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Microorganisms, Volume 8, Issue 10 (October 2020) – 174 articles

Cover Story (view full-size image): Bacteria packaging is a phenomenon observed when undigested bacteria are evacuated in a protozoan’s fecal pellets. The packaged bacteria may be surrounded by a membrane layer that can protect them from physical stress and biocides. Here, we show that the ciliates Tetrahymena pyriformis and T. thermophila can package various species of non-pathogenic bacteria with different characteristics, as previous research in the field has focused almost exclusively on human pathogens. Each of the bacterial strains studied produces a specific pellet morphology, illustrating the complex relationship between bacteria and protozoa. Based on these results, bacteria packaging may be a more widespread phenomenon than previously considered. View this paper
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Article
A Peptide Found in Human Serum, Derived from the C-Terminus of Albumin, Shows Antifungal Activity In Vitro and In Vivo
Microorganisms 2020, 8(10), 1627; https://doi.org/10.3390/microorganisms8101627 - 21 Oct 2020
Cited by 3 | Viewed by 710
Abstract
The growing problem of antimicrobial resistance highlights the need for alternative strategies to combat infections. From this perspective, there is a considerable interest in natural molecules obtained from different sources, which are shown to be active against microorganisms, either alone or in association [...] Read more.
The growing problem of antimicrobial resistance highlights the need for alternative strategies to combat infections. From this perspective, there is a considerable interest in natural molecules obtained from different sources, which are shown to be active against microorganisms, either alone or in association with conventional drugs. In this paper, peptides with the same sequence of fragments, found in human serum, derived from physiological proteins, were evaluated for their antifungal activity. A 13-residue peptide, representing the 597–609 fragment within the albumin C-terminus, was proved to exert a fungicidal activity in vitro against pathogenic yeasts and a therapeutic effect in vivo in the experimental model of candidal infection in Galleria mellonella. Studies by confocal microscopy and transmission and scanning electron microscopy demonstrated that the peptide penetrates and accumulates in Candida albicans cells, causing gross morphological alterations in cellular structure. These findings add albumin to the group of proteins, which already includes hemoglobin and antibodies, that could give rise to cryptic antimicrobial fragments, and could suggest their role in anti-infective homeostasis. The study of bioactive fragments from serum proteins could open interesting perspectives for the development of new antimicrobial molecules derived by natural sources. Full article
(This article belongs to the Special Issue Natural Antimicrobial Compounds)
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Review
Retrospective Analysis on Antimicrobial Resistance Trends and Prevalence of β-lactamases in Escherichia coli and ESKAPE Pathogens Isolated from Arabian Patients during 2000–2020
Microorganisms 2020, 8(10), 1626; https://doi.org/10.3390/microorganisms8101626 - 21 Oct 2020
Cited by 3 | Viewed by 1301
Abstract
The production of diverse and extended spectrum β-lactamases among Escherichia coli and ESKAPE pathogens is a growing threat to clinicians and public health. We aim to provide a comprehensive analysis of evolving trends of antimicrobial resistance and β-lactamases among E. coli and ESKAPE [...] Read more.
The production of diverse and extended spectrum β-lactamases among Escherichia coli and ESKAPE pathogens is a growing threat to clinicians and public health. We aim to provide a comprehensive analysis of evolving trends of antimicrobial resistance and β-lactamases among E. coli and ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acine to bacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) in the Arabian region. A systematic review was conducted in Medline PubMed on papers published between January 2000 and February 2020 on countries in the Arab region showing different antibiotic resistance among E. coli and ESKAPE pathogens. A total of n = 119,144 clinical isolates were evaluated for antimicrobial resistance in 19 Arab countries. Among these clinical isolates, 74,039 belonged to E. coli and ESKAPE pathogen. Distribution of antibiotic resistance among E. coli and ESKAPE pathogens indicated that E. coli (n = 32,038) was the predominant pathogen followed by K. pneumoniae (n = 17,128), P. aeruginosa (n = 11,074), methicillin-resistant S. aureus (MRSA, n = 4370), A. baumannii (n = 3485) and Enterobacter spp. (n = 1574). There were no reports demonstrating Enterococcus faecium producing β-lactamase. Analyses revealed 19 out of 22 countries reported occurrence of ESBL (Extended-Spectrum β-Lactamase) producing E. coli and ESKAPE pathogens. The present study showed significantly increased resistance rates to various antimicrobial agents over the last 20 years; for instance, cephalosporin resistance increased from 37 to 89.5%, fluoroquinolones from 46.8 to 70.3%, aminoglycosides from 40.2 to 64.4%, mono-bactams from 30.6 to 73.6% and carbapenems from 30.5 to 64.4%. An average of 36.9% of the total isolates were reported to have ESBL phenotype during 2000 to 2020. Molecular analyses showed that among ESBLs and Class A and Class D β-lactamases, blaCTX-M and blaOXA have higher prevalence rates of 57% and 52.7%, respectively. Among Class B β-lactamases, few incidences of blaVIM 27.7% and blaNDM 26.3% were encountered in the Arab region. Conclusion: This review highlights a significant increase in resistance to various classes of antibiotics, including cephalosporins, β-lactam and β-lactamase inhibitor combinations, carbapenems, aminoglycosides and quinolones among E. coli and ESKAPE pathogens in the Arab region. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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Review
A Review of Potential Impacts of Climate Change on Coffee Cultivation and Mycotoxigenic Fungi
Microorganisms 2020, 8(10), 1625; https://doi.org/10.3390/microorganisms8101625 - 21 Oct 2020
Cited by 3 | Viewed by 1356
Abstract
Coffee is one of the most traded commodities in the world. It plays a significant role in the global economy, employing over 125 million people. However, it is possible that this vital crop is threatened by changing climate conditions and fungal infections. This [...] Read more.
