Core symbionts, age at inoculation, and diet affect colonization of the bumble bee gut by a common bacterial pathogen

Microbes shape the health of bumble bees, an important group of pollinators including species of conservation concern. Most microbial research on bumble bees has focused on eukaryotic and viral pathogens or the core gut microbiome, a community of host-specialized bacterial symbionts that helps protect hosts against eukaryotic pathogens.
Bumble bees also harbor a third class of microbes: non-core gut bacteria, which are non-host-specific and vary among individuals. Understanding their functional role and how they interact with core symbionts is important for bumble bee ecology and management.
We surveyed non-core bacteria in wild bumble bee workers (Bombus impatiens) and conducted lab experiments with gnotobiotic B. impatiens to examine factors shaping colonization by a focal non-core bacterium (Serratia marcescens) and its consequences for bee health.
Non-core bacteria, including Serratia, frequently occur at high abundance in wild bumble bees, with roughly half of individuals harb..., , , # Core symbionts, host age, and diet affect colonization of the bumble bee gut by a common bacterial pathogen

[https://doi.org/10.5061/dryad.qbzkh18t1](https://doi.org/10.5061/dryad.qbzkh18t1)

## Description of the data and file structure

We measured non-core bacterial prevalence in wild bumble bee workers (*Bombus impatiens*) and conducted lab experiments with gnotobiotic *B. impatiens* workers to examine factors shaping colonization by a focal non-core species (*Serratia marcescens*) and its consequences for bee health.

### Files and variables

#### File: final\_ASV\_table.txt

**Description:** The final amplicon sequence variant table obtained after filtering and removing contaminants.

##### Variables

* sample_name: The name of the sample. Field-collected bees are identified with unique IDs following the format ####_####. Bees from lab experiments are identified with unique IDs following the format MC##_B##.
* All other columns: Headings correspond to a unique identifier (combi...,