Special Issue

Topic: Bioinformatics Applied to Microbiota-based Science

A Special Issue of Microbiome Research Reports

ISSN 2771-5965 (Online)

Submission deadline: 31 Dec 2023

Guest Editor(s)

Dr. Leonardo Mancabelli
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
Dr. Gabriele Andrea Lugli
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.

Special Issue Introduction

During the past two decades, the evolution of DNA sequencing technologies has allowed the gathering of a vast amount of metagenomic data, laying the foundation to study complex microbial communities, also known as microbiomes. At the dawn of the metagenomic classification era, DNA sequences were mainly used to unveil the composition of the bacterial communities inhabiting specific environments through analysis based on the amplification of microbial marker genes. Recently, the more informative shotgun metagenomics approach allowed the reconstruction of the functional contribution of the bacteria harbored in the biological samples without the necessity to compromise data during sample preparation. To date, the interest of the scientific community is rapidly moving to a complete overview of the microbiomes, involving multiple bioinformatic pipelines aiming at understanding complex dynamics between members of the same environmental niche and their host.

This Special Issue aims to gather projects that rely on bioinformatics strategies to investigate bacteria, archaea, protists, and fungi in the frame of microbiome research, highlighting applications in the field of the human microbiome as well as more unexplored microbiomes, such as non-human animals.

We welcome original or review manuscripts, perspectives, opinions, and commentaries on different aspects of this Special Issue, including but not limited to:
Microbiota investigation using bioinformatic approaches:
● Microbial profiling of human and animal microbiomes
● Genome reconstruction of microorganisms from complex environments
● DNA enrichment studies of microbiomes
● Investigation of the microbial dark matter among microbiomes
● Functional profiling of host-related microbiomes
● Host-microbiome and microbiome-microbiome relationships

Bioinformatic pipelines and microbiomes:
● Development of bioinformatic pipeline in the field
● Comparisons between bioinformatic pipelines
● Innovative approaches to microbiome data management

Submission Deadline

31 Dec 2023

Submission Information

Ten articles in the Special Issue are exempt from article processing charges.
For Author Instructions, please refer to https://www.oaepublish.com/mrr/author_instructions
For Online Submission, please login at https://oaemesas.com/login?JournalId=mrr&SpecialIssueId=MRR220810
Submission Deadline: 31 Mar 2023
Contacts: Fiona Chen, Assistant Editor, editorialoffice@mrrjournal.net

Published Articles

Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses

Open Access Original Article DOI: 10.20517/mrr.2023.02 14 Nov 2023
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Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome

Open Access Review DOI: 10.20517/mrr.2023.27 22 Oct 2023
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Comparison of k-mer-based de novo comparative metagenomic tools and approaches

Open Access Original Article DOI: 10.20517/mrr.2023.26 19 Jul 2023
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Connect the dots: sketching out microbiome interactions through networking approaches

Open Access Review DOI: 10.20517/mrr.2023.25 17 Jul 2023
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MEGAnnotator2: a pipeline for the assembly and annotation of microbial genomes

Open Access Original Article DOI: 10.20517/mrr.2022.21 29 Apr 2023
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A tool to assess the mock community samples in 16S rRNA gene-based microbiota profiling studies

Open Access Technical Note DOI: 10.20517/mrr.2022.18 26 Apr 2023
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Microbiome Research Reports
ISSN 2771-5965 (Online)

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All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/