Abstract
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.
Highlights
Microbiome functions are driven by myriad abiotic and biotic forces that span multiple length scales and timescales (Figure 1)
To gain a predictive understanding of how microbial interaction networks are shaped by environmental stimuli and combine to generate community-level properties, we must consider the molecular mechanism of interactions as well as how they change as a function of time and spatial proximity
Linking microbiome composition and function is facilitated by integrating multiple meta-omics techniques, for example, concurrent shotgun metagenomics, metaproteomics, and metabolomics studies to assess which enzymes are producing an observed small molecule of interest and which microbes could produce those enzymes
Summary
Synthetic biology, genetic engineering, computational modeling, meta-omics, microbial interaction network
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