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Microbiol. Res., Volume 15, Issue 1 (March 2024) – 28 articles

Cover Story (view full-size image): Clostridioides difficile is an anaerobic bacterium recognized as the main cause of diarrhea associated with the use of antibiotics in hospitals. The epidemiology of C. difficile infection (CDI) has recently evolved, with an increased incidence of CDI in the community and increased detection of C. difficile from animals, food, and the environment. C. difficile’s genomic evolution is associated with the international emergence and spread of new highly virulent ribotypes (RTs) that have an important impact on global public health and the need for constant monitoring to effectively prevent and control CDI. In this study, the variable cdtR gene was used as a target to develop a molecular beacon-based real-time PCR method to rapidly and easily type C. difficile strains belonging to different RTs and evolutionary clades of One Health importance. View this paper
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9 pages, 687 KiB  
Brief Report
An Evaluation of a SARS-CoV-2 Pseudovirus Neutralization Test and A Comparison to a SARS-CoV-2 Surrogate Virus Neutralization Test in a COVID-19 Long-Term Follow-Up Cohort
by Constant Gillot, Julien Favresse, Clara David, Vincent Maloteau, Jean-Michel Dogne and Jonathan Douxfils
Microbiol. Res. 2024, 15(1), 422-430; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010028 - 21 Mar 2024
Cited by 1 | Viewed by 708
Abstract
Background: The detection of neutralizing anti-SARS-CoV-2 antibodies is important since they represent the subset of antibodies able to prevent the virus to invade human cells. The aim of this study is to evaluate the clinical performances of an in-house pseudovirus neutralization test (pVNT) [...] Read more.
Background: The detection of neutralizing anti-SARS-CoV-2 antibodies is important since they represent the subset of antibodies able to prevent the virus to invade human cells. The aim of this study is to evaluate the clinical performances of an in-house pseudovirus neutralization test (pVNT) versus a commercial surrogate neutralization test (sVNT). Material and Methods: A total of 114 RT-PCR positives samples from 75 COVID-19 patients were analyzed using a pVNT and an sVNT technique. Fifty-six pre-pandemic samples were also analyzed to assess the specificity of the two techniques. An analysis of the repeatability and the reproducibility of the pVNT was also performed. Results: A coefficient of variation (CV) of 10.27% for the repeatability of the pVNT was computed. For the reproducibility test, CVs ranged from 16.12% for low NAbs titer to 6.40% for high NAbs titer. Regarding the clinical sensitivity, 90 RT-PCR positive samples out of 114 were positive with the pVNT (78.94%), and 97 were positive with the sVNT (84.21%). About the clinical specificity, all 56 pre-pandemic samples were negative in both techniques. When comparing the sVNT to the pVNT, the specificity and sensibility were 66.67% (95%CI: 47.81–85.53%) and 98.88% (95%CI: 96.72–99.99%), respectively. Conclusions: The results obtained with the automated sVNT technique are consistent with those obtained with the pVNT technique developed in-house. The results of the various repeatability and reproducibility tests demonstrate the good robustness of the fully manual pVNT technique. Full article
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18 pages, 2121 KiB  
Article
Effects of Biochar and Arbuscular Mycorrhizal Fungi on Soil Health in Chinese Kale (Brassica oleracea var. alboglabra L.) Cultivation
by Kritsana Jatuwong, Worawoot Aiduang, Tanongkiat Kiatsiriroat, Wassana Kamopas and Saisamorn Lumyong
Microbiol. Res. 2024, 15(1), 404-421; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010027 - 12 Mar 2024
Viewed by 1383
Abstract
Biochar and arbuscular mycorrhizal fungi (AMF), a promising environmentally friendly soil enhancer and biostimulant, play a crucial role in sustainable agriculture by influencing soil properties and plant growth. This research investigates the chemical properties of three biochar types [bamboo (BB-char), corn cob (CC-char), [...] Read more.
Biochar and arbuscular mycorrhizal fungi (AMF), a promising environmentally friendly soil enhancer and biostimulant, play a crucial role in sustainable agriculture by influencing soil properties and plant growth. This research investigates the chemical properties of three biochar types [bamboo (BB-char), corn cob (CC-char), and coffee grounds (CG-char)] derived from different biomass sources and their impact on soil quality and Chinese kale growth. The results reveal significant differences in chemical properties among different types of biochar. Particularly, CG-char showed the greatest pH value and phosphorus content, with an average of 10.05 and 0.44%, respectively. On the other hand, CC-char had the highest potassium content, with an average of 2.16%. Incorporating biochar into degraded soil enhances soil structure, promoting porosity and improved texture, as evidenced by scanning electron microscope images revealing distinct porous structures. Soil chemistry analyses in treatment T2–T14 after a 42-day cultivation demonstrate the impact of biochar on pH, electrical conductivity, organic matter, and organic carbon levels in comparison to the control treatment (T1). Furthermore, the research assesses the impact of biochar on Chinese kale growth and photosynthetic pigments. Biochar additions, especially 5% BB-char with AMF, positively influence plant growth, chlorophyll content, and photosynthetic pigment levels. Notably, lower biochar concentrations (5%) exhibit superior effects compared to higher concentrations (10%), emphasizing the importance of optimal biochar application rates. The study also delves into the total phenolic content in Chinese kale leaves, revealing that the synergistic effect of biochar and AMF enhances phenolic compound accumulation. The combination positively influences plant health, soil quality, and nutrient cycling mechanisms. Overall, the research indicates the multifaceted impact of biochar on soil and plant dynamics, emphasizing the need for tailored application strategies to optimize benefits in sustainable agriculture. Full article
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19 pages, 3658 KiB  
Article
Virulence and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli from River Water and Farm Animal Feces near an Agricultural Region in Northwestern Mexico
by Bianca A. Amézquita-López, Marcela Soto-Beltrán, Bertram G. Lee, Edgar F. Bon-Haro, Ofelia Y. Lugo-Melchor and Beatriz Quiñones
Microbiol. Res. 2024, 15(1), 385-403; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010026 - 8 Mar 2024
Viewed by 1451
Abstract
Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens linked to human gastroenteritis worldwide. To aid the development of pathogen control efforts, the present study characterized the genotypic diversity and pathogenic potential of STEC recovered from sources near agricultural fields in Northwest Mexico. [...] Read more.
Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens linked to human gastroenteritis worldwide. To aid the development of pathogen control efforts, the present study characterized the genotypic diversity and pathogenic potential of STEC recovered from sources near agricultural fields in Northwest Mexico. Samples were collected from irrigation river water and domestic animal feces in farms proximal to agricultural fields and were subjected to enrichment followed by immunomagnetic separation and plating on selective media for the recovery of the STEC isolates. Comparative genomic analyses indicated that the recovered STEC with the clinically relevant serotypes O157:H7, O8:H19, and O113:H21 had virulence genes repertoires associated with host cell adherence, iron uptake and effector protein secretion. Subsequent phenotypic characterization revealed multidrug resistance against aminoglycoside, carbapenem, cephalosporin, fluoroquinolone, penicillin, phenicol, and tetracycline, highlighting the need for improved surveillance on the use of antimicrobials. The present study indicated for the first time that river water in the agricultural Culiacan Valley in Mexico is a relevant key route of transmission for STEC O157 and non-O157 with a virulence potential. In addition, feces from domestic farm animals near surface waterways can act as potential point sources of contamination and transport of diverse STEC with clinically relevant genotypes. Full article
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14 pages, 1697 KiB  
Article
Antagonistic Activity of Macrolepiota sp. CS185 against Post-Harvest Fungi of Fig Fruits (Ficus carica L.)
by Guadalupe Gutiérrez-Soto, Iosvany López-Sandin, Jesús Salvador Hernández Ochoa, Carlos Eduardo Hernadez-Luna, Juan Francisco Contreras-Cordero and Carlos Alberto Hernández-Martínez
Microbiol. Res. 2024, 15(1), 371-384; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010025 - 7 Mar 2024
Viewed by 634
Abstract
Macrolepiota sp. CS185 is a basidiomycete with high potential as a biocontrol agent against various phytopathogenic fungi. Regardless of its pronounced potential as a post-harvest fungi biocontrol agent, its activity in tomato seedlings infected with Alternaria alternata has not been well studied. Thus, [...] Read more.
