Five trials (15 total replicates per treatment) were performed. Survival times of weevils in all product treatments were shorter than those of weevils in the water control treatment. Percentages of beetle mortality in the Entrust and BotaniGard treatments were about two-fold higher than in the other treatments. Mean percentages of mycosis for beetles in the BotaniGard, PFR-97, and Met 52 treatments were 90%, 8%, and 5%, respectively. Weevils that consumed BotaniGard-treated leaves caused significantly more leaf damage than weevils that consumed leaves with PFR-97 or Met52. Weevils on leaves treated with Entrust, PyGanic, AzaMax, and Sevin consumed significantly less than those in the fungal and water only treatments. The high mortality rates caused by Entrust and BotaniGard suggest that populations of adult M. undecimpustulatus undatus might be well-managed using these two commercially available biopesticides. Additional testing is needed in the field to corroborate our results obtained under controlled laboratory conditions. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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13 pages, 4601 KiB

Open AccessArticle

Construction of an Escherichia coli Strain Capable of Utilizing Steamed Rice as the Sole Carbon and Energy Source by Extracellular Expression of Amylase and Its Use for the Production of Putrescine

by Hideyuki Suzuki, Nana Iwamoto and Manami Nishimura

Appl. Microbiol. 2023, 3(2), 375-387; https://doi.org/10.3390/applmicrobiol3020026 - 24 Apr 2023

Cited by 1 | Viewed by 4323

Abstract

The amyE gene encoding α-amylase from Bacillus subtilis 168 was fused to several genes, the products of which are membrane proteins to express AmyE extracellularly. Genes of CapA, a subunit of the capsular poly-γ-glutamate synthetase of Bacillus subtilis subsp. natto; YiaT^R232 [...] Read more.

The amyE gene encoding α-amylase from Bacillus subtilis 168 was fused to several genes, the products of which are membrane proteins to express AmyE extracellularly. Genes of CapA, a subunit of the capsular poly-γ-glutamate synthetase of Bacillus subtilis subsp. natto; YiaT^R232, the first 232 residues of YiaT, an outer membrane protein of Escherichia coli K-12; and PgsA, cytidine 5′-diphosphate-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase of B. subtilis subsp. natto, were used. The Escherichia coli strain harboring the plasmid carrying the pgsA-amyE fusion expressed a very high level of amylase not only on the extracellular surface of the cells but also in the medium and the intracellular space and solubilized steamed rice in two days. The N-terminal amino acid sequence of the amylase purified from the culture medium (Ser-Ala-Glu-Thr-Ala) indicated that it was cleaved at the signal peptide cleavage site of AmyE. The strain SH2204, transformed with pKN11 carrying speA (arginine decarboxylase gene), speB (agmatinase gene) and argA^{ATG Y19C} (N-acetylglutamate synthase gene) and pMAN63 carrying pgsA-amyE produced 1.2 mM putrescine from 5 mM arginine by adding 0.5 mM IPTG in eight days. Discarding steamed rice is not only a food loss, but also a waste of renewable, biogenerated resources due to the burning of it with petroleum, increasing carbon dioxide in the atmosphere. The E. coli strain developed in this study can help solve this problem because it can produce an important chemical using steamed rice as the sole carbon and energy source. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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9 pages, 1709 KiB

Open AccessCommunication

The Growth Curve of Microbial Cultures: A Model for a Visionary Reappraisal

by Alberto Schiraldi

Appl. Microbiol. 2023, 3(1), 288-296; https://doi.org/10.3390/applmicrobiol3010020 - 9 Mar 2023

Cited by 2 | Viewed by 3207

Abstract

A phenomenological model of planktonic microbial cultures, reported in previous papers, suggests that the whole growth progress seems planned by the microbial population since a pre-growth latency phase, during which the population level remains at its starting level. This model is in line [...] Read more.