Coffee is one of the most traded commodities in the world. It plays a significant role in the global economy, employing over 125 million people. However, it is possible that this vital crop is threatened by changing climate conditions and fungal infections. This paper reviews how suitable areas for coffee cultivation and the toxigenic fungi species of Aspergillus, Penicillium, and Fusarium will be affected due to climate change. By combining climate models with species distribution models, a number of studies have investigated the future distribution of coffee cultivation. Studies predict that suitable coffee cultivation area could drop by ~50% under representation concentration pathway (RCP) 6.0 by 2050 for both Arabica and Robusta. These findings agree with other studies which also see an altitudinal migration of suitable cultivation areas to cooler regions, but limited scope for latitudinal migration owing to coffee’s inability to tolerate seasonal temperature changes. Increased temperatures will see an overall increase in mycotoxin production such as aflatoxins, particularly in mycotoxigenic fungi (e.g., Aspergillus flavus) more suited to higher temperatures. Arabica and Robusta’s limited ability to relocate means both species will be grown in less suitable climates, increasing plant stress and making coffee more susceptible to fungal infection and mycotoxins. Information regarding climate change parameters with respect to mycotoxin concentrations in real coffee samples is provided and how the changed climate affects mycotoxins in non-coffee systems is discussed. In a few areas where relocating farms is possible, mycotoxin contamination may decrease due to the “parasites lost” phenomenon. More research is needed to include the effect of mycotoxins on coffee under various climate change scenarios, as currently there is a significant knowledge gap, and only generalisations can be made. Future modelling of coffee cultivation, which includes the influence of atmospheric carbon dioxide fertilisation and forest management, is also required; however, all indications show that climate change will have an extremely negative effect on future coffee production worldwide in terms of both a loss of suitable cultivation areas and an increase in mycotoxin contamination. Full article
(This article belongs to the Special Issue Coffee, Fungi, Mycotoxins, and Climate Change)
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Article
Non-Invasive Luciferase Imaging of Type I Interferon Induction in a Transgenic Mouse Model of Biomaterial Associated Bacterial Infections: Microbial Specificity and Inter-Bacterial Species Interactions
Microorganisms 2020, 8(10), 1624; https://doi.org/10.3390/microorganisms8101624 - 21 Oct 2020
Viewed by 724
Abstract
The performance of biomaterials is often compromised by bacterial infections and subsequent inflammation. So far, the conventional analysis of inflammatory processes in vivo involves time-consuming histology and biochemical assays. The present study employed a mouse model where interferon beta (IFN-β) is monitored as [...] Read more.
The performance of biomaterials is often compromised by bacterial infections and subsequent inflammation. So far, the conventional analysis of inflammatory processes in vivo involves time-consuming histology and biochemical assays. The present study employed a mouse model where interferon beta (IFN-β) is monitored as a marker for non-invasive rapid detection of inflammation in implant-related infections. The mouse model comprises subcutaneous implantation of morphologically modified titanium, followed by experimental infections with four taxonomically diverse oral bacteria: Streptococcus oralis, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Treponema denticola (as mono culture or selected mixed-culture). IFN-β expression increased upon infections depending on the type of pathogen and was prolonged by the presence of the implant. IFN-β expression kinetics reduced with two mixed species infections when compared with the single species. Histological and confocal microscopy confirmed pathogen-specific infiltration of inflammatory cells at the implant-tissue interface. This was observed mainly in the vicinity of infected implants and was, in contrast to interferon expression, higher in infections with dual species. In summary, this non-invasive mouse model can be used to quantify longitudinally host inflammation in real time and suggests that the polymicrobial character of infection, highly relevant to clinical situations, has complex effects on host immunity. Full article
(This article belongs to the Special Issue Biofilm Implant Related Infections)
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Article
Effect of a Debaryomyces hansenii and Lactobacillus buchneri Starter Culture on Aspergillus westerdijkiae Ochratoxin A Production and Growth during the Manufacture of Short Seasoned Dry-Cured Ham
Microorganisms 2020, 8(10), 1623; https://doi.org/10.3390/microorganisms8101623 - 21 Oct 2020
Cited by 1 | Viewed by 633
Abstract
Recently, specific dry-cured hams have started to be produced in San Daniele and Parma areas. The ingredients are similar to protected denomination of origin (PDO) produced in San Daniele or Parma areas, and include pork leg, coming from pigs bred in the Italian [...] Read more.
Recently, specific dry-cured hams have started to be produced in San Daniele and Parma areas. The ingredients are similar to protected denomination of origin (PDO) produced in San Daniele or Parma areas, and include pork leg, coming from pigs bred in the Italian peninsula, salt and spices. However, these specific new products cannot be marked as a PDO, either San Daniele or Parma dry cured ham, because they are seasoned for 6 months, and the mark PDO is given only to products seasoned over 13 months. Consequently, these products are called short-seasoned dry-cured ham (SSDCH) and are not branded PDO. During their seasoning period, particularly from the first drying until the end of the seasoning period, many molds, including Eurotium spp. and Penicillium spp., can grow on the surface and work together with other molds and tissue enzymes to produce a unique aroma. Both of these strains typically predominate over other molds. However, molds producing ochratoxins, such as Aspergillus ochraceus and Penicillium nordicum, can simultaneously grow and produce ochratoxin A (OTA). Consequently, these dry-cured hams may represent a potential health risk for consumers. Recently, Aspergillus westerdijkiae has been isolated from SSDCHs, which could represent a potential problem for consumers. Therefore, the aim of this study was to inhibit A. westerdijkiae using Debaryomyces hansenii or Lactobacillus buchneri or a mix of both microorganisms. Six D. hansenii and six L. buchneri strains were tested in vitro for their ability to inhibit A. westerdijkiae. The strains D. hansenii (DIAL)1 and L. buchneri (Lb)4 demonstrated the highest inhibitory activity and were selected for in situ tests. The strains were inoculated or co-inoculated on fresh pork legs for SSDCH production with OTA-producing A. westerdijkiae prior to the first drying and seasoning. At the end of seasoning (six months), OTA was not detected in the SSDCH treated with both microorganisms and their combination. Because both strains did not adversely affect the SSDCH odor or flavor, the combination of these strains are proposed for use as starters to inhibit OTA-producing A. westerdijkiae. Full article
(This article belongs to the Special Issue Food Spoilage Microorganisms: Ecology and Control)
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Review
Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors
Microorganisms 2020, 8(10), 1622; https://doi.org/10.3390/microorganisms8101622 - 21 Oct 2020
Cited by 1 | Viewed by 730
Abstract
Regulation of gene transcription is the initial step in the complex process that controls gene expression within bacteria. Transcriptional control involves the joint effort of RNA polymerases and numerous other regulatory factors. Whether global or local, positive or negative, regulators play an essential [...] Read more.
