Journal Description
Microorganisms
Microorganisms
is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with the Microorganisms, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q2 (Microbiology (medical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.1 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Testimonials: See what our editors and authors say about the Microorganisms.
- Companion journal: Applied Microbiology.
Impact Factor:
4.5 (2022);
5-Year Impact Factor:
4.8 (2022)
Latest Articles
Identification of the Microbiome Associated with Prognosis in Patients with Chronic Liver Disease
Microorganisms 2024, 12(3), 610; https://doi.org/10.3390/microorganisms12030610 (registering DOI) - 19 Mar 2024
Abstract
We investigated the prognostic role of the gut microbiome and clinical factors in chronic liver disease (hepatitis, cirrhosis, and hepatocellular carcinoma [HCC]). Utilizing data from 227 patients whose stool samples were collected over the prior 3 years and a Cox proportional hazards model,
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We investigated the prognostic role of the gut microbiome and clinical factors in chronic liver disease (hepatitis, cirrhosis, and hepatocellular carcinoma [HCC]). Utilizing data from 227 patients whose stool samples were collected over the prior 3 years and a Cox proportional hazards model, we integrated clinical attributes and microbiome composition based on 16S ribosomal RNA sequencing. HCC was the primary cause of mortality, with the Barcelona Clinic Liver Cancer staging system-derived B/C significantly increasing the mortality risk (hazard ratio [HR] = 8.060; 95% confidence interval [CI]: 3.6509–17.793; p < 0.001). Cholesterol levels < 140 mg/dL were associated with higher mortality rates (HR = 4.411; 95% CI: 2.0151–9.6555; p < 0.001). Incertae sedis from Ruminococcaceae showed a protective effect, reducing mortality risk (HR = 0.289; 95% CI: 0.1282 to 0.6538; p = 0.002), whereas increased Veillonella presence was associated with a higher risk (HR = 2.733; 95% CI: 1.1922–6.2664; p = 0.017). The potential of specific bacterial taxa as independent prognostic factors suggests that integrating microbiome data could improve the prognosis and treatment of chronic liver disease. These microbiome-derived markers have prognostic significance independently and in conjunction with clinical factors, suggesting their utility in improving a patient’s prognosis.
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(This article belongs to the Special Issue Advances in Human Microbiomes)
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Harmful and Harmless Soil-Dwelling Fungi Indicate Microhabitat Suitability for Off-Host Ixodid Ticks
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Claire E. Gooding, Layla Gould and Gerhard Gries
Microorganisms 2024, 12(3), 609; https://doi.org/10.3390/microorganisms12030609 (registering DOI) - 19 Mar 2024
Abstract
Following blood meals or questing bouts, hard ticks (Ixodidae) must locate moist off-host microhabitats as refuge. Soil-dwelling fungi, including entomopathogenic Beauveria bassiana (Bb), thrive in moist microhabitats. Working with six species of ixodid ticks in olfactometer bioassays, we tested the hypothesis
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Following blood meals or questing bouts, hard ticks (Ixodidae) must locate moist off-host microhabitats as refuge. Soil-dwelling fungi, including entomopathogenic Beauveria bassiana (Bb), thrive in moist microhabitats. Working with six species of ixodid ticks in olfactometer bioassays, we tested the hypothesis that ticks avoid Bb. Contrary to our prediction, nearly all ticks sought, rather than avoided, Bb-inoculated substrates. In further bioassays with female black-legged ticks, Ixodes scapularis, ticks oriented towards both harmful Bb and harmless soil-dwelling fungi, implying that fungi—regardless of their pathogenicity—signal habitat suitability to ticks. Only accessible Bb-inoculated substrate appealed to ticks, indicating that they sense Bb or its metabolites by contact chemoreception. Bb-inoculated substrate required ≥24 h of incubation before it appealed to ticks, suggesting that they respond to Bb metabolites rather than to Bb itself. Similarly, ticks responded to Bb-inoculated and incubated cellulose but not to sterile cellulose, indicating that Bb detection by ticks hinges on the Bb metabolism of cellulose. 2-Methylisoborneol—a common fungal metabolite with elevated presence in disturbed soils—strongly deterred ticks. Off-host ticks that avoid disturbed soil may lower their risk of physical injury. Synthetic 2-methylisoborneol could become a commercial tick repellent, provided its repellency extends to ticks in diverse taxa.
