Examinando por Materia "Microbial"
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Ítem IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses(BioMed Central Ltd., 2016-12-16) Narayanasamy, S.; Jarosz, Y.; Muller, E.E.L.; Heintz-Buschart, A.; Herold, M.; Kaysen, A.; Laczny, C.C.; Pinel, N.; May, P.; Wilmes, P.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónExisting workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).Ítem Inducible Antibacterial Activity in the Bacillales by Triphenyl Tetrazolium Chloride(Nature Publishing Group, 2020-01-01) Sierra-Zapata L.; Álvarez J.C.; Romero-Tabarez M.; Silby M.W.; Traxler M.F.; Behie S.W.; Pessotti R.C.; Villegas-Escobar V.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónThe world is in the midst of an antimicrobial resistance crisis, driving a need to discover novel antibiotic substances. Using chemical cues as inducers to unveil a microorganism’s full metabolic potential is considered a successful strategy. To this end, we investigated an inducible antagonistic behavior in multiple isolates of the order Bacillales, where large inhibition zones were produced against Ralstonia solanacearum only when grown in the presence of the indicator triphenyl tetrazolium chloride (TTC). This bioactivity was produced in a TTC-dose dependent manner. Escherichia coli and Staphylococcus sp. isolates were also inhibited by Bacillus sp. strains in TTC presence, to a lesser extent. Knockout mutants and transcriptomic analysis of B. subtilis NCIB 3610 cells revealed that genes from the L-histidine biosynthetic pathway, the purine, pyrimidine de novo synthesis and salvage and interconversion routes, were significantly upregulated. Chemical space studied through metabolomic analysis, showed increased presence of nitrogenous compounds in extracts from induced bacteria. The metabolites orotic acid and L-phenylalaninamide were tested against R. solanacearum, E. coli, Staphylococcus sp. and B. subtilis, and exhibited activity against pathogens only in the presence of TTC, suggesting a biotransformation of nitrogenous compounds in Bacillus sp. cells as the plausible cause of the inducible antagonistic behavior. © 2020, The Author(s).Ítem Reviewing microbial behaviors in ecosystems leading to a natural quorum quenching occurrence(INST TECNOLOGIA PARANA, 2017-01-01) Sierra Zapata, Laura; Romero Tabarez, Magally; Correa Alvarez, Javier; Villegas Escobar, Valeska; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónQuorum sensing is considered one of the most important discoveries in cell-to-cell communication. Although revealed in Bacteria, it has been identified as well as a mechanism present in the other two domains, Eukaryota and Archaea. This phenomenon consists mainly of an exchange and sensing of "words" produced by each cell: chemical signals known as autoinducers. The process takes places at high cell densities and confined environments, triggering the expression of specific genes that manifest in a determined phenotype. Quorum sensing has a fundamental importance in the organisms' fitness in natural ecosystems since it activates many of the traits needed by cells to survive under specific conditions, and thus a wide variety of chemical signals, which are detailed throughout the review, have evolved in response to the needs of an organism in the ecosystem it inhabits. As a counterpart, derived from the natural occurrence of quorum sensing, comes it's antagonistic process named quorum quenching. Acting in the exact opposite way, quorum quenching interferes or degrades the autoinducers confusing and stopping communication, hence affecting transcriptional regulation and expression of a specific phenotype. The main reasons for stopping this mechanism go from fading their own signals when perceiving scarce nutrients conditions, to degrading competitors' signals to take advantage in the ecosystem. Some of the most studied purposes and means known up to date to be used by cells for making quorum quenching in their ecosystems is what will be discussed along this review, offering information for future works on quorum quencher molecules bioprospection.Ítem Scale-up from shake flasks to pilot-scale production of the plant growth-promoting bacterium Azospirillum brasilense for preparing a liquid inoculant formulation(SPRINGER, 2013-11-01) Trujillo-Roldan, Mauricio A.; Valdez-Cruz, Norma A.; Gonzalez-Monterrubio, Cesar F.; Acevedo-Sanchez, Eduardo V.; Martinez-Salinas, Carlos; Garcia-Cabrera, Ramses I.; Gamboa-Suasnavart, Ramses A.; Marin-Palacio, Luz D.; Villegas, Jesus; Blancas-Cabrera, Abel; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Azospirillum brasilense has industrial significance as a growth promoter in plants of commercial interest. However, there is no report in the literature disclosing a liquid product produced in pilot-scale bioreactors and is able to be stored at room temperature for more than 2 years. The aim of this work was to scale up a process from a shake flask to a 10-L lab-scale and 1,000-L pilot-scale bioreactor for the production of plant growth-promoting bacterium A. brasilense for a liquid inoculant formulation. Furthermore, this work aimed to determine the shelf life of the liquid formulation stored at room temperature and to increase maize crops yield in greenhouses. Under a constant oxygen mass transfer coefficient (K L a), a fermentation process was successfully scaled up from shake flasks to 10- and 1,000-L bioreactors. A concentration ranging from 3.5 to 7.5 × 108 CFU/mL was obtained in shake flasks and bioreactors, and after 2 years stored at room temperature, the liquid formulation showed one order of magnitude decrease. Applications of the cultured bacteria in maize yields resulted in increases of up to 95 % in corncobs and 70 % in aboveground biomass. © 2013 Springer-Verlag Berlin Heidelberg.Ítem Scale-up from shake flasks to pilot-scale production of the plant growth-promoting bacterium Azospirillum brasilense for preparing a liquid inoculant formulation(SPRINGER, 2013-11-01) Trujillo-Roldan, Mauricio A.; Valdez-Cruz, Norma A.; Gonzalez-Monterrubio, Cesar F.; Acevedo-Sanchez, Eduardo V.; Martinez-Salinas, Carlos; Garcia-Cabrera, Ramses I.; Gamboa-Suasnavart, Ramses A.; Marin-Palacio, Luz D.; Villegas, Jesus; Blancas-Cabrera, Abel; Trujillo-Roldan, Mauricio A.; Valdez-Cruz, Norma A.; Gonzalez-Monterrubio, Cesar F.; Acevedo-Sanchez, Eduardo V.; Martinez-Salinas, Carlos; Garcia-Cabrera, Ramses I.; Gamboa-Suasnavart, Ramses A.; Marin-Palacio, Luz D.; Villegas, Jesus; Blancas-Cabrera, Abel; Universidad EAFIT. Departamento de Ingeniería de Procesos; Procesos Ambientales (GIPAB)Azospirillum brasilense has industrial significance as a growth promoter in plants of commercial interest. However, there is no report in the literature disclosing a liquid product produced in pilot-scale bioreactors and is able to be stored at room temperature for more than 2 years. The aim of this work was to scale up a process from a shake flask to a 10-L lab-scale and 1,000-L pilot-scale bioreactor for the production of plant growth-promoting bacterium A. brasilense for a liquid inoculant formulation. Furthermore, this work aimed to determine the shelf life of the liquid formulation stored at room temperature and to increase maize crops yield in greenhouses. Under a constant oxygen mass transfer coefficient (K L a), a fermentation process was successfully scaled up from shake flasks to 10- and 1,000-L bioreactors. A concentration ranging from 3.5 to 7.5 × 108 CFU/mL was obtained in shake flasks and bioreactors, and after 2 years stored at room temperature, the liquid formulation showed one order of magnitude decrease. Applications of the cultured bacteria in maize yields resulted in increases of up to 95 % in corncobs and 70 % in aboveground biomass. © 2013 Springer-Verlag Berlin Heidelberg.