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Life
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Metagenomics: New Trends and Solutions
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Metagenomics: New Trends and Solutions

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

Deadline for manuscript submissions: closed (20 October 2021) | Viewed by 16448

Special Issue Editors

Dr. Olga Ozoline

E-Mail Website
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
Dr. Anatoly Sorokin

E-Mail Website
Guest Editor
Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
Interests: computational systems biology; whole-genome metabolic models; functional metagenomics; microbial community models

Special Issue Information

Dear Colleagues,

Although metagenomics is one of the youngest areas of knowledge, its contribution to modern biology can hardly be overestimated. 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 strains among harmless bacteria of the same species using alignment-free 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, the complete genomes of bacteriophages, not yet obtained in the form of biological objects, and the context of chromosomes of uncultured bacteria became available. Using new computational approaches, a real prospect has emerged to reconstruct episodes of the ancient history of phage infections based on the order of prokaryotic CRISPR spacers, or, conversely, to predict the spread of pathogenic microorganisms or mobile vectors that create risks of expansion of emerging or re-emerging diseases. The aim of this Special Issue is to collect cutting-edge studies, presenting new experimental and bioinformatics approaches, highlighting the huge heuristic potential of metadata. 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 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. Anatoly Sorokin
Guest Editors

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. 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 (5 papers)