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(This article belongs to the Section Parasitology)
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Active Microbiota of Penaeus stylirostris Larvae: Partially Shaped via Vertical and Horizontal Transmissions and Larval Ontogeny
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Nolwenn Callac, Carolane Giraud, Dominique Pham, Dominique Ansquer, Nelly Wabete and Viviane Boulo
Microorganisms 2024, 12(3), 608; https://doi.org/10.3390/microorganisms12030608 (registering DOI) - 19 Mar 2024
Abstract
During their entire lifecycle, mariculture animals are farmed in water that contains various microorganisms with which they are in close associations. Microbial exchanges between the animals and their surrounding water can occur. However, little is known about the interactions between shrimp larvae and
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During their entire lifecycle, mariculture animals are farmed in water that contains various microorganisms with which they are in close associations. Microbial exchanges between the animals and their surrounding water can occur. However, little is known about the interactions between shrimp larvae and water, and more especially, about larval bacterial selection and microbiota modulation across ontogeny. To address this gap, using HiSeq sequencing targeting the V4 region of the 16S rRNA molecule, we investigated the active prokaryotic diversity and structure of healthy Penaeus stylirostris larvae and seawater. Comparisons between different larval stages revealed evidence of stage-specific microbiotas and biomarkers, a core microbiota common to all stages, and shared taxa between successive stages, suggesting vertical transmission of bacterial taxa. Comparisons between stage-specific microbiotas and core microbiotas with water storages highlighted that many taxa associated with the larvae were originally present in the natural seawater, underlining horizontal transmission of bacteria from water to larvae. As some of these lineages became active at specific larval stages, we suggest that larvae were able to modulate their microbiota. This study provides insight into larvae-microbiota interactions at the larval stage scale.
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(This article belongs to the Special Issue Holobionts in Aquaculture)
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Clinical Profile and Prognosis of Patients with Left-Sided Infective Endocarditis with Surgical Indication Who Are Not Operated
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María de Miguel, Javier López, Isidre Vilacosta, Carmen Olmos, Carmen Sáez, Gonzalo Cabezón, Pablo Zulet, Adrián Jerónimo, Daniel Gómez, Paloma Pulido, Adrián Lozano, Andrea Oña, Itziar Gómez-Salvador and J. Alberto San Román
Microorganisms 2024, 12(3), 607; https://doi.org/10.3390/microorganisms12030607 (registering DOI) - 19 Mar 2024
Abstract
Approximately a quarter of patients with infective endocarditis (IE) who have surgical indication only receive antibiotic treatment. Their short-term prognosis is dismal. We aimed to describe the characteristics of this group of patients to evaluate the mortality according to the cause of rejection
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Approximately a quarter of patients with infective endocarditis (IE) who have surgical indication only receive antibiotic treatment. Their short-term prognosis is dismal. We aimed to describe the characteristics of this group of patients to evaluate the mortality according to the cause of rejection and type of surgical indication and to analyze their prognostic factors of mortality. From 2005 to 2022, 1105 patients with definite left-sided IE were consecutively attended in three tertiary hospitals. Of them, 912 (82.5%) had formal surgical indication according to the most recent European Guidelines available in each period of the study and 303 (33%) only received medical treatment. These were older, had more comorbidities and higher in-hospital (46% vs. 24%; p < 0.001) and one year mortality (57.1% vs. 27.6%; p < 0.001) than operated patients. The main reason for surgical rejection was high surgical risk (57.1%) and the highest mortality when the cause were severe neurological conditions (76%). When the endocarditis team took the decision not to operate (25.5% of the patients), in-hospital (7%) and one-year mortality (17%) were low. In-hospital mortality associated with each surgical indication was 67% in heart failure, 53% in uncontrolled infection and 45% in prevention of embolisms (p < 0.001). Heart failure (OR: 2.26 CI95%: 1.29–3.96; p = 0.005), Staphylococcus aureus (OR: 3.17; CI95%: 1.72–5.86; p < 0.001) and persistent infection (OR: 5.07 CI95%: 2.85–9.03) are the independent risk factors of in-hospital mortality. One third of the patients with left-sided IE and formal surgical indication are rejected for surgery. In-hospital mortality is very high, especially when heart failure is the indication for surgery and when severe neurological conditions the reason for rejection. Short term prognosis of patients rejected by a specialized endocarditis team is favorable.
