Microbiology Research最新文献

{"title":"Novel Bioformulations with Trichoderma lixii to Improve the Growth Dynamics and Biocontrol of the Cowpea Damping-Off Disease","authors":"A. Omara, Fatma M. El-maghraby","doi":"10.3390/microbiolres14040138","DOIUrl":"https://doi.org/10.3390/microbiolres14040138","url":null,"abstract":"Because agricultural wastes are abundant in biologically active substances, they can be used as a substitute source to produce highly valuable products while lowering pollution levels in the environment. Therefore, we aimed at determining the best agricultural wastes to increase the biomass production rate and the effectiveness of the biocontrol strain Trichoderma lixii SARS 111 in a solid-state fermentation system. The potential for its use in enhancing growth dynamics and controlling the Fusarium oxysporum NCAIM-F-00779-caused damping-off disease of cowpea plants grown in greenhouse conditions was also studied. Using a one-factor-at-a-time experiment, five cheap agricultural waste substrates (faba bean, cowpea, sweet potato, pumpkin, and cassava) were studied using the Plackett–Burman design (PBD) and the central composite design (CCD) to optimize the nutritional and growth conditions to maximize the production of Trichoderma conidia. The findings demonstrated that increasing Candida production quantitatively required the use of 3 g of sweet potato, 3 g of cassava, pH 6, 25 °C, and pre-treatment with dH2O. The shelf life and viability of T. lixii strain were measured as log10 CFU g−1 per substrate at room temperature (RT, 25 °C) at the beginning of month 0 and subsequently at 2-month intervals for 12 months. Data showed that the fungal counts increased with the use of 4 g of sweet potato + 2 g of cassava up to 7 months and then sharply decreased, lasting up to 12 months. Additionally, this bioformulation was applied to cowpea plants in a greenhouse experiment, where a significantly higher level of plant growth traits, photosynthetic pigments, antioxidant enzymes, and chemical content in the leaves, as well as lower incidence of the damping-off disease, were noted. Accordingly, it is possible to suggest 4 g of sweet potato and 2 g of cassava as a suitable bioformulation for the industrial-scale production of the T. lixii strain, which may be a potential biocontrol agent for preventing the cowpea damping-off disease caused by F. oxysporum and improving the growth dynamics.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"67 2","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138605057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Detection of Circulating Cell-Free DNA for the Diagnosis of Schistosoma in Immigrants from African Countries in Italy","authors":"Dimartino Valentina, Scopelliti Fernanda, Cattani Caterina, Nicolella Gianluca, Cavani Andrea","doi":"10.3390/microbiolres14040137","DOIUrl":"https://doi.org/10.3390/microbiolres14040137","url":null,"abstract":"The rising migration and travel from and towards endemic areas has brought renewed concerns about many parasitic infections, including neglected tropical diseases, such as schistosomiasis. Although serology is the most widely used method for the screening of schistosomiasis in non-endemic countries, this technique lacks sensitivity, especially to distinguish between past and ongoing infections. More recently, a molecular test based on the detection of Schistosoma cell-free DNA in the serum has been proposed as a diagnostic procedure for parasitosis. To test the performance of a blood PCR assay, this work investigated 102 serum samples collected from migrants coming from endemic areas by using primers specific to genomic regions of S. mansoni and S. haematobium patients. The results were then compared with the detection of specific IgG Abs with serological tests. Molecular analysis detected Schistosoma DNA in 32 patients. Among them, we characterized nine S. haematobium, 20 S. mansoni, and three coinfections. Compared with molecular assay, serological analysis detected specific antibodies against Schistosoma antigens in 52 out of 102 patients. Concordance between the two tests was found in 76 out of 102 patients (74.51%): in particular, both diagnostic tests were positive in 29 patients (28.43%) and negative in 47 (46.08%). The specificity of the molecular test was 94%. Overall, our data suggest that serological diagnosis could be combined with the molecular approach, providing the clinician with the serotyping of the parasite and useful information about the infection as well as the required further diagnostic procedures.