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.

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

“…It is well known that the performance of a microbe during fermentation can be understood by its gene expression. Metatranscriptomic approaches (the use of messenger and non-coding RNAs) provide important insights into regulatory networks and gene expression during the sampling stage, and in combination with the metaproteome and metabolome, the metatranscriptome provides information concerning the activities and functions of microbial communities (Abram, 2015). Using metatranscriptomic analysis, the global gene expression of microbes during the fermentation process can be determined, which helps to understand the key metabolic activities of microbes and to assess the safety of the process.…”

Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology

“…GEMs provide a mechanistic framework for integrating data from multi-omics studies, providing the structure onto which proteomic and transcriptomic data can be mapped—the so-called “context for content” [36]. Essentially, they can be used to unify genomic, transcriptomic, proteomic, metabolomic, and biochemical kinetic information relevant to metabolic models [37–40]. (See, for example, the recent study by Noecker et al [41], which combined taxonomic, genomic, and metabolic data to determine whether shifts in the vaginal microbiome explain shifts in the vaginal metabolome.)…”

Foodomics in microbiological investigations

“…In recent years, systems biology offers a powerful experimental strategy to tackle the exciting task of deciphering structure and function of microbial communities [4 ]. The emerged foodomic approaches have been used to study the food domains through the application of advanced omics technologies to improve consumer's well-being, health, and confidence [5].…”