Macrolepiota sp. CS185 is a basidiomycete with high potential as a biocontrol agent against various phytopathogenic fungi. Regardless of its pronounced potential as a post-harvest fungi biocontrol agent, its activity in tomato seedlings infected with Alternaria alternata has not been well studied. Thus, the present work aimed to evaluate the cultures and supernatants’ antagonistic activity against fig fruits’ post-harvest fungi and antifungal activity production kinetics. The culture antagonistic characteristics were assessed through multiple confrontations, the supernatant concentration effect, and the kinetics of antagonistic action. The multiple confrontations showed differences (p ≤ 0.05) among phytopathogens and over time, with Colletotrichum sp. 2 being the most susceptible. Based on the 9-day incubation profile, the treatment fractions supplemented with a 50% concentration of Macrolepiota sp. CS185 supernatants showed a higher inhibition percentage (%In). Except for Alternaria alternata 1 and 2, the rest of the isolates showed a similar decrease in antagonistic activity up to a certain extent over time. Among all tested strains, Colletotrichum sp. 2 was found with a higher susceptibility. Regarding the production kinetics of antagonistic activity, a triple interaction was observed between the phytopathogen, the age of the Macrolepiota sp. CS 185 culture, and incubation time. In addition, changes in the mycelium growth rate (p ≤ 0.05) along with the higher activity in the supernatants of 20 and 30 days were observed and suggested the production of multiple bioactive metabolites. These results indicate that Macrolepiota sp. CS185 produces antifungal metabolites at different times and could be a suitable candidate to control fig fruits’ post-harvest fungi issues. Full article
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17 pages, 4706 KiB  
Article
Design and Development of Molecular Beacon-Based Real-Time PCR Assays to Identify Clostridioides difficile Types of Main Evolutionary Clades
by Enrico Maria Criscuolo, Fabrizio Barbanti and Patrizia Spigaglia
Microbiol. Res. 2024, 15(1), 354-370; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010024 - 5 Mar 2024
Viewed by 676
Abstract
C. difficile infection (CDI) has an important impact on both human and animal health. The rapid detection and monitoring of C. difficile PCR-ribotypes (RTs) cause of CDI is critical to control and prevent this infection. This study reports the first application of the [...] Read more.
C. difficile infection (CDI) has an important impact on both human and animal health. The rapid detection and monitoring of C. difficile PCR-ribotypes (RTs) cause of CDI is critical to control and prevent this infection. This study reports the first application of the Molecular Beacon (MB)-based real-time PCR method in genotyping important C. difficile RTs of the main evolutionary clades. The cdtR gene was used as target and the cdtR sequences were analyzed after extraction from deposited genomes or were obtained after sequencing from strains of different origin. cdtR alleles were identified after sequence comparisons and MB-based real-time PCR assays were developed to discriminate them. In total, 550 cdtR sequences were compared, 38 SNPs were found, and five different cdtR alleles were identified. In total, one or two alleles were associated to the RTs grouped in the same evolutionary clade. A MB-based real-time assay was designed for each allele and for optimized testing of the C. difficile strains. The results obtained demonstrated that the MB-based real-time PCR assays developed in this study represent a powerful, original, and versatile tool to identify C. difficile types/clades and to monitor changes in the population structure of this important pathogen. Full article
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12 pages, 3624 KiB  
Article
Influence of Organic Matter from Native Fish on the Antimicrobial Efficacy of Sodium Hypochlorite (NaClO) in Reducing Salmonella spp. Population
by Jaqueline Oliveira Reis, Carine Baggio Cavalcante, Nathaly Barros Nunes, Adelino Cunha Neto, Maxsueli Aparecida Moura Machado, Yuri Duarte Porto, Vinicius Silva Castro and Eduardo Eustáquio de Souza Figueiredo
Microbiol. Res. 2024, 15(1), 342-353; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010023 - 29 Feb 2024
Viewed by 907
Abstract
Salmonella spp. is not part of the fish microbiota, being introduced through contaminated water or improper handling. In slaughterhouses, five parts per million (ppm) of free chlorine is recommended in the washing step to eliminate this pathogen. However, Salmonella spp. is still detected [...] Read more.
Salmonella spp. is not part of the fish microbiota, being introduced through contaminated water or improper handling. In slaughterhouses, five parts per million (ppm) of free chlorine is recommended in the washing step to eliminate this pathogen. However, Salmonella spp. is still detected in fish processing plants due to persistent contamination as a result of chlorine–organic matter interactions that reduce chlorine effectiveness. Therefore, this study aimed to test whether organic matter contained in culture media and fish washes interferes with the efficacy of chlorine at 2 and 5 ppm, and what is the time of action required to inactivate ATCC and wild strains of S. typhimurium. For this, the elimination or survival of these strains was investigated when exposed to chlorinated solution for different durations (0, 5, 30, 60, 90 and 120 min) in culture medium, 0.85% saline solution and fish wash (in natura and sterilized). The results showed that the use of 5 ppm of free chlorine is efficient, even when the chlorine remains in contact with the organic matter (washed from the fish), as it reduced the bacterial population by ~5 log log10 CFU/mL of Salmonella spp., showing that this reduction was due to interactions, as long as the chlorine action time was 30 min. Full article
(This article belongs to the Collection Public Health and Quality Aspects Related to Animal Productions)
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16 pages, 9244 KiB  
Article
Optimization of the Conditions for the Transformation of a Bacillus subtilis Strain L11 to Prepare Nano Selenium and Its Preliminary Application in Sheep Feed
by Wenxin Guo, Xinyu Shi, Lu Wang, Xin Cong, Shuiyuan Cheng, Linling Li and Hua Cheng
Microbiol. Res. 2024, 15(1), 326-341; https://doi.org/10.3390/microbiolres15010022 - 26 Feb 2024
Viewed by 1050
Abstract
Selenium nanoparticles (SeNPs) have greater bioavailability and safety than inorganic selenium, and was widely used in medical, agricultural, nutritional supplements, and antibacterial fields. The present study screened a strain L11 producing SeNPs from a selenium rich dairy cow breeding base in Hubei Province, [...] Read more.