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":" 27","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138619421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of Outer Surface Protein Vaccine Candidates of Borrelia burgdorferi for Lyme Disease","authors":"I. Liekniņa, Anna Kozlova, Marina Šaško, I. Akopjana, K. Brangulis, K. Tārs","doi":"10.3390/microbiolres14040136","DOIUrl":"https://doi.org/10.3390/microbiolres14040136","url":null,"abstract":"Lyme disease affects several hundred thousand people worldwide annually, yet there is no registered vaccine for the disease available for human use. The disease is caused by Borrelia burgdorferi sensu lato complex bacteria, which harbor numerous outer surface proteins, and many of which have been targeted for vaccine development. However, to effectively combat various Borrelia species, the target protein should ideally be conserved and located in the chromosome. In this study, we evaluated the potential of seven conservative, chromosome-encoded outer surface proteins as vaccine candidates. Unfortunately, four of the initial candidates could not be produced in E. coli. The remaining BB0028, BB0158, and BB0689 proteins were administered to mice in both the free form and as conjugates with virus-like particles (VLPs). In most cases, high antibody titers were obtained, confirming the good immunogenicity of the selected proteins. However, for BB0158 and BB0689 proteins, adverse effects were observed following the injection of free proteins, which were not observed when they were coupled to VLPs. Bactericidity tests of the obtained antibodies suggested that none of the vaccine candidates could induce the production of bactericidal antibodies.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"22 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139219248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Colombian Fungal Diversity: Untapped Potential for Diverse Applications","authors":"Esteban Charria-Girón, A. Vasco-Palacios, Bibiana Moncada, Y. Marin-Felix","doi":"10.3390/microbiolres14040135","DOIUrl":"https://doi.org/10.3390/microbiolres14040135","url":null,"abstract":"The current list of fungi from Colombia updated in the present review contains a total of 7619 species. The Ascomycota appears as the most diverse group, with 4818 species, followed by the Basidiomycota, with 2555 species. Despite this, we presume that the actual fungal diversity in Colombia could amount to between 105,600 and 300,000 species. Fungi represent an underestimated resource, indispensable for human well-being. Even though the current knowledge on potential applications of Colombian fungi is still limited, the number of studies on areas such as natural products discovery, biological control, and food and beverages, among other biotechnological applications, are increasing. With the current review, we aim to present a comprehensive update on the fungal diversity in Colombia and its potential applications. Colombia’s native fungal biodiversity holds much potential within the country’s current social-economical context, and the future must ensure efforts to preserve both the biodiversity and the untapped resources of the fungi in Colombia, which in alignment with the Sustainable Development Goals (SDGs) might result in new bioeconomy avenues for the country.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"48 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139215496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization and Biological Activities of Yeasts Isolated from Marine Environments","authors":"Woon-Jong Yu, Dawoon Chung, Seung Seob Bae, Y. Kwon, Eun-Seo Cho, Grace Choi","doi":"10.3390/microbiolres14040134","DOIUrl":"https://doi.org/10.3390/microbiolres14040134","url":null,"abstract":"Marine yeasts have versatile applications in the industrial, medical, and environmental fields. However, they have received little attention compared to terrestrial yeasts and filamentous fungi. In this study, a phylogenetic analysis of 11 marine-derived yeasts was conducted using internal transcribed spacers and nuclear large subunit rDNA, and their bioactivities, such as antioxidant, antibacterial, and tyrosinase inhibition activities, were investigated. The 11 marine-derived yeasts were identified to belong to seven species including Geotrichum candidum, Metschnikowia bicuspidata, Papiliotrema fonsecae, Rhodotorula mucilaginosa, Vishniacozyma carnescens, Yamadazyma olivae, and Yarrowia lipolytica, and three strains of these were candidates for new species of the genera Aureobasidium, Rhodotorula, and Vishniacozyma. Most extracts showed antioxidant activity, whereas seven strains exhibited antibacterial activities against Bacillus subtilis. Only Aureobasidium sp. US-Sd3 among the 11 isolates showed tyrosinase inhibition. Metschnikowia bicuspidata BP-Up1 and Yamadazyma olivae K2-6 showed notable radical-scavenging activity, which has not been previously reported. Moreover, Aureobasidium sp. US-Sd3 exhibited the highest antibacterial and tyrosinase inhibitory activities. These results demonstrate the potential of marine-derived yeasts as a source of bioactive compounds for improving industrial applications.