Application of Bioinformatics in Microbiome—2nd Edition

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: 20 July 2025 | Viewed by 228

Special Issue Editor

The ADA Forsyth Institute, Cambridge, MA 02142, USA
Interests: microbiome research; next-generation sequencing; gene markers; genomics; meta-genomics; meta-transcriptomics; bioinformatics analysis; artifical intelligence
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Special Issue Information

Dear Colleagues,

The microorganisms found in a particular environment and their activities are collectively referred to as the microbiome. The advances in sequencing technologies have enabled new means of studying microbiomes; it is now possible to answer the questions of “what is there?”, “what can they do?”, and “what are they doing?” concerning a particular habitat by sequencing its marker genes, meta-genomes, and meta-transcriptomes, respectively. With high-throughput next-generation sequencing (NGS), there has been an explosion of sequencing data, which require novel and efficient computing algorithms, software, and pipelines to process, manage, and interpret their embedded information. Bioinformatics is an interdisciplinary field of science that combines biology, computer science, informatics, mathematics, and statistics to analyze and interpret biological and clinical data. Bioinformatics is not only crucial but essential to extracting meaningful information from cryptic NGS data.

This Special Issue aims to demonstrate the latest developments in bioinformatics in the NGS era that have helped advance our understanding of the microbiome. This second version of this Special Issue also encompasses bioinformatics tools, algorithms, and computing platforms for multi-omics microbiome research. The Issue’s scope includes, but is not limited to, the following topics:

  1. New or improved next-generation sequencing (NGS) technologies that accelerate microbiome research;
  2. New or improved omics and multi-omics technologies that accelerate microbiome research;
  3. New computing algorithms for analyzing NGS and omics data;
  4. Data management platforms (online or standalone desktop databases) for microbiome data;
  5. Pipeline development (a collection of analytic software streamlined from upstream to downstream applications);
  6. Bioinformatics application in the cloud platform;
  7. Artificial intelligence (AI) in microbiome research;
  8. New microbiome research discovery, both medical and non-medical, with a significant bioinformatics component;
  9. Reviews of the above applications.

Dr. Tsute Chen
Guest Editor

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Keywords

  • microbiome
  • microbiota
  • next-generation sequencing
  • genomics
  • meta-genomics
  • meta-transcriptomics
  • taxonomy
  • artificial intelligence
  • bioinformatics

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Published Papers (1 paper)

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Research

16 pages, 2289 KiB  
Article
Taxonomic Diversity and Clinical Correlations in Periapical Lesions by Next-Generation Sequencing Analysis
by Juliana D. Bronzato, Brenda P. F. A. Gomes and Tsute Chen
Genes 2025, 16(7), 775; https://doi.org/10.3390/genes16070775 (registering DOI) - 30 Jun 2025
Abstract
Objectives: The aim of this study was to assess the taxonomic diversity of the microbiota associated with periapical lesions of endodontic origin and to determine whether microbial profiles vary across different populations and clinical characteristics using a unified in silico analysis of next-generation [...] Read more.
Objectives: The aim of this study was to assess the taxonomic diversity of the microbiota associated with periapical lesions of endodontic origin and to determine whether microbial profiles vary across different populations and clinical characteristics using a unified in silico analysis of next-generation sequencing (NGS) data. Methods: Raw 16S rRNA sequencing data from three published studies were retrieved from the NCBI Sequence Read Archive and reprocessed using a standardized bioinformatics pipeline. Amplicon sequence variants were inferred using DADA2, and taxonomic assignments were performed using BLASTN against a curated 16S rRNA reference database. Alpha and beta diversity analyses were conducted using QIIME 2 and R, and differential abundance was assessed with ANCOM-BC2. Statistical comparisons were made based on population, sex, symptomatology, and other clinical metadata. Results: A total of 38 periapical lesion samples yielded 566,223 high-confidence reads assigned to 347 bacterial species. Significant differences in microbial composition were observed between geographic regions (China vs. Spain), sexes, and symptoms. Core species such as Fretibacterium sp. HMT 360 and Porphyromonas endodontalis were prevalent across datasets. Porphyromonas gingivalis and Fusobacterium nucleatum were found in abundance across all three studies. Beta diversity metrics revealed distinct clustering by study and country. Symptomatic lesions were associated with higher abundance of Alloprevotella tannerae and Prevotella oris. Conclusions: The periapical lesion microbiota is taxonomically diverse and varies significantly by geographic and clinical features. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Microbiome—2nd Edition)
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