Dataset DOI: 10.5061/dryad.76hdr7t9b

Description of the data and file structure

We generated transductomics datasets from mouse fecal samples collected during an experiment in which 4-5 week old, male, C57BL/6J mice (n=4) were treated with antibiotics prior to challenge with C. difficile. We collected fecal pellets from the mice immediately before and after an antibiotic treatment in which cefoperazone (0.5 g/mL) was provided in the drinking water for 5 days. After 2 days of antibiotic-washout with fresh drinking water, the mice were orally gavaged with _{1.0e5 C. difficile (strain 630). On day 4 of C. difficile infection (CDI), when toxin mediated inflammation is severe, we collected a final round of fecal pellets from all 4 mice. Each sample collection consisted of two fecal pellets from each mouse replicate. The pellets were manually homogenized in 2mL of SM buffer (100mM NaCl, 8mM MgSO}4_-7H2~O, 50mM TrisHCl) using sterile inoculating loops. The DNA was extracted with the Qiagen PowerFecal Pro kit according to the manufacturer’s instructions.

Files and variables

The sample naming conventions are as follows: the first value specifies the sampling day (1=Pre-ABX, 2=Post-ABX, and 3=CDI) and the second value specifies the replicate/sample number. WC=whole-community (i.e., all the microbes in the sample). All de-replicated and quality filtered MAGs are compressed into the MAGs.zip file.

File: WC1-1_CP05702_L007_contigs.fa

Description: Pre-ABX WC replicate 1

File: WC1-2_CP05702_L007_contigs.fa

Description: Pre-ABX WC replicate 2

File: WC1-6_CP05702_L007_contigs.fa

Description: Pre-ABX WC replicate 6

File: WC1-7_CP05570_S7_L001_contigs.fa

Description: Pre-ABX WC replicate 7

File: WC2-1_CP05702_L007_contigs.fa

Description: Post-ABX WC replicate 1

File: WC2-2_CP05702_L007_contigs.fa

Description: Post-ABX WC replicate 2

File: WC2-6_CP05702_L008_contigs.fa

Description: Post-ABX WC replicate 6

File: WC2-7_CP05570_S8_L001_contigs.fa

Description: Post-ABX WC replicate 7

File: WC3-1_CP05702_L007_contigs.fa

Description: CDI WC replicate 1

File: WC3-2_CP05702_L007_contigs.fa

Description:  CDI WC replicate 2

File: WC3-6_CP05702_L007_contigs.fa

Description:  CDI WC replicate 6

File: WC3-7_CP05570_contigs.fa

Description:  CDI WC replicate 7

File: MAGs.zip

Description: All quality filtered and de-replicated WC MAGs. 

Code/software

We assembled the whole-community metagenomes using MEGAHIT with default parameters. We used differential read coverage to bin the whole-community assemblies. First, we mapped all of the trimmed and decontaminated whole-community reads from all replicates and all conditions to each of the whole-community (WC) assemblies using BBMap with default parameters. The resulting .bam files were sorted with SAMtools sort function then binned with MetaBAT2’s runMetaBat function using default parameters. We de-replicated and quality filtered bins with dRep's dereplicate function using sa=0.95, p=25 and comp=50.

Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).

Bushnell, B. BBMap: A Fast, Accuate, Splice-Aware Aligner. 9th Annual Genomics of Energy & Environmental Meeting, Walnut Creek, CA. (2014).

Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). 

Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019). 

Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017). 

Access information

Other publicly accessible locations of the data:

• The raw sequencing reads used to generate the assemblies are deposited in the sequence Read Archive (SRA) repository under BioProject PRJNA1404639