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Feature Papers in Microbial Genetics in 2024
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Feature Papers in Microbial Genetics in 2024

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (25 July 2024) | Viewed by 1753

Special Issue Editor

Dr. Silvia Turroni

E-Mail Website
Guest Editor
Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro, 6-40126 Bologna, Italy
Interests: human microbiome; gut microbiome; microbial ecology; host–microbiome interactions; probiotics; next-generation sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, “Feature Papers in Microbial Genetics in 2024”, aims to gather together high-quality research articles, review articles, and communications on all aspects of microbial genetics, at the level of both individual microorganisms and microbial communities, from various environments and hosts, and including ancient microbes. We welcome submissions of manuscripts from editorial board members and outstanding scholars invited by the editorial board and editorial office. We aim to develop our Section into an attractive open access publishing platform for microbial genetics research.

Dr. Silvia Turroni
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Genes 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 2600 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

  • microbiome
  • genetics
  • genomics

Published Papers (3 papers)

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Research

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12 pages, 3209 KiB  
Article
Transcriptomic Insights into the Developmental Dynamics of Eimeria acervulina: A Comparative Study of a Precocious Line and the Wild Type
by Ning Zhang, Xiaojin Li, Jie Liu, Linlin Chen, Sixin Zhang, Xianyong Liu, Xinming Tang, Xun Suo and Yuanyuan Zhang
Genes 2024, 15(7), 831; https://doi.org/10.3390/genes15070831 - 24 Jun 2024
Viewed by 464
Abstract
Coccidiosis, a parasitic disease caused by single or multiple Eimeria species, leads to significant economic losses in the poultry industry. The Eimeria life cycle includes schizogony, gametogony, and sporogony. To investigate the dynamics of gene expression and regulatory networks during the development of [...] Read more.
Coccidiosis, a parasitic disease caused by single or multiple Eimeria species, leads to significant economic losses in the poultry industry. The Eimeria life cycle includes schizogony, gametogony, and sporogony. To investigate the dynamics of gene expression and regulatory networks during the development of Eimeria acervulina, we employed time-course transcriptomics to rigorously compare the gene expression patterns between a precocious line (PL) and the wild type (WT) of E. acervulina. The results revealed that the PL enters into gametogony 12 h earlier than the WT, and both the PL and WT exhibited distinct clustering patterns during the development phase. A weighted gene co-expression network analysis (WGCNA) identified genes specifically expressed at four distinct developmental stages, schizogony, gametogony, sporulated oocysts, and unsporulated oocysts, clarifying the key biological processes at each stage. This study used global transcriptome profiling to elucidate molecular variations throughout the E. acervulina life cycle, providing critical insights into molecular characterization and valuable resources for investigating other apicomplexan parasites of public health importance. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2024)
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19 pages, 4828 KiB  
Article
A Proteogenomic Approach to Unravel New Proteins Encoded in the Leishmania donovani (HU3) Genome
by Javier Adán-Jiménez, Alejandro Sánchez-Salvador, Esperanza Morato, Jose Carlos Solana, Begoña Aguado and Jose M. Requena
Genes 2024, 15(6), 775; https://doi.org/10.3390/genes15060775 - 13 Jun 2024
Viewed by 476
Abstract
The high-throughput proteomics data generated by increasingly more sensible mass spectrometers greatly contribute to our better understanding of molecular and cellular mechanisms operating in live beings. Nevertheless, proteomics analyses are based on accurate genomic and protein annotations, and some information may be lost [...] Read more.
The high-throughput proteomics data generated by increasingly more sensible mass spectrometers greatly contribute to our better understanding of molecular and cellular mechanisms operating in live beings. Nevertheless, proteomics analyses are based on accurate genomic and protein annotations, and some information may be lost if these resources are incomplete. Here, we show that most proteomics data may be recovered by interconnecting genomics and proteomics approaches (i.e., following a proteogenomic strategy), resulting, in turn, in an improvement of gene/protein models. In this study, we generated proteomics data from Leishmania donovani (HU3 strain) promastigotes that allowed us to detect 1908 proteins in this developmental stage on the basis of the currently annotated proteins available in public databases. However, when the proteomics data were searched against all possible open reading frames existing in the L. donovani genome, twenty new protein-coding genes could be annotated. Additionally, 43 previously annotated proteins were extended at their N-terminal ends to accommodate peptides detected in the proteomics data. Also, different post-translational modifications (phosphorylation, acetylation, methylation, among others) were found to occur in a large number of Leishmania proteins. Finally, a detailed comparative analysis of the L. donovani and Leishmania major experimental proteomes served to illustrate how inaccurate conclusions can be raised if proteomes are compared solely on the basis of the listed proteins identified in each proteome. Finally, we have created data entries (based on freely available repositories) to provide and maintain updated gene/protein models. Raw data are available via ProteomeXchange with the identifier PXD051920. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2024)
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Other

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8 pages, 1703 KiB  
Perspective
Hope on the Horizon? Aptamers in Diagnosis of Invasive Fungal Infections
by Sadegh Khodavaisy and Jianping Xu
Genes 2024, 15(6), 733; https://doi.org/10.3390/genes15060733 - 3 Jun 2024
Viewed by 410
Abstract
Despite remarkable advances in the diagnosis of invasive fungal infections (IFIs), rapid, specific, sensitive, and cost-effective detection methods remain elusive. Due to their stability, ease of production, and specificity to signature molecules of fungal pathogens, short single-stranded sequences of DNA, RNA, and XNA, [...] Read more.
Despite remarkable advances in the diagnosis of invasive fungal infections (IFIs), rapid, specific, sensitive, and cost-effective detection methods remain elusive. Due to their stability, ease of production, and specificity to signature molecules of fungal pathogens, short single-stranded sequences of DNA, RNA, and XNA, collectively called aptamers, have emerged as promising diagnostic markers. In this perspective, we summarize recent progress in aptamer-based diagnostic tools for IFIs and discuss how these tools could potentially meet the needs and provide economical and simple solutions for point-of-care for better management of IFIs. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2024)
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