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"64 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139245050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are Gastrointestinal Microorganisms Involved in the Onset and Development of Amyloid Neurodegenerative Diseases?","authors":"V. Muronetz, Lidia P. Kurochkina, Evgeniia V. Leisi, S. Kudryavtseva","doi":"10.3390/microbiolres14040131","DOIUrl":"https://doi.org/10.3390/microbiolres14040131","url":null,"abstract":"This review discusses a few examples of specific mechanisms mediating the contribution of the GIT microbiota to the development of amyloid neurodegenerative diseases caused by the pathologic transformation of prion protein, or alpha-synuclein. The effect of the bacterial GroE chaperonin system and phage chaperonins (single-ring OBP and double-ring EL) on prion protein transformation has been described. A number of studies have shown that chaperonins stimulate the formation of cytotoxic amyloid forms of prion protein in an ATP-dependent manner. Moreover, it was found that E. coli cell lysates have a similar effect on prion protein, and the efficiency of amyloid transformation correlates with the content of GroE in cells. Data on the influence of some metabolites synthesized by gut microorganisms on the onset of synucleinopathies, such as Parkinson’s disease, is provided. In particular, the induction of amyloid transformation of alpha-synuclein from intestinal epithelial cells with subsequent prion-like formation of its pathologic forms in nervous tissues featuring microbiota metabolites is described. Possible mechanisms of microbiota influence on the occurrence and development of amyloid neurodegenerative diseases are considered.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"56 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139254915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tannin-Tolerant Saccharomyces cerevisiae Isolated from Traditional Fermented Tea (Miang) of Northern Thailand and Its Feasible Applications","authors":"Kridsada Unban, Natchanon Muangkajang, Pratthana Kodchasee, Apinun Kanpiengjai, Kalidas Shetty, C. Khanongnuch","doi":"10.3390/microbiolres14040133","DOIUrl":"https://doi.org/10.3390/microbiolres14040133","url":null,"abstract":"This study evaluated the ability of a yeast strain isolated from traditional fermented tea leaves (Camellia sinensis var. assamica), Miang from northern Thailand, to grow and produce ethanol in the presence of tannin. Among 43 Miang samples, 25 yeast isolates displayed gas-forming character in the presence of 1% (w/v) tannin, but only ML1-1 and ML1-2 isolates were confirmed as ethanol-producing yeast capable of tannin tolerance. These isolates were further identified to be Pichia occidentalis and Saccharomyces cerevisiae, respectively, based on D1/D2 domain sequence analysis. S. cerevisiae ML1-2 was selected for further studies and exhibited growth at 20–35 °C, pH 4–7, and tolerance to high sugar concentrations of up to 350 g/L. Supplementation of 1% (w/v) tannin had no effect on sugar utilization and ethanol production, while delayed sugar consumption and ethanol production were observed in the reference strain S. cerevisiae TISTR 5088. However, 5 and 10% (w/v) tannin showed inhibitory effects on the growth and ethanol production of the selected yeast isolates. During the fermentation under high tannin conditions derived by mixing Java plum fruit with ground seed, S. cerevisiae ML1-2 showed significant advantages in growth and enhanced the content of ethanol, polyphenols, tannin, and flavonoids compared to S. cerevisiae TISTR 5088. This indicated its potential for high-tannin substrate-based bioconversion for the production of either fuel ethanol or functional alcoholic beverages.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"139 9","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139254731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic Sequencing Analysis of the Effects of Acetylcysteine on the Pig Gut Microbiome","authors":"S. Fu, Xinyue Tian, Jingyang Li, Yuzhen Yuan, Jing He, Chun Peng, Ling Guo, Chun Ye, Yu Liu, Bingbing Zong, Y. Qiu","doi":"10.3390/microbiolres14040132","DOIUrl":"https://doi.org/10.3390/microbiolres14040132","url":null,"abstract":"The gut microbiota is engaged in multiple interactions affecting host health, and gut dysbiosis can lead to many diseases. However, the effects of acetylcysteine (NAC) on the gut microbiome composition in pigs using metagenomic sequencing have not been reported. In this study, we used metagenome sequencing to study the effects of NAC on the pig gut microbiome. Sequencing results showed that microbial diversity was changed after NAC treatment. Antibiotic Resistance Genes Database (ARDB) analysis demonstrated that the main genes modified were macb, tsnr, norm, bl2be-per, vansb and pbp1b in the NAC group. Our data showed that NAC could affect microbial distribution at the phylum, gene and species levels. At the species level, NAC significantly increased the abundances of Megasphaera, Lactobacillus reuteri and Megasphaeraelsdenii and reduced the abundances of Phascolarctobacterium succinatutens, Prevotellacopri and Selenomonasbovis compared with the control group. In addition, Gene Ontology (GO) analysis revealed that in the NAC group, cellular process, metabolic process and single-organism process were the dominant terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that RNA transport, MAPK signaling pathway, cell cycle, glycosylphosphatidylinositol (GPI)-anchor biosynthesis and VEGF signaling pathway were the dominant signaling pathways in the NAC group. In conclusion, our results suggest that NAC may modify the piglet gut microbiome composition and these findings might provide a new strategy for maintaining animal and human health in the future.