scholarly journals Community Structures and Antifungal Activity of Root-Associated Endophytic Actinobacteria of Healthy and Diseased Soybean

2019 ◽  
Vol 7 (8) ◽  
pp. 243 ◽  
Author(s):  
Chongxi Liu ◽  
Xiaoxin Zhuang ◽  
Zhiyin Yu ◽  
Zhiyan Wang ◽  
Yongjiang Wang ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
High Throughput Sequencing ◽  
Antagonistic Activity ◽  
Diseased Plant ◽  
Natural Defense ◽  
Independent Analysis ◽  
Culture Independent ◽  
Potential Reservoir ◽  
Endophytic Actinobacteria

The present study was conducted to examine the influence of a pathogen Sclerotinia sclerotiorum (Lib.) de Bary on the actinobacterial community associated with the soybean roots. A total of 70 endophytic actinobacteria were isolated from the surface-sterilized roots of either healthy or diseased soybeans, and they were distributed under 14 genera. Some rare genera, including Rhodococcus, Kribbella, Glycomyces, Saccharothrix, Streptosporangium and Cellulosimicrobium, were endemic to the diseased samples, and the actinobacterial community was more diverse in the diseased samples compared with that in the heathy samples. Culture-independent analysis of root-associated actinobacterial community using the high-throughput sequencing approach also showed similar results. Four Streptomyces strains that were significantly abundant in the diseased samples exhibited strong antagonistic activity with the inhibition percentage of 54.1–87.6%. A bioactivity-guided approach was then employed to isolate and determine the chemical identity of antifungal constituents derived from the four strains. One new maremycin analogue, together with eight known compounds, were detected. All compounds showed significantly antifungal activity against S. sclerotiorum with the 50% inhibition (EC50) values of 49.14–0.21 mg/L. The higher actinobacterial diversity and more antifungal strains associated with roots of diseased plants indicate a possible role of the root-associated actinobacteria in natural defense against phytopathogens. Furthermore, these results also suggest that the root of diseased plant may be a potential reservoir of actinobacteria producing new agroactive compounds.

scholarly journals House Flies (Musca domestica) Pose a Risk of Carriage and Transmission of Bacterial Pathogens Associated with Bovine Respiratory Disease (BRD)

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 358
Author(s):  
Neupane ◽  
Nayduch ◽  
Zurek
Keyword(s):  
Respiratory Disease ◽  
Pasteurella Multocida ◽  
Bacterial Pathogens ◽  
Bovine Respiratory Disease ◽  
Human Pathogens ◽  
House Flies ◽  
Histophilus Somni ◽  
Culture Independent ◽  
Potential Reservoir

House flies are important nuisance pests in a variety of confined livestock operations. More importantly, house flies are known mechanical vectors of numerous animal and human pathogens. Bovine respiratory disease (BRD) is an economically important, complex illness of cattle associated with several bacteria and viruses. The role of flies in the ecology and transmission of bacterial pathogens associated with BRD is not understood. Using culture-dependent and culture-independent methods, we examined the prevalence of the BRD bacterial complex Mannheimia haemolytica, Pasteurella multocida and Histophilus somni in house flies collected in a commercial feedlot from a pen with cattle exhibiting apparent BRD symptoms. Using both methods, M. haemolytica was detected in 11.7% of house flies, followed by P. multocida (5.0%) and H. somni (3.3%). The presence of BRD bacterial pathogens in house flies suggests that this insect plays a role in the ecology of BRD pathogens and could pose a risk as a potential reservoir and/or a vector of BRD pathogens among individual cattle and in their environment.

scholarly journals Biodeteriogens Characterization and Molecular Analyses of Diverse Funeral Accessories from XVII Century

2020 ◽  
Vol 10 (16) ◽  
pp. 5451 ◽  
Author(s):  
Zuzana Kisová ◽  
Matej Planý ◽  
Jelena Pavlović ◽  
Mária Bučková ◽  
Andrea Puškárová ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Phytopathogenic Fungi ◽  
Metal Corrosion ◽  
Animal Origin ◽  
Organic Substrates ◽  
Illumina Platform ◽  
Buried Objects ◽  
Independent Analysis ◽  
Culture Independent

