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Article: An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community

TitleAn integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community
Authors
KeywordsIntegrated meta-omics
Bisphenol A
Bacterial interactions
Biodegradation
Issue Date2019
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.microbiomejournal.com/
Citation
Microbiome, 2019, v. 7 n. 1, p. article no. 16 How to Cite?
AbstractBackground: Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community—bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses. Results: The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone. Conclusion: The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.
Persistent Identifierhttp://hdl.handle.net/10722/293309
ISSN
2019 Impact Factor: 11.607
2015 SCImago Journal Rankings: 5.701
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYu, K-
dc.contributor.authorYi, S-
dc.contributor.authorLi, B-
dc.contributor.authorGuo, F-
dc.contributor.authorPeng, X-
dc.contributor.authorWang, Z-
dc.contributor.authorWu, Y-
dc.contributor.authorAlvarez-Cohen, L-
dc.contributor.authorZhang, T-
dc.date.accessioned2020-11-23T08:14:54Z-
dc.date.available2020-11-23T08:14:54Z-
dc.date.issued2019-
dc.identifier.citationMicrobiome, 2019, v. 7 n. 1, p. article no. 16-
dc.identifier.issn2049-2618-
dc.identifier.urihttp://hdl.handle.net/10722/293309-
dc.description.abstractBackground: Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communities is a challenging task. Here, we demonstrate an integrated approach of metagenomics, metatranscriptomics, and targeted metabolite analysis to identify the substrates involved in interspecies interactions from a potential cross-feeding model community—bisphenol A (BPA)-biodegrading community, aiming to establish an identification method of microbial interactions in engineering or environmental bioprocesses. Results: The community-level BPA-metabolic pathway was constructed using integrated metagenomics and targeted metabolite analyses. The dynamics of active functions and metabolism of major community members were identified using metagenomic and metatranscriptomic analyses in concert. Correlating the community BPA biodegradation performance to the individual bacterial activities enabled the discovery of substrates involved in a synergistic interaction of cross-feeding between BPA-degrading Sphingonomas species and intermediate users, Pseudomonas sp. and Pusillimonas sp. This proposed synergistic interaction was confirmed by the co-culture of a Sphingonomas sp. and Pseudomonas sp. isolates, which demonstrated enhanced BPA biodegradation compared to the isolate of Sphingonomas sp. alone. Conclusion: The three types of integrated meta-omics analyses effectively revealed the metabolic capability at both community-wide and individual bacterial levels. The correlation between these two levels revealed the hidden connection between apparent overall community performance and the contributions of individual community members and their interactions in a BPA-degrading microbial community. In addition, we demonstrated that using integrated multi-omics in conjunction with culture-based confirmation approach is effective to elucidate the microbial interactions affecting the performance outcome. We foresee this approach would contribute the future application and operation of environmental bioprocesses on a knowledge-based control.-
dc.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.microbiomejournal.com/-
dc.relation.ispartofMicrobiome-
dc.rightsMicrobiome. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectIntegrated meta-omics-
dc.subjectBisphenol A-
dc.subjectBacterial interactions-
dc.subjectBiodegradation-
dc.titleAn integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community-
dc.typeArticle-
dc.identifier.emailZhang, T: zhangt@hkucc.hku.hk-
dc.identifier.authorityZhang, T=rp00211-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s40168-019-0634-5-
dc.identifier.pmid30728080-
dc.identifier.pmcidPMC6366072-
dc.identifier.hkuros319436-
dc.identifier.volume7-
dc.identifier.issue1-
dc.identifier.spagearticle no. 16-
dc.identifier.epagearticle no. 16-
dc.identifier.isiWOS:000458517300001-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl2049-2618-

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