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(This article belongs to the Special Issue The Infective Endocarditis)
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Engineering a Lactobacillus Lysine Riboswitch to Dynamically Control Metabolic Pathways for Lysine Production in Corynebacterium glutamicum
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Qingwei Jiang, Feng Geng, Juan Shen, Ping Zhu, Zhaoxin Lu, Libang Zhou and Fengxia Lu
Microorganisms 2024, 12(3), 606; https://doi.org/10.3390/microorganisms12030606 - 18 Mar 2024
Abstract
Knock-out of genes of metabolic pathways is conventionally used in the metabolic engineering of microorganisms, but it is not applicable for genes of essential pathways. In order to avoid undesirable effects caused by gene deletion, it is attractive to develop riboswitches to dynamically
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Knock-out of genes of metabolic pathways is conventionally used in the metabolic engineering of microorganisms, but it is not applicable for genes of essential pathways. In order to avoid undesirable effects caused by gene deletion, it is attractive to develop riboswitches to dynamically control the metabolic pathways of microbial cell factories. In this regard, the aim of this study is to utilize the lysine riboswitch to control gene expressions of the biosynthetic pathways and by-pathways and thus improve lysine production in Corynebacterium glutamicum. To achieve this, a natural lysine riboswitch from Lactobacillus plantarum (LPRS) was first detected and then fused with RFP to test its functionality. After that, engineered lysine-activated (Lys-A) and lysine-repressed (Lys-R) riboswitches were successfully screened by dual genetic selection. Furthermore, the optimized A263 and R152 were applied to control the expression of aspartate kinase III and homoserine dehydrogenase in the lysine-producing strain C. glutamicum QW45, respectively. In contrast with QW45, the growth of the resulting A263-lysC mutant QW48 was similar to that of QW45; however, the growth of the resulting R357-hom mutant QW54 was slightly inhibited, indicating an inhibition of threonine biosynthesis caused by the riboswitch upon binding of intracellular lysine. Importantly, the lysine production of QW48 and QW54 was, respectively, 35% and 43% higher than that of the parent strain QW45, implying more metabolic flux directed into the lysine synthesis pathway. Finally, the engineered A263 and R357 were simultaneously applied to the same mutant QW55, which greatly improved lysine production. Thus, the approach demonstrated in this work could be principally used as a powerful tool to dynamically control any other undesired metabolic pathways.
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(This article belongs to the Section Microbial Biotechnology)
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One Step Forwards in Knowledge of Blossom Blight Brown Rot Disease: Monilinia spp. SSR Marker Database
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Raminta Antanynienė, Vidmantas Stanys and Birutė Frercks
Microorganisms 2024, 12(3), 605; https://doi.org/10.3390/microorganisms12030605 - 18 Mar 2024
Abstract
A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the
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A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the bioinformatics tool Genome-wide Microsatellite Analyzing Toward Application (GMATA). The database provides information about SSR markers: forward and reverse sequences of the primers, fragment sizes, SSR motifs (and repeats), and the exact locations with the coordinates in the reference genome. This database currently contains information about 39,216 SSR motifs and 26,366 markers. In total, eight primers generated in silico were validated experimentally and they are marked in the database. All scientists can join this collaboration by adding their experimental data. This database is the initial start of organizing Monilinia spp. molecular data worldwide and, in the future, it could be extended by adding more molecular and genomic information.
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(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)
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The Performance of a Modified Anode Using a Combination of Kaolin and Graphite Nanoparticles in Microbial Fuel Cells
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Lea Ouaknin Hirsch, Bharath Gandu, Abhishiktha Chiliveru, Irina Amar Dubrovin, Shmuel Rozenfeld, Alex Schechter and Rivka Cahan
Microorganisms 2024, 12(3), 604; https://doi.org/10.3390/microorganisms12030604 - 18 Mar 2024
Abstract
The bacterial anode in microbial fuel cells was modified by increasing the biofilm’s adhesion to the anode material using kaolin and graphite nanoparticles. The MFCs were inoculated with G. sulfurreducens, kaolin (12.5 g·L−1), and three different concentrations of graphite (0.25,
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The bacterial anode in microbial fuel cells was modified by increasing the biofilm’s adhesion to the anode material using kaolin and graphite nanoparticles. The MFCs were inoculated with G. sulfurreducens, kaolin (12.5 g·L−1), and three different concentrations of graphite (0.25, 1.25, and 2.5 g·L−1). The modified anode with the graphite nanoparticles (1.25 g·L−1) showed the highest electroactivity and biofilm viability. A potential of 0.59, 0.45, and 0.23 V and a power density of 0.54 W·m−2, 0.3 W·m−2, and 0.2 W·m−2 were obtained by the MFCs based on kaolin–graphite nanoparticles, kaolin, and bare anodes, respectively. The kaolin–graphite anode exhibited the highest Coulombic efficiency (21%) compared with the kaolin (17%) and the bare (14%) anodes. Scanning electron microscopy and confocal laser scanning microscopy revealed a large amount of biofilm on the kaolin–graphite anode. We assume that the graphite nanoparticles increased the charge transfer between the bacteria that are in the biofilm and are far from the anode material. The addition of kaolin and graphite nanoparticles increased the attachment of several bacteria. Thus, for MFCs that are fed with wastewater, the modified anode should be prepared with a pure culture of G. sulfurreducens before adding wastewater that includes non-exoelectrogenic bacteria.
