Welcome to MICROBENCH
MICROBENCH is a longitudinal benchmarking resource for human microbiota–associated (HMA) mouse models. Germ-free mice were colonized by fecal microbiota transfer from 10 healthy human donors and profiled by long-read shotgun metagenomics across fecal and intestinal compartments over an 8-week time course. The platform provides interactive tools to explore how faithfully each donor’s gut community transfers to its recipients and how those communities stabilize over time. A central finding is that donor identity dominates recipient microbiome outcomes.
Background
- HMA rodent models are widely used to test microbiome causality, but reported phenotype-transfer rates overstate it
- Donor taxa often fail to colonize, or diverge from donor profiles, in recipients
- Transfer fidelity is rarely quantified across donors, time points, and gut compartments
Aims
- Build a longitudinal metagenomic dataset from 10 donors across fecal and intestinal compartments (Weeks 1–8)
- Quantify donor-to-recipient transfer fidelity over time and tissue
- Release an end-to-end long-read pipeline as a reference for HMA studies and FMT trial design
Materials
- Healthy donor, N=10
- Donor replicate, N=9
- Recipient mouse, N=1,210
- OMM12 control, N=12
- Neg. control, N=8
Availability
- Data: Sequence read archive (SRA) pending
- Code: Zenodo
- Method: BASEN application
- Pipeline: Long-read preprocessing
- Report: Analysis report