Bioinformatics and Omic Data Analysis in Microbial Research, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 787

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Guest Editor
1. Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA
2. Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
Interests: genomics; molecular genetics in eukaryotes and prokaryotes; bacterial diseases affecting poultry
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous successful edition, and aims to further explore the growing role of omics technologies and bioinformatics in advancing microbial research.

This Issue will explore current applications of omics approaches to better understand the roles and functions of microbes in contexts such as ecology, agriculture, disease, homeostasis, or industry. We invite submissions of original research and review articles related to software development, pipeline creation, and/or the application of bioinformatics to address key questions in microbial science.

Submissions may focus on any group of microorganisms—including viruses, bacteria, fungi, protists, and others—using bioinformatics to derive biologically meaningful insights through genomics, proteomics, metabolomics, transcriptomics, or any integrative multi-omics approaches.

Given the essential biological roles of microorganisms, applying omics technologies in these organisms is crucial for advancing our understanding. Relevant topics may include speciation and species complexes, pan genome analyses (including horizontal gene transfer), gene networks, microbiomes, symbiosis, and pathogenesis.

Prof. Dr. Douglas D. Rhoads
Guest Editor

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Keywords

  • bioinformatics
  • microorganisms
  • genomics
  • proteomics
  • metabolomics
  • software pipelines

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Published Papers (1 paper)

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Research

22 pages, 1640 KB  
Article
Proteomic Research of the Stress Response of Saccharomyces cerevisiae W303 Yeast to Metal Ions Eluted from Orthodontic Appliances
by Lara Dežulović, Božena Ćurko-Cofek and Gordana Čanadi Jurešić
Microorganisms 2025, 13(9), 2200; https://doi.org/10.3390/microorganisms13092200 - 19 Sep 2025
Viewed by 645
Abstract
Although orthodontic appliances are widely used in daily practice, they also have their downsides due to the large amount of metal ions released from their surface. In this study, the influence of such released metal ions on the yeast Saccharomyces cerevisiae W303 as [...] Read more.
Although orthodontic appliances are widely used in daily practice, they also have their downsides due to the large amount of metal ions released from their surface. In this study, the influence of such released metal ions on the yeast Saccharomyces cerevisiae W303 as a model organism was investigated. Experimental yeast media in which metal ions (iron, aluminum, nickel, chromium, copper, and manganese) were eluted for 3, 7, 14, and 28 days were prepared and then used for yeast cultivation (up to the early stationary growth phase). The growth, increase, and viability of the cells were tested. The mitochondria were isolated from the spheroplasts, and the mitochondrial proteins were obtained and analyzed by liquid chromatography/mass spectrometry. Fortythree significantly altered proteins were identified. They showed significantly reduced expression in all metal-treated groups compared to the control. The metabolic processes for energy supply (glycolysis, gluconeogenesis, tricarboxylic acid cycle, and adenosine triphosphate synthesis) dominated with 50% of the total amount of significantly altered proteins in all samples, but their proportions changed at different time points. The downregulation of mitochondrial proteins such as Atp1, Atp2, and Pet9 under conditions of metal overload suggests a broader impairment of mitochondrial function. Three levels of response to stress can be observed—at relatively low metal ion concentrations in the medium (3 days of elution, approx. 3 mg/L), at medium concentrations (7 days of elution, approx. 5.5 mg/L), and at high concentrations (>8 mg/L, 14 and 28 days of elution), each affecting a specific group of proteins. The results show that mixtures of metal ions in experimental media led to a specific response (in terms of the amount and type of proteins) in each sample type to combat the provoked stress. Full article
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