Selenium nanoparticles (SeNPs) have greater bioavailability and safety than inorganic selenium, and was widely used in medical, agricultural, nutritional supplements, and antibacterial fields. The present study screened a strain L11 producing SeNPs from a selenium rich dairy cow breeding base in Hubei Province, China. The strain was identified as Bacillus subtilis through physiological, biochemical, and molecular biology analysis. By adjusting the cultivation conditions, the experiment determined the ideal parameters for L11 to efficiently produce SeNPs. These parameters include a pH value of 6, a cultivation temperature of 37 °C, a concentration of 4 mmol/L Na2SeO3, and a cultivation of 48 h. X-ray Photoelectron Spectroscopy (XPS), Scanning Electron Microscope-Energy Dispersive Spectroscopy (SEM-EDS), and Transmission Electron Microscopy (TEM) were used to verify that the Se particles produced by L11 are SeNPs with diameters ranging from 50 to 200 nm. The combination of the protein analysis of different cell components and TEM analysis showed that L11 mainly produces SeNPs through the transformation of the cell’s periplasmic space, cell membrane, and cell wall. Adding the L11 SeNPs complex to sheep feed can significantly enhance the antioxidant activity and immunity of sheep, and increase the Se content in the neck muscles, liver, and spleen tissues. Full article
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12 pages, 4085 KiB  
Article
The Impact of pH Modulation on the Rhizosphere Bacteriome of Maize and Bean
by Rodrigo Reis Moura, Douglas Alfradique Monteiro, Eduardo da Silva Fonseca, Fabiano de Carvalho Balieiro, Fernando Cesário and Caio Tavora Coelho da Costa Rachid
Microbiol. Res. 2024, 15(1), 314-325; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010021 - 20 Feb 2024
Viewed by 752
Abstract
In soils, pH stands as the main factor modulating bacterial communities’ composition. However, most studies address its effects in bulk soils in natural systems, with few focusing on its effects in the rhizosphere of plants. Predicting pH effects in the rhizosphere is an [...] Read more.
In soils, pH stands as the main factor modulating bacterial communities’ composition. However, most studies address its effects in bulk soils in natural systems, with few focusing on its effects in the rhizosphere of plants. Predicting pH effects in the rhizosphere is an important step towards successful microbiome manipulation, aiming to increase crop production. Here, we modulated an acidic soil’s pH to four different ranges (4.7, 5.2, 7.5 and 8.2), while correcting for fertility differences among ranges, thus isolating pH effects from other physicochemical characteristics. Then, two crops with distinct metabolisms (maize and bean) were cultivated in a greenhouse experiment and the effects of pH and cover crops on the rhizosphere bacteriome after 90 days explored through 16S rRNA gene sequencing, aiming to characterize pH effects on the rhizosphere of two different plants across this gradient. Alpha diversity indexes (OTU richness and Shannon index) were statistically different with pH but not crop species, with an interaction among factors. For beta diversity, both pH and crop species were significant modulators of community composition, without an interaction, but pH effects were 2.5 times bigger than those of plant species. Additionally, strong and significant positive correlations were observed between pH and Bacteroidetes and Deltaproteobacteria, while Actinobacteria, Planctomycetes and Acidobacteria were negatively correlated with pH. Regarding OTUs, 27 and 46 were correlated with pH in maize and bean’s rhizosphere, respectively, while 11 were shared between them. Altogether, these results provide valuable information on the isolated effect of pH in the rhizosphere of important crop plants, aiding future microbiome manipulation studies. Full article
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24 pages, 5412 KiB  
Article
Antimycobacterial Drugs as a Novel Strategy to Inhibit Pseudomonas aeruginosa Virulence Factors and Combat Antibiotic Resistance: A Molecular Simulation Study
by Razique Anwer
Microbiol. Res. 2024, 15(1), 290-313; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010020 - 17 Feb 2024
Viewed by 1083
Abstract
Antimicrobial resistance poses a severe threat, particularly in developing countries where the ready availability of drugs and increased consumption lead to improper antibiotic usage, thereby causing a surge in resistance levels compared to developed areas. Despite the past success of antibiotics, their effectiveness [...] Read more.
Antimicrobial resistance poses a severe threat, particularly in developing countries where the ready availability of drugs and increased consumption lead to improper antibiotic usage, thereby causing a surge in resistance levels compared to developed areas. Despite the past success of antibiotics, their effectiveness diminishes with regular use, posing a significant threat to medical efficacy. Pseudomonas aeruginosa, an opportunistic pathogen, triggers various infection-related issues, occurring on occasions including chronic wounds, burn injuries, respiratory problems in cystic fibrosis, and corneal infections. Targeting the quorum sensing (QS) of P. aeruginosa emerges as a strategic approach to combat infections caused by this bacterium. The objective of this study was to check the effect of antimycobacterial drugs against the potential QS targets in P. aeruginosa and identify lead candidates. The antimycobacterial drugs were first examined for the toxicological and pharmacokinetic profile. By virtual screening through molecular docking, delamanid and pretomanid stood out as major candidates. The binding energies of delamanid and pretomanid with LasR were determined to be −8.3 and −10.9 kcal/mol, respectively. The detailed analysis of the complexes of lead compounds were examined through molecular dynamics simulations. The molecular simulations data validated a sustained interaction of lead drugs with target proteins (PqsR, LasI, and LasA) in a physiological environment. The negligible changes in the secondary structure of proteins in presence of hit antimycobacterial drugs further strengthened the stability of the complexes. These findings highlight the potential repurposing of delamanid and pretomanid, specifically in targeting P. aeruginosa quorum-sensing mechanisms. Full article
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17 pages, 1776 KiB  
Article
In Silico Identification of Sugarcane Genome-Encoded MicroRNAs Targeting Sugarcane Mosaic Virus
by Wang Wenzhi, Muhammad Aleem Ashraf, Hira Ghaffar, Zainab Ijaz, Waqar ul Zaman, Huda Mazhar, Maryam Zulfqar and Shuzhen Zhang
Microbiol. Res. 2024, 15(1), 273-289; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010019 - 16 Feb 2024
Viewed by 866
Abstract
Sugarcane mosaic virus (SCMV) (genus, Potyvirus; family, Potyviridae) is widespread, deleterious, and the most damaging pathogen of sugarcane (Saccharum officinarum L. and Saccharum spp.) that causes a substantial barrier to producing high sugarcane earnings. Sugarcane mosaic disease (SCMD) is caused [...] Read more.
Sugarcane mosaic virus (SCMV) (genus, Potyvirus; family, Potyviridae) is widespread, deleterious, and the most damaging pathogen of sugarcane (Saccharum officinarum L. and Saccharum spp.) that causes a substantial barrier to producing high sugarcane earnings. Sugarcane mosaic disease (SCMD) is caused by a single or compound infection of SCMV disseminated by several aphid vectors in a non-persistent manner. SCMV has flexuous filamentous particle of 700–750 nm long, which encapsidated in a positive-sense, single-stranded RNA molecule of 9575 nucleotides. RNA interference (RNAi)-mediated antiviral innate immunity is an evolutionarily conserved key biological process in eukaryotes and has evolved as an antiviral defense system to interfere with viral genomes for controlling infections in plants. The current study aims to analyze sugarcane (Saccharum officinarum L. and Saccharum spp.) locus-derived microRNAs (sof-miRNAs/ssp-miRNAs) with predicted potential for targeting the SCMV +ssRNA-encoded mRNAs, using a predictive approach that involves five algorithms. The ultimate goal of this research is to mobilize the in silico- predicted endogenous sof-miRNAs/ssp-miRNAs to experimentally trigger the catalytic RNAi pathway and generate sugarcane cultivars to evaluate the potential antiviral resistance surveillance ability and capacity for SCMV. Experimentally validated mature sugarcane (S. officinarum, 2n = 8X = 80) and (S. spp., 2n = 100–120) sof-miRNA/ssp-miRNA sequences (n = 28) were downloaded from the miRBase database and aligned with the SCMV genome (KY548506). Among the 28 targeted mature locus-derived sof-miRNAs/ssp-miRNAs evaluated, one sugarcane miRNA homolog, sof-miR159c, was identified to have a predicted miRNA binding site, at nucleotide position 3847 of the SCMV genome targeting CI ORF. To verify the accuracy of the target prediction accuracy and to determine whether the sugarcane sof-miRNA/ssp-miRNA could bind the predicted SCMV mRNA target(s), we constructed an integrated Circos plot. A genome-wide in silico-predicted miRNA-mediated target gene regulatory network was implicated to validate interactions necessary to warrant in vivo analysis. The current work provides valuable computational evidence for the generation of SCMV-resistant sugarcane cultivars. Full article
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26 pages, 1555 KiB  
Review
Microbial Cell Factories: Biodiversity, Pathway Construction, Robustness, and Industrial Applicability
by Rida Chaudhary, Ali Nawaz, Mireille Fouillaud, Laurent Dufossé, Ikram ul Haq and Hamid Mukhtar
Microbiol. Res. 2024, 15(1), 247-272; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010018 - 12 Feb 2024
Viewed by 2275
Abstract
The microbial biosynthesis of proteins, primary metabolites, and chemicals is gaining extraordinary momentum and is presently viewed as an advancing approach in the industrial research sector. Increased threats to the environment and the possibility of declining petroleum assets have switched the spotlight to [...] Read more.
