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Current Research on Omics of Microorganisms
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Current Research on Omics of Microorganisms

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 October 2024) | Viewed by 5671

Special Issue Editor

Prof. Dr. Rosa María Martínez-Espinosa

E-Mail Website
Guest Editor
Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, E-03080 Alicante, Spain
Interests: extremophiles; omics-based technologies; gene regulation; microbial metabolism; carotenoids; polyhydroxyalkanoates; biogeochemical cycles; system biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial physiology and metabolism are the main driving forces sustaining the development and maintenance of the biogeochemical cycles. The accurate description of microbial metabolic pathways allows the potential uses of several microbial species in biotechnological and industrial processes. Due to the relevance of understanding microbial nature and metabolic capabilities and considering the increase in the number of microbial genome sequences that are currently available, this Special Issue focuses on new generation molecular methods and massive data analysis approaches that allow overcoming the frontiers of knowledge regarding microorganisms, either in the context of their natural habitat or by exploring their uses in connection with bioremediation technologies, drugs discovery, and the use of microorganisms as cell factories for the production of compounds of interest, among other potential applications. Consequently, this is a multidisciplinary topic comprising a broad spectrum of disciplines, i.e., systems biology, bioinformatics, biochemistry, microbiology, molecular biology, genetics, chemistry, microbial ecology, and biophysics, with an emphasis on omics-based sciences. Original investigations as well as concise review manuscripts from experts in relevant research fields will be considered for publication.

Prof. Dr. Rosa María Martínez-Espinosa
Guest Editor

Manuscript Submission Information

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Keywords

  • microbial metabolism
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • metabonomics
  • bioinformatics

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Published Papers (5 papers)

