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Microorganisms, Volume 8, Issue 7 (July 2020) – 130 articles

Cover Story (view full-size image): Enteroviral infections have been linked to type 1 diabetes (T1D); its diagnosis peaks in the colder season, where viral infections come together with unfavorable conditions; less sunlight and exercise outside, an increase in cytokines- leading to pro-inflammatory gene networks. Insulin-producing β-cells in the pancreas are specifically permissive to virus infection, resulting in a storm of chemokines and cytokines, subsequent immune cell activation, β-cell destruction and the onset of T1D in genetically predisposed individuals. SARS-CoV-2 can highly infect islet cells, with severe metabolic complications and acute diabetes onset. In this review, we discuss the action of enteroviruses on autoimmunity and β-cell destruction and its crosstalk with genetics. Thanks to Prof. Richard E. Lloyd for kindly providing the enterovirus image. Created using smart server medical art under [...] Read more.
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Article
New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses
Microorganisms 2020, 8(7), 1093; https://doi.org/10.3390/microorganisms8071093 - 21 Jul 2020
Cited by 5 | Viewed by 1321
Abstract
Carnobacterium maltaromaticum and Carnobacterium divergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with [...] Read more.
Carnobacterium maltaromaticum and Carnobacterium divergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with antimicrobial potential by combining genomic and phenotypic approaches on large datasets comprising 12 Carnobacterium species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available Carnobacterium spp. genomes revealed 67 BGCs, distributed according to the species and ecological niches. From zero to six BGCs were predicted per strain and classified into four classes: terpene, NRPS (non-ribosomal peptide synthetase), NRPS-PKS (hybrid non-ribosomal peptide synthetase-polyketide synthase), RiPP (ribosomally synthesized and post-translationally modified peptide). In parallel, the antimicrobial activity of 260 strains from seafood products was evaluated. Among the 60% of active strains, three genomes were sequenced and submitted to a dereplication process. C. inhibens MIP2551 produced a high amountof H2O2, probably thanks to the presence of four oxidase-encoding genes. C. maltaromaticum EBP3019 and SF668 strains were highly efficient against Listeria monocytogenes. A new extracellular 16 kDa unmodified bacteriocin in the EBP3019 strain and five different bacteriocins in SF668 were highlighted. In this study, the overview of antimicrobial BGC and inhibitory activities of Carnobacterium spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications. Full article
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Article
Skin Bacteria Mediate Glycerol Fermentation to Produce Electricity and Resist UV-B
Microorganisms 2020, 8(7), 1092; https://doi.org/10.3390/microorganisms8071092 - 21 Jul 2020
Cited by 8 | Viewed by 2104
Abstract
Bacteria that use electron transport proteins in the membrane to produce electricity in the gut microbiome have been identified recently. However, the identification of electrogenic bacteria in the skin microbiome is almost completely unexplored. Using a ferric iron-based ferrozine assay, we have identified [...] Read more.
Bacteria that use electron transport proteins in the membrane to produce electricity in the gut microbiome have been identified recently. However, the identification of electrogenic bacteria in the skin microbiome is almost completely unexplored. Using a ferric iron-based ferrozine assay, we have identified the skin Staphylococcus epidermidis (S. epidermidis) as an electrogenic bacterial strain. Glycerol fermentation was essential for the electricity production of S. epidermidis since the inhibition of fermentation by 5-methyl furfural (5-MF) significantly diminished the bacterial electricity measured by voltage changes in a microbial fuel cell (MFC). A small-scale chamber with both anode and cathode was fabricated in order to study the effect of ultraviolet-B (UV-B) on electricity production and bacterial resistance to UV-B. Although UV-B lowered bacterial electricity, a prolonged incubation of S. epidermidis in the presence of glycerol promoted fermentation and elicited higher electricity to suppress the effect of UV-B. Furthermore, the addition of glycerol into S. epidermidis enhanced bacterial resistance to UV-B. Electricity produced by human skin commensal bacteria may be used as a dynamic biomarker to reflect the UV radiation in real-time. Full article
(This article belongs to the Special Issue Research Advance in Skin Microbiome)
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Article
Effects of Plasma-Activated Water on Skin Wound Healing in Mice
Microorganisms 2020, 8(7), 1091; https://doi.org/10.3390/microorganisms8071091 - 21 Jul 2020
Cited by 14 | Viewed by 1844
Abstract
Cold atmospheric plasma (CAP) has been widely used in biomedicine during the last two decades. While direct plasma treatment has been reported to promote wound healing, its application can be uneven and inconvenient. In this study, we first activated water with a portable [...] Read more.
Cold atmospheric plasma (CAP) has been widely used in biomedicine during the last two decades. While direct plasma treatment has been reported to promote wound healing, its application can be uneven and inconvenient. In this study, we first activated water with a portable dielectric barrier discharge plasma device and evaluated the inactivation effect of plasma-activated water (PAW) on several kinds of bacteria that commonly infect wounds. The results show that PAW can effectively inactivate these bacteria. Then, we activated tap water and examined the efficacy of PAW on wound healing in a mouse model of full-thickness skin wounds. We found that wound healing in mice treated with PAW was significantly faster compared with the control group. Histological analysis of the skin tissue of mice wounds showed a significant reduction in the number of inflammatory cells in the PAW treatment group. To identify the possible mechanism by which PAW promotes wound healing, we analyzed changes in the profiles of wound bacteria after PAW treatment. The results show that PAW can significantly reduce the abundance of wound bacteria in the treatment group. The results of biochemical blood tests and histological analysis of major internal organs in the mice show that PAW had no obvious side effects. Taken together, these results indicate that PAW may be a new and effective method for promoting wound healing without side effects. Full article
(This article belongs to the Section Medical Microbiology)
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Correction
Correction: Lukša, J., et al. Fungal Microbiota of Sea Buckthorn Berries at Two Ripening Stages and Volatile Profiling of Potential Biocontrol Yeasts. Microorganisms 2020, 8, 456
Microorganisms 2020, 8(7), 1090; https://doi.org/10.3390/microorganisms8071090 - 21 Jul 2020
Cited by 2 | Viewed by 784
Abstract
The authors wish to make the following corrections to this paper [...] Full article
(This article belongs to the Special Issue Applying Metaorganism Studies to the Fruit Microbiome: A New Frontier)
Article
Characterization of Salmonella Phage LPST153 That Effectively Targets Most Prevalent Salmonella Serovars
Microorganisms 2020, 8(7), 1089; https://doi.org/10.3390/microorganisms8071089 - 21 Jul 2020
Cited by 9 | Viewed by 1710
Abstract
Foodborne diseases represent a major risk to public health worldwide. In this study, LPST153, a novel Salmonella lytic phage with halo (indicative of potential depolymerase activity) was isolated by employing Salmonella enterica serovar Typhimurium ATCC 13311 as the host and had excellent lytic [...] Read more.