The microbial biosynthesis of proteins, primary metabolites, and chemicals is gaining extraordinary momentum and is presently viewed as an advancing approach in the industrial research sector. Increased threats to the environment and the possibility of declining petroleum assets have switched the spotlight to microbial cell factories (MCFs). Aside from possessing various advantages over chemical synthesis, such as less toxicity, cheaper methodologies, and an environmentally benign nature, microbes can be cultivated in fermenters, resulting in an effective bioprocessing approach in terms of industrial relevance. As the overwhelming majority of biodiversity is microbial, this review first highlights the microbial biodiversity of industrially vital microorganisms. Then, the paper delineates the production pathways for generating valuable bioproducts via microbial workhorses. Many host cells synthesize bio-compounds as a part of their natural mechanism; however, several techniques have also been developed to attain the desired end product from non-native microbes with selected properties. The microbial biosynthetic pathways can be categorized as native-existing pathways, heterologous pathways, and artificial de novo pathways. Systems metabolic engineering, which integrates metabolic engineering with evolutionary engineering, synthetic biology, and systems biology, has further revolutionized the field of engineering robust phenotypes. The employment of these strategies improves the performance of the strain, eventually achieving high titer and productivity rates of bio-chemicals. Modern trends and tools for exploiting native pathways and designing non-native-created pathways are also briefly discussed in this paper. Finally, the review discusses the use of microbial workhorses for producing a myriad of materials and chemicals, including carboxylic acids, amino acids, plant natural products (PNPs), carotenoids, flavors, and fragrances, unveiling the efficacy of utilizing microbial species to generate sustainable bio-based products. Full article
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11 pages, 1861 KiB  
Article
Assessment of the Possibility of Using Bacterial Strains and Bacteriophages for Epidemiological Studies in the Bioaerosol Environment
by Radosław Wróbel, Monika Andrych-Zalewska, Jędrzej Matla, Justyna Molska, Gustaw Sierzputowski, Agnieszka Szulak, Radosław Włostowski, Adriana Włóka and Małgorzata Rutkowska-Gorczyca
Microbiol. Res. 2024, 15(1), 236-246; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010017 - 6 Feb 2024
Viewed by 727
Abstract
During the COVID-19 pandemic, microbiological controls neglected the spread of viruses through the air. Techniques to identify this threat required additional research to enable control measures to be introduced to protect against the spread of disease through this route. Due to the very [...] Read more.
During the COVID-19 pandemic, microbiological controls neglected the spread of viruses through the air. Techniques to identify this threat required additional research to enable control measures to be introduced to protect against the spread of disease through this route. Due to the very high level of risk occurring during research on the COVID-19 and SARS-CoV-2 viruses, it seems necessary to use analogous microorganisms that will allow, through an experiment, to validate or challenge a method that stops the spread of infectious microorganisms, without unnecessary risk to research staff. The presented work was carried out to assess the possibility of using airborne microorganisms that are safe for humans for this type of research. The work presents the selection process of bacteria and viruses (bacteriophages) that have the greatest potential for use in experimental studies on airborne-droplet transmission indoors, especially in hospital facilities. In the study, it was assumed that determining the survival rates of groups of organisms would allow them to be used as a proxy for studying more dangerous bacteria and viruses. Survival studies of selected microorganisms were carried out, and the paper selected microorganisms with the highest survival rate in a given environment. Full article
(This article belongs to the Topic Antimicrobial Resistance in the Time of COVID-19)
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11 pages, 1422 KiB  
Article
A Role for Secondary Metabolites in Desiccation Tolerance in Lichens
by Nqobile Truelove Ndhlovu, Farida Minibayeva and Richard Peter Beckett
Microbiol. Res. 2024, 15(1), 225-235; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010016 - 20 Jan 2024
Viewed by 1000
Abstract
In lichens, secondary metabolites have been shown to protect against biotic stresses such as pathogen attacks and grazing, and abiotic stresses such as ultraviolet (UV) and high photosynthetically active radiation (PAR). Lichen secondary metabolites are known to have strong antioxidant activity, and while [...] Read more.
In lichens, secondary metabolites have been shown to protect against biotic stresses such as pathogen attacks and grazing, and abiotic stresses such as ultraviolet (UV) and high photosynthetically active radiation (PAR). Lichen secondary metabolites are known to have strong antioxidant activity, and while theoretically they may have roles in tolerance to other abiotic stresses, these roles remain largely unclear. Here, we used the acetone rinsing method to harmlessly remove most of the secondary metabolites from the thalli of six lichen species. This enabled us to compare the effects of desiccation on thalli with and without the presence of secondary metabolites. Results showed that in general, the presence of lichen substances reduces the effects of desiccation stress. For all species, substances significantly improved the photosystem two (PSII) activity of the photobiont during either desiccation or rehydration. In the mycobiont, in four of the six species, the presence of substances reduced membrane damage, which was assessed by measuring ion leakage during rehydration following desiccation. However, in one species, secondary metabolites had no effect, while in another the presence of substances increased membrane damage. Nevertheless, it seems clear that in addition to their more established roles in protecting lichens against pathogen attacks and grazing, lichen substances can also play a role in aiding desiccation tolerance. Full article
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12 pages, 2665 KiB  
Article
COVID-19 Epidemic Process and Evolution of SARS-CoV-2 Genetic Variants in the Russian Federation
by Vasiliy Akimkin, Tatiana A. Semenenko, Svetlana V. Ugleva, Dmitry V. Dubodelov and Kamil Khafizov
Microbiol. Res. 2024, 15(1), 213-224; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010015 - 16 Jan 2024
Cited by 1 | Viewed by 919
Abstract
The COVID-19 pandemic, etiologically related to a new coronavirus, has had a catastrophic impact on the demographic situation on a global scale. The aim of this study was to analyze the manifestations of the COVID-19 epidemic process, the dynamics of circulation, and the [...] Read more.
