Computational protocol: High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community

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Protocol publication

[…] In a recent study, we described a defined intestinal community of 12 murine strains, termed Oligo-Mouse-Microbiota (Oligo-MM12), which permanently colonize gnotobiotic mice over several generations and provide colonization resistance against Salmonella enterica serovar Typhimurium (). This bacterial consortium has been thoroughly characterized by biochemical and molecular methods, and the individual strains have been deposited at the German Culture Collection of Microorganisms and Cell Cultures (DSMZ) (). The genomes of the 12 bacteria were previously sequenced and assembled via different techniques and algorithms (). Since the Oligo-MM12 strains are being used by an increasing number of research groups (, ), the multitude of genome sequences precludes the possibility of a meaningful exchange of data within the scientific community. Thus, there is a strong need for availability and constant update of the Oligo-MM12 reference genomes.It is well recognized that sequences from the Illumina platforms have low error rates, with systematic errors being mainly situated at the end of the reads, but are too short for an efficient complete genome assembly (). On the contrary, the long reads generated by PacBio sequencing are less accurate and contain random errors (). Aiming to create a set of reference genomes, in this study we present the high-quality genome sequences of the Oligo-MM12 bacteria, which were assembled by a hybrid approach combining Illumina and PacBio sequences ().As previously described (), the complete genome sequence of Acutalibacter muris KB18 was obtained on the PacBio RSII platform and assembled using the RS_HGAP_Assembly.3 protocol (default parameters). Error correction was then performed by mapping Illumina reads onto the finished genome with the Burrows–Wheeler Alignment tool (), with subsequent variant calling using CLC Genomics Workbench version 7.0.4. Here, Illumina MiSeq reads () of the remaining 11 bacterial genomes were assembled onto their respective PacBio complete genomes () by applying a reference-guided approach using SPAdes (), with a minimum contig length of 500 bp. Assemblies were evaluated with QUAST (Quality Assessment Tool for genome assemblies) (), and the final genomes were automatically annotated using RAST (Rapid Annotations using Subsystems Technology) (). In future studies, genetic variation, genome evolution, and functional genomics, among other research applications, of the Oligo-MM12 community can be assessed by high-quality analyses. […]

Pipeline specifications

Software tools CLC Genomics Workbench, SPAdes, QUAST, RAST
Application De novo sequencing analysis
Organisms Mus musculus