Regulation of gene transcription is the initial step in the complex process that controls gene expression within bacteria. Transcriptional control involves the joint effort of RNA polymerases and numerous other regulatory factors. Whether global or local, positive or negative, regulators play an essential role in the bacterial cell. For instance, some regulators specifically modify the transcription of virulence genes, thereby being indispensable to pathogenic bacteria. Here, we provide a comprehensive overview of important transcription factors and DNA-binding proteins described for the virulent bacterium Francisella tularensis, the causative agent of tularemia. This is an unexplored research area, and the poorly described networks of transcription factors merit additional experimental studies to help elucidate the molecular mechanisms of pathogenesis in this bacterium, and how they contribute to disease. Full article
(This article belongs to the Special Issue Tularemia: Pathogenesis, Diagnostic, Prevention, and Treatment)
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Article
Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis
Microorganisms 2020, 8(10), 1621; https://doi.org/10.3390/microorganisms8101621 - 21 Oct 2020
Cited by 5 | Viewed by 1164
Abstract
The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, [...] Read more.
The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection. Full article
(This article belongs to the Section Plant Microbe Interactions)
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Review
Rhinovirus Infection in Children with Acute Bronchiolitis and Its Impact on Recurrent Wheezing and Asthma Development
Microorganisms 2020, 8(10), 1620; https://doi.org/10.3390/microorganisms8101620 - 21 Oct 2020
Cited by 2 | Viewed by 681
Abstract
Acute bronchiolitis represents the leading cause of hospitalization in infants. Together with a respiratory syncytial virus, rhinovirus (RV) is one of the most common pathogens associated with bronchiolitis, and its genetic diversity (>150 types) makes the recurrence of RV infections each year quite [...] Read more.
Acute bronchiolitis represents the leading cause of hospitalization in infants. Together with a respiratory syncytial virus, rhinovirus (RV) is one of the most common pathogens associated with bronchiolitis, and its genetic diversity (>150 types) makes the recurrence of RV infections each year quite typical. The frequency of RV infection and co-infection with other viruses and its impact on the clinical course of bronchiolitis have been studied by several authors with controversial results. Some studies demonstrate that multiple virus infections result in more severe clinical presentation and a higher risk of complications, whereas other studies suggest no influence on clinical course. Moreover, RV bronchiolitis has been reported to potentially contribute to the development of long-term sequelae, such as recurrent wheezing and asthma, in the pediatric population. In the present review, we summarize the most recent findings of the role of RV infection in children with acute bronchiolitis, its impact on subsequent asthma development, and the implication in clinical practice. Full article
(This article belongs to the Special Issue Epidemiology of Enterovirus Disease)
Article
Salt Marsh Elevation Drives Root Microbial Composition of the Native Invasive Grass Elytrigia atherica
Microorganisms 2020, 8(10), 1619; https://doi.org/10.3390/microorganisms8101619 - 21 Oct 2020
Cited by 1 | Viewed by 814
Abstract
Elytrigia atherica is a native invasive plant species whose expansion on salt marshes is attributed to genotypic and phenotypic adaptations to non-ideal environmental conditions, forming two ecotypes. It is unknown how E. atherica–microbiome interactions are contributing to its adaptation. Here we investigated [...] Read more.
Elytrigia atherica is a native invasive plant species whose expansion on salt marshes is attributed to genotypic and phenotypic adaptations to non-ideal environmental conditions, forming two ecotypes. It is unknown how E. atherica–microbiome interactions are contributing to its adaptation. Here we investigated the effect of sea-water flooding frequency and associated soil (a)biotic conditions on plant traits and root-associated microbial community composition and potential functions of two E. atherica ecotypes. We observed higher endomycorrhizal colonization in high-elevation ecotypes (HE, low inundation frequency), whereas low-elevation ecotypes (LE, high inundation frequency) had higher specific leaf area. Similarly, rhizosphere and endosphere bacterial communities grouped according to ecotypes. Soil ammonium content and elevation explained rhizosphere bacterial composition. Around 60% the endosphere amplicon sequence variants (ASVs) were also found in soil and around 30% of the ASVs were ecotype-specific. The endosphere of HE-ecotype harbored more unique sequences than the LE-ecotype, the latter being abundant in halophylic bacterial species. The composition of the endosphere may explain salinity and drought tolerance in relation to the local environmental needs of each ecotype. Overall, these results suggest that E. atherica is flexible in its association with soil bacteria and ecotype-specific dissimilar, which may enhance its competitive strength in salt marshes. Full article
(This article belongs to the Special Issue Role of Microorganisms in the Evolution of Animals and Plants)
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Article
Use of Exopolysaccharide-Synthesizing Lactic Acid Bacteria and Fat Replacers for Manufacturing Reduced-Fat Burrata Cheese: Microbiological Aspects and Sensory Evaluation
Microorganisms 2020, 8(10), 1618; https://doi.org/10.3390/microorganisms8101618 - 21 Oct 2020
Cited by 2 | Viewed by 902
Abstract
This study aimed to set-up a biotechnological protocol for manufacturing a reduced-fat Burrata cheese using semi-skimmed milk and reduced-fat cream, in different combinations with exopolysaccharides-synthesizing bacterial starters (Streptococcus thermophilus, E1, or Lactococcus lactis subsp. lactis and Lc. lactis subsp. cremoris [...] Read more.
This study aimed to set-up a biotechnological protocol for manufacturing a reduced-fat Burrata cheese using semi-skimmed milk and reduced-fat cream, in different combinations with exopolysaccharides-synthesizing bacterial starters (Streptococcus thermophilus, E1, or Lactococcus lactis subsp. lactis and Lc. lactis subsp. cremoris, E2) and carrageenan or xanthan. Eight variants of reduced-fat cheese (fat concentration 34–51% lower than traditional full-fat Burrata cheese, used as the control) were obtained using: (i) semi-skimmed milk and reduced-fat cream alone (RC) or in combination with (ii) xanthan (RCX), (iii) carrageenan (RCC), (iv) starter E1 (RCE1), (v) starter E2 (RCE2), (vi) both starters (RCE1-2), (vii) E1 and xanthan (RCXE1), or E1 and carrageenan (RCCE1). Post-acidification occurred for the RCC, RCX, and RCE2 Burrata cheeses, due to the higher number of mesophilic cocci found in these cheeses after 16 days of storage. Overall, mesophilic and thermophilic cocci, although showing cheese variant-depending dynamics, were dominant microbial groups, flanked by Pseudomonas sp. during storage. Lactobacilli, increasing during storage, represented another dominant microbial group. The panel test gave highest scores to RCE1-2 and RCXE1 cheeses, even after 16 days of storage. The 16S-targeted metagenomic analysis revealed that a core microbiota (S. thermophilus, Streptococcus lutetiensis, Lc. lactis, Lactococcus sp., Leuconostoc lactis, Lactobacillus delbrueckii, and Pseudomonas sp.), characterized the Burrata cheeses. A consumer test, based on 105 people, showed that more than 50% of consumers did not distinguish the traditional full-fat from the RCXE1 reduced-fat Burrata cheese. Full article
(This article belongs to the Special Issue Microbial Populations of Fermented Foods)
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Article
Screening Fungal Endophytes Derived from Under-Explored Egyptian Marine Habitats for Antimicrobial and Antioxidant Properties in Factionalised Textiles
Microorganisms 2020, 8(10), 1617; https://doi.org/10.3390/microorganisms8101617 - 21 Oct 2020
Cited by 5 | Viewed by 1538
Abstract
Marine endophytic fungi from under-explored locations are a promising source for the discovery of new bioactivities. Different endophytic fungi were isolated from plants and marine organisms collected from Wadi El-Natrun saline lakes and the Red Sea near Hurghada, Egypt. The isolated strains were [...] Read more.
