Systems-based approaches to unravel multi-species microbial community functioning

Abstract

Some of the most transformative discoveries promising to enable the resolution of this century's grand societal challenges will most likely arise from environmental science and particularly environmental microbiology and biotechnology. Understanding how microbes interact in situ, and how microbial communities respond to environmental changes remains an enormous challenge for science. Systems biology offers a powerful experimental strategy to tackle the exciting task of deciphering microbial interactions. In this framework, entire microbial communities are considered as metaorganisms and each level of biological information (DNA, RNA, proteins and metabolites) is investigated along with in situ environmental characteristics. In this way, systems biology can help unravel the interactions between the different parts of an ecosystem ultimately responsible for its emergent properties. Indeed each level of biological information provides a different level of characterisation of the microbial communities. Metagenomics, metatranscriptomics, metaproteomics, metabolomics and SIP-omics can be employed to investigate collectively microbial community structure, potential, function, activity and interactions. Omics approaches are enabled by high-throughput 21st century technologies and this review will discuss how their implementation has revolutionised our understanding of microbial communities.

Keywords: Metabolomics; Metagenomics; Metaproteomics; Metatranscriptomics; Microbial ecology; Systems biology.

Fig. 1

Systems biology. Integrated analysis of metadata with omics datasets provides access to the metabolic pathways, cellular processes and networks occurring in situ. The extensive datasets generated are then used to build models for the prediction of an ecosystem's response to environmental cues.

Fig. 2

Overview of multi-omics approach. Each level of information (DNA, RNA, proteins and metabolites) provides a different level of characterisation of the microbial community. SIP stands for stable isotope probing. SIP-omics provide insights into elemental fluxes and microbial cross-feeding.