Foodborne diseases represent a major risk to public health worldwide. In this study, LPST153, a novel Salmonella lytic phage with halo (indicative of potential depolymerase activity) was isolated by employing Salmonella enterica serovar Typhimurium ATCC 13311 as the host and had excellent lytic potential against Salmonella. LPST153 is effectively able to lyse most prevalent tested serotypes of Salmonella, including S. Typhimurium, S. Enteritidis, S. Pullorum and S. Gallinarum. Morphological analysis revealed that phage LPST153 belongs to Podoviridae family and Caudovirales order and could completely prevent host bacterial growth within 9 h at multiplicity of infection (MOI) of 0.1, 1, 10 and 100. LPST153 had a latent period of 10 min and a burst size of 113 ± 8 PFU/cell. Characterization of the phage LPST153 revealed that it would be active and stable in some harsh environments or in different conditions of food processing and storage. After genome sequencing and phylogenetic analysis, it is confirmed that LPST153 is a new member of the Teseptimavirus genus of Autographivirinae subfamily. Further application experiments showed that this phage has potential in controlling Salmonella in milk and sausage. LPST153 was also able to inhibit the formation of biofilms and it had the ability to reduce and kill bacteria from inside, including existing biofilms. Therefore, the phage LPST153 could be used as a potential antibacterial agent for Salmonella control in the food industry. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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Article
Granular Calcite Stimulates Natural Mycorrhization and Growth of White Spruce Seedlings in Peat-Based Substrates in Forest Nursery
Microorganisms 2020, 8(7), 1088; https://doi.org/10.3390/microorganisms8071088 - 21 Jul 2020
Cited by 4 | Viewed by 1096
Abstract
The acidity of peat-based substrates used in forest nurseries limits seedling mineral nutrition and growth as well as the activity of microorganisms. To our knowledge, no study has yet evaluated the use of granular calcite as a covering material to increase pH, calcium [...] Read more.
The acidity of peat-based substrates used in forest nurseries limits seedling mineral nutrition and growth as well as the activity of microorganisms. To our knowledge, no study has yet evaluated the use of granular calcite as a covering material to increase pH, calcium and CO2 concentrations in the rhizosphere and ectomycorrhizal development. The objective is to compare different covering treatments on early colonization of the roots by ectomycorrhizal fungi, as well as the growth and calcium nutrition of white spruce seedlings in the forest nursery. Three treatments were used to cover the plant cavities (Silica (29 g/cavity; control treatment), Calcite (24 g/cavity) and calcite+ (31 g/cavity)) and were distributed randomly inside each of the five complete blocks of the experimental design. The results show that calcite stimulates natural mycorrhization. Seedlings grown with calcite have significant gains for several growth and physiological variables, and that the periphery of their root plugs are more colonized by the extramatrical phase of ectomycorrhizal fungi, thus improving root-plug cohesion. The authors discuss the operational scope of the results in relation to the tolerance of seedlings to environmental stress and the improvement of their quality, both in the nursery and in reforestation sites. Full article
(This article belongs to the Special Issue Mycorrhizal Fungi)
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Article
Extracellular Vesicles in Human Preterm Colostrum Inhibit Infection by Human Cytomegalovirus In Vitro
Microorganisms 2020, 8(7), 1087; https://doi.org/10.3390/microorganisms8071087 - 21 Jul 2020
Cited by 8 | Viewed by 1191
Abstract
Breast milk is a complex biofluid that nourishes infants, supports their growth and protects them from diseases. However, at the same time, breastfeeding is a transmission route for human cytomegalovirus (HCMV), with preterm infants being at a great risk of congenital disease. The [...] Read more.
Breast milk is a complex biofluid that nourishes infants, supports their growth and protects them from diseases. However, at the same time, breastfeeding is a transmission route for human cytomegalovirus (HCMV), with preterm infants being at a great risk of congenital disease. The discrepancy between high HCMV transmission rates and the few reported cases of infants with severe clinical illness is likely due to the protective effect of breast milk. The aim of this study was to investigate the anti-HCMV activity of human preterm colostrum and clarify the role of colostrum-derived extracellular vesicles (EVs). Preterm colostrum samples were collected and the EVs were purified and characterized. The in vitro anti-HCMV activity of both colostrum and EVs was tested against HCMV, and the viral replication step inhibited by colostrum-purified EVs was examined. We investigated the putative role EV surface proteins play in impairing HCMV infection using shaving experiments and proteomic analysis. The obtained results confirmed the antiviral action of colostrum against HCMV and demonstrated a remarkable antiviral activity of colostrum-derived EVs. Furthermore, we demonstrated that EVs impair the attachment of HCMV to cells, with EV surface proteins playing a role in mediating this action. These findings contribute to clarifying the mechanisms that underlie the protective role of human colostrum against HCMV infection. Full article
(This article belongs to the Special Issue Cytomegalovirus: Biology and Infection)
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Article
Functional Biodiversity of Yeasts Isolated from Colombian Fermented and Dry Cocoa Beans
Microorganisms 2020, 8(7), 1086; https://doi.org/10.3390/microorganisms8071086 - 21 Jul 2020
Cited by 13 | Viewed by 1907
Abstract
Yeasts play an important role in the cocoa fermentation process. Although the most relevant function is the degradation of sugars and the production of ethanol, there is little understanding of the enzyme activities and attributes that allow them to survive even after drying. [...] Read more.