Marine endophytic fungi from under-explored locations are a promising source for the discovery of new bioactivities. Different endophytic fungi were isolated from plants and marine organisms collected from Wadi El-Natrun saline lakes and the Red Sea near Hurghada, Egypt. The isolated strains were grown on three different media, and their ethyl acetate crude extracts were evaluated for their antimicrobial activity against a panel of pathogenic bacteria and fungi as well as their antioxidant properties. Results showed that most of the 32 fungal isolates initially obtained possessed antimicrobial and antioxidant activities. The most potent antimicrobial extracts were applied to three different cellulose containing fabrics to add new multifunctional properties such as ultraviolet protection and antimicrobial functionality. For textile safety, the toxicity profile of the selected fungal extract was evaluated on human fibroblasts. The 21 strains displaying bioactivity were identified on molecular basis and selected for chemical screening and dereplication, which was carried out by analysis of the MS/MS data using the Global Natural Products Social Molecular Networking (GNPS) platform. The obtained molecular network revealed molecular families of compounds commonly produced by fungal strains, and in combination with manual dereplication, further previously reported metabolites were identified as well as potentially new derivatives. Full article
(This article belongs to the Special Issue Microbial Secondary Metabolites and Biotechnology)
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Correction
Correction: Krauss, J., et al. Epichloë Endophyte Infection Rates and Alkaloid Content in Commercially Available Grass Seed Mixtures in Europe. Microorganisms 2020, 8, 498
Microorganisms 2020, 8(10), 1616; https://doi.org/10.3390/microorganisms8101616 - 21 Oct 2020
Viewed by 613
Abstract
The authors wish to make the following correction to this paper [...] Full article
(This article belongs to the Special Issue Fungal Endophytes and Their Interactions with Plants)
Review
Human mecC-Carrying MRSA: Clinical Implications and Risk Factors
Microorganisms 2020, 8(10), 1615; https://doi.org/10.3390/microorganisms8101615 - 20 Oct 2020
Cited by 4 | Viewed by 895
Abstract
A new methicillin resistance gene, named mecC, was first described in 2011 in both humans and animals. Since then, this gene has been detected in different production and free-living animals and as an agent causing infections in some humans. The possible impact [...] Read more.
A new methicillin resistance gene, named mecC, was first described in 2011 in both humans and animals. Since then, this gene has been detected in different production and free-living animals and as an agent causing infections in some humans. The possible impact that these isolates can have in clinical settings remains unknown. The current available information about mecC-carrying methicillin resistant S. aureus (MRSA) isolates obtained from human samples was analyzed in order to establish its possible clinical implications as well as to determine the infection types associated with this resistance mechanism, the characteristics of these mecC-carrying isolates, their possible relation with animals and the presence of other risk factors. Until now, most human mecC-MRSA infections have been reported in Europe and mecC-MRSA isolates have been identified belonging to a small number of clonal complexes. Although the prevalence of mecC-MRSA human infections is very low and isolates usually contain few resistance (except for beta-lactams) and virulence genes, first isolates harboring important virulence genes or that are resistant to non-beta lactams have already been described. Moreover, severe and even fatal human infection cases have been detected. mecC-carrying MRSA should be taken into consideration in hospital, veterinary and food safety laboratories and in prevention strategies in order to avoid possible emerging health problems. Full article
(This article belongs to the Special Issue Staphylococcal Infections (Host and Pathogenic Factors))
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Article
Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
Microorganisms 2020, 8(10), 1614; https://doi.org/10.3390/microorganisms8101614 - 20 Oct 2020
Viewed by 867
Abstract
In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting [...] Read more.
In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae. Full article
(This article belongs to the Special Issue Biology, Diversity, and Ecology of Methanotrophic Bacteria)
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Article
Mardivirus Infection and Persistence in Feathers of a Chicken Model Harboring a Local Autoimmune Response
Microorganisms 2020, 8(10), 1613; https://doi.org/10.3390/microorganisms8101613 - 20 Oct 2020
Viewed by 521
Abstract
Herpesvirus of turkey (HVT) is commonly used as a vaccine to protect chickens against Marek’s disease. Following vaccination, HVT infects feathers where it can be detected in all chicken lines examined. Unlike the parental Brown line (BL), Smyth line (SL) chickens develop vitiligo, [...] Read more.
Herpesvirus of turkey (HVT) is commonly used as a vaccine to protect chickens against Marek’s disease. Following vaccination, HVT infects feathers where it can be detected in all chicken lines examined. Unlike the parental Brown line (BL), Smyth line (SL) chickens develop vitiligo, due to autoimmune destruction of melanocytes in feathers. Previous reports showed a strong inflammatory response in Smyth chickens’ feathers at vitiligo onset, that subsided once melanocytes were destroyed, and depigmentation was complete. Here, we questioned whether the local autoimmune response in the Smyth model influences HVT infection and persistence in feathers. For this, one-day-old SL and BL chickens were vaccinated with Newcastle disease (rHVT-ND). Vitiligo was scored and HVT loads in pigmented and non-pigmented growing feathers were quantified regularly over 20 weeks. Chickens of both lines showed moderate HVT loads in feathers. At the onset of active vitiligo, the HVT load was significantly higher in SL compared to BL feathers. However, no difference in HVT loads was noticed between pigmented and non-pigmented feathers from SL chickens. Therefore, surprisingly, the inflammatory response in feathers of SL chickens did not inhibit HVT infection and persistence, but on the contrary, temporarily promoted HVT infection in feathers. Full article
(This article belongs to the Special Issue Marek’s Disease Virus)
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Article
Clustering on Human Microbiome Sequencing Data: A Distance-Based Unsupervised Learning Model
Microorganisms 2020, 8(10), 1612; https://doi.org/10.3390/microorganisms8101612 - 20 Oct 2020
Viewed by 802
Abstract
Modeling and analyzing human microbiome allows the assessment of the microbial community and its impacts on human health. Microbiome composition can be quantified using 16S rRNA technology into sequencing data, which are usually skewed and heavy-tailed with excess zeros. Clustering methods are useful [...] Read more.