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(This article belongs to the Special Issue Microbial Fuel Cells: An Update)
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Effect of the Inoculum-to-Substrate Ratio on Putative Pathogens and Microbial Kinetics during the Batch Anaerobic Digestion of Simulated Food Waste
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Saanu Victoria Otite, Bhushan P. Gandhi, Esther Agyabeng Fofie, Alfonso José Lag-Brotons, Lawrence I. Ezemonye, Alastair D. Martin, Roger W. Pickup and Kirk T. Semple
Microorganisms 2024, 12(3), 603; https://doi.org/10.3390/microorganisms12030603 - 18 Mar 2024
Abstract
The effects of the inoculum (anaerobic digestion effluent) to substrate (simulated food waste) ratio (ISR) 4.00 to 0.25 on putative pathogens and microbial kinetics during batch mesophilic anaerobic digestion were investigated. Red fluorescent protein labelled (RFPAKN132) Escherichia coli JM105 was introduced as a
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The effects of the inoculum (anaerobic digestion effluent) to substrate (simulated food waste) ratio (ISR) 4.00 to 0.25 on putative pathogens and microbial kinetics during batch mesophilic anaerobic digestion were investigated. Red fluorescent protein labelled (RFPAKN132) Escherichia coli JM105 was introduced as a marker species, and together with the indigenous Clostridium sp., Enterococcus sp., Escherichia coli, and total coliforms were used to monitor pathogen death kinetics. Quantitative polymerase chain reaction was also used to estimate the bacterial, fungal, and methanogenic gene copies. All the ISRs eliminated E. coli and other coliforms (4 log10 CFU/mL), but ISR 0.25 achieved this within the shortest time (≤2 days), while ISR 1.00 initially supported pathogen proliferation. Up to 1.5 log10 CFU/mL of Clostridium was reduced by acidogenic conditions (ISR 0.25 and 0.50), while Enterococcus species were resistant to the digestion conditions. Fungal DNA was reduced (≥5 log10 copies/mL) and was undetectable in ISRs 4.00, 2.00, and 0.50 at the end of the incubation period. This study has demonstrated that ISR influenced the pH of the digesters during batch mesophilic anaerobic digestion, and that acidic and alkaline conditions achieved by the lower (0.50 and 0.25) and higher (4.00 and 2.00) ISRs, respectively, were critical to the sanitisation of waste.
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(This article belongs to the Section Environmental Microbiology)
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Effects of Salmonella Typhimurium Infection on the Gut Microbiota of Cherry Valley Meat Ducks
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Yue Zheng, Xue Pan, Jialei Hou, Wenchong Shi, Shuhong Sun, Mengze Song and Zheng Gao
Microorganisms 2024, 12(3), 602; https://doi.org/10.3390/microorganisms12030602 - 18 Mar 2024
Abstract
Salmonella infection causes serious economic losses, threatens food safety, and is one of the most important diseases threatening meat duck farming. The gut microbiome is critical in providing resistance against colonization by exogenous microorganisms. Studying the relationship between Salmonella and gut microbiota can
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Salmonella infection causes serious economic losses, threatens food safety, and is one of the most important diseases threatening meat duck farming. The gut microbiome is critical in providing resistance against colonization by exogenous microorganisms. Studying the relationship between Salmonella and gut microbiota can help us better understand the threat of the pathogenic mechanism of Salmonella and provide a more scientific theoretical basis for its prevention and treatment. This study uses Salmonella Typhimurium as the research object and Cherry Valley meat duck as the model with which to study the impact of Salmonella infection on ducks. In this field trial, 2 × 108 CFUs Salmonella Typhimurium were administered to 3-day-old ducks. After infection, duck viscera were collected to detect the colonization of Salmonella, and cecal contents were collected to analyze the changes in gut microbiota. The results show that Salmonella Typhimurium can colonize ducks three days after infection and alter the gut microbiota composition, mainly by increasing the abundance of Ruminococcaceae and Lachnospiraceae. In conclusion, Salmonella Typhimurium infection significantly alters the intestinal microbiota of ducks and poses a serious public health risk.
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(This article belongs to the Section Veterinary Microbiology)
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Effects of Six Natural Compounds and Their Derivatives on the Control of Coccidiosis in Chickens
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Yue Hou, Bo Han, Zehua Lin, Qizheng Liu, Zhenhe Liu, Hongbin Si and Dandan Hu
Microorganisms 2024, 12(3), 601; https://doi.org/10.3390/microorganisms12030601 - 17 Mar 2024
Abstract
Chicken coccidiosis costs the poultry industry over GBP 10 billion per year. The main method of preventing and controlling coccidiosis in chickens continues to be the use of drugs. Unfortunately, the prevalence of drug resistance in the field reduces or even eliminates the
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Chicken coccidiosis costs the poultry industry over GBP 10 billion per year. The main method of preventing and controlling coccidiosis in chickens continues to be the use of drugs. Unfortunately, the prevalence of drug resistance in the field reduces or even eliminates the effectiveness of drugs, and drug residues in the food supply chain can also can be harmful to humans. Therefore, safe and effective anticoccidial drugs are urgently needed. Natural products have many advantages such as being safe, effective and inexpensive and are a sustainable way to control coccidiosis. In this study, the anticoccidial effects of six natural compounds were tested by Eimeria tenella infection. Oocyst production, cecum lesion, body weight gain, feed conversion ratio, and intestinal microbiota were measured. The results showed that nerolidol had a moderate effect on maintaining both body weight gain and feed conversion ratio. Silymarin and dihydroartemisinin showed significant anticoccidial effects by reducing total oocyst output. Dihydroartemisinin also significantly reduced the cecum lesion caused by Eimeria infection, but this compound may be toxic to the host at such informed doses because it decreases growth and survival rates. In addition, both silymarin and dihydroartemisinin partly restored the microbiota after challenge. This indicates that silymarin, dihydroartemisinin, and nerolidol are effective in the control of chicken coccidiosis. Our data provide basic knowledge about the anticoccidial effects of such natural compounds/derivates.