Yeasts play an important role in the cocoa fermentation process. Although the most relevant function is the degradation of sugars and the production of ethanol, there is little understanding of the enzyme activities and attributes that allow them to survive even after drying. The present study explored the functional biodiversity of yeasts associated with Criollo Colombian cocoa fermented beans, able to survive after drying. Twelve species belonging to 10 genera of osmo-, acid-, thermo-, and desiccation-tolerant yeasts were isolated and identified from fermented and dry cocoa beans, with Pichia kudriavzevii and Saccharomyces cerevisiae standing out as the most frequent. For the first time, we reported the presence of Zygosaccharomyces bisporus in cocoa fermented beans. It was found that resistance to desiccation is related to the different degradation capacities of fermentation substrates, which suggests that associative relationships may exist between the different yeast species and their degradation products. Besides, the increased thermotolerance of some species was related to the presence of polyphenols in the medium, which might play a fundamental role in shaping the microbial community composition. Full article
(This article belongs to the Special Issue Microbial Populations of Fermented Foods)
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Article
Impaired Hypothalamic Microglial Activation in Offspring of Antibiotic-Treated Pregnant/Lactating Rats Is Attenuated by Prebiotic Oligofructose Co-Administration
Microorganisms 2020, 8(7), 1085; https://doi.org/10.3390/microorganisms8071085 - 21 Jul 2020
Cited by 3 | Viewed by 1540
Abstract
Microbial colonization of the gut early in life is crucial for the development of the immune and nervous systems, as well as influencing metabolism and weight gain. While early life exposure to antibiotics can cause microbial dysbiosis, prebiotics are non-digestible substrates that selectively [...] Read more.
Microbial colonization of the gut early in life is crucial for the development of the immune and nervous systems, as well as influencing metabolism and weight gain. While early life exposure to antibiotics can cause microbial dysbiosis, prebiotics are non-digestible substrates that selectively promote the growth of beneficial gut microbiota. Our objective was to examine the effects of dietary prebiotic administration on the consequences of maternal antibiotic intake on offspring body weight, behavior, and neuroimmune responses later in life. Sprague-Dawley rat dams were given low-dose penicillin (LDP), prebiotic fiber (10% oligofructose), or both, during the third week of pregnancy and throughout lactation. Anxiety-like behavior, weight gain, body composition, cecal microbiota composition, and microglial responses to lipopolysaccharide (LPS) were assessed in offspring. Male and female prebiotic offspring had lower body weight compared to antibiotic offspring. Maternal antibiotic exposure resulted in lasting effects on select offspring microbiota including a lower relative abundance of Streptococcus, Lactococcus, and Eubacterium at 10 weeks of age. Maternal antibiotic use impaired microglial response to LPS in the hypothalamus compared to control, and this phenotype was reversed with prebiotic. Prebiotic fiber warrants further investigation as an adjunct to antibiotic use during pregnancy. Full article
(This article belongs to the Special Issue Gut Microbiota Dysbiosis)
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Article
Batch and Continuous Lactic Acid Fermentation Based on A Multi-Substrate Approach
Microorganisms 2020, 8(7), 1084; https://doi.org/10.3390/microorganisms8071084 - 21 Jul 2020
Cited by 8 | Viewed by 1860
Abstract
The utilisation of waste materials and industrial residues became a priority within the bioeconomy concept and the production of biobased chemicals. The aim of this study was to evaluate the feasibility to continuously produce L-lactic acid from different renewable substrates, in a multi-substrate [...] Read more.
The utilisation of waste materials and industrial residues became a priority within the bioeconomy concept and the production of biobased chemicals. The aim of this study was to evaluate the feasibility to continuously produce L-lactic acid from different renewable substrates, in a multi-substrate strategy mode. Based on batch experiments observations, Bacillus coagulans A534 strain was able to continuously metabolise acid whey, sugar beet molasses, sugar bread, alfalfa press green juice and tapioca starch. Additionally, reference experiments showed its behaviour in standard medium. Continuous fermentations indicated that the highest productivity was achieved when molasses was employed with a value of 10.34 g·L−1·h−1, while the lactic acid to sugar conversion yield was 0.86 g·g−1. This study demonstrated that LA can be efficiently produced in continuous mode regardless the substrate, which is a huge advantage in comparison to other platform chemicals. Full article
(This article belongs to the Special Issue Substrate Tolerant Fermentations)
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Article
Characterization of Pediococcus acidilactici PFC69 and Lactococcus lactis PFC77 Bacteriocins and Their Antimicrobial Activities in Tarhana Fermentation
Microorganisms 2020, 8(7), 1083; https://doi.org/10.3390/microorganisms8071083 - 21 Jul 2020
Cited by 6 | Viewed by 1221
Abstract
Tarhana is a traditional cereal product fermented by lactic acid bacteria (LAB) and yeast strains that has gained special interest recently as an infant nutrition. Tarhana contains wheat flour, yogurt, and various vegetables that might create a microbiological toxicological risk, especially for Bacillus [...] Read more.
Tarhana is a traditional cereal product fermented by lactic acid bacteria (LAB) and yeast strains that has gained special interest recently as an infant nutrition. Tarhana contains wheat flour, yogurt, and various vegetables that might create a microbiological toxicological risk, especially for Bacillus cereus and Staphylococcus aureus. In this study, characterization of the metabolites responsible for antibacterial activity of Pediococcus acidilactici PFC69 and Lactococcus lactis PFC77 strains obtained from tarhana was performed, and antibacterial effects were detected against B. cereus ATCC 11778 and S. aureus ATCC 29213 during the fermentation. A total of 12,800 AU/mL antibacterial activity was observed for the supernatants of the PFC69 and PFC77 strains that were found to be stable at high temperature and in low pH conditions and sensitive to proteases, suggesting the antimicrobial metabolite is a bacteriocin. These bacteriocins were further purified and their molecular sizes were determined as 4.5 and 3.5 kDa, respectively. Importantly, inoculation of PFC69 and PFC77 to tarhana dough significantly decreased B. cereus ATCC 11778 and S. aureus ATCC 29213 amounts from the fifth day of fermentation compared to the control dough samples. P. acidilactici PFC69 and L. lactis PFC77 strains were concluded as bioprotective cultures for tarhana and these strains were offered for other cereal-based fermentations. Full article
(This article belongs to the Special Issue Antimicrobial Interventions for Raw and Processed Foods)
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Article
Analysis of Cytoplasmic and Secreted Proteins of Staphylococcus aureus Revealed Adaptive Metabolic Homeostasis in Response to Changes in the Environmental Conditions Representative of the Human Wound Site
Microorganisms 2020, 8(7), 1082; https://doi.org/10.3390/microorganisms8071082 - 20 Jul 2020
Cited by 2 | Viewed by 997
Abstract
The pathogenesis of Staphylococcus aureus is mainly attributed to its capability to adjust to changes in environmental conditions, including those present on human skin or within a wound site. This study investigated the changes in the cytoplasmic and secreted proteins in S. aureus [...] Read more.
