Systems biology approach to elucidation of contaminants biodegradation in complex samples- integration of high-resolution analytical and molecular tools

Gauchotte-Lindsay, C. , Aspray, T. J., Knapp, M. and Ijaz, U. Z. (2019) Systems biology approach to elucidation of contaminants biodegradation in complex samples- integration of high-resolution analytical and molecular tools. Faraday Discussions, 218, pp. 481-504. (doi: 10.1039/C9FD00020H) (PMID:31140531)

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We present here a data-driven systems biology framework to the rational design of biotechnological solutions for contaminated environments with the aim of understanding the interactions and mechanisms underpinning the role of microbial communities in the biodegradation of contaminated soils. We have considered a multi-omics approach which employs novel in silico tools to combine high-throughput sequencing data (16S rRNA amplicons) with the chemical data including high-resolution analytical data generated by comprehensive two-dimensional gas chromatography (GCxGC). To assess this approach, we have considered a matching dataset with both microbiological and chemical signatures available for samples from two former manufactured gas plant sites. On this dataset, we applied the numerical procedures informed by ecological principles (predominantly diversity measures) as well as recently published statistical approaches that give discriminatory features and their correlations by maximizing the covariances between multiple datasets on the same sample space. In particular, we have utilized sparse projection to latent discriminant analysis and its derivative to multiple datasets, an N-integration algorithm called DIABLO. Our results indicate microbial community structure dependent on the contaminated environment and unravel promising interactions of some of the microbial species with the biodegradation potential. To the best of our knowledge, this is the first study that incorporates with microbiome an unprecedented high-level distribution of hydrocarbons obtained through GC x GC.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Gauchotte-Lindsay, Professor Caroline and Ijaz, Dr Umer
Authors: Gauchotte-Lindsay, C., Aspray, T. J., Knapp, M., and Ijaz, U. Z.
College/School:College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:Faraday Discussions
Publisher:Royal Society of Chemistry
ISSN (Online):1364-5498
Published Online:29 March 2019
Copyright Holders:Copyright © 2019 The Authors
First Published:First published in Faraday Discussions 218:481-504
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
652772Understanding microbial community through in situ environmental 'omic data synthesisUmer Zeeshan IjazNatural Environment Research Council (NERC)NE/L011956/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR
621352Synthetic Biology applications to Water Supply and RemediationSteven BeaumontEngineering and Physical Sciences Research Council (EPSRC)EP/K038885/1VPO VICE PRINCIPAL RESEARCH & ENTERPRISE