Biology subjects

Zepeda Mendoza, M. L.

Publications and source records attributed to Zepeda Mendoza, M. L..

3 recordsLinked to original sources

bioRxiv2019

Uncovering the dynamic mechanisms of the Pseudomonas aeruginosa quorum sensing and virulence networks using Boolean modelling

IntroductionPseudomonas aeruginosa is an opportunistic pathogen with an extraordinary metabolic adaptability and a large repertoire of virulence factors that allow it to cause acute and chronic infections. Treatment of P. aeruginosa infections often fail due to its antibiotic resistance mechanisms, thus novel strategies aim at targeting virulence factors instead of growth-related features. However, there is currently not a clear understanding of the dynamic nature inherent to the wiring of its virulence networks.\n\nResultsIn this study, we manually reconstructed the signalling and transcriptional regulatory networks of 12 acute (incl. pyocin and elastase) and 8 chronic virulence factors (incl. biofilm), and the 4 quorum sensing (QS) systems of P. aeruginosa. Using Boolean modelling (BM), we unveiled the important roles that stochasticity and node connectivity play in the networks inherent dynamicity and robustness. We showed that both the static interactions, as well as the time when the interactions take place, are important features in the QS network. In addition, we found that the virulence factors of the acute networks are under strict repression, or under an activation that is non-strict or oscillatory, while the chronic networks favour the repression of the virulence factor, with only moderate activation under certain conditions.\n\nConclusionIn conclusion, our in silico-modelling framework provided us with a system-level view of the P. aeruginosa virulence and QS networks to gain new insights into the various mechanisms that support its pathogenicity and response to stressors targeting these networks. Thus, we suggest that BM provides an invaluable tool to guide the design of new treatments against P. aeruginosa.

bioinformatics↗

bioRxiv2017

Influence of Oenococcus oeni and Brettanomyces bruxellensis on Aged Wine Microbial Taxonomic and Functional Profiles

In the wine making process, the interactions between lactic acid bacteria (LAB), yeast and other wine microflora have an impact on the wine quality. In this study, we investigate the influence of the LAB Oenococcus oeni and the spoilage yeast Brettanomyces bruxellensis on the microbial community of a Cabernet Sauvignon wine. We generated metagenomic datasets from inoculations of three strains of B. bruxellensis, in combination with two O. oeni strains, one with and one without cinnamoyl esterase activity. This esterase activity releases hydroxycinnamic acids (HCAs) that can subsequently be processed by some B. bruxellensis strains able to generate off-flavor compounds. We evaluated the influence of the O. oeni and B. bruxellensis on the microbial taxonomic and functional potential profile, particularly regarding off-flavor formation due to HCAs. We found that the effect on the microbial profiles depends on i) the O. oeni and B. bruxellensis strains being combined and ii) the abundance they reach in the final wine, which depends on certain unidentified conditions. We confirmed that the potential of B. bruxellensis to produce off-flavor compounds from HCAs depends on the strain. Interestingly, the samples without microbial inoculants also had this potential, suggesting that native grape microbiota could also influence the levels of HCA. We also found that the presence of B. bruxellensis does not interfere with the malolactic fermentation of the evaluated O. oeni strains, which leads to a less acidic taste. We show that metagenomic approaches can help uncover the complex wine microbial community traits, such as flavor, impacted by the simultaneous presence of O. oeni and B. bruxellensis.

microbiology↗

bioRxiv2017

Protective role of the vulture facial and gut microbiomes aid adaptation to scavenging

BackgroundVultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial and gut microbiomes from the black and turkey vultures. We characterized i) the functional potential and taxonomic diversity of their microbiomes, ii) the potential pathogenic challenges they face, and iii) elements in the microbiome that could play a protective role to the vultures face and gut.\n\nResultsWe found elements involved in diseases, such as periodontitis and pneumonia (more abundant in the face), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing health beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasites and antiinsectisides in the face. Based on the identified phages, we suggest that phages aid in the control, and possibly elimination as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we also identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role though biofilm formation played by Fusobacteria and Clostridia in the gut.\n\nConclusionsOur results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.

bioinformatics↗