Simple animal models are emerging as valuable tools for microbiome research. In this Review, Douglas discusses the opportunity for microbiome research on the traditional biomedical models Drosophila melanogaster, Caenorhabditis elegans and zebrafish. Other systems, for example, hydra, squid and the honeybee, are valuable alternative models to address specific questions.
Microbiome tractability and translation
The microbiome is diverse, not only in its microbial members but also in its functions, and it has important roles in human health and disease and in ecosystem functioning. Yet, translating knowledge of the microbiome and its associations with the state of the host into applications and therapies has been challenging. In large part, successful translation relies on tractable methods and systems that enable systematic and controlled testing of hypotheses and interventions. Therefore, in this Focus issue Nature Reviews Microbiology explores strategies, tools and approaches that make microbiome research more tractable and that will pave the way towards successful translation of microbiota-based therapeutics and applications.
This Nature Reviews Microbiology Focus is editorially independent, produced with financial support from the Kellogg Company, a third party.
Microbiome engineering has many potential applications, ranging from agriculture to medicine. In this Review, Lawson, McMahon and colleagues guide us through the design–build–test–learn cycle that has been successful in many disciplines and explain how it applies to microbiome engineering.
In this Review, Kolodziejczyk, Zheng and Elinav describe the latest advances in understanding diet–microbiota interactions, the individuality of gut microbiota composition and how this knowledge could be harnessed for personalized nutrition strategies to improve human health.
Going from description of the diversity and disease associations of the human gut microbiota towards functional understanding and applications is challenging. In this Review, Raes and colleagues present synthetic ecology approaches that reduce the complexity and advance translation of human gut microbiota research.
News & Comment
Microbiome research has attracted considerable attention, partially because of the potential to manipulate the microbiome for human health. To fulfil this promise, tractable methods and cautious interpretation of results are needed.
Faecal microbiota transplant (FMT) is now accepted as an effective treatment for Clostridioides difficile infections. With the increasing number of FMT treatments and clinical trials for other indications there is an urgent need for standardized regulations to ensure patient safety and focused development of safer, rationally designed, microbiota-based medicines.
Three recent studies highlight how the gut microbiome responds to dietary change, with potential consequences for host–microbiota interactions.
A study reports the generation of synthetic ‘phagebodies’ with a broadened host range that were able to target naturally occurring phage-resistant bacterial mutants.
This study reports the feasibility of vaginal microbiome transplantation from healthy donors as treatment for patients suffering from symptomatic, intractable and recurrent bacterial vaginosis.
This study shows that sublethal doses of ciprofloxacin enhanced aggregation of bacterial cells, which resulted in their increased expulsion from the gut by the mechanical activity of the intestine.
This study explores the response of the gut microbiota to dietary fibres and presents new biosensors that can measure microbial fibre use in vivo.
This study links a histone deacetylase and the gut microbiota to the circadian regulation of host metabolism.
This study finds that gut segmented filamentous bacteria prevent and cure rotavirus infection in immunodeficient mice.
A recent study finds that probiotic yeasts can inhibit virulence of several non-albicans Candida species, including mutidrug-resistant Candida auris.
This study observed that the functional diversity of core and accessory genes in the soil microbiome are governed by distinct processes.
This month’s Under the Lens explores how recent developments in sample preparation are aiding and advancing the imaging of host–microorganism interactions.