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Comment
. 2025 Apr 15;122(15):e2502663122.
doi: 10.1073/pnas.2502663122. Epub 2025 Apr 7.

Mixing microbiomes in vitro reveals rules of community assembly

Alyssa H Mitchell  1   2 , Tami D Lieberman  1   2
Affiliations
Comment

Mixing microbiomes in vitro reveals rules of community assembly

Alyssa H Mitchell et al. Proc Natl Acad Sci U S A. .
No abstract available

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Conflict of interest statement

Competing interests statement:The authors declare no competing interest.

Figures

Fig. 1.
Fig. 1.
The high number of species in complex microbiomes decreases the availability of private resources and increases the likelihood of dose-dependent dynamics. (A) To systematically study the role of dose-dependent invasion into complex microbiome communities, Goldman et al. (10) mixed stable human stool-derived in vitro communities across ratios spanning six orders of magnitude. Similar follow-up experiments were performed with individual species. (B) 16S rRNA sequencing was performed to track relative abundances of individual sequence variants (ASVs, roughly corresponding to species) in these mixed communities. Many ASVs were not unique to a sample and thus could not be tracked across mixtures (not shown). The remaining ASVs could be categorized as noisy, dose-independent, or dose-dependent. Cartoon examples shown with the percent of all ASVs assigned to each category. (C) A two-species consumer–resource model revealed that competition for shared resources can drive dose dependence. This is further explored in experiments. (D) Gradually increasing complexity in both models and experiments, the authors demonstrated that increasing the number of species in a community directly enhances colonizer dose dependence by limiting available exclusive (unshared) resources.
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