Functional characterization of prokaryotic dark matter: the road so far and what lies ahead
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-g...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Current Research in Microbial Sciences |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666517422000566 |
| _version_ | 1811188454365593600 |
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| author | Pedro Escudeiro Christopher S. Henry Ricardo P.M. Dias |
| author_facet | Pedro Escudeiro Christopher S. Henry Ricardo P.M. Dias |
| author_sort | Pedro Escudeiro |
| collection | DOAJ |
| description | Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications. |
| first_indexed | 2024-04-11T14:19:06Z |
| format | Article |
| id | doaj.art-6b68dd3e933247eb8beb5ff4156d3d81 |
| institution | Directory Open Access Journal |
| issn | 2666-5174 |
| language | English |
| last_indexed | 2024-04-11T14:19:06Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Research in Microbial Sciences |
| spelling | doaj.art-6b68dd3e933247eb8beb5ff4156d3d812022-12-22T04:19:07ZengElsevierCurrent Research in Microbial Sciences2666-51742022-01-013100159Functional characterization of prokaryotic dark matter: the road so far and what lies aheadPedro Escudeiro0Christopher S. Henry1Ricardo P.M. Dias2BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, PortugalArgonne National Laboratory, Lemont, Illinois, USA; University of Chicago, Chicago, Illinois, USABioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal; iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal; Corresponding author.Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.http://www.sciencedirect.com/science/article/pii/S2666517422000566Functional GenomicsMetagenomicsMicrobial Dark MatterBiotechnological Potential |
| spellingShingle | Pedro Escudeiro Christopher S. Henry Ricardo P.M. Dias Functional characterization of prokaryotic dark matter: the road so far and what lies ahead Current Research in Microbial Sciences Functional Genomics Metagenomics Microbial Dark Matter Biotechnological Potential |
| title | Functional characterization of prokaryotic dark matter: the road so far and what lies ahead |
| title_full | Functional characterization of prokaryotic dark matter: the road so far and what lies ahead |
| title_fullStr | Functional characterization of prokaryotic dark matter: the road so far and what lies ahead |
| title_full_unstemmed | Functional characterization of prokaryotic dark matter: the road so far and what lies ahead |
| title_short | Functional characterization of prokaryotic dark matter: the road so far and what lies ahead |
| title_sort | functional characterization of prokaryotic dark matter the road so far and what lies ahead |
| topic | Functional Genomics Metagenomics Microbial Dark Matter Biotechnological Potential |
| url | http://www.sciencedirect.com/science/article/pii/S2666517422000566 |
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