Modeling and analyzing human microbiome allows the assessment of the microbial community and its impacts on human health. Microbiome composition can be quantified using 16S rRNA technology into sequencing data, which are usually skewed and heavy-tailed with excess zeros. Clustering methods are useful in personalized medicine by identifying subgroups for patients stratification. However, there is currently a lack of standardized clustering method for the complex microbiome sequencing data. We propose a clustering algorithm with a specific beta diversity measure that can address the presence-absence bias encountered for sparse count data and effectively measure the sample distances for sample stratification. Our distance measure used for clustering is derived from a parametric based mixture model producing sample-specific distributions conditional on the observed operational taxonomic unit (OTU) counts and estimated mixture weights. The method can provide accurate estimates of the true zero proportions and thus construct a precise beta diversity measure. Extensive simulation studies have been conducted and suggest that the proposed method achieves substantial clustering improvement compared with some widely used distance measures when a large proportion of zeros is presented. The proposed algorithm was implemented to a human gut microbiome study on Parkinson’s diseases to identify distinct microbiome states with biological interpretations. Full article
(This article belongs to the Special Issue New Methods in Microbial Research)
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Article
The Microbiota Profile in Inflamed and Non-Inflamed Ileal Pouch–Anal Anastomosis
Microorganisms 2020, 8(10), 1611; https://doi.org/10.3390/microorganisms8101611 - 20 Oct 2020
Cited by 1 | Viewed by 670
Abstract
The objective was to determine the bacterial composition in inflamed and non-inflamed pouches for comparison to the microbiota of healthy individuals. Pouch patients and healthy individuals were included between November 2017 and June 2019 at the Department of Gastrointestinal Surgery, Aalborg University Hospital, [...] Read more.
The objective was to determine the bacterial composition in inflamed and non-inflamed pouches for comparison to the microbiota of healthy individuals. Pouch patients and healthy individuals were included between November 2017 and June 2019 at the Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark. A faecal sample was collected from all participants for microbiota analysis using 16S rRNA amplicon sequencing. Overall, 38 participants were included in the study. Eleven patients with a normally functioning pouch, 9 patients with chronic pouchitis, 6 patients with familial adenomatous polyposis, and 12 healthy individuals. Patients with chronic pouchitis had overall lower microbial diversity and richness compared to patients with a normal pouch function (p < 0.001 and p = 0.009) and healthy individuals (p < 0.001 and p < 0.001). No significant difference was found between patients with familial adenomatous polyposis and chronic pouchitis (microbial diversity p = 0.39 and richness p = 0.78). Several taxa from the family Enterobacteriaceae, especially genus Escherichia, were associated primarily with patients with chronic pouchitis, while taxa from the genus Bacteroides primarily were associated with healthy individuals and patients with a normally functioning pouch. Finally, a microbial composition gradient could be established from healthy individuals through patients with normal pouch function and familial adenomatous polyposis to patients with chronic pouchitis. Full article
(This article belongs to the Section Gut Microbiota)
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Communication
Detailed Molecular Interactions of Favipiravir with SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza Virus Polymerases In Silico
Microorganisms 2020, 8(10), 1610; https://doi.org/10.3390/microorganisms8101610 - 20 Oct 2020
Cited by 6 | Viewed by 1864
Abstract
Favipiravir was initially developed as an antiviral drug against influenza and is currently used in clinical trials against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (COVID-19). This agent is presumably involved in RNA chain termination during influenza virus replication, although the molecular interactions [...] Read more.
Favipiravir was initially developed as an antiviral drug against influenza and is currently used in clinical trials against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection (COVID-19). This agent is presumably involved in RNA chain termination during influenza virus replication, although the molecular interactions underlying its potential impact on the coronaviruses including SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) remain unclear. We performed in silico studies to elucidate detailed molecular interactions between favipiravir and the SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza virus RNA-dependent RNA polymerases (RdRp). As a result, no interactions between favipiravir ribofuranosyl-5′-triphosphate (F-RTP), the active form of favipiravir, and the active sites of RdRps (PB1 proteins) from influenza A (H1N1)pdm09 virus were found, yet the agent bound to the tunnel of the replication genome of PB1 protein leading to the inhibition of replicated RNA passage. In contrast, F-RTP bound to the active sites of coronavirus RdRp in the presence of the agent and RdRp. Further, the agent bound to the replicated RNA terminus in the presence of agent, magnesium ions, nucleotide triphosphate, and RdRp proteins. These results suggest that favipiravir exhibits distinct mechanisms of action against influenza virus and various coronaviruses. Full article
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Article
Biofilm Produced In Vitro by Piscirickettsia salmonis Generates Differential Cytotoxicity Levels and Expression Patterns of Immune Genes in the Atlantic Salmon Cell Line SHK-1
Microorganisms 2020, 8(10), 1609; https://doi.org/10.3390/microorganisms8101609 - 20 Oct 2020
Viewed by 950
Abstract
Piscirickettsia salmonis is the causative agent of Piscirickettsiosis, an infectious disease with a high economic impact on the Chilean salmonid aquaculture industry. This bacterium produces biofilm as a potential resistance and persistence strategy against stressful environmental stimuli. However, the in vitro culture conditions [...] Read more.
Piscirickettsia salmonis is the causative agent of Piscirickettsiosis, an infectious disease with a high economic impact on the Chilean salmonid aquaculture industry. This bacterium produces biofilm as a potential resistance and persistence strategy against stressful environmental stimuli. However, the in vitro culture conditions that modulate biofilm formation as well as the effect of sessile bacteria on virulence and immune gene expression in host cells have not been described for P. salmonis. Therefore, this study aimed to analyze the biofilm formation by P. salmonis isolates under several NaCl and iron concentrations and to evaluate the virulence of planktonic and sessile bacteria, together with the immune gene expression induced by these bacterial conditions in an Atlantic salmon macrophage cell line. Our results showed that NaCl and Fe significantly increased biofilm production in the LF-89 type strain and EM-90-like isolates. Additionally, the planktonic EM-90 isolate and sessile LF-89 generated the highest virulence levels, associated with differential expression of il-1β, il-8, nf-κb, and iκb-α genes in SHK-1 cells. These results suggest that there is no single virulence pattern or gene expression profile induced by the planktonic or sessile condition of P. salmonis, which are dependent on each strain and bacterial condition used. Full article
(This article belongs to the Section Biofilm)
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Article
An Alcohol Dehydrogenase 3 (ADH3) from Entamoeba histolytica Is Involved in the Detoxification of Toxic Aldehydes
Microorganisms 2020, 8(10), 1608; https://doi.org/10.3390/microorganisms8101608 - 19 Oct 2020
Cited by 1 | Viewed by 831
Abstract
Recently, a putative alcohol dehydrogenase 3, termed EhADH3B of the Entamoeba histolytica isolate HM-1:IMSS was identified, which is expressed at higher levels in non-pathogenic than in pathogenic amoebae and whose overexpression reduces the virulence of pathogenic amoebae. In an in silico analysis performed [...] Read more.
