Metagenomics: New Trends and Solutions: 2nd Edition

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (29 September 2023) | Viewed by 2202

Special Issue Editors


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Guest Editor
Institute of Cell Biophysics, Russian Academy of Sciences, Moscow 142290, Russia
Interests: molecular microbiology; secreted RNAs; bioinformatics in promoter modeling; taxonomic analysis of natural microbiota
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino Scientific Center for Biological Research RAS, Pushchino, Russia
Interests: genomic studies; molecular biology; transcriptional regulation; biochemistry

Special Issue Information

Dear Colleagues,

Metagenomics, as a field of research, emerged quite recently, showing significant progress in the description of microbial communities inhabiting a great variety of environments. Initially based on 16S rRNA phylotyping, aimed at assessing the biodiversity of natural microbiomes at the species or genus level, it can now reveal pathogenic or biotechnologically relevant strains among harmless bacteria of the same species using alignment-free computational approaches. Genome-resolved metagenomics can identify genetic mobility and metabolic interactions within complex communities, and metagenome-assembled genomes (MAGs) appeared as a new category of genomic data. By employing long-read sequencing, complete genomes of bacteriophages, not yet obtained in the form of biological objects, and the context of chromosomes of so far uncultured bacteria became available. Novel computational approaches allowed for real prospects in the reconstruction of ancient episodes of phage infections based on the order of prokaryotic CRISPR spacers, or, conversely, help to predict the spread of pathogenic microorganisms or mobile vectors that create risks of expansion of emerging or re-emerging diseases. The patterns of microbial consortia in the framework of historic development of life on Earth and, in particular, the human race, are also of high interest. A particularly intriguing emphasis in metagenomics is connected with mutual events of transcript-based signaling and regulation between particular microorganisms in complex communities, as well as between prokaryotes and their hosts.

The aim of this Special Issue is to present advanced new experimental and bioinformatics studies, highlighting the huge heuristic potential of metadata and proposing the means for improvement of their interpretation. Considering them as a resource of new genomic information, we also encourage the submission of papers formulating new ideas and hypotheses about what kind of hidden genomic information can be extracted from metagenomics data.

The scope of the Special Issue includes, but is not limited to:

  • Biodiversity of microbiomes in different ecological niches;
  • Intraspecies polymorphism in natural biotopes;
  • Alignment-free approaches in metagenomics;
  • New genome assembly from metagenome;
  • Predictive approaches in metagenomics;
  • Metagenome-based metabolomics;
  • Metadata resources  

Dr. Olga Ozoline
Dr. Konstantin S. S. Shavkunov
Guest Editors

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. Life 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

  • biodiversity of microbiomes in different ecological niches
  • intraspecies polymorphism in natural biotopes
  • alignment-free approaches in metagenomics
  • new genome assembly from metagenome
  • predictive approaches in metagenomics
  • metagenome-based metabolomics
  • metadata resources

Published Papers (1 paper)

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Research

24 pages, 1530 KiB  
Article
Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products
by Jolien D’aes, Marie-Alice Fraiture, Bert Bogaerts, Sigrid C. J. De Keersmaecker, Nancy H. C. J. Roosens and Kevin Vanneste
Life 2022, 12(12), 1971; https://doi.org/10.3390/life12121971 - 25 Nov 2022
Cited by 5 | Viewed by 1781
Abstract
Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several [...] Read more.
Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several rapid alerts at the European level. The aim of this study was to investigate the added value of shotgun metagenomic high-throughput sequencing to confirm and extend the results of classical analysis methods for the genomic characterization of unauthorized GMM. By combining short- and long-read metagenomic sequencing, two transgenic constructs were characterized, with insertions of alpha-amylase genes originating from B. amyloliquefaciens and B. licheniformis, respectively, and a transgenic construct with a protease gene insertion originating from B. velezensis, which were all present in all four investigated samples. Additionally, the samples were contaminated with up to three unculturable Bacillus strains, carrying genetic modifications that may hamper their ability to sporulate. Moreover, several samples contained viable Bacillus strains. Altogether these contaminations constitute a considerable load of antimicrobial resistance genes, that may represent a potential public health risk. In conclusion, our study showcases the added value of metagenomics to investigate the quality and safety of complex commercial microbial fermentation products. Full article
(This article belongs to the Special Issue Metagenomics: New Trends and Solutions: 2nd Edition)
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