Decoding the microbiome: advances in genetic manipulation for gut bacteria

As the importance of the gastrointestinal microbiome in human health and disease has been revealed via association studies, genetic manipulation tools for gut bacteria are much needed to define mechanisms and show causality.Exogenous DNA delivery and DNA manipulation using traditional strategies and novel clustered regularly interspaced short palindromic repeats (CRISPR)-Cas-based approaches have shown tractability in both model bacteria and non-model (‘wild’) bacteria.The development of genetic manipulation tools in gut bacteria is crucial to overcome barriers to ‘taming’ the microbiome, which allows us not only to understand host–microbiome interactions but also to accelerate microbiome engineering for novel therapeutics. Studies of the gut microbiota have revealed associations between specific bacterial species or community compositions with health and disease, yet the causal mechanisms underlying microbiota gene–host interactions remain poorly understood. This is partly due to limited genetic manipulation (GM) tools for gut bacteria. Here, we review current advances and challenges in the development of GM approaches, including clustered regularly interspaced short palindromic repeats (CRISPR)-Cas and transposase-based systems in either model or non-model gut bacteria. By overcoming barriers to ‘taming’ the gut microbiome, GM tools allow molecular understanding of host–microbiome associations and accelerate microbiome engineering for clinical treatment of cancer and metabolic disorders. Finally, we provide perspectives on the future development of GM for gut microbiome species, where more effort should be placed on assembling a generalized GM pipeline to accelerate the application of groundbreaking GM tools in non-model gut bacteria towards both basic understanding and clinical translation.