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(This article belongs to the Special Issue Parasitic Diseases in Husbandry Animals and Relevant Antiparasitic Treatment)
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Open AccessReview
A Mini-Review on the Common Antiviral Drug Targets of Coronavirus
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Jun Wang, Qinghe Zhu, Xiaoxu Xing and Dongbo Sun
Microorganisms 2024, 12(3), 600; https://doi.org/10.3390/microorganisms12030600 - 17 Mar 2024
Abstract
Coronaviruses in general are a zoonotic pathogen with significant cross-species transmission. They are widely distributed in nature and have recently become a major threat to global public health. Vaccines are the preferred strategy for the prevention of coronaviruses. However, the rapid rate of
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Coronaviruses in general are a zoonotic pathogen with significant cross-species transmission. They are widely distributed in nature and have recently become a major threat to global public health. Vaccines are the preferred strategy for the prevention of coronaviruses. However, the rapid rate of virus mutation, large number of prevalent strains, and lag in vaccine development contribute to the continuing frequent occurrence of coronavirus diseases. There is an urgent need for new antiviral strategies to address coronavirus infections effectively. Antiviral drugs are important in the prevention and control of viral diseases. Members of the genus coronavirus are highly similar in life-cycle processes such as viral invasion and replication. These, together with the high degree of similarity in the protein sequences and structures of viruses in the same genus, provide common targets for antiviral drug screening of coronaviruses and have led to important advances in recent years. In this review, we summarize the pathogenic mechanisms of coronavirus, common drugs targeting coronavirus entry into host cells, and common drug targets against coronaviruses based on biosynthesis and on viral assembly and release. We also describe the common targets of antiviral drugs against coronaviruses and the progress of antiviral drug research. Our aim is to provide a theoretical basis for the development of antiviral drugs and to accelerate the development and utilization of commonly used antiviral drugs in China.
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(This article belongs to the Section Virology)
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RNA Interference Therapeutics for Chronic Hepatitis B: Progress, Challenges, and Future Prospects
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Laura Sneller, Christine Lin, Angie Price, Shyam Kottilil and Joel V. Chua
Microorganisms 2024, 12(3), 599; https://doi.org/10.3390/microorganisms12030599 - 17 Mar 2024
Abstract
Chronic hepatitis B (CHB) is a global health challenge that can result in significant liver-related morbidity and mortality. Despite a prophylactic vaccine being available, patients already living with CHB often must engage in lifelong therapy with nucleoside analogues. However, the potential of RNA
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Chronic hepatitis B (CHB) is a global health challenge that can result in significant liver-related morbidity and mortality. Despite a prophylactic vaccine being available, patients already living with CHB often must engage in lifelong therapy with nucleoside analogues. However, the potential of RNA interference (RNAi) therapeutics as a promising avenue for CHB treatment is being explored. RNAi, particularly using small interfering RNA (siRNA), targets viral RNA that can be used to inhibit hepatitis B virus (HBV) replication. Several candidates are currently being studied and have exhibited varying success in reducing hepatitis B surface antigen (HBsAg) levels, with some showing sustained HBsAg loss after cessation of therapy. The dynamic evolution of RNAi therapy presents a promising trajectory for the development of effective and sustained treatments for CHB. This review highlights recent findings on RNAi therapeutics, including modifications for stability, various delivery vectors, and specific candidates currently in development.