A historical crypt offers us a particular view of the conditions of some buried materials (in this case textiles) and the various biogenic phenomena to which they were subjected over the centuries. In addition, significant knowledge can come by studying the DNA of buried objects which allows the recognition of materials, but also to reveal some practice of the funeral ceremony. In this study, the deteriorating microbial communities colonizing various funeral textile items were identified and characterized using microscopic observation, cultivation, polymerase chain reaction (PCR) and sequencing, hydrolytic tests; and culture-independent analysis (high-throughput sequencing, MinION platform). Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. The combination of all these techniques permitted the identification of a complex microbiota composed by dangerous degradative microorganisms able to hydrolyze various organic substrates such as fibroin, keratin, and cellulose. Bacteria responsible for metal corrosion and bio-mineralization, and entomopathogenic and phytopathogenic fungi. The analysis of aDNA identified the animal component used in bodice manufacturing, the plant utilized as ornament and probably the season of this fatal event.

scholarly journals High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

2013 ◽  
Vol 79 (10) ◽  
pp. 3148-3155 ◽  
Author(s):  
Danilo Ercolini
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Food Microbiology ◽  
Acid Extraction ◽  
Food Research ◽  
Independent Analysis ◽  
Culture Independent ◽  
Depth Study ◽  
Current Scenario ◽  
Recent Trends

ABSTRACTFollowing recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.

Questions on the role of biofilms for the adaptation of microorganisms to unfavorable environmental factors by the example of P. aeruginosa

2020 ◽  
Vol 99 (4) ◽  
pp. 379-383
Author(s):  
Vasily N. Afonyushkin ◽  
N. A. Donchenko ◽  
Ju. N. Kozlova ◽  
N. A. Davidova ◽  
V. Yu. Koptev ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Environmental Factors ◽  
Barrier Function ◽  
Infectious Agent ◽  
Antagonistic Activity ◽  
The Body ◽  
Main Function ◽  
Pathogenic Potential ◽  
The Face

Pseudomonas aeruginosa is a widely represented species of bacteria possessing of a pathogenic potential. This infectious agent is causing wound infections, fibrotic cystitis, fibrosing pneumonia, bacterial sepsis, etc. The microorganism is highly resistant to antiseptics, disinfectants, immune system responses of the body. The responses of a quorum sense of this kind of bacteria ensure the inclusion of many pathogenicity factors. The analysis of the scientific literature made it possible to formulate four questions concerning the role of biofilms for the adaptation of P. aeruginosa to adverse environmental factors: Is another person appears to be predominantly of a source an etiological agent or the source of P. aeruginosa infection in the environment? Does the formation of biofilms influence on the antibiotic resistance? How the antagonistic activity of microorganisms is realized in biofilm form? What is the main function of biofilms in the functioning of bacteria? A hypothesis has been put forward the effect of biofilms on the increase of antibiotic resistance of bacteria and, in particular, P. aeruginosa to be secondary in charcter. It is more likely a biofilmboth to fulfill the function of storing nutrients and provide topical competition in the face of food scarcity. In connection with the incompatibility of the molecular radii of most antibiotics and pores in biofilm, biofilm is doubtful to be capable of performing a barrier function for protecting against antibiotics. However, with respect to antibodies and immunocompetent cells, the barrier function is beyond doubt. The biofilm is more likely to fulfill the function of storing nutrients and providing topical competition in conditions of scarcity of food resources.

Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

2020 ◽  
Vol 15 ◽  
Author(s):  
Na Wang ◽  
Yukun Li ◽  
Sijing Liu ◽  
Liu Gao ◽  
Chang Liu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Functional Study ◽  
Regulation Network ◽  
Glucagon Like Peptide 1 ◽  
G Protein Coupled ◽  
Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

scholarly journals Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 396
Author(s):  
Ewa Sajnaga ◽  
Marcin Skowronek ◽  
Agnieszka Kalwasińska ◽  
Waldemar Kazimierczak ◽  
Karolina Ferenc ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Entomopathogenic Nematodes ◽  
Bacterial Species ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Bacterial Phyla ◽  
Melolontha Melolontha

This study focused on the potential relationships between midgut microbiota of the common cockchafer Melolontha melolontha larvae and their resistance to entomopathogenic nematodes (EPN) infection. We investigated the bacterial community associated with control and unsusceptible EPN-exposed insects through nanopore sequencing of the 16S rRNA gene. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant bacterial phyla within the complex and variable midgut microbiota of the wild M. melolontha larvae. The core microbiota was found to include 82 genera, which accounted for 3.4% of the total number of identified genera. The EPN-resistant larvae differed significantly from the control ones in the abundance of many genera belonging to the Actinomycetales, Rhizobiales, and Clostridiales orders. Additionally, the analysis of the microbiome networks revealed different sets of keystone midgut bacterial genera between these two groups of insects, indicating differences in the mutual interactions between bacteria. Finally, we detected Xenorhabdus and Photorhabdus as gut residents and various bacterial species exhibiting antagonistic activity against these entomopathogens. This study paves the way to further research aimed at unravelling the role of the host gut microbiota on the output of EPN infection, which may contribute to enhancement of the efficiency of nematodes used in eco-friendly pest management.

scholarly journals Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. 565
Author(s):  
Anindita Lahiri ◽  
Brian R. Murphy ◽  
Trevor R. Hodkinson
Keyword(s):  
Community Composition ◽  
Environmental Effects ◽  
High Throughput Sequencing ◽  
Fungal Community Composition ◽  
Species Identity ◽  
Ash Dieback ◽  
Hymenoscyphus Fraxineus ◽  
Culture Independent ◽  
The Impact ◽  
Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

scholarly journals Synthetic Histidine-Rich Peptides Inhibit Candida Species and Other Fungi In Vitro: Role of Endocytosis and Treatment Implications

2006 ◽  
Vol 50 (8) ◽  
pp. 2797-2805 ◽  
Author(s):  
Jingsong Zhu ◽  
Paul W. Luther ◽  
Qixin Leng ◽  
A. James Mixson
Keyword(s):  
Nucleic Acid ◽  
Antifungal Activity ◽  
Antifungal Agents ◽  
Fungal Growth ◽  
Nucleic Acid Delivery ◽  
Histatin 5 ◽  
Ph Buffering ◽  
Endosomal Acidification

ABSTRACT A family of histidine-rich peptides, histatins, is secreted by the parotid gland in mammals and exhibits marked inhibitory activity against a number of Candida species. We were particularly interested in the mechanism by which histidine-rich peptides inhibit fungal growth, because our laboratory has synthesized a variety of such peptides for drug and nucleic acid delivery. In contrast to naturally occurring peptides that are linear, peptides made on synthesizers can be varied with respect to their degrees of branching. Using this technology, we explored whether histidine-lysine (HK) polymers of different complexities and degrees of branching affect the growth of several species of Candida. Polymers with higher degrees of branching were progressively more effective against Candida albicans, with the four-branched polymer, H2K4b, most effective. Furthermore, H2K4b accumulated efficiently in C. albicans, which may indicate its ability to transport other antifungal agents intracellularly. Although H2K4b had greater antifungal activity than histatin 5, their mechanisms were similar. Toxicity in C. albicans induced by histatin 5 or branched HK peptides was markedly reduced by 4,4′-diisothiocyanato-stilbene-2,2′-disulfonate, an inhibitor of anion channels. We also determined that bafilomycin A1, an inhibitor of endosomal acidification, significantly decreased the antifungal activity of H2K4b. This suggests that the pH-buffering and subsequent endosomal-disrupting properties of histidine-rich peptides have a role in their antifungal activity. Moreover, the ability of the histidine component of these peptides to disrupt endosomes, which allows their escape from the lysosomal pathway, may explain why these peptides are both effective antifungal agents and nucleic acid delivery carriers.

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