Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Open accessAbstract
Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.
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Sequence-based approaches to assess microbial composition include biomarker approaches that focus on a single kingdom-specific ubiquitous microbial gene or region that exhibits sequence hypervariability, such as the 16S ribosomal RNA gene in bacteria or the interspacer region in fungi.
“Sequence‐based approaches to assess microbial composition include biomarker approaches that focus on a single kingdom‐specific ubiquitous microbial gene or region that exhibits sequence hypervariability (eg, the 16S ribosomal RNA gene in bacteria or the interspacer region in fungi).71”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [71]
Alcohol-containing mouthwashes can exacerbate bad breath by reducing production of saliva in the mouth.
“Furthermore, alcohol‐containing mouthwashes can exacerbate bad breath, a common driver of mouthwash use, by reducing production of saliva in the mouth.”
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References 278 · Cited by 314
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- Authors
- Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C.
- Affiliations
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Buchrieser, Carmen
- Venue
- Microbial Genomics
- Publisher
- Microbiology Society
- Published
- 2020-08-01
- Volume
- 6
- Issue
- 8
- Pages
- mgen000409
- ISSN
- 2057-5858 (ISSN-L)
- PMC
- PMC7641418
- OpenAlex
- W3045315617
- Cited by
- 314
- References
- 278
- Citations by year
- 2026: 51 · 2025: 83 · 2024: 84 · 2023: 48 · 2022: 26 · 2021: 21 · 2020: 1
- FWCI
- 2.28
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbial Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- Funders
- Agence Nationale de la Recherche (ANR-10-LABX-62-IBEID)
- Fondation pour la Recherche Médicale (EQU201903007847)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- metagenomics, marker gene sequencing, whole genome shotgun sequencing, microbial ecology, microbial diversity, microbial community composition, taxonomic identification, functional potential, culture-independent methods, bioinformatics software
- MeSH terms
- Whole Genome Sequencing, Genetic Markers, Software, Computational Biology, Metagenome, Metagenomics, High-Throughput Nucleotide Sequencing, Microbiota
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