Figure 1: High-throughput cultivation of feces from humanized mice yields stable, complex, and reproducible microbial communities.

A) Experimental setup. germ-free mice were colonized with feces from a single human donor (“humanized”). Fecal samples from humanized mice were inoculated into anaerobic batch culture and passaged with dilution every 48 h to derive SICs.

B) In vitro passaging produces stable and complex SICs. Family-level compositions of a representative SIC derived from the feces of MD mouse 1 during 16 rounds of in vitro passaging in BHI.

C) In vitro passaging can produce an SIC that resembles the fecal inoculum. Family-level relative abundances (mean of passages 4–16) for the SIC in (B) compared with the fecal inoculum from which it originated.

D) In vitro-passaged SICs are highly reproducible. ASV-level relative abundances for two technical replicates of the SIC in (B) after 7 passages. R and p were computed using only ASVs present in both samples.

Relative abundances <10⁻⁴ in (C,D) were set to 10⁻⁴ for visualization.