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Metagenomics and Metatranscriptomics
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Metagenomics and Metatranscriptomics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 24031

Special Issue Editor

Prof. Dr. Valerio Fulci

E-Mail Website
Guest Editor
Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
Interests: non-coding RNA; microRNA; epitranscriptomics; metagenomics; NGS; epigenomics

Special Issue Information

Dear Colleagues,

Metagenomics is a rapidly evolving field and current technological advances provide new opportunities to investigate microbiomes for clinical, ecological, phylogenetic and biotechnological purposes. Despite huge sequencing and sampling efforts by the scientific community we are still far from a comprehensive characterization of microbial genomes and transcriptomes. The growing amount of data generated requires continuous improvement of bioinformatic tools and innovative approaches to improve data resolution. This IJMS special issue will be focused on the methodological and bioinformatic challenges of shotgun metagenomics.

Topics of interest include (but are not limited to):

  • innovative metagenomics protocols
  • applications of third generation NGS platforms (e.g. PacBio, Nanopore)
  • computational and/or experimental strategies to characterize epigenetic modifications in microbial communities
  • computational and/or experimental strategies to characterize epitranscriptomic modifications in microbial communities
  • single cell metagenomics approaches or analytical tools
  • pipelines introducing significant advantages in metagenomic data analysis
  • comparative analysis of emerging metagenomics techniques
  • viral genome characterization and assembly through NGS sequencing
  • tools for metagenomic/metatranscriptomic data integration with metabolomics/proteomics

Prof. Dr. Valerio Fulci
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • Metatranscriptomics
  • Shotgun metagenomics
  • Single cell metagenomics
  • Integrative biology
  • Epitranscriptomics
  • Virome
  • Microbiome
  • Third generation sequencing
  • Bioinformatics
  • Metabolomics
  • Long reads
  • Proteomics

Published Papers (6 papers)

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Editorial

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2 pages, 166 KiB  
Editorial
Meta’omics: Challenges and Applications
by Valerio Fulci
Int. J. Mol. Sci. 2022, 23(12), 6486; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126486 - 10 Jun 2022
Viewed by 1136
Abstract
Metagenomics and metatranscriptomics are emerging as key disciplines towards a fully understanding the complex relationships between living organisms belonging to different kingdoms [...] Full article
(This article belongs to the Special Issue Metagenomics and Metatranscriptomics)

