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A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data
Open accessAbstract
The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data. This review summarizes the most commonly used bioinformatics tools for the assembly and annotation of metagenomic sequence data with the aim of discovering novel genes.
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“The rumen also remains a source of valuable bioactives for the biotechnology industry, and metagenomics is a key tool for such bioprospecting (Oyama et al., 2017; Roumpeka et al., 2017).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Roumpeka et al., 2017
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Cites
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“After removing repetitive sequences and low-quality regions, MG-RAST maps sequence data to three non-redundant databases and creates a phylogenetic profile of the metagenomic sample.”
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“Megahit (Li et al., 2015) uses a very similar approach to IDBA-UD, but takes advantage of succinct de Bruijn graphs (Bowe et al., 2012) and GPUs, which lowers the memory requirements and increases speed, respectively.”
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“MetaVelvet authors reported longer N50 sizes, higher cover rates of genomes (compared to other metagenome and single genome assemblers) and high numbers of predicted proteins (by MetaGene gene finding software, Noguchi et al., 2006).”
MethodInfluentialSpace/time trade-offs in hash coding with allowable errors
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“Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database connecting genomic, biochemical and phenotypical information from multiple individual databases (Kanehisa et al., 2008).”
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“There are extensive population of microorganisms, encompassing bacteria, archaea, fungi, protozoa, and viruses in rumi-nant GIT [8, 9].”
Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety
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Macroecological dynamics of skin microbiota
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Metadata
- Authors
- Roumpeka, D. D., Wallace, R. J., Escalettes, F., Fotheringham, I., & Watson, M.
- Affiliations
- Roslin Institute (GB)
- University of Aberdeen (GB)
- Ingenza (United Kingdom) (GB)
- Corresponding author
- Roumpeka, Despoina D.
- ORCID
- Watson, Mick
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2017-03-06
- Volume
- 8
- Pages
- 23-23
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC5337752
- OpenAlex
- W2595593998
- Cited by
- 199
- References
- 74
- Citations by year
- 2026: 14 · 2025: 18 · 2024: 23 · 2023: 14 · 2022: 24 · 2021: 34 · 2020: 19 · 2019: 25 · 2018: 22 · 2017: 5
- FWCI
- 1.89
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Funders
- Biotechnology and Biological Sciences Research Council (BBS/E/D/20310000, BB/J004243/1, BB/L016389/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
- Keywords
- metagenomics, bioinformatics software, bioprospecting, microbiome, metagenome assembly, metagenome annotation, gene discovery, microbial community structure
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