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Microbial Genomics in the Omics Era

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 531

Special Issue Editor


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Guest Editor
Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
Interests: meta-genomics; microbial ecology

Special Issue Information

Dear Colleagues,

The unprecedented growth of microbial DNA/RNA sequences in the past fifty years is accompanied by an ever-growing need to analyze vast quantities of such data rapidly and accurately. There have been signficant advances in DNA sequencing technology in recent decades, moving from the traditional Sanger sequencing to a number of high-throughput next-generation sequencing technologies. Alongside the rapid generation of microbial DNA/RNA sequences, other biological data have expanded rapidly, such as protein sequences and protein structures. Analyzing vast quantities of these biological data in order to decipher their meaning, test hypotheses and generate novel ideas requires the most advanced bioinformatics tools. Thirty years ago, some knowledge of computer programming and inputing commands was required in order to use state-of-the-art bioinformatics tools. However, in the last twenty years, bioinformatics tools have gradually become more user-friendly. In this Special Issue, we aim to collect original research articles and reviews that involve the development and use of these bioinformatics tools in the study of microbial species, their community structure, interactions and functional attributes.

Dr. Surajit De Mandal
Guest Editor

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Keywords

  • microbe
  • bioinformatics
  • DNA
  • RNA
  • protein
  • sequencing
  • structure
  • omics

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Published Papers (1 paper)

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Research

22 pages, 2834 KiB  
Article
Antibiotic Resistance and Genetic Determinants of Helicobacter pylori in Oman: Insights from Phenotypic and Whole-Genome Analysis
by Amal Al-Hinai, Meher Rizvi, Said A. Al-Busafi, Masoud Kashoob, Zakariya Al-Muharrmi, Ahmed Al-Darmaki and Zaaima Al-Jabri
Int. J. Mol. Sci. 2025, 26(12), 5628; https://doi.org/10.3390/ijms26125628 - 12 Jun 2025
Viewed by 278
Abstract
Helicobacter pylori antibiotic resistance data in Oman are limited yet crucial for effective treatment selection. The genetic diversity within H. pylori influences its pathogenicity and clinical outcomes. This study evaluates resistance patterns and genetic determinants to guide treatment strategies. This study assessed antibiotic [...] Read more.
Helicobacter pylori antibiotic resistance data in Oman are limited yet crucial for effective treatment selection. The genetic diversity within H. pylori influences its pathogenicity and clinical outcomes. This study evaluates resistance patterns and genetic determinants to guide treatment strategies. This study assessed antibiotic susceptibility in 15 H. pylori isolates (from 169 clinical samples) from naïve and treatment-failed patients. Resistance to clarithromycin (CLA), amoxicillin (AMX), metronidazole (MTZ), tetracycline, rifampicin (RIF), and levofloxacin (LEV) was tested alongside genetic analysis of virulence and resistance-associated mutations by whole-genome sequencing (WGS). Among the 15 resistant isolates, 20% were resistant to one antibiotic, 33.3% to two, 20% to three, and 26.6% to four antibiotics. MTZ resistance was universal among single-drug resistant isolates (100%). AMX-MTZ dual resistance was present in 60%, while triple resistance (CLA-AMX-MTZ) was present in 66.7%. Quadruple resistance (CLA-AMX-MTZ-RIF) was present in 75%. WGS revealed 23S rRNA mutations in 33.3% of CLA-resistant strains and pbp-1 mutations in 66.6% of AMX-resistant strains. MTZ resistance was linked to rdxA/frxA mutations, while RIF and LEV resistance correlated with rpoB (65.7%) and gyrA (20%) mutations, respectively. The genotype–phenotype agreement was insignificant (p = 1). High mutation heterogeneity, virulence factors, and environmental influences contribute to resistance. Further studies on host–pathogen interactions are needed to understand resistance mechanisms. Full article
(This article belongs to the Special Issue Microbial Genomics in the Omics Era)
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