Research

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19 pages, 3658 KiB  
Article
16S rRNA of Mucosal Colon Microbiome and CCL2 Circulating Levels Are Potential Biomarkers in Colorectal Cancer
by Carmela Nardelli, Ilaria Granata, Marcella Nunziato, Mario Setaro, Fortunata Carbone, Claudio Zulli, Vincenzo Pilone, Ettore Domenico Capoluongo, Giovanni Domenico De Palma, Francesco Corcione, Giuseppe Matarese, Francesco Salvatore and Lucia Sacchetti
Int. J. Mol. Sci. 2021, 22(19), 10747; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910747 - 04 Oct 2021
Cited by 16 | Viewed by 3168
Abstract
Colorectal cancer (CRC) is one of the most common malignancies in the Western world and intestinal dysbiosis might contribute to its pathogenesis. The mucosal colon microbiome and C-C motif chemokine 2 (CCL2) were investigated in 20 healthy controls (HC) and 20 CRC patients [...] Read more.
Colorectal cancer (CRC) is one of the most common malignancies in the Western world and intestinal dysbiosis might contribute to its pathogenesis. The mucosal colon microbiome and C-C motif chemokine 2 (CCL2) were investigated in 20 healthy controls (HC) and 20 CRC patients using 16S rRNA sequencing and immunoluminescent assay, respectively. A total of 10 HC subjects were classified as overweight/obese (OW/OB_HC) and 10 subjects were normal weight (NW_HC); 15 CRC patients were classified as OW/OB_CRC and 5 patients were NW_CRC. Results: Fusobacterium nucleatum and Escherichia coli were more abundant in OW/OB_HC than in NW_HC microbiomes. Globally, Streptococcus intermedius, Gemella haemolysans, Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were significantly increased in CRC patient tumor/lesioned tissue (CRC_LT) and CRC patient unlesioned tissue (CRC_ULT) microbiomes compared to HC microbiomes. CCL2 circulating levels were associated with tumor presence and with the abundance of Fusobacterium nucleatum, Bacteroides fragilis and Gemella haemolysans. Our data suggest that mucosal colon dysbiosis might contribute to CRC pathogenesis by inducing inflammation. Notably, Fusobacterium nucleatum, which was more abundant in the OW/OB_HC than in the NW_HC microbiomes, might represent a putative link between obesity and increased CRC risk. Full article
(This article belongs to the Special Issue Metagenomics and Metatranscriptomics)
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19 pages, 5452 KiB  
Article
Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes
by Yeonhwa Jo, Chang-Gi Back, Kook-Hyung Kim, Hyosub Chu, Jeong Hun Lee, Sang Hyun Moh and Won Kyong Cho
Int. J. Mol. Sci. 2021, 22(13), 6791; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22136791 - 24 Jun 2021
Cited by 7 | Viewed by 2304
Abstract
Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues [...] Read more.
Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study. Full article
(This article belongs to the Special Issue Metagenomics and Metatranscriptomics)
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11 pages, 1438 KiB  
Article
Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments
by Rebecca Ansorge, Giovanni Birolo, Stephen A. James and Andrea Telatin
Int. J. Mol. Sci. 2021, 22(10), 5309; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105309 - 18 May 2021
Cited by 12 | Viewed by 4721
Abstract
The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for [...] Read more.
The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as ‘Amplicon Sequence Variants’ (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic. Full article
(This article belongs to the Special Issue Metagenomics and Metatranscriptomics)
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19 pages, 1804 KiB  
Article
Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer
by Pamela Vernocchi, Tommaso Gili, Federica Conte, Federica Del Chierico, Giorgia Conta, Alfredo Miccheli, Andrea Botticelli, Paola Paci, Guido Caldarelli, Marianna Nuti, Paolo Marchetti and Lorenza Putignani
Int. J. Mol. Sci. 2020, 21(22), 8730; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21228730 - 19 Nov 2020
Cited by 72 | Viewed by 9768
Abstract
Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role in disease progression through immune response, inflammation and metabolism modulation. This study focused on the use of network analysis and weighted gene co-expression network [...] Read more.
Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role in disease progression through immune response, inflammation and metabolism modulation. This study focused on the use of network analysis and weighted gene co-expression network analysis (WGCNA) to identify the biological interaction between the gut ecosystem and its metabolites that could impact the immunotherapy response in non-small cell lung cancer (NSCLC) patients undergoing second-line treatment with anti-PD1. Metabolomic data were merged with operational taxonomic units (OTUs) from 16S RNA-targeted metagenomics and classified by chemometric models. The traits considered for the analyses were: (i) condition: disease or control (CTRLs), and (ii) treatment: responder (R) or non-responder (NR). Network analysis indicated that indole and its derivatives, aldehydes and alcohols could play a signaling role in GM functionality. WGCNA generated, instead, strong correlations between short-chain fatty acids (SCFAs) and a healthy GM. Furthermore, commensal bacteria such as Akkermansia muciniphila, Rikenellaceae, Bacteroides, Peptostreptococcaceae, Mogibacteriaceae and Clostridiaceae were found to be more abundant in CTRLs than in NSCLC patients. Our preliminary study demonstrates that the discovery of microbiota-linked biomarkers could provide an indication on the road towards personalized management of NSCLC patients. Full article
(This article belongs to the Special Issue Metagenomics and Metatranscriptomics)
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Other

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7 pages, 241 KiB  
Case Report
Mycobacterium chelonae Infection Identified by Metagenomic Next-Generation Sequencing as the Probable Cause of Acute Contained Rupture of a Biological Composite Graft—A Case Report
by Andrea C. Büchler, Vladimir Lazarevic, Nadia Gaïa, Myriam Girard, Friedrich Eckstein, Adrian Egli, Sarah Tschudin Sutter and Jacques Schrenzel
Int. J. Mol. Sci. 2022, 23(1), 381; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010381 - 29 Dec 2021
Cited by 5 | Viewed by 1693
Abstract
We present the case of a 72-year-old female patient with acute contained rupture of a biological composite graft, 21 months after replacement of the aortic valve and the ascending aorta due to an aortic dissection. Auramine-rhodamine staining of intraoperative biopsies showed acid-fast bacilli, [...] Read more.
We present the case of a 72-year-old female patient with acute contained rupture of a biological composite graft, 21 months after replacement of the aortic valve and the ascending aorta due to an aortic dissection. Auramine-rhodamine staining of intraoperative biopsies showed acid-fast bacilli, but classical culture and molecular methods failed to identify any organism. Metagenomic analysis indicated infection with Mycobacterium chelonae, which was confirmed by target-specific qPCR. The complexity of the sample required a customized bioinformatics pipeline, including cleaning steps to remove sequences of human, bovine ad pig origin. Our study underlines the importance of multiple testing to increase the likelihood of pathogen identification in highly complex samples. Full article
(This article belongs to the Special Issue Metagenomics and Metatranscriptomics)
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