Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications

Abstract

The human gut harbors native microbial communities, forming a highly complex ecosystem. Synthetic microbial communities (SynComs) of the human gut are an assembly of microorganisms isolated from human mucosa or fecal samples. In recent decades, the ever-expanding culturing capacity and affordable sequencing, together with advanced computational modeling, started a ''golden age'' for harnessing the beneficial potential of SynComs to fight gastrointestinal disorders, such as infections and chronic inflammatory bowel diseases. As simplified and completely defined microbiota, SynComs offer a promising reductionist approach to understanding the multispecies and multikingdom interactions in the microbe-host-immune axis. However, there are still many challenges to overcome before we can precisely construct SynComs of designed function and efficacy that allow the translation of scientific findings to patients' treatments. Here, we discussed the strategies used to design, assemble, and test a SynCom, and address the significant challenges, which are of microbiological, engineering, and translational nature, that stand in the way of using SynComs as live bacterial therapeutics.

Keywords: human gut microbiome; live bacterial therapeutic; rational design; synthetic microbial consortium.

Figure 1.

The known beneficial effects of the gut microbiota on crucial functions in human health. Circles represent the main functional categories as identified in this review. Arrows with dashed lines indicate a relationship between functions of interest. Functions can have overlapping categories if they are defined in multiple categories.

Figure 2.

Overview on the strategies for designing, assembling, and testing SynComs. (A) The top-down approach starts at the inoculum and microbial composition profiling, followed by the selection and iteration cycle in which bacteria are added to an animal model, isolated, and subsequently sequenced for a further iteration cycle or ultimately the description of an adapted SynCom (Atarashi et al. 2013). (B) The bottom-up approach uses existing knowledge on the metagenome, abundances, and growth parameters of candidate microorganisms. Furthermore, when the SynCom is required to have a specific function, the candidate microorganisms can be adjusted accordingly (van der Lelie et al. 2021). The designed SynCom then enters iteration cycles in the in-vitro setting, being cultured in batches and sequenced to understand the composition. Lastly, the SynCom is tested in an in-vivo setting, being introduced to a murine model. The SynCom is then extracted from the model and sequenced after an incubation or experimental period. The functional profile is also checked to ensure the SynCom performed as expected. From there, feedback from the results can be used to start the iteration cycles again.

Figure 3.

Design flowchart for the creation of SynComs. Blocks indicate steps to create a SynCom. Arrows indicate relationships, dashed arrow indicates a shortcut. Starting at the design phase, there are many factors that change the initial composition of a SynCom, most notably being the aim of the research that the SynCom will be used for, the design strategy used, and the observational data used. From there, an in-silico approach can help to predict the behavior of the SynCom and design the species and conditions, but could be skipped. Then, in-vitro testing commences, culturing the microorganisms and preparing them for the final step. In this final step, the SynCom is added to a test environment, which range from bioreactors to murine models and everything in between. The results from these experiments can next be fed back into the starting block, using prior knowledge for the initial design of a new SynCom.