Recently, a putative alcohol dehydrogenase 3, termed EhADH3B of the Entamoeba histolytica isolate HM-1:IMSS was identified, which is expressed at higher levels in non-pathogenic than in pathogenic amoebae and whose overexpression reduces the virulence of pathogenic amoebae. In an in silico analysis performed in this study, we assigned EhADH3B to a four-member ADH3 family, with ehadh3b present as a duplicate (ehadh3ba/ehadh3bb). In long-term laboratory cultures a mutation was identified at position 496 of ehadh3ba, which codes for a stop codon, which was not the case for amoebae isolated from human stool samples. When using transfectants that overexpress or silence ehadh3bb, we found no or little effect on growth, size, erythrophagocytosis, motility, hemolytic or cysteine peptidase activity. Biochemical characterization of the recombinant EhADH3Bb revealed that this protein forms a dimer containing Ni2+ or Zn2+ as a co-factor and that the enzyme converts acetaldehyde and formaldehyde in the presence of NADPH. A catalytic activity based on alcohols as substrates was not detected. Based on the results, we postulate that EhADH3Bb can reduce free acetaldehyde released by hydrolysis from bifunctional acetaldehyde/alcohol dehydrogenase-bound thiohemiacetal and that it is involved in detoxification of toxic aldehydes produced by the host or the gut microbiota. Full article
(This article belongs to the Special Issue Virulence and Parasitism of Parasitic Protozoa)
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Article
Effects of Different Stress Parameters on Growth and on Oleuropein-Degrading Abilities of Lactiplantibacillus plantarum Strains Selected as Tailored Starter Cultures for Naturally Table Olives
Microorganisms 2020, 8(10), 1607; https://doi.org/10.3390/microorganisms8101607 - 19 Oct 2020
Cited by 1 | Viewed by 613
Abstract
The use of β-glucosidase positive strains, as tailored-starter cultures for table olives fermentation, is a useful biotechnological tool applied to accelerate the debittering process. Nowadays, strains belonging to Lactiplantibacillus plantarum species are selected for their high versatility and tolerance to stress conditions. The [...] Read more.
The use of β-glucosidase positive strains, as tailored-starter cultures for table olives fermentation, is a useful biotechnological tool applied to accelerate the debittering process. Nowadays, strains belonging to Lactiplantibacillus plantarum species are selected for their high versatility and tolerance to stress conditions. The present study investigated the effect of different stress factors (pH, temperature and NaCl) on growth and on oleuropein-degrading abilities of selected L. plantarum strains. In addition, the presence of the beta-glucosidase gene was investigated by applying a PCR based approach. Results revealed that, overall, the performances of the tested strains appeared to be robust toward the different stressors. However, the temperature of 16 °C significantly affected the growth performance of the strains both singularly and in combination with other stressing factors since it prolongs the latency phase and reduces the maximum growth rate of strains. Similarly, the oleuropein degradation was mainly affected by the low temperature, especially in presence of low salt content. Despite all strains displayed the ability to reduce the oleuropein content, the beta-glucosidase gene was detected in five out of the nine selected strains, demonstrating that the ability to hydrolyze the oleuropein is not closely related to the presence of beta-glucosidase. Data of the present study suggest that is extremely important to test the technological performances of strains at process conditions in order to achieve a good selection of tailored starter cultures for table olives. Full article
(This article belongs to the Special Issue Microbial Populations of Fermented Foods)
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Article
Electrically Charged Disinfectant Containing Calcium Hydrogen Carbonate Mesoscopic Crystals as a Potential Measure to Control Xanthomonas campestris pv. campestris on Cabbage Seeds
Microorganisms 2020, 8(10), 1606; https://doi.org/10.3390/microorganisms8101606 - 19 Oct 2020
Viewed by 1133
Abstract
Xanthomonas campestris pv. campestris (Xcc) is an important seed-borne bacterial pathogen that causes black rot in brassica. Current seed disinfection methods for Xcc have disadvantages; chemical treatment has associated environmental risks, hot water immersion reduces germination, and dry heat treatment is [...] Read more.
Xanthomonas campestris pv. campestris (Xcc) is an important seed-borne bacterial pathogen that causes black rot in brassica. Current seed disinfection methods for Xcc have disadvantages; chemical treatment has associated environmental risks, hot water immersion reduces germination, and dry heat treatment is protracted. Here, we treated Xcc-contaminated seeds with CAC-717, a recently developed disinfectant produced by applying an electric field and water flow to distilled water containing calcium hydrogen carbonate to produce mesoscopic crystals. The decimal reduction time (D-value) of Xcc suspension (8.22 log10 colony forming units (CFU)/mL) by CAC-717 treatment was 0.319 min. Treatment of Xcc-contaminated cabbage seeds at 25 °C for 30 min with CAC-717 significantly reduced bacterial cell numbers recovered from the seeds (0.36 log10 CFU/mL (SEM (standard error of the mean) = 0.23 log10 CFU/mL)) compared with distilled water treatment (3.52 log10 CFU/mL (SEM = 0.12 log10 CFU/mL)). Moreover, there was a lower incidence of black rot after treatment with CAC-717 (26.67% ± 3.33%) versus distilled water (56.67% ± 8.82%). For non-contaminated seeds, there was no significant difference in germination rate and plant stem length between distilled water and CAC-717 treatment after 5 days of cultivation. In conclusion, CAC-717 is a promising seed disinfectant without deleterious effects on germination or plant growth. Full article
(This article belongs to the Section Microbial Biotechnology)
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Article
Effects of Wormwood (Artemisia montana) Essential Oils on Digestibility, Fermentation Indices, and Microbial Diversity in the Rumen
Microorganisms 2020, 8(10), 1605; https://doi.org/10.3390/microorganisms8101605 - 18 Oct 2020
Viewed by 843
Abstract
This study investigated the effects of essential oil (EO) from three Korean wormwood (Artemisia Montana) plants on in vitro ruminal digestibility, fermentation, and microbial diversity. Dried (0.5 g) soybean meal (SBM) or bermudagrass hay (BGH) were incubated in buffered rumen fluid [...] Read more.
