microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes
Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Bioinformatics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2022.918853/full |
| _version_ | 1811288471620288512 |
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| author | Ulas Karaoz Eoin L. Brodie Eoin L. Brodie |
| author_facet | Ulas Karaoz Eoin L. Brodie Eoin L. Brodie |
| author_sort | Ulas Karaoz |
| collection | DOAJ |
| description | Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes. |
| first_indexed | 2024-04-13T03:37:08Z |
| format | Article |
| id | doaj.art-0948c109b2dc429292bfb6990fd3bd59 |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-04-13T03:37:08Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj.art-0948c109b2dc429292bfb6990fd3bd592022-12-22T03:04:18ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472022-07-01210.3389/fbinf.2022.918853918853microTrait: A Toolset for a Trait-Based Representation of Microbial GenomesUlas Karaoz0Eoin L. Brodie1Eoin L. Brodie2Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesEarth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesDepartment of Environmental Science, Policy and Management, University of California, Berkeley, CA, United StatesRemote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.https://www.frontiersin.org/articles/10.3389/fbinf.2022.918853/fullfunctional traitsfunctional guildsecological strategytrait-based modelprofile hidden markov modelmicrobial genome |
| spellingShingle | Ulas Karaoz Eoin L. Brodie Eoin L. Brodie microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes Frontiers in Bioinformatics functional traits functional guilds ecological strategy trait-based model profile hidden markov model microbial genome |
| title | microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes |
| title_full | microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes |
| title_fullStr | microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes |
| title_full_unstemmed | microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes |
| title_short | microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes |
| title_sort | microtrait a toolset for a trait based representation of microbial genomes |
| topic | functional traits functional guilds ecological strategy trait-based model profile hidden markov model microbial genome |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2022.918853/full |
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