DOI: 10.5061/dryad.x0k6djhq5
title: Metagenome assembled genomes from mouse gut microbiota

description: The source of protein in a person's diet affects their total life
 expectancy. However, the mechanisms by which dietary protein sources
 differentially impact human health and life expectancy are poorly
 understood. Dietary choices impact the composition and function of the
 intestinal microbiota that ultimately modulate host health. This raises
 the possibility that health outcomes based on dietary protein sources
 might be driven by interactions between dietary protein and the gut
 microbiota. In this study, we determined the effects of seven different
 sources of dietary protein on the gut microbiota of male and female mice
 (C57BL/6J) using an integrated metagenomics-metaproteomics approach. In
 order of feeding, the diets were 20% soy protein, 20% casein protein, 20%
 brown rice protein, 40% soy protein, 20% yeast protein, 40% casein
 protein, 20% pea protein, 20% egg white protein, and 20% chicken bone
 protein. We fed a total of 10-12 mice each diet for one week and then
 collected a fecal sample at the end of the week before proceeding to the
 next diet. We then analyzed the fecal samples using an integrated
 metagenomics-metaproteomics approach that included generating a
 genome-resolved metagenome with metagenome assembled genomes (MAGs). This
 data set represents all the MAGs generated in this study. To generate the
 MAGs, we pooled DNA extracted from feces taken from each mouse cage (four
 cages in total) across four different diets (20% rice, 40% soy, 20% yeast,
 40% casein). We sent the DNA to be sequenced at the NCSU GSL and generated
 between 51,152,549 and 74,618,259 paired-end reads (150bp x 2) per sample
 using a NovaSeq 6000 Sequencing System, Illumina. We analyzed these reads
 using a genome-resolved metagenomic pipeline, which included read QC,
 assembly using metaSPAdes and MEGAHIT, binning using MetaBAT 2, and bin
 quality checking using CheckM. This data set includes the metagenomic
 assemblies for each cage, a co-assembly, and 454 MAGs with a completion
 score of &gt;30% and a contamination scores of &lt;10% if the
 completion score was 50% and &lt;5% if the completion score was
 between 30-50%. We also include a re-assembled Bacteroides
 thetaiotaomicron genome along with its associated reads and checkM scores
 and a BinGroupingTableWithGTDB.txt file that includes the bin identifiers,
 the species cluster group at 95% ANI, CheckM scores, and GTDB taxonomy
 information. This data set represents a group of MAGs that could be used
 along with other metagenomic measurements as part of a catalog of the
 C57BL/6J mouse microbiota.
description: We fed conventional C57BL/6J mice a series of defined diets where
 the source of dietary protein was the only difference, which made up
 twenty or forty percent of the diet. The dietary protein sources used were
 purified protein. The diets were fed to 12 mice across four cages for one
 week each. A fecal sample was collected at the end of each week. The diets
 were fed in this order: standard chow, 20% soy, 20% casein, 20% rice, 40%
 soy, 20% yeast, 40% casein, 20% pea, 20% egg white protein, 20% chicken
 bone broth, and lastly at the end of the experiment half of the mice were
 fed the 20% soy and half the mice the 20% casein diet again as a control.
 We pooled samples by cage from the 20% rice diet, 40% soy diet, 20% yeast
 diet, and 40% casein diet to generate four metagenomes, one for each cage.
 DNA was extracted with the QIAamp DNA stool mini kit (Qiagen) and
 sequenced the DNA on an Illumina NovaSeq 6000 sequencer.
 We assembled raw reads using a genome-resolved metagenomics
 approach. We removed PhiX74 (NCBI GenBank accession CP004084.1) and mouse
 genome (mm10) contaminating sequences using BBSplit and removed adapters
 using BBDuk (BBMap, Version 38.06), parameters: mink = 6, minlength =20
 (Bushnell,
 2014). We assembled decontaminated reads individually using
 MetaSPAdes (v3.12.0) -k 33,55,99 (Nurk et
 al., 2017) and co-assembled them using MEGAHIT (v1.2.4) –kmin 31
 –k-step 10 (D. Li et
 al., 2015). We mapped reads from all four samples to all five
 assemblies using bbmap, and binned the contigs using MetaBAT (v2.12.1)
 (Kang
 et al., 2019). We assessed the quality of the bins using CheckM
 (v1.1.3) (Parks et
 al., 2015) and automatically accepted medium quality bins with a
 completion score greater than 50% and less than 10% (Bowers et
 al., 2017). Since the purpose of this was to assign proteins to
 species, we further accepted bins that were greater than &gt;30%
 complete and &lt;5% contaminated. We clustered the bins into species
 groups by 95% ANI using dRep (v2.6.2) (Olm et
 al., 2017, 2020) and assigned taxonomy using GTDB-Tk (v1.3.0,
 ref r95) (Chaumeil
 et al., 2020). We reassembled the Bacteroides
 thetaiotaomicron genome by mapping the reads from one of our metagenomic
 samples to all the contigs that we identified as belonging to B. theta
 using BBSplit (BBMap, Version 38.06). We then assembled reads that mapped
 to B. theta using metaSPAdes to assemble a new genome.
description: # Metagenome assembled genomes from mouse gut microbiota
 [https://doi.org/10.5061/dryad.x0k6djhq5](https://doi.org/10.5061/dryad.x0k6djhq5) Here we provide assemblies and MAGs assembled from four metagenome samples sequenced from pooled DNA. DNA was extracted from mice across four cages that were fed different sources of dietary protein. ## Description of the data and file structure This data set includes four single-sample assemblies and one co-assembly, and 454 metagenome assembled genomes with a CheckM completion score of &gt;30% and a contamination score of &lt;10%.  The table “BinGroupingTableWithGTDB.txt” provided with this submission contains the file names for the bins, their species group cluster based on 95% ANI, their CheckM scores, and their GTDB taxonomic assignment. We also included data for a re-assembly of *Bacteroides thetaiotaomicron*. This includes the assembly, the reads that mapped to *Bacteroides thetaiotaomicron* used to assemble the genome, and then a table called CheckMResultOfSPADESAssembly.txt that analyzed the outputs from SPAdes. The completion contamination scores for the re-assembly are 98.28% completion and 0.76%.  ## Sharing/Access information These metagenomes were used as part of a database used to search metaproteomes, which have been deposited to the ProteomeXchange Consortium via the PRIDE [(Perez-Riverol et al., 2022)](https://www.zotero.org/google-docs/?6OGT01) partner repository with the dataset identifier PXD041586. The raw reads used to build these MAGs were deposited to SRA as part of the bioproject PRJNA1026909.