This study investigated the effects of essential oil (EO) from three Korean wormwood (Artemisia Montana) plants on in vitro ruminal digestibility, fermentation, and microbial diversity. Dried (0.5 g) soybean meal (SBM) or bermudagrass hay (BGH) were incubated in buffered rumen fluid (40 mL) for 72 h with or without EO (5 mg/kg) from Ganghwa (GA), Injin (IN), or San (SA) wormwood (Experiment 1). Both SA and IN improved (p < 0.05) dry matter digestibility (DMD) of BGH, while GA reduced (p < 0.05) total short-chain fatty acid of BGH and SBM. Besides, SA increased (p < 0.05) numbers of Ruminococcus albus and Streptococcus bovis in SBM. Experiment 2 examined different doses (0, 0.1, 1, and 10 mg/kg) of SA, the most promising EO from Experiment 1. Applying SA at 10 mg/kg gave the highest DMD (L; p < 0.01) and neutral detergent fiber (Q; p < 0.05) digestibility for BGH. Applying SA at 1 mg/kg gave the highest R. albus population (Q; p < 0.05) in SBM. Therefore, SA was better than GA and IN at improving rumen fermentation, and the 0.1 to 1 and 10 mg/kg doses improved ruminal fermentation and in vitro digestibility of SBM and BGH, respectively. Full article
(This article belongs to the Section Gut Microbiota)
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Article
Spatial Changes in Microbial Communities along Different Functional Zones of a Free-Water Surface Wetland
Microorganisms 2020, 8(10), 1604; https://doi.org/10.3390/microorganisms8101604 - 18 Oct 2020
Cited by 2 | Viewed by 838
Abstract
Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical conditions, and vegetation, [...] Read more.
Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical conditions, and vegetation, one can expect the presence of distinct microbiomes across different CW zones. Here, we investigated spatial changes in microbiomes along different functional zones of a free-water surface wetland located in Moscow, Russia. The microbiome structure was analyzed using Illumina MiSeq amplicon sequencing. We also determined particle diameter and surface area of sediments, as well as chemical composition of organic pollutants in different CW zones. Specific organic particle aggregates similar to activated sludge flocs were identified in the sediments. The highest accumulation of hydrocarbons was found in the zones with predominant sedimentation of fine fractions. Phytofilters had the highest rate of organic pollutants decomposition and predominance of Smithella, Ignavibacterium, and Methanothrix. The sedimentation tank had lower microbial diversity, and higher relative abundances of Parcubacteria, Proteiniclasticum, and Macellibacteroides, as well as higher predicted abundances of genes related to methanogenesis and methanotrophy. Thus, spatial changes in microbiomes of constructed wetlands can be associated with different types of wastewater treatment processes. Full article
(This article belongs to the Special Issue Precision Microbiomics: Environment to Human Health)
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Article
Combined Comparative Genomics and Gene Expression Analyses Provide Insights into the Terpene Synthases Inventory in Trichoderma
Microorganisms 2020, 8(10), 1603; https://doi.org/10.3390/microorganisms8101603 - 18 Oct 2020
Cited by 10 | Viewed by 1248
Abstract
Trichoderma is a fungal genus comprising species used as biocontrol agents in crop plant protection and with high value for industry. The beneficial effects of these species are supported by the secondary metabolites they produce. Terpenoid compounds are key players in the interaction [...] Read more.
Trichoderma is a fungal genus comprising species used as biocontrol agents in crop plant protection and with high value for industry. The beneficial effects of these species are supported by the secondary metabolites they produce. Terpenoid compounds are key players in the interaction of Trichoderma spp. with the environment and with their fungal and plant hosts; however, most of the terpene synthase (TS) genes involved in their biosynthesis have yet not been characterized. Here, we combined comparative genomics of TSs of 21 strains belonging to 17 Trichoderma spp., and gene expression studies on TSs using T. gamsii T6085 as a model. An overview of the diversity within the TS-gene family and the regulation of TS genes is provided. We identified 15 groups of TSs, and the presence of clade-specific enzymes revealed a variety of terpenoid chemotypes evolved to cover different ecological demands. We propose that functional differentiation of gene family members is the driver for the high number of TS genes found in the genomes of Trichoderma. Expression studies provide a picture in which different TS genes are regulated in many ways, which is a strong indication of different biological functions. Full article
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Communication
A Preliminary Study on the Presence of Salmonella in Lymph Nodes of Sows at Processing Plants in the United States
Microorganisms 2020, 8(10), 1602; https://doi.org/10.3390/microorganisms8101602 - 18 Oct 2020
Cited by 1 | Viewed by 684
Abstract
Salmonella-contaminated lymph nodes (LN), when included into edible meat products, are a potential source of Salmonella foodborne disease. In this survey, ventral superficial cervical and mandibular LN were tested for the presence of Salmonella from two sow processing plants in the midwestern [...] Read more.
Salmonella-contaminated lymph nodes (LN), when included into edible meat products, are a potential source of Salmonella foodborne disease. In this survey, ventral superficial cervical and mandibular LN were tested for the presence of Salmonella from two sow processing plants in the midwestern United States. Results indicate that both LN can be contaminated with Salmonella; mandibular LN have higher prevalence (p < 0.05) of Salmonella than cervical LN (16% vs. 0.91%), and the majority (>90%) of Salmonella isolates are pan-susceptible or resistant to one antimicrobial, while 9.78% of isolates were multi-drug-resistant (MDR-resistant to three or more classes of antimicrobials). Intervention methods to prevent foodborne disease could include elimination of these LN from pork products or inclusion of LN only into products that are destined for cooking. Integrated multi-faceted intervention methods need to be developed to reduce Salmonella in the food chain. Full article
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Article
Bacterial Community Dynamics Distinguish Poultry Compost from Dairy Compost and Non-Amended Soils Planted with Spinach
Microorganisms 2020, 8(10), 1601; https://doi.org/10.3390/microorganisms8101601 - 18 Oct 2020
Cited by 4 | Viewed by 865
Abstract
The aim of this study was to determine whether and how poultry litter compost and dairy manure compost alter the microbial communities within field soils planted with spinach. In three successive years, separate experimental plots on two fields received randomly assigned compost treatments [...] Read more.
