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Microorganisms
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Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition
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Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition

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

Deadline for manuscript submissions: 28 February 2025 | Viewed by 7703

Special Issue Editor

Dr. Rajeev K. Azad

E-Mail Website
Guest Editor
1. Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
2. BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA
3. Department of Mathematics, University of North Texas, Denton, TX 76203, USA
Interests: plants bioinformatics; computational genomics, genome evolution, pathogenomics, metagenomics; gene prediction, structural variation detection, disease gene identification
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue "Microbial Genome Analysis and Interpretation Using Computational Approaches”.

The focus of this Special Issue is on the computational analysis and interpretation of microbial genomes. Deciphering information obscured within the genomes of microorganisms is critical to understanding factors underlying the versatile phenotypic traits they possess. Interrogation of genomes or metagenomes also provides insights into interactions among microorganisms and between organisms and the environments they dwell in. For this Special Issue, we invite researchers across the globe to contribute research articles or reviews pertaining to the development and/or application of computational methods to unraveling microbes through (meta)genome analysis.

Dr. Rajeev K. Azad
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial genome
  • whole-genome sequencing
  • bioinformatics

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Related Special Issue

Published Papers (7 papers)

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Research

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21 pages, 7528 KiB  
Article
Genomic Characterization of Bacillus sp. THPS1: A Hot Spring-Derived Species with Functional Features and Biotechnological Potential
by Samuel Mwakisha Mwamburi, Sk Injamamul Islam, Nguyen Dinh-Hung, Orathai Dangsawat, Rapeewan Sowanpreecha, Luu Tang Phuc Khang, Napatsorn Montha, Phatthanaphong Therdtatha, Sefti Heza Dwinanti, Patima Permpoonpattana and Nguyen Vu Linh
Microorganisms 2024, 12(12), 2476; https://doi.org/10.3390/microorganisms12122476 - 2 Dec 2024
Viewed by 528
Abstract
Bacillus sp. THPS1 is a novel strain isolated from a high-temperature hot spring in Thailand, exhibiting distinctive genomic features that enable adaptation to an extreme environment. This study aimed to characterize the genomic and functional attributes of Bacillus sp. THPS1 to understand its [...] Read more.
Bacillus sp. THPS1 is a novel strain isolated from a high-temperature hot spring in Thailand, exhibiting distinctive genomic features that enable adaptation to an extreme environment. This study aimed to characterize the genomic and functional attributes of Bacillus sp. THPS1 to understand its adaptation strategies and evaluate its potential for biotechnological applications. The draft genome is 5.38 Mbp with a GC content of 35.67%, encoding 5606 genes, including those linked to stress response and sporulation, which are essential for survival in high-temperature conditions. Phylogenetic analysis and average nucleotide identity (ANI) values confirmed its classification as a distinct species within the Bacillus genus. Pangenome analysis involving 19 others closely related thermophilic Bacillus species identified 1888 singleton genes associated with heat resistance, sporulation, and specialized metabolism, suggesting adaptation to nutrient-deficient, high-temperature environments. Genomic analysis revealed 12 biosynthetic gene clusters (BGCs), including those for polyketides and non-ribosomal peptides, highlighting its potential for synthesizing secondary metabolites that may facilitate its adaptation. Additionally, the presence of three Siphoviridae phage regions and 96 mobile genetic elements (MGEs) suggests significant genomic plasticity, whereas the existence of five CRISPR arrays implies an advanced defense mechanism against phage infections, contributing to genomic stability. The distinctive genomic features and functional capacities of Bacillus sp. THPS1 make it a promising candidate for biotechnological applications, particularly in the production of heat-stable enzymes and the development of resilient bioformulations. Full article
(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)
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14 pages, 2998 KiB  
Article
Planctomycetes of the Genus Singulisphaera Possess Chitinolytic Capabilities
by Anastasia A. Ivanova, Daniil G. Naumoff, Irina S. Kulichevskaya, Andrey L. Rakitin, Andrey V. Mardanov, Nikolai V. Ravin and Svetlana N. Dedysh
Microorganisms 2024, 12(7), 1266; https://doi.org/10.3390/microorganisms12071266 - 22 Jun 2024
Viewed by 940
Abstract
Planctomycetes of the genus Singulisphaera are common inhabitants of soils and peatlands. Although described members of this genus are characterized as possessing hydrolytic capabilities, the ability to degrade chitin has not yet been reported for these bacteria. In this study, a novel Singulisphaera [...] Read more.
Planctomycetes of the genus Singulisphaera are common inhabitants of soils and peatlands. Although described members of this genus are characterized as possessing hydrolytic capabilities, the ability to degrade chitin has not yet been reported for these bacteria. In this study, a novel Singulisphaera representative, strain Ch08, was isolated from a chitinolytic enrichment culture obtained from a boreal fen in Northern European Russia. The 16S rRNA gene sequence of this isolate displayed 98.2% similarity to that of Singulisphaera acidiphila MOB10T. Substrate utilization tests confirmed that strain Ch08 is capable of growth on amorphous chitin. The complete genome of strain Ch08 determined in this study was 10.85 Mb in size and encoded two predicted chitinases, which were only distantly related to each other and affiliated with the glycoside hydrolase family GH18. One of these chitinases had a close homologue in the genome of S. acidiphila MOB10T. The experimental verification of S. acidiphila MOB10T growth on amorphous chitin was also positive. Transcriptome analysis performed with glucose- and chitin-growth cells of strain Ch08 showed upregulation of the predicted chitinase shared by strain Ch08 and S. acidiphila MOB10T. The gene encoding this protein was expressed in Escherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The ability to utilize chitin, a major constituent of fungal cell walls and arthropod exoskeletons, appears to be one of the previously unrecognized ecological functions of Singulisphaera-like planctomycetes. Full article