The pathogenesis of Staphylococcus aureus is mainly attributed to its capability to adjust to changes in environmental conditions, including those present on human skin or within a wound site. This study investigated the changes in the cytoplasmic and secreted proteins in S. aureus that occurred in response to alterations in the environmental parameters that could be found in the human wound site. In total, sixty differentially regulated cytoplasmic proteins were detected using a label-free quantification approach, and these proteins were classified into ten molecular functions: protein biosynthesis, glycolysis, signal transduction, metabolism, cell cycle, transport, energy generation, cell anchorage, nucleotide biosynthesis and unknown. These changes represented characteristic protein profiles when evaluated by principal component analysis. The bacterium responded to elevated NaCl at pH 6 by decreasing the abundance of the majority of cytoplasmic proteins, while at pH 8 there was an increase in the levels of cytoplasmic proteins in comparison to the untreated cells. The analysis of the secreted proteins showed that there was a high degree of difference in both the intensity and the distribution of many individual protein bands in response to environmental challenges. From these results, it was deduced that specific metabolic homeostasis occurred under each combination of defined environmental conditions. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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Article
Molecular Characterization, Intra-Species Diversity and Abundance of Freshwater Plesiomonas shigelloides Isolates
Microorganisms 2020, 8(7), 1081; https://doi.org/10.3390/microorganisms8071081 - 20 Jul 2020
Cited by 3 | Viewed by 998
Abstract
Molecular signatures of Plesiomonas shigelloides strain specific to pathogenic and nonpathogenic variants are not well established till present. There is a need for intra-species barcoding of P. shigelloides to aid infection control. This study aims at characterizing and assessing intra-species diversity and abundance [...] Read more.
Molecular signatures of Plesiomonas shigelloides strain specific to pathogenic and nonpathogenic variants are not well established till present. There is a need for intra-species barcoding of P. shigelloides to aid infection control. This study aims at characterizing and assessing intra-species diversity and abundance of P. shigelloides isolated from three freshwaters in the Eastern Cape Province. The study used a Plesiomonas-specific PCR to characterize the isolates. Intra-species (dis)similarities were assessed using ERIC-PCR and (GTG)5-PCR techniques. The DNA fingerprints produced were electrophoresed, digitized, and documented via computer-assisted pattern analysis. The fingerprints were analyzed using neighbor-joining clustering (NJC) based on Euclidean similarity index. Results revealed 80%, 83.64%, and 80% of the water samples from Tyhume, Kat, and Kubusie rivers, respectively, positive for P. shigelloides isolation. The prevalence of P. shigelloides from sites ranged from 13.5% to 88.9%. NJC delineated 48 isolates to 8 clades (ERIC-fingerprints) and 34 isolates into 7 clades ((GTG)5-fingerprints). The relative abundance of unique strains ranged from 6.3% to 22.9% via the two methods. Both fingerprinting approaches have strain-differentiating potential for P. shigelloides, however ERIC-PCR possessed higher resolution (D = 37.46) advantage over (GTG)5-PCR (D = 29.64). In conclusion, the study achieved intra-species diversity and abundance of P. shigelloides from aquatic milieu and provide further opportunity for intra-species-specific barcoding. Full article
(This article belongs to the Section Environmental Microbiology)
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Article
Biological Control of Verticillium Wilt on Olive Trees by the Salt-Tolerant Strain Bacillus velezensis XT1
Microorganisms 2020, 8(7), 1080; https://doi.org/10.3390/microorganisms8071080 - 20 Jul 2020
Cited by 11 | Viewed by 2330
Abstract
Verticillium wilt, caused by the pathogen Verticillium dahliae, is extremely devastating to olive trees (Olea europea). Currently, no successful control measure is available against it. The objective of this work was to evaluate the antifungal activity of Bacillus velezensis XT1, [...] Read more.
Verticillium wilt, caused by the pathogen Verticillium dahliae, is extremely devastating to olive trees (Olea europea). Currently, no successful control measure is available against it. The objective of this work was to evaluate the antifungal activity of Bacillus velezensis XT1, a well-characterized salt-tolerant biocontrol strain, against the highly virulent defoliating V. dahliae V024. In vitro, strain XT1 showed to reduce fungal mycelium from 34 to 100%, depending on if the assay was conducted with the supernatant, volatile compounds, lipopeptides or whole bacterial culture. In preventive treatments, when applied directly on young olive trees, it reduced Verticillium incidence rate and percentage of severity by 54 and ~80%, respectively. It increased polyphenol oxidase (PPO) activity by 395%, indicating an enhancement of disease resistance in plant tissues, and it decreased by 20.2% the number of fungal microsclerotia in soil. In adult infected trees, palliative inoculation of strain XT1 in the soil resulted in a reduction in Verticillium symptom severity by ~63%. Strain XT1 is biosafe, stable in soil and able to colonize olive roots endophytically. All the traits described above make B. velezensis XT1 a promising alternative to be used in agriculture for the management of Verticillium wilt. Full article
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Article
Biosynthesis and Antimicrobial Activity of Pseudodesmin and Viscosinamide Cyclic Lipopeptides Produced by Pseudomonads Associated with the Cocoyam Rhizosphere
Microorganisms 2020, 8(7), 1079; https://doi.org/10.3390/microorganisms8071079 - 20 Jul 2020
Cited by 6 | Viewed by 1756
Abstract
Pseudomonas cyclic lipopeptides (CLPs) are encoded non-ribosomally by biosynthetic gene clusters (BGCs) and possess diverse biological activities. In this study, we conducted chemical structure and BGC analyses with antimicrobial activity assays for two CLPs produced by Pseudomonas strains isolated from the cocoyam rhizosphere [...] Read more.