A phenomenological model of planktonic microbial cultures, reported in previous papers, suggests that the whole growth progress seems planned by the microbial population since a pre-growth latency phase, during which the population level remains at its starting level. This model is in line with recent suggestions about the behavior of complex systems, as long as it allows for the gathering of the growth trends of a number of real batch cultures in a single master plot of reduced variables, in spite of their metabolic and physiological differences. One important issue of the model concerns the origin of the time scale for the microbes that can differ from that for the observer. The present paper reports some consequences of the model in view of its potential use in predictive microbiology and proposes an extension to the steady and decay phases of the culture evolution suggesting that, consistent with the assumptions about the growth phase, the decay occurs by a scan of the cell generation steps. This view leads to the conclusion that the steady phase between growth and decay trends actually corresponds to the loss of the oldest cell generations, which represents minor fractions of the microbial population. Such early decay is almost undetectable in a log scale, looking like a steady phase. To account for cases that show a broad maximum instead of an intermediate steady trend, a single continuous function, still related to the model, can describe the whole growth and decay trend of the microbial culture. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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13 pages, 343 KiB

Open AccessArticle

Hydrolytic Enzyme Production and Susceptibility to Antifungal Compounds of Opportunistic Candida parapsilosis Strains Isolated from Cucurbitaceae and Rosaceae Fruits

by Anna Glushakova, Aleksey Kachalkin and Evgenia Rodionova

Appl. Microbiol. 2023, 3(1), 199-211; https://doi.org/10.3390/applmicrobiol3010014 - 28 Jan 2023

Cited by 4 | Viewed by 2456

Abstract

Endophytic yeast species were studied in the internal tissues of ripe cultivated vegetables and fruits. A total of 19 yeast species, 11 ascomycete species, and 8 basidiomycete species were observed in the internal tissues of all fruits examined. The opportunistic yeast Candida parapsilosis [...] Read more.

Endophytic yeast species were studied in the internal tissues of ripe cultivated vegetables and fruits. A total of 19 yeast species, 11 ascomycete species, and 8 basidiomycete species were observed in the internal tissues of all fruits examined. The opportunistic yeast Candida parapsilosis was present in all plants studied. Several virulence factors (production of hydrolytic enzymes and sensitivity to antifungal agents) were examined in all 107 isolates of C. parapsilosis from the internal tissues of fruits. The most virulent isolates were found in vegetables. C. parapsilosis is widespread in nature and is often isolated from a variety of non-human sources. It is frequently involved in invasive infections that seriously affect human health. This species poses a high risk to immunocompromised individuals, such as HIV patients and surgical patients or children whose immune systems are not sufficiently mature. Since virulent isolates of Candida parapsilosis have been found in vegetables and fruits; their raw consumption may not be safe. Finally, we emphasize the importance of ongoing phenotypic and genetic studies of endophytic isolates of Candida parapsilosis and their comparison with clinical isolates. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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11 pages, 3502 KiB

Open AccessArticle

The Effects of Atrazine, Diuron, Fluazifop-P-butyl, Haloxyfop-P-methyl, and Pendimethalin on Soil Microbial Activity and Diversity

by Paul G. Dennis, Tegan Kukulies, Christian Forstner, Fabien Plisson, Geoff Eaglesham and Anthony B. Pattison

Appl. Microbiol. 2023, 3(1), 79-89; https://doi.org/10.3390/applmicrobiol3010007 - 16 Jan 2023

Cited by 5 | Viewed by 2560

Abstract

Understanding the impacts of herbicides on soil microbial communities is important, as these organisms mediate a wide range of ecosystem services. Here, we investigated whether the diversity and function of soil microbial communities were significantly influenced by one-off applications of atrazine, diuron, fluazifop- [...] Read more.

Understanding the impacts of herbicides on soil microbial communities is important, as these organisms mediate a wide range of ecosystem services. Here, we investigated whether the diversity and function of soil microbial communities were significantly influenced by one-off applications of atrazine, diuron, fluazifop-P-butyl, haloxyfop-P-methyl and pendimethalin as pure compounds at their recommended doses over multiple time points (1, 3, 7, 14, 30 and 60 days). Phylogenetic marker gene sequencing revealed that none of the herbicides influenced the numbers of bacterial and archaeal taxa or the evenness of their abundances. Similarly, none of the herbicides influenced the composition of bacterial and archaeal communities, except for diuron, fluazifop-P-methyl and pendimethalin, which were associated with larger relative abundances of a small number of OTUs on day 30 only. Functionally, none of the herbicides significantly influenced fluorescein diacetate hydrolysis (FDA) and beta-glucosidase activities or the induced respiratory responses of soil microbial communities to a range of substrates. These data indicate that the active herbicide ingredients tested may have minimal non-target effects when applied once at their recommended dose. Given their frequent use, it is important to next consider whether these herbicides have more pronounced effects at higher doses and application frequencies. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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12 pages, 2090 KiB