The COVID-19 pandemic, etiologically related to a new coronavirus, has had a catastrophic impact on the demographic situation on a global scale. The aim of this study was to analyze the manifestations of the COVID-19 epidemic process, the dynamics of circulation, and the rate of the spread of new variants of the SARS-CoV-2 virus in the Russian Federation. Retrospective epidemiological analysis of COVID-19 incidence from March 2020 to fall 2023 and molecular genetic monitoring of virus variability using next-generation sequencing technologies and bioinformatics methods were performed. Two phases of the pandemic, differing in the effectiveness of anti-epidemic measures and the evolution of the biological properties of the pathogen, were identified. Regularities of SARS-CoV-2 spread were determined, and risk territories (megacities), risk groups, and factors influencing the development of the epidemic process were identified. It was found that with each subsequent cycle of disease incidence rise, the pathogenicity of SARS-CoV-2 decreased against the background of the increasing infectiousness of SARS-CoV-2. Data on the mutational variability of the new coronavirus were obtained using the Russian platform of viral genomic information aggregation (VGARus) deployed at the Central Research Institute of Epidemiology. Monitoring the circulation of SARS-CoV-2 variants in Russia revealed the dominance of Delta and Omicron variants at different stages of the pandemic. Data from molecular genetic studies are an essential component of epidemiologic surveillance for making management decisions to prevent the further spread of SARS-CoV-2 and allow for prompt adaptation to pandemic control tactics. Full article
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17 pages, 2648 KiB  
Article
Promising Eco-Friendly Nanoparticles for Managing Bottom Rot Disease in Lettuce (Lactuca sativa var. longifolia)
by Nashwa A. H. Fetyan, Tarek A. Essa, Tamer M. Salem, Ahmed Aboueloyoun Taha, Samah Fawzy Elgobashy, Nagwa A. Tharwat and Tamer Elsakhawy
Microbiol. Res. 2024, 15(1), 196-212; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010014 - 16 Jan 2024
Cited by 3 | Viewed by 908
Abstract
Developing innovative, eco-friendly fungicide alternatives is crucial to mitigate the substantial threat fungal pathogens pose to crop yields. In this study, we assessed the in vitro effectiveness of SiO2, CuO, and γFe2O3 nanoparticles against Rhizoctonia solani. Furthermore, [...] Read more.
Developing innovative, eco-friendly fungicide alternatives is crucial to mitigate the substantial threat fungal pathogens pose to crop yields. In this study, we assessed the in vitro effectiveness of SiO2, CuO, and γFe2O3 nanoparticles against Rhizoctonia solani. Furthermore, greenhouse experiments were conducted in artificially infested soil to evaluate the in vivo impact of nanoparticles under study. Two application methods were employed: soil drenching with 10 mL per pot at concentrations of 50, 100, and 200 mg L−1, and seedling dipping in nanoparticle suspensions at each concentration combined with soil drench. The combined treatment of 200 mg L−1 γFe2O3 or CuO nanoparticles showed the highest in vitro antifungal activity. Conversely, SiO2 nanoparticles demonstrated the lowest in vitro activity. Notably, the application of 200 mg/L SiO2 via the dipping and soil drenching methods decreased counts of silicate-solubilizing bacteria and Azospirillum spp. Whereas, application of 100 mg L−1 γFe2O3 nanoparticles via soil drenching increased soil bacterial counts, and CuO nanoparticles at 50 mg L−1 through dipping and soil drenching had the highest dehydrogenase value. γFe2O3 nanoparticles improved plant photosynthetic pigments, reduced malondialdehyde levels, and minimized membrane leakage in lettuce plants. A root anatomical study showed that 200 mg L−1 CuO nanoparticles induced toxicity, whereas 200 mg L−1 γFe2O3 or SiO2 nanoparticles positively affected root diameter, tissue structure, and various anatomical measurements in lettuce roots. γFe2O3 nanoparticles hold promise as a sustainable alternative for managing crop diseases. Full article
(This article belongs to the Special Issue Plants, Mycorrhizal Fungi, and Bacteria)
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9 pages, 391 KiB  
Communication
Effects of Glomus fasciculatum, Azotobacter chroococcum and Vermicompost Leachate on the Production and Quality of Tomato Fruit
by Alejandro Alarcón-Zayas, Luis Guillermo Hernández-Montiel, Diana Medina-Hernández, Edgar Omar Rueda-Puente, Wilson Geobel Ceiro-Catasú and Ramón Jaime Holguín-Peña
Microbiol. Res. 2024, 15(1), 187-195; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010013 - 11 Jan 2024
Viewed by 871
Abstract
Arbuscular mycorrhizal fungi, plant-growth-promoting bacteria (PGPB) and vermicompost constitute important environmental and economic resources for improving the production and quality of tomato fruits. The present research aims to determine the single and combined effect of Glomus fasciculatum (Gf) fungus, Azotobacter chroococcum (Azot), PGPB [...] Read more.
Arbuscular mycorrhizal fungi, plant-growth-promoting bacteria (PGPB) and vermicompost constitute important environmental and economic resources for improving the production and quality of tomato fruits. The present research aims to determine the single and combined effect of Glomus fasciculatum (Gf) fungus, Azotobacter chroococcum (Azot), PGPB and vermicompost leachate (VL) organic fertilizer on the yield and quality of tomato fruit. Thus, an open-field experiment was established with seven treatments, a control and three replicates. Total soluble solids, vitamin C, acidity, fruit mass and fruit diameter were evaluated as fruit quality variables; the yield was recorded and estimated in tons per hectare−1. The results showed that Gf, Azot and VL were effective in promoting tomato yield and fruit quality. As a trend, the triple combination (Gf + Azot + VL) evidently obtained the highest values of total soluble solids, vitamin C and fruit acidity. The range of improvement concerning the fruit size was 66.6% (single treatment) compared to 78.5% (triple combination). The maximum yield of 54.5 t/ha−1 was recorded for the Gf + Azot + VL combination. Therefore, G. fasciculatum, A. chroococcum and VL are considered useful as organic alternatives for open-field tomato biofertilization programs in tropical countries. Full article
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13 pages, 1774 KiB  
Article
Biogas Dynamics and Microbial Composition Employing Different Inocula and Substrates in Continuous Stirred-Tank Reactors
by Fayyaz Ali Shah, Roderick I. Mackie and Qaisar Mahmood
Microbiol. Res. 2024, 15(1), 174-186; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010012 - 9 Jan 2024
Viewed by 899
Abstract
The current investigation delved into the utilization of cattle and municipal sanitary inocula for anaerobic digestion of poultry wastes, addressing a crucial and pragmatic challenge in waste management. The emphasis on poultry waste is pertinent due to its well-documented impediments in anaerobic digestion, [...] Read more.
The current investigation delved into the utilization of cattle and municipal sanitary inocula for anaerobic digestion of poultry wastes, addressing a crucial and pragmatic challenge in waste management. The emphasis on poultry waste is pertinent due to its well-documented impediments in anaerobic digestion, attributed to heightened levels of ammonia and volatile fatty acids (VFAs). The strategic selection of cattle and municipal sanitary inocula suggests an approach aimed at bolstering the anaerobic digestion process. In this study, we evaluated the use of cattle and municipal sanitary inocula for the anaerobic digestion of various poultry wastes, which is often challenged by high levels of ammonia and volatile fatty acids (VFAs). The substrates tested included belt waste (Poultry A), poultry litter plus feed residues (Poultry B), tray hatchery ©, and stillage. These substrates were processed in two continuous stirred tank reactors (CSTRs), R-1 (with antibiotic monensin) and R-2 (without monensin). Initially, both reactors operated with the same hydraulic retention time (HRT), using a substrate ratio of stillage: belt: tray hatchery (S:B:T) of 70:15:15. On the 41st day, the HRT was adjusted to 20 days, and the substrate ratio was changed to S:A:T 70:40:40. The specific methane yield for R-1 started at 10.768 L g−1 COD, but decreased to 2.65 L g−1 COD by the end of the experiment. For R-2, the specific methane yield varied between 0.45 L g−1 COD and 0.243 L g−1 COD. Microbial composition in the reactors changed over time. In R-1, bacteroides were consistently dominant, while firmicutes were less abundant compared to R-2. Proteobacteria were initially low in abundance, but spirochetes were found in both reactors throughout the experiment. The study concluded that Poultry B substrates, due to their rich nutrient and trace element composition, are suitable for biogas plants. Municipal sanitary inocula also showed promise due to their resilience in high ammonia concentrations. Further research into biofilm interactions is recommended to better understand microbial responses to high ammonia concentrations, which can lead to propionate production in anaerobic digestion (AD). Full article
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10 pages, 2650 KiB  
Case Report
First Occurrence of Coffee Leaf Rust Caused by Hemileia vastatrix on Coffee in Saudi Arabia
by Khalid Alhudaib and Ahmed Mahmoud Ismail
Microbiol. Res. 2024, 15(1), 164-173; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010011 - 8 Jan 2024
Viewed by 1295
Abstract
Coffee leaf rust (CLR) is a major disease of Arabica coffee caused by the biotrophic fungus Hemileia vastatrix. Jazan region in Saudi Arabia has long been one of the last coffee-producing regions in the world free of this disease. In August 2023, [...] Read more.