Pseudomonas cyclic lipopeptides (CLPs) are encoded non-ribosomally by biosynthetic gene clusters (BGCs) and possess diverse biological activities. In this study, we conducted chemical structure and BGC analyses with antimicrobial activity assays for two CLPs produced by Pseudomonas strains isolated from the cocoyam rhizosphere in Cameroon and Nigeria. LC-MS and NMR analyses showed that the Pseudomonas sp. COR52 and A2W4.9 produce pseudodesmin and viscosinamide, respectively. These CLPs belong to the Viscosin group characterized by a nonapeptidic moiety with a 7-membered macrocycle. Similar to other Viscosin-group CLPs, the initiatory non-ribosomal peptide synthetase (NRPS) gene of the viscosinamide BGC is situated remotely from the other two NRPS genes. In contrast, the pseudodesmin genes are all clustered in a single genomic locus. Nano- to micromolar levels of pseudodesmin and viscosinamide led to the hyphal distortion and/or disintegration of Rhizoctonia solani AG2-2 and Pythium myriotylum CMR1, whereas similar levels of White Line-Inducing Principle (WLIP), another member of the Viscosin group, resulted in complete lysis of both soil-borne phytopathogens. In addition to the identification of the biosynthetic genes of these two CLPs and the demonstration of their interaction with soil-borne pathogens, this study provides further insights regarding evolutionary divergence within the Viscosin group. Full article
(This article belongs to the Special Issue Microbial Biosurfactants)
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Review
Cytomegalovirus and Inflammatory Bowel Diseases (IBD) with a Special Focus on the Link with Ulcerative Colitis (UC)
Microorganisms 2020, 8(7), 1078; https://doi.org/10.3390/microorganisms8071078 - 20 Jul 2020
Cited by 14 | Viewed by 2514
Abstract
Cytomegalovirus (CMV) infects approximately 40% of adults in France and persists lifelong as a latent agent in different organs, including gut. A close relationship is observed between inflammation that favors viral expression and viral replication that exacerbates inflammation. In this context, CMV colitis [...] Read more.
Cytomegalovirus (CMV) infects approximately 40% of adults in France and persists lifelong as a latent agent in different organs, including gut. A close relationship is observed between inflammation that favors viral expression and viral replication that exacerbates inflammation. In this context, CMV colitis may impact the prognosis of patients suffering from inflammatory bowel diseases (IBDs), and notably those with ulcerative colitis (UC). In UC, the mucosal inflammation and T helper cell (TH) 2 cytokines, together with immunomodulatory drugs used for controlling flare-ups, favor viral reactivation within the gut, which, in turn, increases mucosal inflammation, impairs corticoid and immunosuppressor efficacy (the probability of steroid resistance is multiplied by more than 20 in the case of CMV colitis), and enhances the risk for colectomy. This review emphasizes the virological tools that are recommended for exploring CMV colitis during inflammatory bowel diseases (IBD) and underlines the interest of using ganciclovir for treating flare-ups associated to CMV colitis in UC patients. Full article
(This article belongs to the Special Issue Cytomegalovirus: Biology and Infection)
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Communication
Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile
Microorganisms 2020, 8(7), 1077; https://doi.org/10.3390/microorganisms8071077 - 20 Jul 2020
Cited by 4 | Viewed by 1616
Abstract
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) [...] Read more.
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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Article
Understanding Stress Response to High-Arsenic Gold-Bearing Sulfide Concentrate in Extremely Metal-Resistant Acidophile Sulfobacillus thermotolerans
Microorganisms 2020, 8(7), 1076; https://doi.org/10.3390/microorganisms8071076 - 19 Jul 2020
Cited by 10 | Viewed by 1304
Abstract
Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense [...] Read more.
Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense strategies of the acidophilic bacterium Sulfobacillus thermotolerans, which dominates microbial communities functioning in industrial biooxidation processes at >35 °C, against the toxic effect of the high-arsenic gold-bearing sulfide concentrate. In addition to extreme metal resistance, this acidophile proved to be one of the most As-tolerant microorganisms. Comparative proteomic analysis indicated that 30 out of 33 differentially expressed proteins were upregulated in response to the ore concentrate, while the synthesis level of the functional proteins required for cell survival was not negatively affected. Despite a high level of cellular metal(loid) accumulation, no specific metal(loid)-resistant systems were regulated. Instead, several proteins involved in the metabolic pathways and stress response, including MBL fold metallo-hydrolase, sulfide:quinone oxidoreductase, and GroEL chaperonin, may play crucial roles in resistance to the sulfide ore concentrate and arsenic, in particular. This study provides the first data on the microbial responses to sulfide ore concentrates and advances our understanding of defense mechanisms against toxic compounds in acidophiles. Full article
(This article belongs to the Section Microbial Biotechnology)
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Article
Taking Screenshots of the Invisible: A Study on Bacterial Contamination of Mobile Phones from University Students of Healthcare Professions in Rome, Italy
Microorganisms 2020, 8(7), 1075; https://doi.org/10.3390/microorganisms8071075 - 19 Jul 2020
Cited by 8 | Viewed by 1589
Abstract
Mobile phones (MPs) are commonly used both in the personal and professional life. We assessed microbiological contamination of MPs from 108 students in healthcare professions (HPs), in relation to their demographic characteristics and MPs handling habits, collected by means of a questionnaire. Cultural [...] Read more.
Mobile phones (MPs) are commonly used both in the personal and professional life. We assessed microbiological contamination of MPs from 108 students in healthcare professions (HPs), in relation to their demographic characteristics and MPs handling habits, collected by means of a questionnaire. Cultural and biochemical tests were performed, and statistical analyses were carried out. Staphylococci were present in 85% of MPs, Enterococci in 37%, Coliforms in 6.5%; E. coli was never detected. Staphylococcus epidermidis was the most frequently isolated staphylococcal species (72% of MPs), followed by S. capitis (14%), S. saprophyticus, S. warneri, S. xylosus (6%), and by S. aureus (4%). Heterotrophic Plate Counts (HPC) at 37 °C, ranged from 0 to 1.2 × 104 CFU/dm2 (mean = 362 CFU/dm2). In univariate analysis, the male gender only was significantly associated with higher HPCs and enterococcal contamination. Multiple linear regression models explained only 17% and 16% of the HPC 37 °C and staphylococcal load variability, respectively. Developing specific guidelines for a hygienic use of MPs in clinical settings, for preventing cross-infection risks, is advisable, as well as introducing specific training programs to HP students. MPs decontamination procedures could also be implemented in the community. Full article
(This article belongs to the Section Public Health Microbiology)
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Article
Functional Identification and Evolutionary Analysis of Two Novel Plasmids Mediating Quinolone Resistance in Proteus vulgaris
Microorganisms 2020, 8(7), 1074; https://doi.org/10.3390/microorganisms8071074 - 18 Jul 2020
Cited by 4 | Viewed by 1058
Abstract
Plasmid-mediated quinolone resistance (PMQR) remains one of the main mechanisms of bacterial quinolone resistance and plays an important role in the transmission of antibiotic resistance genes (ARGs). In this study, two novel plasmids, p3M-2A and p3M-2B, which mediate quinolone resistance in Proteus vulgaris [...] Read more.