Open AccessArticle

Whole Genome Sequencing Evidences High Rates of Relapse in Clostridioides difficile Infection Caused by the Epidemic Ribotype 106

by Loreto Suárez-Bode, Carla López-Causapé, Ricardo M. Arcay, Antonio Oliver and Ana Mena

Appl. Microbiol. 2023, 3(1), 64-75; https://doi.org/10.3390/applmicrobiol3010005 - 14 Jan 2023

Cited by 1 | Viewed by 2136

Abstract

An increasing prevalence and spread of Clostridioides difficile infection (CDI) caused by DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or by the higher resistance rates observed for some strains. Based on the results of our previous [...] Read more.

An increasing prevalence and spread of Clostridioides difficile infection (CDI) caused by DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or by the higher resistance rates observed for some strains. Based on the results of our previous study where RT106 showed higher recurrence rates than other relevant ribotypes, a genetic analysis by whole-genome sequencing (WGS) of primary and recurrent RT106 isolates from ten patients was performed to determine whether the higher rate of recurrence associated with RT106 is due to relapses, caused by the same strain, or reinfections, caused by different strains. MLST profiles, resistance mutations, and phylogenetic relatedness were determined by comparative single nucleotide variant (SNV) analysis. All isolates were classified as ST42, and those belonging to the same patient were isogenic, with one exception; strains belonging to different patients were not with two exceptions, pointing to putative transmission events. Phylogenetic analysis also suggested the presence of similar local epidemic lineages associated with moxifloxacin resistance, except for one patient whose isolates clustered with different nonresistant US strains. Our results show that recurrent CDIs caused by RT06/ST42 are mainly due to relapses caused by the primary strains, showing the higher capacity of RT106/ST42 to persist and cause recurrences as compared to other ribotypes. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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13 pages, 793 KiB

Open AccessArticle

Selected Antimicrobial Peptides Inhibit In Vitro Growth of Campylobacter spp.

by John Eric Line, Bruce S. Seal and Johnna K. Garrish

Appl. Microbiol. 2022, 2(4), 688-700; https://doi.org/10.3390/applmicrobiol2040053 - 21 Sep 2022

Cited by 1 | Viewed by 2262

Abstract

Campylobacter is a major cause of acute human diarrheal illness. Broiler chickens constitute a primary reservoir for C. jejuni leading to human infection. Consequently, there is a need for developing novel intervention methods. Antimicrobial peptides (AMP) are small proteins which have evolved in [...] Read more.

Campylobacter is a major cause of acute human diarrheal illness. Broiler chickens constitute a primary reservoir for C. jejuni leading to human infection. Consequently, there is a need for developing novel intervention methods. Antimicrobial peptides (AMP) are small proteins which have evolved in most lifeforms to provide defense against microbial infections. To date, over 3000 AMP have been discovered; however, few of them have been analyzed specifically for ability to kill campylobacters. We selected and evaluated a set of 11 unique chemically synthesized AMP for ability to inhibit growth of C. jejuni. Six of the AMP we tested produced zones of inhibition on lawns of C. jejuni. These AMP included: NRC-13, RL-37, Temporin L, Cecropin–Magainin, Dermaseptin, and C₁₂K-2β₁₂. In addition, MIC were determined for Cecropin–Magainin, RL-37 and C₁₂K-2β₁₂ against 15 isolates of Campylobacter representing the three most common pathogenic strains. MIC for campylobacters were approximately 3.1 µg/mL for AMP RL-37 and C₁₂K-2β₁₂. MIC were slightly higher for the Cecropin–Magainin AMP in the range of 12.5 to 100 µg/mL. These AMP are attractive subjects for future study and potential in vivo delivery to poultry to reduce Campylobacter spp. populations. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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Review

Jump to: Research, Other

21 pages, 2018 KiB

Open AccessReview

Yeast and Virus-like Particles: A Perfect or Imperfect Couple?

by Sara Brachelente, Alvaro Galli and Tiziana Cervelli

Appl. Microbiol. 2023, 3(3), 805-825; https://doi.org/10.3390/applmicrobiol3030056 - 14 Jul 2023

Cited by 1 | Viewed by 4138

Abstract

Virus-like particles (VLPs) comprise viral structural proteins that self-assemble to form a particle similar to the native virus capsid. Since their discovery, they have been employed mainly as vaccines to prevent viral infection because they can elicit an immune response. Besides their use [...] Read more.

