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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: 20 October 2024 | Viewed by 2067

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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
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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

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Keywords

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

Published Papers (2 papers)

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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
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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 888
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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