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(This article belongs to the Section Virology)
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Identification and Pathogenicity of Fusarium Fungi Associated with Dry Rot of Potato Tubers
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Olga Gavrilova, Aleksandra Orina, Ilya Trubin and Tatiana Gagkaeva
Microorganisms 2024, 12(3), 598; https://doi.org/10.3390/microorganisms12030598 - 16 Mar 2024
Abstract
Dry rot of potato tubers is a harmful disease caused by species of the Fusarium genus. Studies on the composition and features of Fusarium spp. that cause the disease in Russia are limited. Thirty-one Fusarium strains belonging to the F. sambucinum species complex
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Dry rot of potato tubers is a harmful disease caused by species of the Fusarium genus. Studies on the composition and features of Fusarium spp. that cause the disease in Russia are limited. Thirty-one Fusarium strains belonging to the F. sambucinum species complex (FSAMSC) and F. solani species complex (FSSC) were accurately identified using multilocus phylogenetic analysis of the tef and rpb2 loci, and their physiological characteristics were studied in detail. As a result, 21 strains of F. sambucinum s. str. and 1 strain of F. venenatum within the FSAMSC were identified. Among the analyzed strains within the FSSC, one strain of F. mori, four strains of F. noneumartii, and two strains of both F. stercicola and F. vanettenii species were identified. This is the first record of F. mori on potato as a novel host plant, and the first detection of F. noneumartii and F. stercicola species in Russia. The clear optimal temperature for the growth of the strains belonging to FSAMSC was noted to be 25 °C, with a growth rate of 11.6–15.0 mm/day, whereas, for the strains belonging to FSSC, the optimal temperature range was between 25 and 30 °C, with a growth rate of 5.5–14.1 mm/day. The distinctive ability of F. sambucinum strains to grow at 5 °C has been demonstrated. All analyzed Fusarium strains were pathogenic to potato cv. Gala and caused extensive damage of the tuber tissue at an incubation temperature of 23 °C for one month. Among the fungi belonging to the FSAMSC, the F. sambucinum strains were more aggressive and caused 23.9 ± 2.2 mm of necrosis in the tubers on average compared to the F. venenatum strain—17.7 ± 1.2 mm. Among the fungi belonging to the FSSC, the F. noneumartii strains were the most aggressive and caused 32.2 ± 0.8 mm of necrosis on average. The aggressiveness of the F. mori, F. stercicola, and especially the F. vanettenii strains was significantly lower: the average sizes of damage were 17.5 ± 0.5 mm, 17.2 ± 0.2 mm, and 12.5 ± 1.7 mm, respectively. At an incubation temperature of 5 °C, only the F. sambucinum strains caused tuber necroses in the range of 6.7 ± 0.5–15.9 ± 0.8 mm.
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(This article belongs to the Special Issue Molecular Identification and Phylogeny of Crops Pathogenic Fungi)
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Removal of Phenol by Rhodococcus opacus 1CP after Dormancy: Insight into Enzymes’ Induction, Specificity, and Cells Viability
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Natalia S. Egozarian, Elena V. Emelyanova, Nataliya E. Suzina, Olesya I. Sazonova, Valentina N. Polivtseva, Tatiana O. Anokhina, Yonghong Wu and Inna P. Solyanikova
Microorganisms 2024, 12(3), 597; https://doi.org/10.3390/microorganisms12030597 - 16 Mar 2024
Abstract
Biodegradation of phenol is an effective method for removing this toxicant from contaminated sites. Phenol is a toxic compound for living cells, so many bacteria degrade phenol in relatively low concentrations, up to 0.75 g L−1. The Rhodococcus opacus strain 1CP
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Biodegradation of phenol is an effective method for removing this toxicant from contaminated sites. Phenol is a toxic compound for living cells, so many bacteria degrade phenol in relatively low concentrations, up to 0.75 g L−1. The Rhodococcus opacus strain 1CP is an effective destructor of a wide range of pollutants. In the absence of a carbon source in the medium, cells of the R. opacus 1CP strain easily form cyst-like resting cells (CLC). The purpose of this work was to evaluate the viability of cells during long-term storage and the efficiency of the process of phenol destruction by R. opacus 1CP cells germinating after dormancy. Resting cells were obtained by simple cultivation in a rich medium followed by storage under static conditions. This is a simple approach to obtain a large amount of biomass. Decomposition of phenol proceeded via catechol followed by ortho-cleavage of aromatic ring. The induction of three phenol hydroxylases was detected by RT-PCR in cells germinated in a mineral medium with phenol as the carbon source. The stability of the genome of cells germinating after dormancy is shown by box-PCR. Dormant R. opacus 1CP cells, both suspended and immobilized, can be directly used for the decomposition of phenol after 4–12 months storage. In addition to phenol, after 9 months of storage, immobilized germinating cells easily metabolized 4-chlorophenol and 2,4,6-trichlorophenol. The results demonstrate a potential and simple approach toward achieving long-term storage of cells for further use in bioremediation.
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(This article belongs to the Section Microbial Biotechnology)
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Open AccessReview
Therapy of Mycobacterium abscessus Infections in Solid Organ Transplant Patients
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Lubna Osman, Christopher Lopez, Yoichiro Natori, Shweta Anjan, Julia Bini Viotti and Jacques Simkins
Microorganisms 2024, 12(3), 596; https://doi.org/10.3390/microorganisms12030596 - 16 Mar 2024
Abstract
Mycobacterium abscessus complex (MABC), a rapidly growing Mycobacterium, is one of the most common causes of non-tuberculous mycobacteria (NTM) infections in the United States of America, and it has been associated with a wide spectrum of infections in immunocompetent and immunosuppressed individuals.
