A survey of computational approaches for characterizing microbial interactions in microbial mats
Abstract In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degr...
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| Format: | Article |
| Language: | English |
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BMC
2025-06-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03634-2 |
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| author | Vanesa L. Perillo Michael Nute Nicolae Sapoval Kristen D. Curry Logan Golia Yongze Yin Huw A. Ogilvie Luay Nakhleh Santiago Segarra Devaki Bhaya Diana G. Cuadrado Todd J. Treangen |
| author_facet | Vanesa L. Perillo Michael Nute Nicolae Sapoval Kristen D. Curry Logan Golia Yongze Yin Huw A. Ogilvie Luay Nakhleh Santiago Segarra Devaki Bhaya Diana G. Cuadrado Todd J. Treangen |
| author_sort | Vanesa L. Perillo |
| collection | DOAJ |
| description | Abstract In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats. |
| format | Article |
| id | doaj-art-d5a8bbddf32f4a2797fc024686bed616 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-d5a8bbddf32f4a2797fc024686bed6162025-08-20T03:47:14ZengBMCGenome Biology1474-760X2025-06-0126112010.1186/s13059-025-03634-2A survey of computational approaches for characterizing microbial interactions in microbial matsVanesa L. Perillo0Michael Nute1Nicolae Sapoval2Kristen D. Curry3Logan Golia4Yongze Yin5Huw A. Ogilvie6Luay Nakhleh7Santiago Segarra8Devaki Bhaya9Diana G. Cuadrado10Todd J. Treangen11Instituto Argentino de Oceanografía (IADO-CONICET-UNS)Department of Computer Science, Rice UniversityDepartment of Computer Science, Rice UniversityDepartment of Computer Science, Rice UniversityDepartment of Computer Science, Rice UniversityDepartment of Computer Science, Rice UniversityDepartment of Computer Science, Rice UniversityDepartment of Computer Science, Rice UniversityDepartment of Electrical and Computer Engineering, Rice UniversityDepartment of Plant Biology, Carnegie Institution for ScienceInstituto Argentino de Oceanografía (IADO-CONICET-UNS)Department of Computer Science, Rice UniversityAbstract In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.https://doi.org/10.1186/s13059-025-03634-2Transdisciplinary studiesComputational modelsMicrobial matsMicrobial evolutionEnvironmental dataMicrobial ecology |
| spellingShingle | Vanesa L. Perillo Michael Nute Nicolae Sapoval Kristen D. Curry Logan Golia Yongze Yin Huw A. Ogilvie Luay Nakhleh Santiago Segarra Devaki Bhaya Diana G. Cuadrado Todd J. Treangen A survey of computational approaches for characterizing microbial interactions in microbial mats Genome Biology Transdisciplinary studies Computational models Microbial mats Microbial evolution Environmental data Microbial ecology |
| title | A survey of computational approaches for characterizing microbial interactions in microbial mats |
| title_full | A survey of computational approaches for characterizing microbial interactions in microbial mats |
| title_fullStr | A survey of computational approaches for characterizing microbial interactions in microbial mats |
| title_full_unstemmed | A survey of computational approaches for characterizing microbial interactions in microbial mats |
| title_short | A survey of computational approaches for characterizing microbial interactions in microbial mats |
| title_sort | survey of computational approaches for characterizing microbial interactions in microbial mats |
| topic | Transdisciplinary studies Computational models Microbial mats Microbial evolution Environmental data Microbial ecology |
| url | https://doi.org/10.1186/s13059-025-03634-2 |
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