Draft Genome Sequences of the Altered Schaedler Flora, a Defined Bacterial Community from Gnotobiotic Mice

The altered Schaedler flora (ASF) is a bacterial community that supports normal growth and development of gnotobiotic mice. We report here the draft genome sequences of the 8 bacteria that comprise the ASF.

health of the host has been known for decades. Roles of the GI microbiota include nutrient acquisition, protection against pathogens, and immune system development. Recent studies have added to our understanding by providing new mechanistic insights into host-microbiota interactions (1,2). A significant challenge to these studies moving forward is the high abundance and diversity of bacterial species that colonize the mammalian GI tract, which is dominated by members of the phyla Bacteroidetes and Firmicutes (3). Recently, there has been renewed interest in the gnotobiotic mouse model, represented by the altered Schaedler flora (ASF), for the study of how gut bacteria impact the host (4)(5)(6)(7)(8)(9)(10).
The ASF mouse model is derived from the work of Schaedler et al., who colonized germfree mice with a consortium of bacteria that originated from conventional mice (11). Motivated by efforts by the National Cancer Institute (NCI) to generate mice colonized with a standardized microbiota, the ASF was subsequently derived from the original Schaedler flora, which comprised eight bacterial species. The ASF also consists of eight separate bacterial species, which were isolated from Swiss outbred mice, and includes four species not present in the original community (12). The ASF has subsequently been characterized by 16S rRNA sequence analysis to better determine the phylogeny of the members (13) and by quantitative PCR to assess the abundance, stability, and spatial distribution throughout the GI tract (14,15). To further develop the ASF model as a resource for gut microbiota studies, we have determined the genome sequences of each of the bacterial species, which represent the first genome sequences of a complete mammalian GI bacterial community.
Whole-genome shotgun sequencing was done using Illumina sequencing technology to generate draft sequences for the 8 ASF strains, as summarized in Table 1. Genomic sequence reads were generated on an Illumina HiSeq 2000 machine. Data consisted of two libraries: one 180-bp insert paired-end library (16) and a large-insert, robotically size-selected, 3-to 5-kbp jumping library (17).
Genome consensus was built de novo using ALLPATHS-LG (18) with default parameters, except for Lactobacillus bacterium ASF360, for which Velvet was used due to lack of jumping libraries for ASF360. Original assembly consensus was improved and corrected for Mucispirillum schaedleri ASF457 and Firmicutes bacterium ASF500 using the Pilon assembly improvement tool (D. Ward, unpublished data). Assemblies were analyzed using the GAEMR (http://www.broadinstitute.org/software/gaemr/) assembly evaluation package and manually reviewed for quality.
Protein-coding genes were predicted with Prodigal (19) and filtered to remove genes with at least 70% overlap of tRNAs or rRNAs, which were identified using tRNAscan-SE (20) and RNAmmer (21), respectively. Gene product names were assigned Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers shown in Table 1.

ACKNOWLEDGMENTS
We thank the Broad Institute Sequencing Platform for generating the data for this work. We thank the Broad Institute Genome Sequencing and Analysis team for project management and assembly and annotation of sequence data.
This project has been funded in part with federal funds from the National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services, under grants U54HG003067 (Broad Institute) and R01GM099537 (to G.J.P.).