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Microorganisms
Special Issues
Revealing Microbial Networks: Bioinformatics Insights into Microbiomes
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Revealing Microbial Networks: Bioinformatics Insights into Microbiomes

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 2255

Special Issue Editor

Dr. Vagner Fonseca

E-Mail Website
Guest Editor
Department of Exact and Earth Sciences, University of the State of Bahia, Salvador 41150-000, Brazil
Interests: bioinformatics; viral evolution; molecular epidemiology; mathematical models; phylogenetic and phylodynamic tree

Special Issue Information

Dear Colleagues,

I am delighted to invite you to contribute to a Special Issue of Microorganisms within the Microbiomes Section, titled "Revealing Microbial Networks: Bioinformatics Insights into Microbiomes". This distinctive issue aims to showcase cutting-edge genomic and epidemiological data on global microbial strains and offer a real-time snapshot of the ever-evolving microbial landscape. As the Guest Editor, I am eager to curate a collection that explores the dynamic interactions within microbiomes, highlighting the pivotal roles played by various organisms beyond viruses and fungi.

We welcome original research, reviews, and methodological advancements utilizing bioinformatics to unravel the complexities of microbial communities within microbiomes. We aim to deepen our comprehension of how these diverse microorganisms influence host systems and ecosystems, providing insights into their diversity, functions, and ecological significance.

Contributions may span a broad spectrum, including studies on metagenomics, metatranscriptomics, and bioinformatic tools customized for various microbial microbiomes. Your research has the potential to significantly advance our understanding of microbiome dynamics.

Dr. Vagner Fonseca
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. Microorganisms 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 2700 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

  • microbiomes
  • bioinformatics analysis
  • metagenomics
  • microbial communities
  • genomic dynamics
  • microbiome dynamics
  • global microbial strains
  • ecological significance
  • metagenomics
  • metatranscriptomics
  • host–microbe interactions

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (2 papers)

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Research

14 pages, 3165 KiB  
Article
New Iflavirus Species Characterized from Mosquitoes Captured in the Sao Paulo Zoological Facilities
by Lilian de Oliveira Guimarães, Santana Lobato Bahia, Geovani de Oliveira Ribeiro, Endrya do Socorro Foro Ramos, Fabiola Villanova, Vanessa dos Santos Morais, Juliana Telles-de-Deus, Vanessa Christe Helfstein, Jesus Maia dos Santos, Ramendra Pati Pandey, Xutao Deng, Eric Delwart, Vera Lucia Fonseca de Camargo-Neves, Antonio Charlys da Costa, Karin Kirchgatter and Élcio Leal
Microorganisms 2024, 12(9), 1749; https://doi.org/10.3390/microorganisms12091749 - 23 Aug 2024
Viewed by 835
Abstract
Metagenomic studies of mosquito viromes demonstrated a more diverse composition than just an exclusive composition of pathogenic arboviruses transmitted to humans. In our study, the virome of 866 female mosquitoes collected throughout 2020 at the São Paulo Zoo, located in the city of [...] Read more.
Metagenomic studies of mosquito viromes demonstrated a more diverse composition than just an exclusive composition of pathogenic arboviruses transmitted to humans. In our study, the virome of 866 female mosquitoes collected throughout 2020 at the São Paulo Zoo, located in the city of São Paulo/SP—Brazil, was obtained. Specifically, in this paper, we describe a new virus found by viral RNA extraction and next-generation MiSeq sequencing of a group of 23 specimens of Anopheles (Nys.) strodei. The complete genome with a length of 9709 nucleotides was characterized by a positive orientation and a single strand, with a single large ORF, which encodes a polyprotein of 2987 amino acids. The phylogenetic analysis showed an association with the viral family Iflaviridae and the Riboviria realm. We carried out comparisons with translated sequences of the capsid regions of other iflavirus, and the identities in relation to our sequence were below the minimum limit of 90%, indicating that possibly it is a new species of iflavirus. Our findings contribute to expanding knowledge of virome composition among mosquito species in Brazil and globally. Moreover, we provide a viral genome reference specific to this geographic region and Culicidae family of mosquitoes. This resource facilitates future in silico recognition and assembly of viral genomes within metagenomic datasets. Full article
(This article belongs to the Special Issue Revealing Microbial Networks: Bioinformatics Insights into Microbiomes)
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14 pages, 4005 KiB  
Article
Metagenomic Characterization and Comparative Analysis of Removable Denture-Wearing and Non-Denture-Wearing Individuals in Healthy and Diseased Periodontal Conditions
by Ho-Hin Wong, Chun-Ho Hung, Jason Yip and Tong-Wah Lim
Microorganisms 2024, 12(6), 1197; https://doi.org/10.3390/microorganisms12061197 - 13 Jun 2024
Cited by 2 | Viewed by 1026
Abstract
Removable denture wearers are at an increased risk of developing periodontal diseases due to biofilm deposition and microbial colonization on the denture surface. This study aimed to characterize and compare the metagenomic composition of saliva in denture wearers with different periodontal statuses. Twenty-four [...] Read more.
Removable denture wearers are at an increased risk of developing periodontal diseases due to biofilm deposition and microbial colonization on the denture surface. This study aimed to characterize and compare the metagenomic composition of saliva in denture wearers with different periodontal statuses. Twenty-four community-dwelling elders were recruited and grouped into denture wearers with active periodontitis (APD), non-denture wearers with active periodontitis (APXD), denture wearers with stable periodontal health conditions (SPCD), and non-denture wearers with stable periodontal health conditions (SPCXD). Saliva samples were collected and underwent Type IIB restriction-site-associated DNA for microbiome (2bRAD-M) metagenomic sequencing to characterize the species-resolved microbial composition. Alpha diversity analysis based on the Shannon index revealed no significant difference between groups. Beta diversity analysis using the Jaccard distance matrix was nearly significantly different between denture-wearing and non-denture-wearing groups (p = 0.075). Some respiratory pathogens, including Streptococcus agalactiae and Streptococcus pneumoniae, were detected as the top 30 species in saliva samples. Additionally, LEfSe analysis revealed a substantial presence of pathogenic bacteria in denture groups. In the cohort of saliva samples collected from community-dwelling elders, a remarkable abundance of certain opportunistic pathogens was detected in the microbial community. Full article
(This article belongs to the Special Issue Revealing Microbial Networks: Bioinformatics Insights into Microbiomes)
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