Coffee leaf rust (CLR) is a major disease of Arabica coffee caused by the biotrophic fungus Hemileia vastatrix. Jazan region in Saudi Arabia has long been one of the last coffee-producing regions in the world free of this disease. In August 2023, CLR was initially observed in coffee plantations located in Fyfa district one of the main coffee-producing mountains of Jazan region. The source of the infection is unknown, however CLR could have entered Jazan from the nearest coffee-producing locations that haven the pathogen. During a scheduled survey in August 2023, symptoms were observed including yellowish-orange lesions that frequently combined to form chlorotic lesions and exhibited the powdery appearance of yellow uredospores on the abaxial surface of leaves. The uredospores and teliospores were microscopically examined and their morphology matched the previously published description for H. vastatrix. The identity of H. vastatrix specimens was further confirmed based on PCR amplification and sequencing of ITS, sharing a 99–100% identity with previously published sequences, as belonging to H. vastatrix. The pathogenicity of H. vastatrix specimens was investigated on Coffee arabica plants under growth chamber conditions, and all were pathogenic relative to control, with 100% of disease incidence, therefore fulfilling Koch’s postulates. Based on our findings, this is the first documentation of H. vastatrix causing CLR in Saudi Arabia. Full article
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12 pages, 706 KiB  
Article
Screening of Microorganisms from Wastes and Identification of the Optimal Substrate for Biosurfactant Production
by Liliya Biktasheva, Alexander Gordeev, Anastasia Kirichenko, Polina Kuryntseva and Svetlana Selivanovskaya
Microbiol. Res. 2024, 15(1), 152-163; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010010 - 6 Jan 2024
Viewed by 1033
Abstract
The production of biosurfactants from organic wastes has received significant attention due to its potential cost savings. This study involved the isolation of biosurfactant-producing microorganisms from waste sources. The surfactant properties of the 37 studied isolates were assessed by reducing surface tension and [...] Read more.
The production of biosurfactants from organic wastes has received significant attention due to its potential cost savings. This study involved the isolation of biosurfactant-producing microorganisms from waste sources. The surfactant properties of the 37 studied isolates were assessed by reducing surface tension and their emulsifying properties, determined by the emulsification index E24. We assessed the ability of these isolated strains to produce biosurfactants using various waste substrates, namely potato peelings, waste cooking oil and sunflower cake. Our results showed that sunflower cake exhibited better growth and biosurfactant production for most of the strains studied. This highlights that sunflower cake is a potentially effective and economical substrate for the production of biosurfactants. The most effective strains allowing to achieve an emulsification index above 50% and reduce surface tension below 40 mN m−1 were Enterobacter sp. 2pp, strain 2wfo, Peribacillus sp. 1mo, Sphingomonas sp. 2mo, Ochrobactrum sp. 5mo, Shouchella sp. 6mo, Bacillus sp. 1os, Bacillus sp. 2os. Among these strains, both previously known strains as biosurfactant producers and previously unknown strains were found. Thus, we found that among representatives of the genus Sphingomonas there are effective producers of biosurfactants. The highest yield of biosurfactant on a medium with glycerol and glucose was shown by the Bacillus sp. 2os strain of 0.501 and 0.636 g L−1, respectively. Full article
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15 pages, 320 KiB  
Review
Updates on Staphylococcal Vaccines
by Alexandru Scafa-Udriste, Mircea-Ioan Popa and Gabriela-Loredana Popa
Microbiol. Res. 2024, 15(1), 137-151; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010009 - 28 Dec 2023
Cited by 1 | Viewed by 1351
Abstract
Staphylococcus aureus, a prevalent human pathogen and a leading cause of hospital-acquired infections, is increasingly evolving antibiotic-resistant strains, increasing mortality and morbidity rates. Anti-staphylococcal vaccine research for prevention and treatment has become a priority. Antibodies against specific S. aureus components, toxins, and [...] Read more.
Staphylococcus aureus, a prevalent human pathogen and a leading cause of hospital-acquired infections, is increasingly evolving antibiotic-resistant strains, increasing mortality and morbidity rates. Anti-staphylococcal vaccine research for prevention and treatment has become a priority. Antibodies against specific S. aureus components, toxins, and polysaccharides have demonstrated encouraging results in animal studies regarding protection against colonization or infection. However, human immunization trials have yielded less optimistic outcomes, with no anti-staphylococcal having passed clinical trials up to now. Although multiple formulation attempts triggered strong antibody responses, the vaccines could not effectively prevent S. aureus infections. This article delves into the results of immunotherapeutic strategies against S. aureus in both animal and human studies, discussing the feasibility of adequate immunization approaches against S. aureus in humans. Full article
17 pages, 2431 KiB  
Article
Automated Protocol for Monitoring Droplets and Fomites on Surfaces
by Federica Valeriani, Lory Marika Margarucci, Francesca Ubaldi, Gianluca Gianfranceschi and Vincenzo Romano Spica
Microbiol. Res. 2024, 15(1), 120-136; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010008 - 27 Dec 2023
Viewed by 960
Abstract
During the COVID-19 pandemic, extensive efforts focused on developing a better understanding of indirect transmission routes, environmental monitoring of fomites, and suitable surveillance strategies, providing new perspectives to also face other communicable diseases. Rapid methods for monitoring environmental contamination are strongly needed to [...] Read more.
During the COVID-19 pandemic, extensive efforts focused on developing a better understanding of indirect transmission routes, environmental monitoring of fomites, and suitable surveillance strategies, providing new perspectives to also face other communicable diseases. Rapid methods for monitoring environmental contamination are strongly needed to support risk assessment, epidemiological surveillance and prevent infections from spreading. We optimized and automatized a protocol based on fomite detection by qPCR, using a microbial-signature approach based on marker genes belonging to the microbiota of droplets or different biological fluids. The procedure was implemented by exploiting the available tools developed for SARS-CoV-2 tracing, such as flocked swab sampling, real-time PCR equipment and automatic extraction of nucleic acids. This approach allowed scaling up, simplifying, and speeding up the extraction step of environmental swabs, processing at least 48 samples within 45 min vs. 90 min for about 24 samples by manual protocols. A comparison of microflora data by Next-Generation Sequencing (NGS) strongly supports the effectiveness of this semiautomated extraction procedure, providing good quality DNA with comparable representation of species as shown by biodiversity indexes. Today, equipment for qPCR is widely available and relatively inexpensive; therefore this approach may represent a promising tool for hospital hygiene in surveilling fomites associated with SARS-CoV-2 or other pathogen’s transmission. Full article
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11 pages, 5627 KiB  
Communication
Comparative Analysis of Healthy Gut Microbiota in German and Korean Populations: Insights from Large-Scale Cohort Studies
by Min Kee Son, Yuri Song, Jin Chung and Hee Sam Na
Microbiol. Res. 2024, 15(1), 109-119; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010007 - 26 Dec 2023
Viewed by 962
Abstract
Healthy individuals often have different gut microbiota, and these differences can be influenced by their country of origin or their race. This study aimed to compare the gut microbiota compositions of healthy Germans and Koreans using 16S rRNA sequencing data extracted from public [...] Read more.