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Mycobacterium abscessus complex (MABC), a rapidly growing Mycobacterium, is one of the most common causes of non-tuberculous mycobacteria (NTM) infections in the United States of America, and it has been associated with a wide spectrum of infections in immunocompetent and immunosuppressed individuals. Eradicating MABC is very challenging, even with prolonged combination therapies. The management of MABC infections in solid organ transplant (SOT) patients is usually complex given their net state of immunosuppression, associated comorbidities, and potential drug–drug interactions, among other things. In this manuscript, we discussed the antimicrobial management of pulmonary and extrapulmonary MABC infections. In addition, we reviewed promising novel therapies such as clofazimine, omadacycline, bedaquiline, and inhaled tigecycline that could join the existing antimicrobial armamentarium to fight this infection associated with significant morbidity and mortality. However, further studies are needed, especially among the immunocompromised host.
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(This article belongs to the Special Issue Mycobacterium abscessus: Current Knowledgement on an Emerging Pathogen)
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Physicochemical Properties and Microbiome of Vineyard Soils from DOP Ribeiro (NW Spain) Are Influenced by Agricultural Management
by
Pilar Blanco, Isaac Rodríguez, Victoria Fernández-Fernández, María Ramil, David Castrillo, Marta Acín-Albiac, Irene Adamo, Clara Fernández-Trujillo, Beatriz García-Jiménez, Alberto Acedo, Noemi Calvo-Portela, Andrea Parente-Sendín, Lara Acemel-Míguez and Flora Alonso-Vega
Microorganisms 2024, 12(3), 595; https://doi.org/10.3390/microorganisms12030595 - 16 Mar 2024
Abstract
Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of
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Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of vineyards from DOP Ribeiro on the soil’s condition. Samples from soils under three different management systems were collected, and the main soil physicochemical properties were evaluated. A selection of 50 pesticides were investigated by liquid chromatography with tandem mass spectrometry. The bacterial and fungal microbiomes were characterized through amplicon sequencing. The results show that organic agriculture positively influences soil pH and the concentration of some nutrients compared to conventional management. Our microbiome analysis demonstrated that transitioning from conventional to organic management significantly improves several BeCrop® indexes related to key microbial metabolism and soil bio-sustainability. Such a transition does not affect soil alpha diversity, but leads to a higher interconnected microbial network structure. Moreover, differential core genera and species for each management system are observed. In addition, the correlation of the microbiome with geographical distance is evidence of the existence of different microbial terroirs within DOP Ribeiro. Indeed, sustainable management leads to higher nutrient availability and enhances soil health in the short term, while lowering pesticide usage.
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(This article belongs to the Special Issue Advances in Soil Microbiome 2.0)
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Investigation of Yellow Fever Virus at the Human–Animal Interface after a Zika Virus Outbreak in Midwest Brazil
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Lis Alvarez Baranowski, Helver Gonçalves Dias, Débora Familiar-Macedo, Gilberto Sabino-Santos, Heitor Miraglia Herrera, Renata Dezengrini Slhessarenko, Flávia Barreto dos Santos and Alex Pauvolid-Corrêa
Microorganisms 2024, 12(3), 594; https://doi.org/10.3390/microorganisms12030594 - 16 Mar 2024
Abstract
Following the first report of zika virus in March 2015, Brazil experienced its largest sylvatic yellow fever outbreak between 2016 and 2019. This study aimed to investigate the circulation of yellow fever virus (YFV) in non-human primates (NHPs) and mosquitoes collected in urban
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Following the first report of zika virus in March 2015, Brazil experienced its largest sylvatic yellow fever outbreak between 2016 and 2019. This study aimed to investigate the circulation of yellow fever virus (YFV) in non-human primates (NHPs) and mosquitoes collected in urban parks and other metropolitan areas of midwest Brazil between 2017 and 2018. Whole blood samples from 80 NHPs, including 48 black-tailed marmosets (Mico melanurus) and 2332 mosquitoes from six different genera, were collected in the states of Mato Grosso (MT) and Mato Grosso do Sul (MS) and then tested for YFV by RT-qPCR. Additionally, 23 plasma samples of NHPs were tested for neutralizing antibodies for YFV by a plaque reduction neutralization test (PRNT). No YFV RNA or neutralizing antibodies for YFV were detected in NHPs and mosquitoes from MT and MS. The continuous monitoring of YFV circulation in different species of NHPs and vectors in urban areas is instrumental to quickly assess potentially unknown maintenance cycles of yellow fever at the human–animal interface in Brazil.
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(This article belongs to the Special Issue Emerging Viruses: New Challenges in Detection, Prevention and Control)
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Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis
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Lucas Rafael Santana Pinheiro, Érika Dayane Leal Rodrigues, Francisco Amilton dos Santos Paiva, Ana Cecília Ribeiro Cruz, Daniele Barbosa de Almeida Medeiros, Alexandre do Rosário Casseb, Sandro Patroca da Silva and Livia Medeiros Neves Casseb
Microorganisms 2024, 12(3), 593; https://doi.org/10.3390/microorganisms12030593 - 16 Mar 2024
Abstract
Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from
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Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats.