(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)
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16 pages, 5541 KiB  
Article
Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients
by Vaidehi Pusadkar, Anirudh Mazumder, Abhijay Azad, Deepti Patil and Rajeev K. Azad
Microorganisms 2024, 12(6), 1058; https://doi.org/10.3390/microorganisms12061058 - 24 May 2024
Viewed by 1325
Abstract
COVID-19, caused by SARS-CoV-2, results in respiratory and cardiopulmonary infections. There is an urgent need to understand not just the pathogenic mechanisms of this disease but also its impact on the physiology of different organs and microbiomes. Multiple studies have reported the effects [...] Read more.
COVID-19, caused by SARS-CoV-2, results in respiratory and cardiopulmonary infections. There is an urgent need to understand not just the pathogenic mechanisms of this disease but also its impact on the physiology of different organs and microbiomes. Multiple studies have reported the effects of COVID-19 on the gastrointestinal microbiota, such as promoting dysbiosis (imbalances in the microbiome) following the disease’s progression. Deconstructing the dynamic changes in microbiome composition that are specifically correlated with COVID-19 patients remains a challenge. Motivated by this problem, we implemented a biomarker discovery pipeline to identify candidate microbes specific to COVID-19. This involved a meta-analysis of large-scale COVID-19 metagenomic data to decipher the impact of COVID-19 on the human gut and respiratory microbiomes. Metagenomic studies of the gut and respiratory microbiomes of COVID-19 patients and of microbiomes from other respiratory diseases with symptoms similar to or overlapping with COVID-19 revealed 1169 and 131 differentially abundant microbes in the human gut and respiratory microbiomes, respectively, that uniquely associate with COVID-19. Furthermore, by utilizing machine learning models (LASSO and XGBoost), we demonstrated the power of microbial features in separating COVID-19 samples from metagenomic samples representing other respiratory diseases and controls (healthy individuals), achieving an overall accuracy of over 80%. Overall, our study provides insights into the microbiome shifts occurring in COVID-19 patients, shining a new light on the compositional changes. Full article
(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)
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14 pages, 1224 KiB  
Article
In-Host Flat-like Quasispecies: Characterization Methods and Clinical Implications
by Josep Gregori, Sergi Colomer-Castell, Marta Ibañez-Lligoña, Damir Garcia-Cehic, Carolina Campos, Maria Buti, Mar Riveiro-Barciela, Cristina Andrés, Maria Piñana, Alejandra González-Sánchez, Francisco Rodriguez-Frias, Maria Francesca Cortese, David Tabernero, Ariadna Rando-Segura, Tomás Pumarola, Juan Ignacio Esteban, Andrés Antón and Josep Quer
Microorganisms 2024, 12(5), 1011; https://doi.org/10.3390/microorganisms12051011 - 17 May 2024
Cited by 3 | Viewed by 1438
Abstract
The repeated failure to treat patients chronically infected with hepatitis E (HEV) and C (HCV) viruses, despite the absence of resistance-associated substitutions (RAS), particularly in response to prolonged treatments with the mutagenic agents of HEV, suggests that quasispecies structure may play a crucial [...] Read more.
The repeated failure to treat patients chronically infected with hepatitis E (HEV) and C (HCV) viruses, despite the absence of resistance-associated substitutions (RAS), particularly in response to prolonged treatments with the mutagenic agents of HEV, suggests that quasispecies structure may play a crucial role beyond single point mutations. Quasispecies structured in a flat-like manner (referred to as flat-like) are considered to possess high average fitness, occupy a significant fraction of the functional genetic space of the virus, and exhibit a high capacity to evade specific or mutagenic treatments. In this paper, we studied HEV and HCV samples using high-depth next-generation sequencing (NGS), with indices scoring the different properties describing flat-like quasispecies. The significance of these indices was demonstrated by comparing the values obtained from these samples with those from acute infections caused by respiratory viruses (betacoronaviruses, enterovirus, respiratory syncytial viruses, and metapneumovirus). Our results revealed that flat-like quasispecies in HEV and HCV chronic infections without RAS are characterized by numerous low-frequency haplotypes with no dominant one. Surprisingly, these low-frequency haplotypes (at the nucleotide level) exhibited a high level of synonymity, resulting in much lower diversity at the phenotypic level. Currently, clinical approaches for managing flat-like quasispecies are lacking. Here, we propose methods to identifying flat-like quasispecies, which represents an essential initial step towards exploring alternative treatment protocols for viruses resistant to conventional therapies. Full article
(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)
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19 pages, 13091 KiB  
Article
Comparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group
by Taiquan Wang, Yiling Shi, Mengzhuo Zheng and Jinshui Zheng
Microorganisms 2024, 12(5), 986; https://doi.org/10.3390/microorganisms12050986 - 14 May 2024
Viewed by 1595
Abstract
The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual [...] Read more.
The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin–antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group. Full article
(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)
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Review

