DOI: 10.5061/dryad.4qrfj6qn8
title: Metagenomes and metagenome-assembled genomes from Onthophagus taurus

description: 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.
description: Wild-caught <em>Onthophagus taurus</em> 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. <br>All MAG
 assemblies with completion above 90% (n=16) are stored on NCBI in
 BioProject PRJNA1117517 as BioSamples SAMN41896156-SAMN41896171.
description: # Metagenomes and metagenome-assembled genomes from Onthophagus taurus
 [https://doi.org/10.5061/dryad.4qrfj6qn8](https://doi.org/10.5061/dryad.4qrfj6qn8) ## Description of the data and file structure "summary_statistics.csv" contains statistics and characterizations related to the metagenomically assembled genomes from this project. Rows 1-4 are identifiers used to differentiate sample quality, NCBI sample information, and by what name they're referred to in manuscript text and figures. Rows 5-11 contain summary statistics (base-pairs, contig number, N50, L50, G-C content, Completeness, and Contamination) from Quast v4.4 and CheckM v1.0.18 Row 12 quantifies predicted protein-coding sequences from RASTtk v1.073 Rows 13-19 shows taxonomic classification across each level (Domain to Species) from GRDB-Tk v1.7.0 Rows 20-25 shows the percentage of sample sequencing reads that align to that metagenomically assembled genome using Bowtie2 v2.3.2 Rows 26-33, column 1 gives definitions of terms and programs used to gain statistics. Bacterial_Taxa.zip and Fungal_Taxa.zip contain .csv files with Kaiju outputs. Both folder has 6 .csv files with the total abundances of phyla, class, order, family, genus, and species across the 5 samples. Table: Data included in repository. Assembly files in parentheses represent samples with &gt;90% completion, located on NCBI | **Identifier** | **Assembly File (.fa)** | **RASTtk Output File (.GFF)** | | :----------------------- | :--------------------------- | :---------------------------- | | Pseudomaricurvus | (SAMN41896156) | Pseudomaricurvus.gff | | Frigididesulfovibrio | (SAMN41896157) | Frigididesulfovibrio.gff | | Proteiniphilum  | (SAMN41896158) | Proteiniphilum.gff | | Moraxellaceae | (SAMN41896159) | Moraxellaceae.gff | | Paludibacteraceae_B | (SAMN41896160) | Paludibacteraceae_B.gff | | Alphaproteobacteria | (SAMN41896161) | Alphaproteobacteria.gff | | Christensenellales_A | (SAMN41896162) | Christensenellales_A.gff | | Gemmatimonadaceae | (SAMN41896163) | Gemmatimonadaceae.gff | | Dysgonomonas | (SAMN41896164) | Dysgonomonas.gff | | Desulfovibrionaceae | (SAMN41896165) | Desulfovibrionaceae.gff | | Massilibacteroides | (SAMN41896166) | Massilibacteroides.gff | | Negativicutes | (SAMN41896167) | Negativicutes.gff | | Crocinitomicaceae | (SAMN41896168) | Crocinitomicaceae.gff | | Saccharospirillaceae | (SAMN41896169) | Saccharospirillaceae.gff | | Azobacteroidaceae | (SAMN41896170) | Azobacteroidaceae.gff | | Saezia | (SAMN41896171) | Saezia.gff | | Parachlamydiaceae | Parachlamydiaceae.fa | Parachlamydiaceae.gff | | Fluviicola | Fluviicola.fa | Fluviicola.gff | | Pseudomonas | Pseudomonas.fa | Pseudomonas.gff | | Ruminococcaceae WRAV01 | Ruminococcaceae_WRAV01.fa | Ruminococcaceae_WRAV01.gff | | Lachnospiraceae | Lachnospiraceae.fa | Lachnospiraceae.gff | | Paludibacteraceae_A | Paludibacteraceae_A.fa | Paludibacteraceae_A.gff | | Ruminococcaceae | Ruminococcaceae.fa | Ruminococcaceae.gff | | Devosiaceae | Devosiaceae.fa | Devosiaceae.gff | | Caryophanon | Caryophanon.fa | Caryophanon.gff | | Ruminococcaceae JAAYCI01 | Ruminococcaceae_JAAYCI01.fa | Ruminococcaceae_JAAYCI01.gff | | Croceibacterium | Croceibacterium.fa | Croceibacterium.gff | | Polyangiales | Polyangiales.fa | Polyangiales.gff | | Christensenellales_B | Christensenellales_B.fa | Christensenellales_B.gff | | Fimivivens | Fimivivens.fa | Fimivivens.gff | | Stenotrophomonas | Stenotrophomonas.fa | Stenotrophomonas.gff | | Saccharimonadales | Saccharimonadales.fa | Saccharimonadales.gff | **August-6th-2025:** Added Bacterial_Taxa.zip and Fungal_Taxa.zip. Which contains .csv files for access to the Kaiju output. Both folders have 6 .csv files with the total abundances of phyla, class, order, family, genus, and species across the 5 samples.