Virus-like particles (VLPs) comprise viral structural proteins that self-assemble to form a particle similar to the native virus capsid. Since their discovery, they have been employed mainly as vaccines to prevent viral infection because they can elicit an immune response. Besides their use as vaccines, their application in cancer prevention and drug delivery is under intensive investigation. They can be produced in different systems such as bacteria, mammalian, plant, insect, and yeast cells. The main hurdle for their use is establishing a platform for production because many variables need to be considered. First, VLPs must be effective in the action for which they are constructed, depending on the nature of the VLPs. Second, the production platform must be suitable for safe and high-scale production. Yeast has been shown to be a valuable tool in VLP production, as it is able to express heterologous proteins efficiently and its manipulation is cheap and easy. Several species have been employed for this purpose. In the present review, we analyze the features of different yeast species and how they have been used to produce VLPs. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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19 pages, 801 KiB

Open AccessReview

Perspectives on Using a Competitive Exclusion Approach to Control Listeria monocytogenes in Biological Soil Amendments of Animal Origin (BSAAO): A Review

by Hongye Wang, Jinge Huang and Xiuping Jiang

Appl. Microbiol. 2023, 3(3), 786-804; https://doi.org/10.3390/applmicrobiol3030055 - 14 Jul 2023

Viewed by 1549

Abstract

Biological soil amendments of animal origin (BSAAO), such as animal waste or animal-waste-based composts, may contain foodborne pathogens such as Listeria monocytogenes. Due to the ubiquitous nature of Listeria, it is essential to understand the behavior of L. monocytogenes in BSAAO [...] Read more.

Biological soil amendments of animal origin (BSAAO), such as animal waste or animal-waste-based composts, may contain foodborne pathogens such as Listeria monocytogenes. Due to the ubiquitous nature of Listeria, it is essential to understand the behavior of L. monocytogenes in BSAAO in order to develop preharvest prevention strategies to reduce pathogen contamination. As biological control agents, competitive exclusion (CE) microorganisms have been widely utilized in agriculture to control plant- or foodborne pathogens. Due to the diverse microbial community, animal wastes and composts are the potential sources for isolating CE strains for pathogen control. To explore the potential of using CE to control L. monocytogenes in BSAAO, we thoroughly reviewed the studies on the fate of L. monocytogenes in the agriculture field, and in the isolation and identification of CE from different matrices, and the applications of CE as a biological control method. Future studies using a next-generation sequencing approach to identify and characterize CE strains in complex microbial communities can provide a comprehensive picture of the microbial interactions between invading pathogens and the indigenous microbiota in BSAAO. This comprehensive review will provide insight into the development of effective biological control measures for preventing L. monocytogenes contamination in the agricultural field and enhancing food safety. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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17 pages, 1258 KiB

Open AccessReview

Fungal Pigments: Their Diversity, Chemistry, Food and Non-Food Applications

by Waill Elkhateeb and Ghoson Daba

Appl. Microbiol. 2023, 3(3), 735-751; https://doi.org/10.3390/applmicrobiol3030051 - 12 Jul 2023

Cited by 5 | Viewed by 4635

Abstract

Colorants have many applications in food, cosmetics, pharmaceutics, textile, paints, plastics, paper, ink and photographic industries. Colorants are classified according to their solubility into dyes and pigments. Those of natural origin have many advantages over synthetic ones, as natural colorants usually do not [...] Read more.

