Shotgun metagenomic sequencing was carried out on Onthophagus taurus larval gut sections, female adult midgut, and pedestal (a maternally-provisioned fecal pellet provided to offspring). Here we present the fasta sequences of 16 metagenomically assembled genomes, which fell below the NCBI completion threshold, as well as the 32 GFF protein predictions and annotations, resulting from RASTtk analysis of all 32 genomes assembled in the study, and .csv files containing the abundance of bacteria and fungal taxa across samples, from Kaiju.

Wild-caught Onthophagus taurus were collected and maintained in the lab. Pedestals (n=17), from the brood balls these individuals produced, were collected, pooled, and DNA was extracted using a Qiagen DNeasy PowerSoil Pro Kit. Larval gut sections (fore-, mid-, and hindgut; n=5), and adult female midguts (n=4), dissected from F1 offspring, were processed to enrich for bacteria before a modified phenol-chloroform extracted was used to extract DNA. The NEBNext Ultra II Kit protocol was used to size select FNA fragments, using Serapure beads, and to generate libraries. DNA was sequenced on the NextSeq500 sequencer using 300 PE cycles. 

Sequences were quality controlled with Trimomatic v0.36 to remove adapter sequences and low quality reads. Assembly was carried out on KBase, where sequences were assembled with metaSPAdes v1.3.4 and binned into metagenomically assembled genomes using CONCOCT v1.3.4, MaxBins2 v1.1.1, and MetaBAT2 v2.3.0 with bin optimization with DAS Tool v1.1.2. Finally, RASTtk v1.073 was used for protein prediction and annotation. 

Assembles with below 90% completion, and all RASTtk output files are stored here. 
All MAG assemblies with completion above 90% (n=16) are stored on NCBI in BioProject PRJNA1117517 as BioSamples SAMN41896156-SAMN41896171.