Healthy individuals often have different gut microbiota, and these differences can be influenced by their country of origin or their race. This study aimed to compare the gut microbiota compositions of healthy Germans and Koreans using 16S rRNA sequencing data extracted from public sources. Two cohorts, comprising 1592 samples (804 Germans and 788 Koreans), were analyzed for alpha and beta diversity, core microbiome, and abundances of specific taxa. The Prevotella enterotype was more prevalent in Koreans, and significant diversity differences were observed depending on cohorts and enterotypes. The core microbiomes across all enterotypes and cohorts included Bacteroides, Faecalibacterium, Parabacteroides, and Lachnospira. Several common core microbiomes were also found depending on enterotype. Koreans exhibited higher abundances of Faecalibacterium, Prevotella, and Bacteroides, while Germans had higher abundances of Blautia, Subdoligranulum, and Agathobacter. Distinctive microbiomes were identified by enterotype. The study enhances comprehension of gut microbiome variations linked to enterotype and geographical factors, and emphasizes the need for additional research to establish correlations between specific microbial properties and individual health status. Full article
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18 pages, 427 KiB  
Article
Assess the Diagnostic Accuracy of GeneXpert to Detect Mycobacterium tuberculosis and Rifampicin-Resistant Tuberculosis among Presumptive Tuberculosis and Presumptive Drug Resistant Tuberculosis Patients
by Venkateswari Ramachandra, Usharani Brammacharry, Aaina Muralidhar, Anbazhagi Muthukumar, Revathi Mani, Muthuraj Muthaiah, Govindarajan Soundappan and Asha Frederick
Microbiol. Res. 2024, 15(1), 91-108; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010006 - 22 Dec 2023
Viewed by 1038
Abstract
GeneXpert MTB/RIF is a rapid molecular diagnostic tool capable of simultaneously detecting Mycobacterium tuberculosis and rifampicin resistance. This study aimed to assess the diagnostic precision of GeneXpert MTB/RIF assay to detect pulmonary and extrapulmonary tuberculosis and evaluate the performance for detecting of rifampicin [...] Read more.
GeneXpert MTB/RIF is a rapid molecular diagnostic tool capable of simultaneously detecting Mycobacterium tuberculosis and rifampicin resistance. This study aimed to assess the diagnostic precision of GeneXpert MTB/RIF assay to detect pulmonary and extrapulmonary tuberculosis and evaluate the performance for detecting of rifampicin resistance. Of 37,695 samples, 7156 (18.98%) were tuberculosis-positive, and 509 (7.11%) were rifampicin-resistant. The sensitivity, specificity, positive predictive value, negative predictive value, disease prevalence, and accuracy of the GeneXpert MTB/RIF assay for pulmonary tuberculosis were 99.87% (95%CI: 99.75–99.94), 99.92% (95%CI: 99.88–99.95), 99.71% (95%CI: 99.54–99.82), 99.97% (95%CI: 99.93–99.98), 21.38% (95%CI: 20.92–21.86), and 99.91% (95%CI: 99.87–99.94), respectively. For extrapulmonary tuberculosis, the sensitivity, specificity, PPV, NPV, disease prevalence, and accuracy of GeneXpert MTB/RIF assay accounted for 99.45% (95%CI: 98.73–99.82), 99.84% (95%CI: 99.73–99.92), 98.70% (95%CI: 97.73–99.25), 99.93% (95%CI: 99.84–99.97), 10.64% (95%CI: 9.99–11.31), and 99.80% (95%CI: 99.68–99.88), respectively. Despite its high sensitivity for detecting tuberculosis and rifampicin resistance, GeneXpert MTB/RIF had contradictory results for 20.5% of cases among patients with smear-negative results and 54.9% of cases among patients with a high risk of multidrug-resistant tuberculosis. Of 46% fluoroquinolone-resistant cases, 16.56% (26/157) were multidrug-resistant tuberculosis isolates, and 4.02% (20/498) were isoniazid-resistant, a characteristic distribution leading to about 17.2% of fluoroquinolone-resistance events and relevant marker gyr-A mutations in MDR tuberculosis isolates. Further, our study indicated that increased fluoroquinolone resistance among rifampicin-resistant and isoniazid-resistant tuberculosis endangers the success of newly endorsed MDR-TB regimens. Full article
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25 pages, 3552 KiB  
Review
Bioactive Diepoxy Metabolites and Highly Oxygenated Triterpenoids from Marine and Plant-Derived Bacteria and Fungi
by Valery M. Dembitsky
Microbiol. Res. 2024, 15(1), 66-90; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010005 - 21 Dec 2023
Viewed by 1148
Abstract
This article explores the diverse array of biologically active compounds derived from microbial symbionts, particularly focusing on the isolation and characterization of diepoxides, highly oxygenated triterpenoids, secosteroids, ergostane-type steroids, and meroterpenoids from various marine and plant-derived fungi. We highlight significant discoveries such as [...] Read more.
This article explores the diverse array of biologically active compounds derived from microbial symbionts, particularly focusing on the isolation and characterization of diepoxides, highly oxygenated triterpenoids, secosteroids, ergostane-type steroids, and meroterpenoids from various marine and plant-derived fungi. We highlight significant discoveries such as vitamin D variants from fungal species, unique sesterterpenoids from mangrove endophytic fungi, and secosteroids with potential medicinal applications. The study delves into the structural uniqueness and bioactivities of these compounds, including their anti-inflammatory, antibacterial, antifungal, antiviral, and cytotoxic effects. Notable findings include the isolation of compounds with significant activity against cancer cell lines, the inhibition of acetylcholinesterase, and promising antifouling properties. This work underscores the potential of microbial symbionts as a rich source of novel bioactive compounds with diverse therapeutic applications, highlighting the importance of marine and fungal biodiversity in drug discovery and development. Full article
(This article belongs to the Special Issue Bioactive Secondary Metabolites of Microbial Symbionts)
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16 pages, 2335 KiB  
Article
Genome Sequence and Characterisation of Peribacillus sp. Strain AS_2, a Bacterial Endophyte Isolated from Alectra sessiliflora
by Mehabo Penistacia Maela and Mahloro Hope Serepa-Dlamini
Microbiol. Res. 2024, 15(1), 50-65; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010004 - 21 Dec 2023
Cited by 2 | Viewed by 1409
Abstract
Peribacillus sp. AS_2, a leaf endophytic bacterium isolated from the medicinal plant Alectra sessiliflora, was previously identified using the 16S rRNA gene sequence. The draft genome of AS_2 had a 5,482,853 bp draft circular chromosome, 43 contigs, N50 of 360,633 bp [...] Read more.
