In vivo augmentation of a complex gut bacterial community

Abstract

Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex but not both, limiting their utility. In accompanying work, we constructed a complex synthetic community (104 strains, hCom1) containing the most common taxa in the human gut microbiome. Here, we used an iterative experimental process to improve hCom1 by filling open metabolic and/or anatomical niches. When we colonized germ-free mice with hCom1 and then challenged it with a human fecal sample, the consortium exhibited surprising stability; 89% of the cells and 58% of the taxa derive from the original community, and the pre- and post-challenge communities share a similar overall structure. We used these data to construct a second version of the community, adding 22 strains that engrafted following fecal challenge and omitting 7 that dropped out (119 strains, hCom2). In gnotobiotic mice, hCom2 exhibited increased stability to fecal challenge and robust colonization resistance against pathogenic Escherichia coli. Mice colonized by hCom2 versus human feces are similar in terms of microbiota-derived metabolites, immune cell profile, and bacterial density in the gut, suggesting that this consortium is a prototype of a model system for the human gut microbiome.

Resource competition predicts assembly of in vitro gut bacterial communities

“…For the same model community studied here (Aranda-Díaz et al ., 2022), the effects of the addition of simple carbon sources on community dynamics could be quantitatively explained by the monoculture growth behaviors of isolates on those carbon sources, implying that competition for resources again drove community dynamics. When a separate synthetic community of >100 gut commensals colonizing germ-free mice was challenged by a human fecal sample via gavage, the relative abundances of species that persisted post-challenge were highly correlated with their pre-challenge values (Cheng et al, 2021). This observation mirrors the tight distribution of z -scores in dropout assemblies and the compositional similarity of refilled communities, which together show that the removal or addition of a species typically did not affect community composition.…”

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

“…Next steps include further technical developments (both wet lab and in silico ) 24,58 to enhance the throughput and optimize the in-to-output ratio of cultivation approaches, especially regarding rapid and precise identification of isolates. Large-scale cultivation studies 5 still report a low depth of cultivation per individual sample, and yet-unpublished work on the development of high-complexity SYNs 59 is based on isolates of various origins. Further efforts are thus required to reach the goal of personalized microbiome-based research and applications using isolates.…”

Mapping the T cell repertoire to a complex gut bacterial community

“…hCom1d and hCom2d were prepared from individual strain stocks as described previously 26 . For germ-free mouse experiments, strains were revived from frozen stocks and cultured for 48 h anaerobically in an atmosphere consisting of 10% CO2, 5% H2, and 85% N2.…”

“…For germ-free mouse experiments, strains were revived from frozen stocks and cultured for 48 h anaerobically in an atmosphere consisting of 10% CO2, 5% H2, and 85% N2. Strains were propagated in sterile 2.2-mL 96-well deep well plates in their respective growth medium ( Supplementary Table 1 ): Mega Medium 26 supplemented with 400 μM vitamin K2,or Chopped Meat Medium supplemented with Mega Medium carbohydrate mix 26 and 400 μM vitamin K2. The optical density at 600 nm (OD600) of each revived strain was measured.…”

“…Metagenomic sequencing and sequence analysis were performed as described previously 26 . In brief, fecal pellets were collected from mice into sterile tubes.…”