Plasmid-mediated quinolone resistance (PMQR) remains one of the main mechanisms of bacterial quinolone resistance and plays an important role in the transmission of antibiotic resistance genes (ARGs). In this study, two novel plasmids, p3M-2A and p3M-2B, which mediate quinolone resistance in Proteus vulgaris strain 3M (P3M) were identified. Of these, only p3M-2B appeared to be a qnrD-carrying plasmid. Both p3M-2A and p3M-2B could be transferred into Escherichia coli, and the latter caused a twofold change in ciprofloxacin resistance, according to the measured minimum inhibitory concentration (MIC). Plasmid curing/complementation and qRT-PCR results showed that p3M-2A can directly regulate the expression of qnrD in p3M-2B under treatment with ciprofloxacin, in which process, ORF1 was found to play an important role. Sequence alignments and phylogenetic analysis revealed the evolutionary relationships of all reported qnrD-carrying plasmids and showed that ORF1–4 in p3M-2B is the most conserved backbone for the normal function of qnrD-carrying plasmids. The identified direct repeats (DR) suggested that, from an evolutionary perspective, p3M-2B may have originated from the 2683-bp qnrD-carrying plasmid and may increase the possibility of plasmid recombination and then of qnrD transfer. To the best of our knowledge, this is the first identification of a novel qnrD-carrying plasmid isolated from a P. vulgaris strain of shrimp origin and a plasmid that plays a regulatory role in qnrD expression. This study also sheds new light on plasmid evolution and on the mechanism of horizontal transfer of ARGs encoded by plasmids. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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Article
Maturational Changes Alter Effects of Dietary Phytase Supplementation on the Fecal Microbiome in Fattening Pigs
Microorganisms 2020, 8(7), 1073; https://doi.org/10.3390/microorganisms8071073 - 18 Jul 2020
Cited by 4 | Viewed by 1296
Abstract
Age-related successions in the porcine gut microbiome may modify the microbial response to dietary changes. This may especially affect the bacterial response to essential nutrients for bacterial metabolism, such as phosphorus (P). Against this background, we used phytase supplementation (0 or 650 phytase [...] Read more.
Age-related successions in the porcine gut microbiome may modify the microbial response to dietary changes. This may especially affect the bacterial response to essential nutrients for bacterial metabolism, such as phosphorus (P). Against this background, we used phytase supplementation (0 or 650 phytase units/kg complete feed) to alter the P availability in the hindgut and studied the dietary response of the fecal bacterial microbiome from the early to late fattening period. Fecal DNA were isolated after 0, 3, 5 and 10 weeks and the V3-V4 region of the 16S rRNA gene was sequenced. Permutational analysis of variance showed distinct bacterial communities for diet and week. Alpha-diversity and taxonomy indicated progressing maturation of the bacterial community with age. Prevotellaceae declined, whereas Clostridiaceae and Ruminococcaceae increased from weeks 0 to 3, 5, and 10, indicating changes in fiber-digesting capacities with age. Phytase affected all major bacterial taxa but reduced species richness (Chao1) and diversity (Shannon and Simpson). To conclude, present results greatly support the importance of available P for bacterial proliferation, including fibrolytic, lactic acid- and butyrate-producing genera, in pigs. Results also emphasize the necessity to assess bacterial responses to dietary manipulation at several time points throughout the fattening period. Full article
(This article belongs to the Special Issue Gut Microbiota Development in Farm Animals)
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Review
Molecular Mechanisms Involved in the Multicellular Growth of Ustilaginomycetes
Microorganisms 2020, 8(7), 1072; https://doi.org/10.3390/microorganisms8071072 - 18 Jul 2020
Cited by 6 | Viewed by 1570
Abstract
Multicellularity is defined as the developmental process by which unicellular organisms became pluricellular during the evolution of complex organisms on Earth. This process requires the convergence of genetic, ecological, and environmental factors. In fungi, mycelial and pseudomycelium growth, snowflake phenotype (where daughter cells [...] Read more.
Multicellularity is defined as the developmental process by which unicellular organisms became pluricellular during the evolution of complex organisms on Earth. This process requires the convergence of genetic, ecological, and environmental factors. In fungi, mycelial and pseudomycelium growth, snowflake phenotype (where daughter cells remain attached to their stem cells after mitosis), and fruiting bodies have been described as models of multicellular structures. Ustilaginomycetes are Basidiomycota fungi, many of which are pathogens of economically important plant species. These fungi usually grow unicellularly as yeasts (sporidia), but also as simple multicellular forms, such as pseudomycelium, multicellular clusters, or mycelium during plant infection and under different environmental conditions: Nitrogen starvation, nutrient starvation, acid culture media, or with fatty acids as a carbon source. Even under specific conditions, Ustilago maydis can form basidiocarps or fruiting bodies that are complex multicellular structures. These fungi conserve an important set of genes and molecular mechanisms involved in their multicellular growth. In this review, we will discuss in-depth the signaling pathways, epigenetic regulation, required polyamines, cell wall synthesis/degradation, polarized cell growth, and other cellular-genetic processes involved in the different types of Ustilaginomycetes multicellular growth. Finally, considering their short life cycle, easy handling in the laboratory and great morphological plasticity, Ustilaginomycetes can be considered as model organisms for studying fungal multicellularity. Full article
(This article belongs to the Special Issue Microbial Cell Wall)
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Article
Biofilm Production by Enterotoxigenic Strains of Bacillus cereus in Different Materials and under Different Environmental Conditions
Microorganisms 2020, 8(7), 1071; https://doi.org/10.3390/microorganisms8071071 - 17 Jul 2020
Cited by 2 | Viewed by 1047
Abstract
Foodborne illnesses, such as infections or food poisoning, can be caused by bacterial biofilms present in food matrices or machinery. The production of biofilms by several strains of Bacillus cereus on different materials under different culture conditions was determined, as well as the [...] Read more.
Foodborne illnesses, such as infections or food poisoning, can be caused by bacterial biofilms present in food matrices or machinery. The production of biofilms by several strains of Bacillus cereus on different materials under different culture conditions was determined, as well as the relationship of biofilms with motility, in addition to the enterotoxigenic profile and candidate genes that participate in the production of biofilms. Biofilm production of B. cereus strains was determined on five materials: glass, polystyrene, polyethylene, polyvinylchloride (PVC), PVC/glass; in three culture media: Phenol red broth, tryptic soy broth, and brain heart infusion broth; in two different temperatures (37 °C and 25 °C), and in two different oxygen conditions (oxygen and CO2 tension). Furthermore, the strains were molecularly characterized by end-point polymerase chain reaction. Motility was determined on semi-solid agar. The B. cereus strains in this study were mainly characterized as enterotoxigenic strains; statistically significant differences were found in the PVC material and biofilm production. Motility was positively associated with the production of biofilm in glass/PVC. The sipW and tasA genes were found in two strains. The results of this study are important in the food industry because the strains carry at least one enterotoxin gene and produce biofilms on different materials Full article
(This article belongs to the Section Biofilm)
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Article
Mycobacterium bovis Infection in Red Foxes in Four Animal Tuberculosis Endemic Areas in France
Microorganisms 2020, 8(7), 1070; https://doi.org/10.3390/microorganisms8071070 - 17 Jul 2020
Cited by 9 | Viewed by 1041
Abstract
In France, animal tuberculosis (TB) due to Mycobacterium bovis (M. bovis) affects a multi-host community that include cattle and wildlife species such as wild boars (Sus scrofa), badgers (Meles meles), or wild deer (Cervus elaphus, Capreolus [...] Read more.