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Research

14 pages, 1085 KiB  
Article
CRISPR-Cas Systems in Gut Microbiome of Children with Autism Spectrum Disorders
by Natalia V. Zakharevich, Mikhail S. Nikitin, Alexey S. Kovtun, Vsevolod O. Malov, Olga V. Averina, Valery N. Danilenko and Irena I. Artamonova
Life 2022, 12(3), 367; https://doi.org/10.3390/life12030367 - 03 Mar 2022
Cited by 2 | Viewed by 2004
Abstract
The human gut microbiome is associated with various diseases, including autism spectrum disorders (ASD). Variations of the taxonomical composition in the gut microbiome of children with ASD have been observed repeatedly. However, features and parameters of the microbiome CRISPR-Cas systems in ASD have [...] Read more.
The human gut microbiome is associated with various diseases, including autism spectrum disorders (ASD). Variations of the taxonomical composition in the gut microbiome of children with ASD have been observed repeatedly. However, features and parameters of the microbiome CRISPR-Cas systems in ASD have not been investigated yet. Here, we demonstrate such an analysis in order to describe the overall changes in the microbiome CRISPR-Cas systems during ASD as well as to reveal their potential to be used in diagnostics and therapy. For the systems identification, we used a combination of the publicly available tools suited for completed genomes with subsequent filtrations. In the considered data, the microbiomes of children with ASD contained fewer arrays per Gb of assembly than the control group, but the arrays included more spacers on average. CRISPR arrays from the microbiomes of children with ASD differed from the control group neither in the fractions of spacers with protospacers from known genomes, nor in the sets of known bacteriophages providing protospacers. Almost all bacterial protospacers of the gut microbiome systems for both children with ASD and the healthy ones were located in prophage islands, leaving no room for the systems to participate in the interspecies competition. Full article
(This article belongs to the Special Issue Metagenomics: New Trends and Solutions)
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22 pages, 6492 KiB  
Article
The Influence of Kerosene on Microbiomes of Diverse Soils
by Pavel V. Shelyakin, Ivan N. Semenkov, Maria N. Tutukina, Daria D. Nikolaeva, Anna V. Sharapova, Yulia V. Sarana, Sergey A. Lednev, Alexander D. Smolenkov, Mikhail S. Gelfand, Pavel P. Krechetov and Tatiana V. Koroleva
Life 2022, 12(2), 221; https://doi.org/10.3390/life12020221 - 31 Jan 2022
Cited by 10 | Viewed by 3896
Abstract
One of the most important challenges for soil science is to determine the limits for the sustainable functioning of contaminated ecosystems. The response of soil microbiomes to kerosene pollution is still poorly understood. Here, we model the impact of kerosene leakage on the [...] Read more.
One of the most important challenges for soil science is to determine the limits for the sustainable functioning of contaminated ecosystems. The response of soil microbiomes to kerosene pollution is still poorly understood. Here, we model the impact of kerosene leakage on the composition of the topsoil microbiome in pot and field experiments with different loads of added kerosene (loads up to 100 g/kg; retention time up to 360 days). At four time points we measured kerosene concentration and sequenced variable regions of 16S ribosomal RNA in the microbial communities. Mainly alkaline Dystric Arenosols with low content of available phosphorus and soil organic matter had an increased fraction of Actinobacteriota, Firmicutes, Nitrospirota, Planctomycetota, and, to a lesser extent, Acidobacteriota and Verrucomicobacteriota. In contrast, in highly acidic Fibric Histosols, rich in soil organic matter and available phosphorus, the fraction of Acidobacteriota was higher, while the fraction of Actinobacteriota was lower. Albic Luvisols occupied an intermediate position in terms of both physicochemical properties and microbiome composition. The microbiomes of different soils show similar response to equal kerosene loads. In highly contaminated soils, the proportion of anaerobic bacteria-metabolizing hydrocarbons increased, whereas the proportion of aerobic bacteria decreased. During the field experiment, the soil microbiome recovered much faster than in the pot experiments, possibly due to migration of microorganisms from the polluted area. The microbial community of Fibric Histosols recovered in 6 months after kerosene had been loaded, while microbiomes of Dystric Arenosols and Albic Luvisols did not restore even after a year. Full article
(This article belongs to the Special Issue Metagenomics: New Trends and Solutions)
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17 pages, 2648 KiB  
Article
An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics
by Anastasiia Rusanova, Victor Fedorchuk, Stepan Toshchakov, Svetlana Dubiley and Dmitry Sutormin
Life 2022, 12(1), 25; https://doi.org/10.3390/life12010025 - 24 Dec 2021
Cited by 4 | Viewed by 3548
Abstract
Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed [...] Read more.
Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed the microbiomes and viromes of cold-water sympatric sponges Isodictya palmata (n = 2), Halichondria panicea (n = 3), and Halichondria sitiens (n = 3) by 16S and shotgun metagenomics. We showed that the bacterial and viral communities associated with these White Sea sponges are species-specific and different from the surrounding water. Extensive mining of bacterial antiphage defense systems in the metagenomes revealed a variety of defense mechanisms. The abundance of defense systems was comparable in the metagenomes of the sponges and the surrounding water, thus distinguishing the White Sea sponges from those inhabiting the tropical seas. We developed a network-based approach for the combined analysis of CRISPR-spacers and protospacers. Using this approach, we showed that the virus–host interactions within the sponge-associated community are typically more abundant (three out of four interactions studied) than the inter-community interactions. Additionally, we detected the occurrence of viral exchanges between the communities. Our work provides the first insight into the metagenomics of the three cold-water sponge species from the White Sea and paves the way for a comprehensive analysis of the interactions between microbial communities and associated viruses. Full article
(This article belongs to the Special Issue Metagenomics: New Trends and Solutions)
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19 pages, 3416 KiB  
Article
Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity
by Maria Frolova, Sergey Yudin, Valentin Makarov, Olga Glazunova, Olga Alikina, Natalia Markelova, Nikolay Kolzhetsov, Timur Dzhelyadin, Viktoria Shcherbakova, Vladimir Trubitsyn, Valery Panyukov, Alexandr Zaitsev, Sergey Kiselev, Konstantin Shavkunov and Olga Ozoline
Life 2021, 11(11), 1246; https://doi.org/10.3390/life11111246 - 17 Nov 2021
Cited by 4 | Viewed by 2401
Abstract
Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for [...] Read more.
Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this “rare” strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes. Full article
(This article belongs to the Special Issue Metagenomics: New Trends and Solutions)
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19 pages, 2079 KiB  
Article
Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane
by Alexander Y. Merkel, Nikolay A. Chernyh, Nikolai V. Pimenov, Elizaveta A. Bonch-Osmolovskaya and Alexander I. Slobodkin
Life 2021, 11(9), 953; https://doi.org/10.3390/life11090953 - 11 Sep 2021
Cited by 16 | Viewed by 2922
Abstract
Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. [...] Read more.
Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea. Full article
(This article belongs to the Special Issue Metagenomics: New Trends and Solutions)
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