Microbiome diversity protects against pathogens by nutrient blocking

The human gut microbiome plays an important role in resisting colonisation of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonisation of two major bacterial pathogens, both in vitro and in gnotobiotic mice. While single species alone had negligible effects, colonisation resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explain these ecological patterns via the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Further, we apply our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities., Various methods were used to collect data provided in this dataset including plate-reader based measurments of optical density or luminescence, flow cytometry, colony counting, and metagenomic sequencing. Raw data is provided in this dataset and allows re-plotting of figures in the manuscript., , # Microbiome diversity protects against pathogens by nutrient blocking

[https://doi.org/10.5061/dryad.pnvx0k6v8](https://doi.org/10.5061/dryad.pnvx0k6v8)

Give a brief summary of dataset contents, contextualized in experimental procedures and results.

## Description of the data and file structure

These files provide the necessary data to recreate the figures in the associated manuscript, and also provides additional raw data.

**LEAD CONTACT**: Prof. Kevin R Foster. Departments of Biology and Biochemistry, University of Oxford, Oxford, United Kingdom, [e-mail]

**DATE AND LOCATION OF DATA COLLECTION**: 01/2020 - 04/2023, University of Oxford, United Kingdom

**BACKGROUND FOR DATA**: The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonization of two major bacterial pathogens, both in vitro and in...