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"162 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139258402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Natural Products from Marine Actinomycete Genus Salinispora Might Inhibit 3CLpro and PLpro Proteins of SARS-CoV-2: An In Silico Evidence","authors":"Omkar Pokharkar, G. Zyryanov, M. Tsurkan","doi":"10.3390/microbiolres14040130","DOIUrl":"https://doi.org/10.3390/microbiolres14040130","url":null,"abstract":"Among the oldest marine species on the planet, the genus Salinispora is often encountered inhabiting sediments and other marine creatures in tropical and subtropical marine settings. This bacterial genus produces a plethora of natural products. The purpose of this study was to examine the potential for salinispora-based natural products (NPs) to combat the SARS-CoV-2 virus. The RCSB PDB was used to obtain the crystal structures of proteins 3CLpro and PLpro. All 125 NPs were obtained from online databases. Using Autodock Vina software v1.2.0 the molecular docking process was carried out after the proteins and ligands were prepared. Assessments of binding affinities and interacting amino acids were rigorously examined prior to MD simulations. The docking experiments revealed 35 NPs in total for both 3CLpro and PLpro, with high docking scores ranging from −8.0 kcal/mol to −9.0 kcal/mol. However, a thorough binding residue analyses of all docked complexes filtered nine NPs showing strong interactions with HIS: 41 and CYS: 145 of 3CLpro. Whereas, for PLpro, merely six NPs presented good interactions with residues CYS: 111, HIS: 272, and ASP: 286. Further research was conducted on residue–residue and ligand–residue interactions in both the filtered docked complexes and the Apo-protein structures using the Protein Contacts Atlas website. All complexes were found to be stable in CABS-flex 2.0 MD simulations conducted at various time frames (50, 125, 500, and 1000 cycles). In conclusion, salinaphthoquinone B appears to be the most promising metabolite, based on favorable amino acid interactions forming stable confirmations towards 3CLpro and PLpro enzymes, acting as a dual inhibitor.","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"38 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139274794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Poly(3-hydroxybutyrate) Biosynthesis from [U-13C6]D-Glucose by Ralstonia eutropha NCIMB 11599 and Recombinant Escherichia coli","authors":"Ramamoorthi M. Sivashankari, Yuki Miyahara, Takeharu Tsuge","doi":"10.3390/microbiolres14040129","DOIUrl":"https://doi.org/10.3390/microbiolres14040129","url":null,"abstract":"The use of stable isotope-labeled polymers in in situ biodegradation tests provides detailed information on the degradation process. As isotope-labeled raw chemicals are generally expensive, it is desirable to prepare polymer samples with high production yields and high isotope-labeling ratios. The biodegradable plastic poly[(R)-3-hydroxybutyrate)] (P(3HB)) is produced by microorganisms. In this study, to produce carbon 13 (13C)-labeled P(3HB) from [U-13C6]D-glucose (13C-glucose), the culture conditions needed for high production yields and high 13C-labeling ratios were investigated using Ralstonia eutropha NCIMB 11599 and recombinant Escherichia coli JM109. We found that over 10 g/L of P(3HB) could be obtained when these microorganisms were cultured in Luria-Bertani (LB3) medium containing 3 g/L NaCl and 40 g/L 13C-glucose, while 1.4–4.7 g/L of P(3HB) was obtained when a mineral salt (MS) medium containing 20 g/L 13C-glucose was used. The 13C-labeling ratio of P(3HB) was determined by 1H nuclear magnetic resonance and gas chromatography-mass spectrometry (GC-MS), and both analytical methods yielded nearly identical results. High 13C-labeling ratios (97.6 atom% by GC-MS) were observed in the MS medium, whereas low 13C-labeling ratios (88.8–94.4 atom% by GC-MS) were observed in the LB3 medium. Isotope effects were observed for the P(3HB) content in cells cultured in the LB3 medium and the polydispersity of P(3HB).","PeriodicalId":43788,"journal":{"name":"Microbiology Research","volume":"37 14","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135038691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}