Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis
Abstract Background Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensivel...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-04-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5469-8 |
| _version_ | 1818325575606992896 |
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| author | Dongmei Ai Xiaoxin Li Hongfei Pan Jiamin Chen Jacob A. Cram Li C. Xia |
| author_facet | Dongmei Ai Xiaoxin Li Hongfei Pan Jiamin Chen Jacob A. Cram Li C. Xia |
| author_sort | Dongmei Ai |
| collection | DOAJ |
| description | Abstract Background Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities. Methods We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third “mediator” variable. These “mediator” variables appear to modulate the associations between pairs of bacteria. Results Using this analysis, we were able to assess the OTUs’ ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors. Conclusions By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa). |
| first_indexed | 2024-12-13T11:46:40Z |
| format | Article |
| id | doaj.art-a1f9481cbd624b44a8ab7e02ff8bf015 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T11:46:40Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-a1f9481cbd624b44a8ab7e02ff8bf0152022-12-21T23:47:29ZengBMCBMC Genomics1471-21642019-04-0120S211712810.1186/s12864-019-5469-8Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysisDongmei Ai0Xiaoxin Li1Hongfei Pan2Jiamin Chen3Jacob A. Cram4Li C. Xia5School of Mathematics and Physics, University of Science and Technology BeijingSchool of Mathematics and Physics, University of Science and Technology BeijingSchool of Mathematics and Physics, University of Science and Technology BeijingDepartment of Medicine, Stanford University School of MedicineCenter for Environmental Science, University of MarylandDepartment of Medicine, Stanford University School of MedicineAbstract Background Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities. Methods We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third “mediator” variable. These “mediator” variables appear to modulate the associations between pairs of bacteria. Results Using this analysis, we were able to assess the OTUs’ ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors. Conclusions By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).http://link.springer.com/article/10.1186/s12864-019-5469-8Liquid associationLocal similarity analysisMicrobial ecologyTime series dataThree-way association |
| spellingShingle | Dongmei Ai Xiaoxin Li Hongfei Pan Jiamin Chen Jacob A. Cram Li C. Xia Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis BMC Genomics Liquid association Local similarity analysis Microbial ecology Time series data Three-way association |
| title | Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis |
| title_full | Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis |
| title_fullStr | Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis |
| title_full_unstemmed | Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis |
| title_short | Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis |
| title_sort | explore mediated co varying dynamics in microbial community using integrated local similarity and liquid association analysis |
| topic | Liquid association Local similarity analysis Microbial ecology Time series data Three-way association |
| url | http://link.springer.com/article/10.1186/s12864-019-5469-8 |
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