Identification of multidimensional Boolean patterns in microbial communities
Abstract Background Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an essential function affecting multiple other community members through se...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-09-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40168-020-00853-6 |
| _version_ | 1828917994943676416 |
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| author | George Golovko Khanipov Kamil Levent Albayrak Anna M. Nia Renato Salomon Arroyo Duarte Sergei Chumakov Yuriy Fofanov |
| author_facet | George Golovko Khanipov Kamil Levent Albayrak Anna M. Nia Renato Salomon Arroyo Duarte Sergei Chumakov Yuriy Fofanov |
| author_sort | George Golovko |
| collection | DOAJ |
| description | Abstract Background Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an essential function affecting multiple other community members through secondary metabolism. Since microbial community members are often simultaneously involved in multiple relations, not all interaction patterns for such microorganisms are expected to exhibit a visually uninterrupted pattern. As a result, such relations cannot be detected using traditional correlation, mutual information, principal coordinate analysis, or covariation-based network inference approaches. Results We present a novel pattern-specific method to quantify the strength and estimate the statistical significance of two-dimensional co-presence, co-exclusion, and one-way relation patterns between abundance profiles of two organisms as well as extend this approach to allow search and visualize three-, four-, and higher dimensional patterns. The proposed approach has been tested using 2380 microbiome samples from the Human Microbiome Project resulting in body site-specific networks of statistically significant 2D patterns as well as revealed the presence of 3D patterns in the Human Microbiome Project data. Conclusions The presented study suggested that search for Boolean patterns in the microbial abundance data needs to be pattern specific. The reported presence of multidimensional patterns (which cannot be reduced to a combination of two-dimensional patterns) suggests that multidimensional (multi-organism) relations may play important roles in the organization of microbial communities, and their detection (and appropriate visualization) may lead to a deeper understanding of the organization and dynamics of microbial communities. Video Abstract |
| first_indexed | 2024-12-13T21:01:35Z |
| format | Article |
| id | doaj.art-81797e0b3c704f6491e278184e388ae5 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-13T21:01:35Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-81797e0b3c704f6491e278184e388ae52022-12-21T23:31:35ZengBMCMicrobiome2049-26182020-09-018111010.1186/s40168-020-00853-6Identification of multidimensional Boolean patterns in microbial communitiesGeorge Golovko0Khanipov Kamil1Levent Albayrak2Anna M. Nia3Renato Salomon Arroyo Duarte4Sergei Chumakov5Yuriy Fofanov6Department of Pharmacology and Toxicology, University of Texas Medical Branch–GalvestonDepartment of Pharmacology and Toxicology, University of Texas Medical Branch–GalvestonDepartment of Pharmacology and Toxicology, University of Texas Medical Branch–GalvestonDepartment of Molecular Biophysics, University of Texas Medical Branch–GalvestonDepartment of Physics, University of GuadalajaraDepartment of Physics, University of GuadalajaraDepartment of Pharmacology and Toxicology, University of Texas Medical Branch–GalvestonAbstract Background Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an essential function affecting multiple other community members through secondary metabolism. Since microbial community members are often simultaneously involved in multiple relations, not all interaction patterns for such microorganisms are expected to exhibit a visually uninterrupted pattern. As a result, such relations cannot be detected using traditional correlation, mutual information, principal coordinate analysis, or covariation-based network inference approaches. Results We present a novel pattern-specific method to quantify the strength and estimate the statistical significance of two-dimensional co-presence, co-exclusion, and one-way relation patterns between abundance profiles of two organisms as well as extend this approach to allow search and visualize three-, four-, and higher dimensional patterns. The proposed approach has been tested using 2380 microbiome samples from the Human Microbiome Project resulting in body site-specific networks of statistically significant 2D patterns as well as revealed the presence of 3D patterns in the Human Microbiome Project data. Conclusions The presented study suggested that search for Boolean patterns in the microbial abundance data needs to be pattern specific. The reported presence of multidimensional patterns (which cannot be reduced to a combination of two-dimensional patterns) suggests that multidimensional (multi-organism) relations may play important roles in the organization of microbial communities, and their detection (and appropriate visualization) may lead to a deeper understanding of the organization and dynamics of microbial communities. Video Abstracthttp://link.springer.com/article/10.1186/s40168-020-00853-6MicrobiomeMultidimensional Boolean patternsMicrobial communitiesCo-exclusionCo-presencePattern-specific score |
| spellingShingle | George Golovko Khanipov Kamil Levent Albayrak Anna M. Nia Renato Salomon Arroyo Duarte Sergei Chumakov Yuriy Fofanov Identification of multidimensional Boolean patterns in microbial communities Microbiome Microbiome Multidimensional Boolean patterns Microbial communities Co-exclusion Co-presence Pattern-specific score |
| title | Identification of multidimensional Boolean patterns in microbial communities |
| title_full | Identification of multidimensional Boolean patterns in microbial communities |
| title_fullStr | Identification of multidimensional Boolean patterns in microbial communities |
| title_full_unstemmed | Identification of multidimensional Boolean patterns in microbial communities |
| title_short | Identification of multidimensional Boolean patterns in microbial communities |
| title_sort | identification of multidimensional boolean patterns in microbial communities |
| topic | Microbiome Multidimensional Boolean patterns Microbial communities Co-exclusion Co-presence Pattern-specific score |
| url | http://link.springer.com/article/10.1186/s40168-020-00853-6 |
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