Colorants have many applications in food, cosmetics, pharmaceutics, textile, paints, plastics, paper, ink and photographic industries. Colorants are classified according to their solubility into dyes and pigments. Those of natural origin have many advantages over synthetic ones, as natural colorants usually do not induce allergies or other health problems. In addition, their consumption in the food and drug industries is fortified with nutritional and health benefits as the majority of them possess antioxidant activity or can be used to produce some vitamins. Plants, animals, insects and microorganisms are rich sources of colorants. However, microbial pigments are favored over other natural pigments due to their higher yield, stability, economical production. Therefore, we focus in this review on fungal pigments, the history of their use, their chemistry and their applications in food and non-food fields. Additionally, the ability of the fungal genus, Epicoccum, to produce pigments is discussed. Moreover, the challenges and future prospects concerning fungal pigment production are highlighted in detail. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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24 pages, 27286 KiB

Open AccessReview

β-Lactams and Ureas as Cross Inhibitors of Prokaryotic Systems

by Monika I. Konaklieva and Balbina J. Plotkin

Appl. Microbiol. 2023, 3(3), 605-628; https://doi.org/10.3390/applmicrobiol3030043 - 25 Jun 2023

Viewed by 1436

Abstract

β-Lactams in the last thirty years have been viewed as universal acylating agents of serine and cysteine enzymes of both prokaryotic and eukaryotic systems. More recently, their use has been propelled by the COVID-19 pandemic, thus broadening their application as inhibitors of viral [...] Read more.

β-Lactams in the last thirty years have been viewed as universal acylating agents of serine and cysteine enzymes of both prokaryotic and eukaryotic systems. More recently, their use has been propelled by the COVID-19 pandemic, thus broadening their application as inhibitors of viral enzymes. The urea-based drugs have been extensively studied as inhibitors of the aforementioned enzymes. The focus of this review is the last decade’s drug discovery strategies, as well as new strategies that show utility in the expansion of β-lactams and ureas in the development of new antimicrobial and antiviral drugs. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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13 pages, 3608 KiB

Open AccessReview

Asteltoxins: Synthesis and Biological Studies

by Eslam R. El-Sawy, Gilbert Kirsch and Mohamed S. Abdel-Aziz

Appl. Microbiol. 2023, 3(3), 592-604; https://doi.org/10.3390/applmicrobiol3030042 - 21 Jun 2023

Cited by 1 | Viewed by 1728

Abstract

Asteltoxins belong to a group of polyene pyrone mycotoxins that are known to be potent inhibitors of mitochondrial ATP synthesis and ATP hydrolysis. Asteltoxin A was first isolated from the toxic maize cultures of Aspergillus stellatus. Several attempts have been made to [...] Read more.

Asteltoxins belong to a group of polyene pyrone mycotoxins that are known to be potent inhibitors of mitochondrial ATP synthesis and ATP hydrolysis. Asteltoxin A was first isolated from the toxic maize cultures of Aspergillus stellatus. Several attempts have been made to synthesize asteltoxin A, starting with the synthesis of a bis(tetrahydrofuran) moiety that has been demonstrated previously in biosynthetic studies. This review highlights the fungal sources of asteltoxins, similar asteltoxins, biosynthetic pathways, their synthetic trials, and their biological activities. This review is the first of its kind covering the periods from 1979 to 2023. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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11 pages, 483 KiB

Open AccessReview

Psychobiotics as an Intervention in the Treatment of Irritable Bowel Syndrome: A Systematic Review

by Weronika Gwioździk, Paulina Helisz, Mateusz Grajek and Karolina Krupa-Kotara

Appl. Microbiol. 2023, 3(2), 465-475; https://doi.org/10.3390/applmicrobiol3020032 - 15 May 2023

Cited by 3 | Viewed by 2520

Abstract

Today’s perceived excess of work versus rest and excessive stressful situations are one of the potential factors for an increasing number of gastrointestinal disorders. Although the prevalence of irritable bowel syndrome (IBS) varies widely, it is assumed that up to 15% of the [...] Read more.