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15 pages, 2896 KiB  
Article
Pangenome-Wide Association Study in the Chlamydiaceae Family Reveals Key Evolutionary Aspects of Their Relationship with Their Hosts
by Rosalba Salgado-Morales, Karla Barba-Xochipa, Fernando Martínez-Ocampo, Edgar Dantán-González, Armando Hernández-Mendoza, Manuel Quiterio-Trenado, Magdalena Rodríguez-Santiago and Abraham Rivera-Ramírez
Int. J. Mol. Sci. 2024, 25(23), 12671; https://doi.org/10.3390/ijms252312671 - 26 Nov 2024
Viewed by 252
Abstract
The Chlamydiaceae are a family of obligate intracellular bacteria known for their unique biphasic developmental cycle. Chlamydial are associated with various host organisms, including humans, and have been proposed as emerging pathogens. Genomic studies have significantly enhanced our understanding of chlamydial biology, host [...] Read more.
The Chlamydiaceae are a family of obligate intracellular bacteria known for their unique biphasic developmental cycle. Chlamydial are associated with various host organisms, including humans, and have been proposed as emerging pathogens. Genomic studies have significantly enhanced our understanding of chlamydial biology, host adaptation, and evolutionary processes. In this study, we conducted a complete pangenome association analysis (pan-GWAS) using 101 genomes from the Chlamydiaceae family to identify differentially represented genes in Chlamydia and Chlamydophila, revealing their distinct evolutionary strategies for interacting with eukaryotic hosts. Our analysis identified 289 genes with differential abundance between the two clades: 129 showed a strong association with Chlamydia and 160 with Chlamydophila. Most genes in Chlamydia were related to the type III secretion system, while Chlamydophila genes corresponded to various functional categories, including translation, replication, transport, and metabolism. These findings suggest that Chlamydia has developed a high dependence on mammalian cells for replication, facilitated by a complex T3SS for intracellular manipulation. In contrast, the metabolic and functional diversity in Chlamydophila allows it to colonize a broad range of hosts, such as birds, reptiles, amphibians, and mammals, making it a less specialized clade. Full article
(This article belongs to the Special Issue Current Research on Omics of Microorganisms)
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25 pages, 4840 KiB  
Article
Mechanism of Intracellular Elemental Sulfur Oxidation in Beggiatoa leptomitoformis, Where Persulfide Dioxygenase Plays a Key Role
by Tatyana S. Rudenko, Liubov I. Trubitsina, Vasily V. Terentyev, Ivan V. Trubitsin, Valentin I. Borshchevskiy, Svetlana V. Tishchenko, Azat G. Gabdulkhakov, Alexey A. Leontievsky and Margarita Yu. Grabovich
Int. J. Mol. Sci. 2024, 25(20), 10962; https://doi.org/10.3390/ijms252010962 - 11 Oct 2024
Viewed by 597
Abstract
Representatives of the colorless sulfur bacteria of the genus Beggiatoa use reduced sulfur compounds in the processes of lithotrophic growth, which is accompanied by the storage of intracellular sulfur. However, it is still unknown how the transformation of intracellular sulfur occurs in Beggiatoa [...] Read more.
Representatives of the colorless sulfur bacteria of the genus Beggiatoa use reduced sulfur compounds in the processes of lithotrophic growth, which is accompanied by the storage of intracellular sulfur. However, it is still unknown how the transformation of intracellular sulfur occurs in Beggiatoa representatives. Annotation of the genome of Beggiatoa leptomitoformis D-402 did not identify any genes for the oxidation or reduction of elemental sulfur. By searching BLASTP, two putative persulfide dioxygenase (PDO) homologs were found in the genome of B. leptomitoformis. In some heterotrophic prokaryotes, PDO is involved in the oxidation of sulfane sulfur. According to HPLC-MS/MS, the revealed protein was reliably detected in a culture sample grown only in the presence of endogenous sulfur and CO2. The recombinant protein from B. leptomitoformis was active in the presence of glutathione persulfide. The crystal structure of recombinant PDO exhibited consistency with known structures of type I PDO. Thus, it was shown that B. leptomitoformis uses PDO to oxidize endogenous sulfur. Additionally, on the basis of HPLC-MS/MS, RT-qPCR, and the study of PDO reaction products, we predicted the interrelation of PDO and Sox-system function in the oxidation of endogenous sulfur in B. leptomitoformis and the connection of this process with energy metabolism. Full article
(This article belongs to the Special Issue Current Research on Omics of Microorganisms)
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21 pages, 3605 KiB  
Article
Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics
by Haixia Li, Tong Liang, Yongju Liu, Pengfei Wang, Shaojuan Wang, Min Zhao and Ying Zhang
Int. J. Mol. Sci. 2024, 25(16), 9013; https://doi.org/10.3390/ijms25169013 - 19 Aug 2024
Viewed by 958
Abstract
Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance [...] Read more.
Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes. Full article
(This article belongs to the Special Issue Current Research on Omics of Microorganisms)
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23 pages, 4128 KiB  
Article
Genomic Insights into Cyanide Biodegradation in the Pseudomonas Genus
by Lara P. Sáez, Gema Rodríguez-Caballero, Alfonso Olaya-Abril, Purificación Cabello, Conrado Moreno-Vivián, María Dolores Roldán and Víctor M. Luque-Almagro
Int. J. Mol. Sci. 2024, 25(8), 4456; https://doi.org/10.3390/ijms25084456 - 18 Apr 2024
Cited by 1 | Viewed by 1213
Abstract
Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas [...] Read more.
Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation. Full article
(This article belongs to the Special Issue Current Research on Omics of Microorganisms)
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12 pages, 7120 KiB  
Article
Fine-Tuning of DADA2 Parameters for Multiregional Metabarcoding Analysis of 16S rRNA Genes from Activated Sludge and Comparison of Taxonomy Classification Power and Taxonomy Databases
by Wiktor Babis, Jan P. Jastrzebski and Slawomir Ciesielski
Int. J. Mol. Sci. 2024, 25(6), 3508; https://doi.org/10.3390/ijms25063508 - 20 Mar 2024
Viewed by 1690
Abstract
Taxonomic classification using metabarcoding is a commonly used method in microbiological studies of environmental samples and during monitoring of biotechnological processes. However, it is difficult to compare results from different laboratories, due to the variety of bioinformatics tools that have been developed and [...] Read more.
Taxonomic classification using metabarcoding is a commonly used method in microbiological studies of environmental samples and during monitoring of biotechnological processes. However, it is difficult to compare results from different laboratories, due to the variety of bioinformatics tools that have been developed and used for data analysis. This problem is compounded by different choices regarding which variable region of the 16S rRNA gene and which database is used for taxonomic identification. Therefore, this study employed the DADA2 algorithm to optimize the preprocessing of raw data obtained from the sequencing of activated sludge samples, using simultaneous analysis of three frequently used regions of 16S rRNA (V1–V3, V3–V4, V4–V5). Additionally, the study evaluated which variable region and which of the frequently used microbial databases for taxonomic classification (Greengenes2, Silva, RefSeq) more accurately classify OTUs into taxa. Adjusting the values of selected parameters of the DADA2 algorithm, we obtained the highest possible numbers of OTUs for each region. Regarding biodiversity within regions, the V3–V4 region had the highest Simpson and Shannon indexes, and the Chao1 index was similar to that of the V1–V3 region. Beta-biodiversity analysis revealed statistically significant differences between regions. When comparing databases for each of the regions studied, the highest numbers of taxonomic groups were obtained using the SILVA database. These results suggest that standardization of metabarcoding of short amplicons may be possible. Full article
(This article belongs to the Special Issue Current Research on Omics of Microorganisms)
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