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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: closed (20 March 2026) | Viewed by 4076

Special Issue Editor


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Guest Editor
1. Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
2. Associate Professor, Department of Microbiology, Shri Davara University, Raipur 493661, Chhattisgarh, India
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 (3 papers)

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Research

20 pages, 2817 KB  
Article
Unveiling Metabolic Capability and Growth Adaptation of Monascus purpureus NP1 Through Genomic Sequencing and Comparative Analysis
by Haisu Hu, Preecha Patumcharoenpol, Kangsadan Boonprab, Amornthep Kingkaw, Yu Zhang, Kamonporn Masawang and Wanwipa Vongsangnak
Int. J. Mol. Sci. 2026, 27(8), 3670; https://doi.org/10.3390/ijms27083670 - 20 Apr 2026
Viewed by 173
Abstract
Monascus sp. NP1 is a significant filamentous fungus with valuable properties for food industries. Initially isolated from the fermented rice product ang-kak, this strain is known for its ability to produce natural pigments. In this study, we therefore sequenced its genome together with [...] Read more.
Monascus sp. NP1 is a significant filamentous fungus with valuable properties for food industries. Initially isolated from the fermented rice product ang-kak, this strain is known for its ability to produce natural pigments. In this study, we therefore sequenced its genome together with the 26S rRNA D1/D2 domain and ITS fragment for identifying species of Monascus sp. NP1, and further conducted functional annotations of its overall genes related to metabolic capability and growth adaptation using comparative genomics. As a result, promisingly, the NP1 strain was identified as Monascus purpureus with the genome sequences, which was shown to be 23.54 Mb with a GC content of 49.01%. Genome annotation predicted 8031 protein-encoding genes. Comparative genomics between NP1 and 11 other related strains revealed 6024 core groups, 2204 accessory groups, and 5 strain-specific groups. Metabolic pathway analysis promisingly showed carbohydrate metabolism as the most enriched category, particularly central carbon metabolism involving key precursors, e.g., acetyl-CoA and pyruvate that support energy generation and the biosynthesis of pigments, fatty acids, and lipids. These findings highlighted the metabolic versatility and adaptive growth potential of M. purpureus NP1. This study provides key genetic insights into the cellular functions of M. purpureus NP1, laying the groundwork for exploring metabolic properties. It offers a comprehensive understanding for developing targeted applications of M. purpureus NP1 as an alternative fungal cell factory in food and nutrition. Full article
(This article belongs to the Special Issue Microbial Genomics in the Omics Era)
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22 pages, 3365 KB  
Article
How to Unmask an Unknown: The Restriction-Modification System MhoVII of Mycoplasma hominis Expresses Two Complementary Methylation Activities in One Enzyme
by Lars Vogelgsang, Dana Bäcker, Sebastian Alexander Scharf, Azlan Nisar, Alexander T. Dilthey and Birgit Henrich
Int. J. Mol. Sci. 2026, 27(3), 1591; https://doi.org/10.3390/ijms27031591 - 5 Feb 2026
Viewed by 614
Abstract
Restriction–modification (RM) systems contribute to genome plasticity in Mycoplasma hominis, a facultative pathogen with an extremely small but highly heterogeneous genome. The MhoVII RM system, which contains a fusion of two methyltransferases (MTases), M1 and M2, was recently identified within a [...] Read more.
Restriction–modification (RM) systems contribute to genome plasticity in Mycoplasma hominis, a facultative pathogen with an extremely small but highly heterogeneous genome. The MhoVII RM system, which contains a fusion of two methyltransferases (MTases), M1 and M2, was recently identified within a family of Type II RM systems, but its specificity and biological function remained unknown. Phylogenetic analysis revealed that M1 and M2 belong to distinct MTase classes clustering within the YhdJ and MTaseD12 branches, respectively. In this study, the dissemination, expression and function of the MhoVII system was analyzed in detail using Oxford Nanopore-based methylation analysis, recombinant expression of the individual RM components in Escherichia coli, and methylation-sensitive restriction assays. It was thus possible to demonstrate that M1 and M2 methylate the complementary non-palindromic motifs GATG and CATC, and that the associated restriction endonuclease cleaves only DNA lacking 6mA methylation at these sites. The transcriptional analysis of mid-to-late logarithmic cultures indicated a polycistronic organization of the MhoVII genes, and GATG/CATC-driven methylation analysis revealed culture-dependent methylation differences, suggesting a post-transcriptional regulation, whereas in the infection of HeLa cells, MhoVII transcription was highest at the beginning and was then gradually downregulated in the later stages of infection. These findings establish MhoVII as a previously uncharacterized Type II RM system. Full article
(This article belongs to the Special Issue Microbial Genomics in the Omics Era)
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22 pages, 2834 KB  
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
Cited by 2 | Viewed by 2433
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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