The aim of this study was to determine whether and how poultry litter compost and dairy manure compost alter the microbial communities within field soils planted with spinach. In three successive years, separate experimental plots on two fields received randomly assigned compost treatments varying in animal origin: dairy manure (DMC), poultry litter (PLC), or neither (NoC). The composition and function of bacterial and fungal communities were characterized by the amplicon sequencing of marker genes and by the ecoenzyme activity, respectively. The temporal autocorrelation within and among years was adjusted by principal response curves (PRC) to analyze the effect of compost on community composition among treatments. Bacteria in the phylum Bacteriodetes, classes Flavobacteriia and Spingobacteriales (Fluviicola, Flavobacteriia, and Pedobacter), were two to four times more abundant in soils amended with PLC than DMC or NoC consistently among fields and years. Fungi in the phylum Ascomycota were relatively abundant, but their composition was field-specific and without treatment differences. The ecoenzyme data verify that the effects of PLC and DMC on soil communities are based on their microbial composition and not a response to the C source or nutrient content of the compost. Full article
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Article
In silico Investigation on the Inhibiting Role of Nicotine/Caffeine by Blocking the S Protein of SARS-CoV-2 Versus ACE2 Receptor
Microorganisms 2020, 8(10), 1600; https://doi.org/10.3390/microorganisms8101600 - 17 Oct 2020
Cited by 7 | Viewed by 2139
Abstract
In this paper, we studied the in silico interaction of angiotensin-converting enzyme 2 (ACE2) human receptor with two bioactive compounds, i.e., nicotine and caffeine, via molecular dynamic (MD) simulations. The simulations reveal the efficient blocking of ACE2 by caffeine and nicotine in the [...] Read more.
In this paper, we studied the in silico interaction of angiotensin-converting enzyme 2 (ACE2) human receptor with two bioactive compounds, i.e., nicotine and caffeine, via molecular dynamic (MD) simulations. The simulations reveal the efficient blocking of ACE2 by caffeine and nicotine in the exposure to the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have selected the two most important active sites of ACE2-S protein, i.e., 6LZG and 6VW1, which are critically responsible in the interaction of S protein to the receptor and thus, we investigated their interaction with nicotine and caffeine through MD simulations. Caffeine and nicotine are interesting structures for interactions because of their similar structure to the candidate antiviral drugs. Our results reveal that caffeine or nicotine in a specific molar ratio to 6LZG shows a very strong interaction and indicate that caffeine is more efficient in the interaction with 6LZG and further blocking of this site against S protein binding. Further, we investigated the interaction of ACE2 receptor- S protein with nicotine or caffeine when mixed with candidate or approved antiviral drugs for SARS-CoV-2 therapy. Our MD simulations suggest that the combination of caffeine with ribavirin shows a stronger interaction with 6VW1, while in case of favipiravir+nicotine, 6LZG shows potent efficacy of these interaction, proposing the potent efficacy of these combinations for blocking ACE2 receptor against SARS-CoV-2. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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Article
Identification and Elimination of the Clinically Relevant Multi-Resistant Environmental Bacteria Ralstonia insidiosa in Primary Cell Culture
Microorganisms 2020, 8(10), 1599; https://doi.org/10.3390/microorganisms8101599 - 17 Oct 2020
Viewed by 691
Abstract
In times of spreading multidrug-resistant bacteria, species identification and decontamination of cell cultures can be challenging. Here, we describe a mobile cell culture contaminant with “black dot”-like microscopic appearance in newly established irreplaceable hybridoma cell lines and its identification. Using 16S rRNA gene [...] Read more.
In times of spreading multidrug-resistant bacteria, species identification and decontamination of cell cultures can be challenging. Here, we describe a mobile cell culture contaminant with “black dot”-like microscopic appearance in newly established irreplaceable hybridoma cell lines and its identification. Using 16S rRNA gene sequencing, species-specific PCRs, whole genome sequencing (WGS), and MALDI-TOF mass spectrometry, the contaminant was identified as the ubiquitous environmental and clinically relevant Gram-negative bacterium Ralstonia insidiosa (R. insidiosa), a strong biofilm producer. Further characterizations by transmission electron microscopy (TEM) and biochemical API test were not conclusive. Whole genome sequencing of our R. insidiosa isolate revealed numerous drug-resistance determinants. Genome-wide comparison to other Ralstonia species could not unambiguously designate our isolate to R. insidiosa (<95% average nucleotide identity) suggesting a potential novel species or subspecies, closely related to R. insidiosa and R. pickettii. After determining the antibiotic susceptibility profile, the hybridoma cell culture was successfully decontaminated with ciprofloxacin without affecting antibody production. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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Article
Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability
Microorganisms 2020, 8(10), 1598; https://doi.org/10.3390/microorganisms8101598 - 17 Oct 2020
Cited by 3 | Viewed by 1233
Abstract
G-rich DNA repeats that can form G-quadruplex structures are prevalent in bacterial genomes and are frequently associated with regulatory regions of genes involved in virulence, antigenic variation, and antibiotic resistance. These sequences are also inherently mutagenic and can lead to changes affecting cell [...] Read more.
G-rich DNA repeats that can form G-quadruplex structures are prevalent in bacterial genomes and are frequently associated with regulatory regions of genes involved in virulence, antigenic variation, and antibiotic resistance. These sequences are also inherently mutagenic and can lead to changes affecting cell survival and adaptation. Transcription of the G-quadruplex-forming repeat (G3T)n in E. coli, when mRNA comprised the G-rich strand, promotes G-quadruplex formation in DNA and increases rates of deletion of G-quadruplex-forming sequences. The genomic instability of G-quadruplex repeats may be a source of genetic variability that can influence alterations and evolution of bacteria. The DNA chaperone Hfq is involved in the genetic instability of these G-quadruplex sequences. Inactivation of the hfq gene decreases the genetic instability of G-quadruplex, demonstrating that the genomic instability of this regulatory element can be influenced by the E. coli highly pleiotropic Hfq protein, which is involved in small noncoding RNA regulation pathways, and DNA organization and packaging. We have shown previously that the protein binds to and stabilizes these sequences, increasing rates of their genomic instability. Here, we extend this analysis to characterize the role of the C-terminal domain of Hfq protein in interaction with G-quadruplex structures. This allows to better understand the function of this specific region of the Hfq protein in genomic instability. Full article
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