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14 pages, 1357 KiB  
Review
Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology
by Yanhua Han, Jinling He, Minghui Li, Yunjuan Peng, Hui Jiang, Jiangchao Zhao, Ying Li and Feilong Deng
Microorganisms 2024, 12(12), 2482; https://doi.org/10.3390/microorganisms12122482 - 2 Dec 2024
Viewed by 337
Abstract
Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio’s high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the [...] Read more.
Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio’s high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing’s ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications. Full article
(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)
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Other

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15 pages, 3345 KiB  
Project Report
Looking for Pathogens in Dust from North Africa Arriving in the French West Indies Using Metabarcoding and Cultivable Analysis
by Yann Reynaud, Andric Gelasse, Luc Multigner, Philippe Quénel, Antoine Talarmin and Stéphanie Guyomard-Rabenirina
Microorganisms 2024, 12(10), 2111; https://doi.org/10.3390/microorganisms12102111 - 21 Oct 2024
Viewed by 856
Abstract
Periodically, the French West Indies receive dust originating from North Africa (NA). Microorganisms associated with desert dust can be transported over long distances through the atmosphere and could represent a means for the remote colonization of new habitats by putatively pathogenic microorganisms. The [...] Read more.
Periodically, the French West Indies receive dust originating from North Africa (NA). Microorganisms associated with desert dust can be transported over long distances through the atmosphere and could represent a means for the remote colonization of new habitats by putatively pathogenic microorganisms. The aim of this study was to determine the diversity and frequency of microbial agents (bacteria, eukaryotes) in NA dusts and the potential threat toward human and/or animal health by comparing microbial air composition during dust events and in control samples. In 2017 and 2018, 16 samples were collected during seven NA dust episodes and there were 9 controls. The microbial composition of the samples was characterized using a cultivable approach and by metabarcoding analyses (16S and 18S). A greater bacterial load and greater diversity were observed during the dust events, and some genera were significantly associated with the events. Some, such as Geodermatophilus, can be considered signature species of NA dust. No pathogenic species were found with the cultivable approach, whereas the metabarcoding analyses highlighted the presence of several potentially pathogenic species or known human pathogens such as Naegleria fowleri. Full article
(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)
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