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(This article belongs to the Special Issue Advances in Viral Metagenomics)
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Enhancing Benzo[a]pyrene Degradation by Pantoea dispersa MSC14 through Biostimulation with Sodium Gluconate: Insights into Mechanisms and Molecular Regulation
by
La Lai, Shuqi Li, Shaoping Zhang, Manchun Liu, Lianwei Xia, Yuan Ren and Tangbing Cui
Microorganisms 2024, 12(3), 592; https://doi.org/10.3390/microorganisms12030592 - 15 Mar 2024
Abstract
We investigated biostimulation as an effective strategy for enhancing the degradation efficiency of recalcitrant organic compounds, with MSC14 (a novel polycyclic aromatic hydrocarbon degrading bacterium Pantoea dispersa MSC14) as the study material. Here, we investigated the impact of sodium gluconate on MSC14-mediated degradation
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We investigated biostimulation as an effective strategy for enhancing the degradation efficiency of recalcitrant organic compounds, with MSC14 (a novel polycyclic aromatic hydrocarbon degrading bacterium Pantoea dispersa MSC14) as the study material. Here, we investigated the impact of sodium gluconate on MSC14-mediated degradation of B[a]p. This study focused on the application of sodium gluconate, a biostimulant, on MSC14, targeting Benzo[a]pyrene (B[a]p) as the model pollutant. In this study, the novel PAHs-degrading bacterium P. dispersa MSC14 demonstrated the capability to degrade 24.41% of B[a]p after 4 days. The addition of the selected sodium gluconate stimulant at a concentration of 4 g/L stimulated MSC14 to degrade 54.85% of B[a]p after 16 h. Intermediate metabolites were analyzed using gas chromatography-mass spectrometry to infer the degradation pathway. The findings indicated that sodium gluconate promoted the intracellular transport of B[a]p by MSC14, along with the secretion of biosurfactants, enhancing emulsification and solubilization capabilities for improved B[a]p dissolution and degradation. Further analysis through transmission electron microscopy (TEM) and scanning electron microscopy (SEM) revealed the formation of a biofilm by MSC14 and an increase in flagella as a response to B[a]p stress. Transcriptome profiling elucidated the interplay of quorum sensing systems, chemotaxis systems, and flagellar systems in the degradation mechanism. Additionally, the study uncovered the molecular basis of B[a]p transport, degradation pathways, metabolic changes, and genetic regulation. In summary, the addition of sodium gluconate promotes the degradation of B[a]p by P. dispersa MSC14, offering the advantages of being rapid, efficient, and cost-effective. This research provides an economically viable approach for the remediation of petroleum hydrocarbon pollution, with broad potential applications.
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(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)
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Impact of Swabbing Location, Self-Swabbing, and Food Intake on SARS-CoV-2 RNA Detection
by
Sarah Dräger, Flavio Bruni, Melina Bernasconi, Anya Hammann-Hänni, Vlastimil Jirasko, Alexander Tanno, Yves Blickenstorfer, Karoline Leuzinger, Hans H. Hirsch and Michael Osthoff
Microorganisms 2024, 12(3), 591; https://doi.org/10.3390/microorganisms12030591 - 15 Mar 2024
Abstract
This study compared SARS-CoV-2 RNA loads at different anatomical sites, and the impact of self-swabbing and food intake. Adult symptomatic patients with SARS-CoV-2 or non-SARS-CoV-2 respiratory tract infection were included between 2021 and 2022. Patients performed a nasal and buccal swab before a
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This study compared SARS-CoV-2 RNA loads at different anatomical sites, and the impact of self-swabbing and food intake. Adult symptomatic patients with SARS-CoV-2 or non-SARS-CoV-2 respiratory tract infection were included between 2021 and 2022. Patients performed a nasal and buccal swab before a professionally collected nasopharyngeal/oropharyngeal swab (NOPS). Buccal swabs were collected fasting and after breakfast in a subgroup of patients. SARS-CoV-2 RNA loads were determined by nucleic acid testing. Swabbing convenience was evaluated using a survey. The median age of 199 patients was 54 years (interquartile range 38–68); 42% were female and 52% tested positive for SARS-CoV-2. The majority of patients (70%) were hospitalized. The mean SARS-CoV-2 RNA load was 6.6 log10 copies/mL (standard deviation (SD), ±1.5), 5.6 log10 copies/mL (SD ± 1.9), and 3.4 log10 copies/mL (SD ± 1.9) in the professionally collected NOPS, and self-collected nasal and buccal swabs, respectively (p < 0.0001). Sensitivity was 96.1% (95% CI 90.4–98.9) and 75.3% (95% CI 63.9–81.8) for the nasal and buccal swabs, respectively. After food intake, SARS-CoV-2 RNA load decreased (p = 0.0006). Buccal swabbing was the preferred sampling procedure for the patients. In conclusion, NOPS yielded the highest SARS-CoV-2 RNA loads. Nasal self-swabbing emerged as a reliable alternative in contrast to buccal swabs. If buccal swabs are used, they should be performed before food intake.
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(This article belongs to the Section Medical Microbiology)
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