Genome Sequence of “Candidatus Arthromitus” sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions

“Candidatus Arthromitus” spp., also known as segmented filamentous bacteria (SFB), are noncultivable, spore-forming, Clostridia-related commensal bacteria that colonize the digestive tracts of many animal species (1). SFB typically form filaments that are solidly anchored in gut epithelial cells (2), notably in the ileum. In mice, SFB play a key role in the postnatal maturation of gut innate and adaptive immune functions, and notably, they can induce a strong IgA response (3, 4) and the recruitment and activation of intraepithelial CD8⁺ T lymphocytes (5) and lamina propria CD4⁺ T cells (6, 7; reviewed in reference 8).

Here, we report the complete genome sequence of the mouse-specific isolate “Candidatus Arthromitus” sp. SFB-mouse-NL. While an earlier sequenced mouse SFB isolate from Japan was shown to elicit a T helper (Th) 17 immune response in the intestinal lamina propria of C57BL/6 mice (7), the present strain, an independent isolate from The Netherlands (9), was reported to not only induce a strong Th17 response but also to foster Th1, Th2, and regulatory T-cell responses in C3H/HeN mice (6). To define whether the observed differences may be related to genetic variations between the two SFB isolates, we determined the genome sequence of strain SFB-mouse-NL.

DNA was isolated from fecal material from SFB-monocolonized mice using a modified version of the protocol described in Morita et al. (10). The DNA was sequenced using Illumina paired-end sequencing technology. The sequence reads were filtered using CLC and BOWTIE (11) to eliminate mouse genome sequences, and they were assembled using CLC, ABySS (12), and SOAPdenovo (13), yielding 40 scaffolds >1,000 bp with high BLASTn scoring to existing SFB genome sequences. Finishing was performed using GAP4 of the Staden package (14) through iterative selection of read pair mapping to scaffold extremities and independent de novo assembly of these reads by SOAP. The scaffolds were also ordered using Mauve aligner (15), with earlier published SFB genome sequences as the reference, and some sequence gaps bridged by PCR performed on the basis of this alignment and sequencing of the PCR products. Genome annotation was performed using RAST (16).

The genome of “Candidatus Arthromitus” sp. SFB-mouse-NL consists of one circular chromosome (1,654,902 bp) with 1,598 predicted coding sequences (CDS). The genome contains 4 (partial) prophages. A comparative analysis of the “Candidatus Arthromitus” sp. SFB-mouse-NL genome and two complete and 7 incomplete other SFB genomes retrieved from NCBI (http://www.ncbi.nlm.nih.gov/genomes/) using MUMmer (17) and Mauve (18) revealed that the SFB-mouse-NL genome is distinct (0.4% of overall nucleotide divergence) from the other genomes (which show <0.2% of overall nucleotide divergence among them).

We thank Laurence Ma for technical assistance in DNA sequencing, as well as Jean-Michel Batto and Pierre Leonard for help in computing.

This project was supported by the French National Research Agency (ANR) (contract ANR-10-BLAN-1317) and INRA AIP Bio-Resources.