Today’s perceived excess of work versus rest and excessive stressful situations are one of the potential factors for an increasing number of gastrointestinal disorders. Although the prevalence of irritable bowel syndrome (IBS) varies widely, it is assumed that up to 15% of the general population may be affected. Symptoms resulting from IBS take the form of pain, including difficulties with bowel movements, bloating, and a feeling of overflowing in the intestines. These symptoms have a negative impact on patients’ quality of life, so any possible intervention supported by Evidence-Based Medicine should effectively contribute to their improvement. In the following review, the authors compile the current knowledge based on the findings of researchers from around the world. The topic of probiotic therapy is increasingly discussed in the field of lower gastrointestinal disorders, and thus the authors discover links between probiotic strains and the improvement of health quality in patients with IBS, taking into consideration the ways it affects patients’ mental health. As a result, a systematic review was prepared based on 60 items of recent literature, of which more than 80% were published in the last 5 years. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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17 pages, 1027 KiB

Open AccessReview

Phycoremediation Processes for Secondary Effluent from Sewage Treatment Plants Using Photosynthetic Microorganisms: A Review

by Lina Susana Pérez-Mora, Lauris del Carmen Mejia-da-Silva, Eleane de Almeida Cezare-Gomes, Évellin do Espirito Santo, Aline Kirie Gohara-Beirigo, Marcelo Chuei Matsudo, Bruno Monteiro Nardin, Célia Leite Sant’Anna and João Carlos Monteiro de Carvalho

Appl. Microbiol. 2023, 3(2), 400-416; https://doi.org/10.3390/applmicrobiol3020028 - 28 Apr 2023

Cited by 3 | Viewed by 2746

Abstract

Taking into account the worrying scenario of water scarcity, it is essential to enable more efficient technologies for wastewater treatment. Wastewater may be treated by conventional biological processes that remove pathogenic organisms, particulate and soluble organic compounds, and other components. However, secondary effluents [...] Read more.

Taking into account the worrying scenario of water scarcity, it is essential to enable more efficient technologies for wastewater treatment. Wastewater may be treated by conventional biological processes that remove pathogenic organisms, particulate and soluble organic compounds, and other components. However, secondary effluents from treatment plants may still contain toxic elements or high concentrations of inorganic nutrients (mainly nitrogen and phosphorus), which enable the growth of photosynthetic microorganisms in water bodies, resulting in eutrophication. In this context, cultivation of photosynthetic microorganisms in secondary wastewater from sewage treatment allows the removal of nutrients from such wastewater, reducing the possibility of eutrophication. Moreover, microalgal biomass, produced in this tertiary wastewater treatment, may be harvested by different methods with the potential for different applications, such as fertilizer and biofuel. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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9 pages, 1246 KiB

Open AccessBrief Report

A Brief Snapshot of Aspergillus Section Nigri Isolated from Brazilian Peanuts and Soil

by Fernanda Rodrigues, Josué J. Silva, Beatriz T. Iamanaka, Ligia M. Martins and Marta H. Taniwaki

Appl. Microbiol. 2023, 3(2), 476-484; https://doi.org/10.3390/applmicrobiol3020033 - 17 May 2023

Viewed by 1518

Abstract

The occurrence of mycotoxigenic species in peanuts is a major concern, and has been investigated in depth for many years. However, most studies focus on the occurrence of aflatoxigenic fungi, such as Aspergillus section Flavi. The present study aimed to clarify the [...] Read more.

The occurrence of mycotoxigenic species in peanuts is a major concern, and has been investigated in depth for many years. However, most studies focus on the occurrence of aflatoxigenic fungi, such as Aspergillus section Flavi. The present study aimed to clarify the occurrence of Aspergillus section Nigri, a group that harbors species capable of producing ochratoxin A (OTA), which has scarcely been investigated in peanuts. A total of 52 peanut samples, collected in the field and from storage, were analyzed. Aspergillus section Nigri was isolated from 64% and 100% of field and storage samples, respectively, and 218 strains were obtained. Based on the multiloci phylogeny of the CaM and BenA loci, six species of Aspergillus section Nigri were identified: A. brasiliensis, A. niger, A. neoniger, A. welwitschiae, A. costaricaensis, and A. japonicus. The incidence of ochratoxigenic strains was 5.0% (11/218), and only A. niger and A. welwitschiae were able to produce OTA. The presence of OTA in peanuts was found in 6 field and 8 storage samples, with levels ranging from 0.106 to 0.387 and 0.090 to 0.160 µg/kg, respectively. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology)

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