**Background:** The human gut microbiota is a highly complex ecosystem whose imbalance has been linked to various diseases. Establishing causality and mechanistic understanding is extremely challenging due to this inherent complexity. Synthetic microbial communities (SynComs)—consortia of two or more known microbial species under defined conditions—offer a reductionist approach to study functional, ecological, and structural concepts of native microbiota while maintaining key features of natural communities. This review systematically discusses strategies to design, assemble, and test SynComs of the human gut, along with the microbiological, engineering, and translational challenges that remain.
**Methods:** The authors review published SynCom studies from 2008 to 2021, categorizing design strategies into top-down (abundance-based) and bottom-up (function-oriented) approaches. Top-down design identifies the most abundant bacteria from sequencing data and assembles a subset capturing native diversity. Bottom-up design focuses on assessing individual species' functions and assembling species to achieve specific emergent behaviors, such as anti-inflammatory properties. The review covers testing systems including germ-free rodents, bioreactors, microplate cultures, and emerging tools such as computational modeling and gut microphysiological systems (organ-on-a-chip).
**Key Results:** The review catalogs 34 reported SynComs ranging from 2 to 104 species, spanning 2–5 phyla (primarily Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia). Firmicutes and Bacteroidetes represent approximately 90% of microbial sequences in the human gut. The SIHUMI consortium (7–8 species) stably colonized germ-free rats and was successfully transferred from mother to offspring, though short-chain fatty acid production was substantially lower than in human feces; introducing butyrate producers increased butyrate production by 56% but did not reach human fecal levels. Atarashi et al. (2013) iteratively reduced a 23-strain consortium to 17 Clostridia strains that induced Treg cell differentiation in mice; neither monoculture nor random subsets had comparable effects, indicating emergent community behavior. The 17-strain SynCom attenuated colon shortening, reduced histological disease features, and lowered mortality in a TNBS-induced colitis mouse model. Cheng et al. (2021) constructed a 104-species SynCom using only two media and a new algorithm (NinjaMap) for strain quantification, showing remarkable reproducibility. Perez et al. (2021) assembled MCC100 (100 species) and found it increased alpha diversity in elderly fecal microbiota in bioreactors, though it also increased opportunistic pathogens from Escherichia and Shigella genera. The RePOOPulate consortium (33 species) induced CDI symptom remission in two patients lasting 24–26 weeks post-treatment, with reduced C. difficile toxin production confirmed in one patient. GUT-103 (17 members) and GUT-108 (11 members) were designed to integrate multiple functions including short-chain fatty acid production, tryptophan metabolite synthesis, secondary bile acid synthesis, and antimicrobial release. Computational modeling efforts using generalized Lotka–Volterra models showed good agreement with experimental validations for 12-species consortia, though predicting tri-culture dynamics from monoculture data alone remained challenging.
**Clinical Implications:** SynComs represent a promising alternative to fecal microbiota transplant (FMT) for treating dysbiosis and gastrointestinal disorders, offering a defined, safer, and more reproducible therapeutic approach. The first human trials with RePOOPulate demonstrated feasibility of SynComs for CDI treatment, though larger clinical trials are needed. SynComs may reduce the global need for antibiotics by increasing microbiome resilience to pathogens. Key challenges include: ensuring stable engraftment (recipient factors and donor–recipient complementarity are critical determinants); achieving native-like functional output (e.g., butyrate production); expanding culturomics beyond Western-lifestyle individuals; deploying validated predictive models to shorten design phases; and developing advanced in-vitro models (gut-on-a-chip, organoids) to reduce reliance on animal testing, facilitated by the US FDA Modernization Act of 2021. Future research should also address multikingdom SynComs including fungi, viruses, and archaea.