Metagenomics and Metatranscriptomics: Recent Advances and Emerging Technologies

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: closed (20 August 2023) | Viewed by 7541

Special Issue Editors

Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center, Alexander Fleming 34 Fleming Street, Vari, 16672 Athens, Greece
Interests: molecular modeling; molecular dynamics; protein-protein docking; protein-ligand docking; drug design; biological networks; protein sequence; protein structure; sequence analysis; lipids; membranes; membrane proteins; amyloid fibrils; protein aggregation; biophysics; computational biology; bioinformatics
Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
Interests: human genetics; complex diseases; statistical genetics; metagenomics; molecular genetics/biomarkers

Special Issue Information

Dear Colleagues,

Metagenomics is the study of metagenomes, defined as the total amount of genomic material in an environmental sample. Metagenomic (DNA) and metatranscriptomic (RNA) shotgun sequencing of complex biological samples has emerged as a prevalent source of information in the study and classification of microorganisms, as well as a treasure trove of novel sequence data. Advances in high-throughput shotgun sequencing technologies have improved the quality and reduced the cost of the method, resulting in a significant increase of the available metagenome and metatranscriptome sequences. All of the above has led to the application of metagenomics and metatranscriptomics to a wide range of biological fields, from ecology and biotechnology to disease diagnosis and treatment, drug design and, most recently, large-scale protein 3D structure modeling.

This Special Issue, titled “Metagenomics and Metatranscriptomics: recent advances and emerging technologies”, welcomes the submission of manuscripts on the study of metagenomes and metratranscriptomes, their applications, the novel advances in the field and the challenges faced. Both original research papers and reviews are welcome.  Manuscripts describing the development of novel approaches and methods, either experimental or computational, or the application of metagenomics and metatrascriptomics to other fields (e.g. protein 3D structure modeling, environmental biology etc.) are especially encouraged.

Dr. Fotis Baltoumas
Prof. Dr. Chiara Scapoli
Guest Editors

Manuscript Submission Information

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Published Papers (4 papers)

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14 pages, 2465 KiB  
Article
Single-Cell Transcriptome Analysis of H5N1-HA-Stimulated Alpaca PBMCs
Biomolecules 2023, 13(1), 60; https://doi.org/10.3390/biom13010060 - 28 Dec 2022
Cited by 1 | Viewed by 2409
Abstract
Avian influenza A virus H5N1 is a highly pathogenic and persistently a major threat to global health. Vaccines and antibodies targeting hemagglutinin (HA) protein are the primary management strategies for the epidemic virus. Although camelids possess unique immunological features, the immune response induced [...] Read more.
Avian influenza A virus H5N1 is a highly pathogenic and persistently a major threat to global health. Vaccines and antibodies targeting hemagglutinin (HA) protein are the primary management strategies for the epidemic virus. Although camelids possess unique immunological features, the immune response induced by specific antigens has not yet been thoroughly investigated. Herein, we immunized an alpaca with the HA antigen of the H5N1 virus and performed single-cell transcriptome profiling for analysis of longitudinal peripheral blood mononuclear cell (PBMCs) behavior using single-cell sequencing technology (scRNA-seq). We revealed multiple cellular immunities during the immunization. The monocytes continued to expand after immunization, while the plasma cells reached their peak three days after the second antigen stimulation. Both monocytes and B cells were stimulated by the HA antigen and produced cell-type-specific cytokines to participated in the immune response. To our knowledge, this is the first study to examine the HA-specific immunological dynamics of alpaca PBMCs at the single-cell level, which is beneficial for understanding the anti-viral immune system and facilitating the development of more potent vaccines and antibodies in camelid animals. Full article
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15 pages, 2637 KiB  
Article
Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections
Biomolecules 2023, 13(1), 6; https://doi.org/10.3390/biom13010006 - 20 Dec 2022
Cited by 1 | Viewed by 1651
Abstract
This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using [...] Read more.
This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein–Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19. Full article
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14 pages, 3034 KiB  
Article
Molecular Structure and Phylogenetic Analyses of the Plastomes of Eight Sorbus Sensu Stricto Species
Biomolecules 2022, 12(11), 1648; https://doi.org/10.3390/biom12111648 - 07 Nov 2022
Cited by 1 | Viewed by 1155
Abstract
Sorbus L. is a genus of controversy on its taxonomic concept due to great variations in morphological characteristics. Sorbus sensu stricto species, being monophyletic, are characterized as pinnate leaves. However, phylogenetic relationships of these species are somewhat fluid based on morphological characteristics and [...] Read more.
Sorbus L. is a genus of controversy on its taxonomic concept due to great variations in morphological characteristics. Sorbus sensu stricto species, being monophyletic, are characterized as pinnate leaves. However, phylogenetic relationships of these species are somewhat fluid based on morphological characteristics and genetic markers. In this study, the chloroplast (cp) genomes of eight Sorbus s. str. species were characterized and compared with those of twelve released species in this genus. Our results indicated that the plastomes of the twenty Sorbus species had a conserved quadripartite structure, and 129 annotated genes had the same order and showed a good collinearity. Additionally, numerous SSRs were observed in the cp genome of each Sorbus species; most of the sequence variations appeared in non-coding regions, and four intergenic regions were identified as mutation spots. By contrast, protein-coding genes showed low variations under purifying selection. The phylogenetic and molecular-dating analysis showed that Sorbus was resolved into two major clades, in which S. americana forms one clade originating at 51.78 Ma, and the rest of Sorbus formed another clade, splitting at 36.77 Ma into two sister groups with high support values. These results provide a basis for further studying the phylogenetic relationship and biogeography of Sorbus species. Full article
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12 pages, 2273 KiB  
Brief Report
Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics
Biomolecules 2023, 13(10), 1505; https://doi.org/10.3390/biom13101505 - 11 Oct 2023
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Abstract
Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson’s disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed [...] Read more.
Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson’s disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed to improve sample collection and preservation, and provide high DNA quality and quantity for downstream analysis. As metagenomic studies are today performed on a large number of samples, the next evolution to increase study throughput is with DNA extraction automation. In this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. While similar DNA yields were observed between the protocols, our semi-automated DNA protocol generated significantly higher DNA fragment sizes. Moreover, we showed that the oral microbiome composition was equivalent between DNA extraction methods, even at the species level. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome. Full article
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