In France, animal tuberculosis (TB) due to Mycobacterium bovis (M. bovis) affects a multi-host community that include cattle and wildlife species such as wild boars (Sus scrofa), badgers (Meles meles), or wild deer (Cervus elaphus, Capreolus capreolus). The involvement of foxes in the epidemiology of TB is fairly described in countries facing multispecies concerns. After the discovery of grouped cases of TB in foxes in a French TB endemic region, a study was implemented in the core of four TB endemic areas in Dordogne, Charente, Landes (departments of Nouvelle-Aquitaine region), and Côte-d’Or (Burgundy-Franche-Comté region). No infected fox was found in Côte-d’Or (n = 146), where in parallel TB in cattle and other wild species became sparse in the last years. In contrast, in Dordogne, Charente, and Landes, 13 (n = 184), 9 (n = 98) and 7 (n = 140) foxes were found infected by M. bovis, respectively, corresponding to 7.1% (CI95% 3.8–11.8%), 9.2% (4.3–16.7%) and 5.0% (CI95% 2.0–10.0%) prevalence rates, respectively. These infection rates are comparable with those observed in badgers and wild boar in these same three areas (ranging from 9 to 13.2% and 4.3 to 17.9%, respectively), where the number of cattle outbreaks has increased in the last 10-15 years. In each area, the genotypes of foxes’ M. bovis isolates were the same as those in local cattle and other wildlife species. None of the infected foxes presented TB-like gross lesions. M. bovis was found in the mesenteric lymph nodes of 28 foxes (68%). For the 12 foxes where retropharyngeal and respiratory lymph nodes were analyzed separately, M. bovis was present in the respiratory lymph nodes of eight individuals. With regard to excretion, appropriate samples were available for 12 infected foxes from Dordogne. M. bovis DNA was detected in the feces of five of these animals, four of which were infected in the mesenteric lymph nodes. Combined with the knowledge on the biology and ecology of foxes, the results of this study suggest that in areas where infection in cattle is still active in France, foxes might play a role of spillover host in the epidemiology of M. bovis. Full article
(This article belongs to the Special Issue Wildlife Microbiology 2.0)
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Review
Can We Harness Immune Responses to Improve Drug Treatment in Leishmaniasis?
Microorganisms 2020, 8(7), 1069; https://doi.org/10.3390/microorganisms8071069 - 17 Jul 2020
Cited by 7 | Viewed by 1844
Abstract
Leishmaniasis is a vector-borne parasitic disease that has been neglected in priority for control and eradication of malaria, tuberculosis, and HIV/AIDS. Collectively, over one seventh of the world’s population is at risk of being infected with 0.7–1.2 million new infections reported annually. Clinical [...] Read more.
Leishmaniasis is a vector-borne parasitic disease that has been neglected in priority for control and eradication of malaria, tuberculosis, and HIV/AIDS. Collectively, over one seventh of the world’s population is at risk of being infected with 0.7–1.2 million new infections reported annually. Clinical manifestations range from self-healing cutaneous lesions to fatal visceral disease. The first anti-leishmanial drugs were introduced in the 1950′s and, despite several shortcomings, remain the mainstay for treatment. Regardless of this and the steady increase in infections over the years, particularly among populations of low economic status, research on leishmaniasis remains under funded. This review looks at the drugs currently in clinical use and how they interact with the host immune response. Employing chemoimmunotherapeutic approaches may be one viable alternative to improve the efficacy of novel/existing drugs and extend their lifespan in clinical use. Full article
(This article belongs to the Special Issue Treatment of Leishmaniasis)
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Article
In vitro Edwardsiella piscicida CK108 Transcriptome Profiles with Subinhibitory Concentrations of Phenol and Formalin Reveal New Insights into Bacterial Pathogenesis Mechanisms
Microorganisms 2020, 8(7), 1068; https://doi.org/10.3390/microorganisms8071068 - 17 Jul 2020
Cited by 8 | Viewed by 1431
Abstract
Phenol and formalin are major water pollutants that are frequently discharged into the aquatic milieu. These chemicals can affect broad domains of life, including microorganisms. Aquatic pollutants, unlike terrestrial pollutants, are easily diluted in water environments and exist at a sub-inhibitory concentration (sub-IC), [...] Read more.
Phenol and formalin are major water pollutants that are frequently discharged into the aquatic milieu. These chemicals can affect broad domains of life, including microorganisms. Aquatic pollutants, unlike terrestrial pollutants, are easily diluted in water environments and exist at a sub-inhibitory concentration (sub-IC), thus not directly inhibiting bacterial growth. However, they can modulate gene expression profiles. The sub-IC values of phenol and formalin were measured by minimal inhibitory concentration (MIC) assay to be 0.146% (1.3 mM) and 0.0039% (0.38 mM), respectively, in Edwardsiella piscicida CK108, a Gram-negative fish pathogen. We investigated the differentially expressed genes (DEG) by RNA-seq when the cells were exposed to the sub-ICs of phenol and formalin. DEG analyses revealed that genes involved in major virulence factors (type I fimbriae, flagella, type III and type VI secretion system) and various cellular pathways (energy production, amino acid synthesis, carbohydrate metabolism and two-component regulatory systems) were up- or downregulated by both chemicals. The genome-wide gene expression data corresponded to the results of a quantitative reverse complementary-PCR and motility assay. This study not only provides insight into how a representative fish pathogen, E. piscicida CK108, responds to the sub-ICs of phenol and formalin but also shows the importance of controlling chemical pollutants in aquatic environments. Full article
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Review
Regulation of Host Immune Responses against Influenza A Virus Infection by Mitogen-Activated Protein Kinases (MAPKs)
Microorganisms 2020, 8(7), 1067; https://doi.org/10.3390/microorganisms8071067 - 17 Jul 2020
Cited by 13 | Viewed by 1622
Abstract
Influenza is a major respiratory viral disease caused by infections from the influenza A virus (IAV) that persists across various seasonal outbreaks globally each year. Host immune response is a key factor determining disease severity of influenza infection, presenting an attractive target for [...] Read more.