Peribacillus sp. AS_2, a leaf endophytic bacterium isolated from the medicinal plant Alectra sessiliflora, was previously identified using the 16S rRNA gene sequence. The draft genome of AS_2 had a 5,482,853 bp draft circular chromosome, 43 contigs, N50 of 360,633 bp and an average G + C% content of 40.5%. Whole genome sequencing and phenotypic analysis showed that AS_2 was Gram-positive, endospore-forming, motile, and rod-shaped and it showed a high sequence similarity with P. frigoritolerans DSM 8801T. Genomic digital DNA–DNA hybridisation (dDDH) between strain AS_2 and Peribacillus frigoritolerans DSM 8801T and P. castrilensis N3T was 84.8% and 79.2%, respectively, and the average nucleotide identity (ANI) of strain AS_2 with P. frigoritolerans DSM 8801T and P. castrilensis N3T was 97.0% and 96.7%, respectively. The antiSMASH software predicted a total of eight secondary metabolite gene clusters comprising non-ribosomal peptide synthetase (NRPS) type koranimine, terpenes, and siderophore clusters. Strain AS_2 also displayed genes involved in endophytic lifestyle and antibiotic resistance gene clusters such as small multidrug resistance antibiotic efflux pumps (qacJs). Using the multilocus sequence analysis (MLSA), together with the phenotypic data and genomic analysis, we demonstrated that strain AS_2 is a subspecies of P. frigoritolerans DSM 8801T. Genome sequencing of Peribacillus sp. AS_2 from medicinal plants provides valuable genomic information and allows us to further explore its biotechnological applications. Full article
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17 pages, 1660 KiB  
Article
Biodegradation of Free Cyanide by a New Isolated Alkaliphilic Bacillus licheniformis Strain
by Daniel Uribe-Ramírez, Eliseo Cristiani-Urbina and Liliana Morales-Barrera
Microbiol. Res. 2024, 15(1), 33-49; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010003 - 21 Dec 2023
Viewed by 759
Abstract
Microbial treatment of free-cyanide-polluted wastewater is a cost-effective, efficient, and eco-friendly method. Free-cyanide-degrading microbial cultures were isolated from different sources using batch-enrichment culture techniques, with acetate as the carbon source. Five microbial cultures were able to tolerate and grow at 1500 mg/L free [...] Read more.
Microbial treatment of free-cyanide-polluted wastewater is a cost-effective, efficient, and eco-friendly method. Free-cyanide-degrading microbial cultures were isolated from different sources using batch-enrichment culture techniques, with acetate as the carbon source. Five microbial cultures were able to tolerate and grow at 1500 mg/L free cyanide, which was used as the only nitrogen source under strongly alkaline conditions (pH = 11). Among them, one bacterial strain (B11) was selected for further study because of its high free-cyanide-biodegradation efficiency. Bacterial strain B11 was molecularly identified as Bacillus licheniformis CDBB B11. Free cyanide inhibited the growth rate of B. licheniformis CDBB B11 at initial cyanide concentrations >75 mg/L. Despite this, the bacterial strain demonstrated 100% cyanide-biodegradation efficiency at initial cyanide concentrations ranging from 25 to 75 mg/L, which decreased to 32% as the initial cyanide concentration increased from 75 to 1500 mg/L. Free-cyanide biodegradation corresponds to bacterial growth and ammonia accumulation in the culture medium. The alkaliphilic B. licheniformis CDBB B11 strain is a robust candidate for the detoxification of free-cyanide-laden wastewater because it tolerates and efficiently degrades free cyanide at concentrations of up to 1500 mg/L. Full article
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13 pages, 1445 KiB  
Article
Properties of Potential Plant-Growth-Promoting Bacteria and Their Effect on Wheat Growth Promotion (Triticum aestivum) and Soil Characteristics
by Elena Voronina, Ekaterina Sokolova, Irina Tromenschleger, Olga Mishukova, Inna Hlistun, Matvei Miroshnik, Oleg Savenkov, Maria Buyanova, Ilya Ivanov, Maria Galyamova and Natalya Smirnova
Microbiol. Res. 2024, 15(1), 20-32; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010002 - 19 Dec 2023
Cited by 1 | Viewed by 1054
Abstract
Plant-growth-promoting bacteria are an important economic and environmental resource as biofertilizers that can stimulate plant growth and improve agricultural yields. In this study, potential plant growth-promoting bacteria were isolated from soil samples collected in Russia. Strains that manifested active growth on a nitrogen-free [...] Read more.
Plant-growth-promoting bacteria are an important economic and environmental resource as biofertilizers that can stimulate plant growth and improve agricultural yields. In this study, potential plant growth-promoting bacteria were isolated from soil samples collected in Russia. Strains that manifested active growth on a nitrogen-free medium, the Pikovskaya medium (with insoluble phosphates) and CAS (Chrome Azurol S) agar, were selected for the study. All bacterial isolates were identified by 16S rRNA gene sequencing analysis. Seventeen bacterial isolates of different species were purified and quantified for their ability to grow on nitrogen-free media; dissolve phosphate; and produce ammonium, indole-3-acetic acid, siderophores, and antifungal activity. Principal component analysis identified three groups of strains: one with the maximum signs of providing “plant nutrition”; one with signs of “antimicrobial activity”; and a group “without outstanding signs”. All 17 strains were involved in experiments involving growing inoculated wheat seeds (Triticum aestivum) in pots under natural environmental conditions, and were assessed by their effect on the wheat growth and yield as well as on the chemical composition of the soil. For the “plant nutrition” group, regression analysis revealed a connection between indicators of plant growth, ear length, and ammonium accumulation in the soil. However, in other groups, there were also strains showing a positive effect on plant growth, which suggests the necessity of involving additional factors to predict the ability of strains to affect plants when screened in the laboratory. Full article
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19 pages, 2328 KiB  
Article
Genome-Wide Identification of Cotton MicroRNAs Predicted for Targeting Cotton Leaf Curl Kokhran Virus-Lucknow
by Muhammad Aleem Ashraf, Judith K. Brown, Muhammad Shahzad Iqbal and Naitong Yu
Microbiol. Res. 2024, 15(1), 1-19; https://0-doi-org.brum.beds.ac.uk/10.3390/microbiolres15010001 - 19 Dec 2023
Viewed by 984
Abstract
Cotton leaf curl Kokhran virus (CLCuKoV) (genus, Begomovirus; family, Geminiviridae) is one of several plant virus pathogens of cotton (Gossypium hirsutum L.) that cause cotton leaf curl disease in Pakistan. Begomoviruses are transmitted by the whitefly Bemisia tabaci cryptic species [...] Read more.
Cotton leaf curl Kokhran virus (CLCuKoV) (genus, Begomovirus; family, Geminiviridae) is one of several plant virus pathogens of cotton (Gossypium hirsutum L.) that cause cotton leaf curl disease in Pakistan. Begomoviruses are transmitted by the whitefly Bemisia tabaci cryptic species group and cause economic losses in cotton and other crops worldwide. The CLCuKoV strain, referred to as CLCuKoV-Bur, emerged in the vicinity of Burewala, Pakistan, and was the primary causal virus associated with the second CLCuD epidemic in Pakistan. The monopartite ssDNA genome of (2.7 Kb) contains six open reading frames that encode four predicted proteins. RNA interference (RNAi)-mediated antiviral immunity is a sequence-specific biological process in plants and animals that has evolved to combat virus infection. The objective of this study was to design cotton locus-derived microRNA (ghr-miRNA) molecules to target strains of CLCuKoV, with CLCuKoV-Lu, as a typical CLCuD-begomovirus genome, predicted by four algorithms, miRanda, RNA22, psRNATarget, and RNA hybrid. Mature ghr-miRNA sequences (n = 80) from upland cotton (2n = 4x = 52) were selected from miRBase and aligned with available CLCuKoV-Lu genome sequences. Among the 80 cotton locus-derived ghr-miRNAs analyzed, ghr-miR2950 was identified as the most optimal, effective ghr-miRNA for targeting the CLCuKoV-Lu genome (nucleotide 82 onward), respectively, based on stringent criteria. The miRNA targeting relies on the base pairing of miRNA–mRNA targets. Conservation and potential base pairing of binding sites with the ghr-miR2950 were validated by multiple sequence alignment with all available CLCuKoV sequences. A regulatory interaction network was constructed to evaluate potential miRNA–mRNA interactions with the predicted targets. The efficacy of miRNA targeting of CLCuKoV was evaluated in silico by RNAi-mediated mRNA cleavage. This predicted targets for the development of CLCuD-resistant cotton plants. Full article
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