Influenza is a major respiratory viral disease caused by infections from the influenza A virus (IAV) that persists across various seasonal outbreaks globally each year. Host immune response is a key factor determining disease severity of influenza infection, presenting an attractive target for the development of novel therapies for treatments. Among the multiple signal transduction pathways regulating the host immune activation and function in response to IAV infections, the mitogen-activated protein kinase (MAPK) pathways are important signalling axes, downstream of various pattern recognition receptors (PRRs), activated by IAVs that regulate various cellular processes in immune cells of both innate and adaptive immunity. Moreover, aberrant MAPK activation underpins overexuberant production of inflammatory mediators, promoting the development of the “cytokine storm”, a characteristic of severe respiratory viral diseases. Therefore, elucidation of the regulatory roles of MAPK in immune responses against IAVs is not only essential for understanding the pathogenesis of severe influenza, but also critical for developing MAPK-dependent therapies for treatment of respiratory viral diseases. In this review, we will summarise the current understanding of MAPK functions in both innate and adaptive immune response against IAVs and discuss their contributions towards the cytokine storm caused by highly pathogenic influenza viruses. Full article
(This article belongs to the Special Issue The Biology of Influenza Viruses)
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Article
A Weakened Immune Response to Synthetic Exo-Peptides Predicts a Potential Biosecurity Risk in the Retrieval of Exo-Microorganisms
Microorganisms 2020, 8(7), 1066; https://doi.org/10.3390/microorganisms8071066 - 17 Jul 2020
Viewed by 6974
Abstract
The discovery of liquid water at several locations in the solar system raises the possibility that microbial life may have evolved outside Earth and as such could be accidently introduced into the Earth’s ecosystem. Unusual sugars or amino acids, like non-proteinogenic isovaline and [...] Read more.
The discovery of liquid water at several locations in the solar system raises the possibility that microbial life may have evolved outside Earth and as such could be accidently introduced into the Earth’s ecosystem. Unusual sugars or amino acids, like non-proteinogenic isovaline and α-aminoisobutyric acid that are vanishingly rare or absent from life forms on Earth, have been found in high abundance on non-terrestrial carbonaceous meteorites. It is therefore conceivable that exo-microorganisms might contain proteins that include these rare amino acids. We therefore asked whether the mammalian immune system would be able to recognize and induce appropriate immune responses to putative proteinaceous antigens that include these rare amino acids. To address this, we synthesised peptide antigens based on a backbone of ovalbumin and introduced isovaline and α-aminoisobutyric acid residues and demonstrated that these peptides can promote naïve OT-I cell activation and proliferation, but did so less efficiently than the canonical peptides. This is relevant to the biosecurity of missions that may retrieve samples from exoplanets and moons that have conditions that may be permissive for life, suggesting that accidental contamination and exposure to exo-microorganisms with such distinct proteomes might pose an immunological challenge. Full article
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Article
Tick-Borne Encephalitis Virus and Its European Distribution in Ticks and Endothermic Mammals
Microorganisms 2020, 8(7), 1065; https://doi.org/10.3390/microorganisms8071065 - 17 Jul 2020
Cited by 11 | Viewed by 1666
Abstract
Tick-borne encephalitis (TBE) is the most common viral tick-borne disease in Europe causing thousands of human infections every year. Available risk maps in Europe are solely based on human incidences, but often underestimate areas with TBE virus circulation as shown by several autochthonous [...] Read more.
Tick-borne encephalitis (TBE) is the most common viral tick-borne disease in Europe causing thousands of human infections every year. Available risk maps in Europe are solely based on human incidences, but often underestimate areas with TBE virus circulation as shown by several autochthonous cases detected outside known risk areas. A dataset of more than 1300 georeferenced TBE virus detections in ticks and mammals except for humans was compiled and used to estimate the probability of TBE virus presence in Europe. For this, a random forests model was implemented using temperature- and precipitation-dependent bioclimatic variables of the WorldClim dataset, altitude, as well as land cover of the ESA GlobCover dataset. The highest probabilities of TBE virus presence were identified in Central Europe, in the south of the Nordic countries, and in the Baltic countries. The model performance was evaluated by an out-of-bag error (OOB) of 0.174 and a high area under the curve value (AUC) of 0.905. The TBE virus presence maps may subsequently be used to estimate the risk of TBE virus infections in humans and can support decision-makers to identify TBE risk areas and to encourage people to take appropriate actions against tick bites and TBE virus infections. Full article
(This article belongs to the Special Issue Tick-Borne Encephalitis)
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Communication
A Novel Multiplex qRT-PCR Assay to Detect SARS-CoV-2 Infection: High Sensitivity and Increased Testing Capacity
Microorganisms 2020, 8(7), 1064; https://doi.org/10.3390/microorganisms8071064 - 17 Jul 2020
Cited by 26 | Viewed by 2947
Abstract
Rapid and sensitive screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to limit the spread of the global pandemic we are facing. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is currently used for the clinical diagnosis of SARS-CoV-2 infection using [...] Read more.
Rapid and sensitive screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to limit the spread of the global pandemic we are facing. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is currently used for the clinical diagnosis of SARS-CoV-2 infection using nasopharyngeal swabs, tracheal aspirates, or bronchoalveolar lavage (BAL) samples. Despite the high sensitivity of the qRT-PCR method, false negative outcomes might occur, especially in patients with a low viral load. Here, we developed a multiplex qRT-PCR methodology for the simultaneous detection of SARS-CoV-2 genome (N gene) and of the human RNAse P gene as internal control. We found that multiplex qRT-PCR was effective in detecting SARS-Cov-2 infection in human specimens with 100% sensitivity. Notably, patients with few copies of SARS-CoV-2 RNA (<5 copies/reaction) were successfully detected by the novel multiplex qRT-PCR method. Finally, we assessed the efficacy of multiplex qRT-PCR on human nasopharyngeal swabs without RNA extraction. Collectively, our results provide evidence of a novel and reliable tool for SARS-CoV-2 RNA detection in human specimens, which allows the testing capacity to be expanded and the RNA extraction step to be bypassed. Full article
(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)
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