Abstract
Eggerthella sp. strain YY7918 was isolated from the intestinal flora of a healthy human. It metabolizes daidzein (a soybean isoflavonoid) and produces S-equol, which has stronger estrogenic activities than daidzein. Here, we report the finished and annotated genomic sequence of this organism.
GENOME ANNOUNCEMENT
The complete genomic sequence of Eggerthella sp. strain YY7918 (8) was determined by a whole-genome shotgun strategy with the Sanger method. Genomic libraries containing 2-kb inserts were constructed with pTS1 plasmids, and 36,480 sequences were generated, providing 8.1-fold coverage from both ends of the genomic clones. Sequence reads were assembled with the Phred-Phrap-Consed program (1). Remaining gaps between contigs were closed by direct sequencing of the fosmid clones. Prediction and annotation of protein-coding genes were performed by MiGAP (6).
The genome of strain YY7918 consists of a circular 3,123,671-bp chromosome with 56.2% GC content and contains 2,680 predicted protein-coding sequences (CDSs) but no plasmid. It also has 2 sets of rRNA operons and 44 tRNA genes. The strain possesses two sets of clustered, regularly interspaced short palindromic repeats. Similarity at the sequence level (1,772 CDSs) was observed between strain YY7918 and the closely related type strain Eggerthella lenta VPI0255 (GenBank accession no. CP001726) (3), with overall genome synteny. However, a reciprocal BLASTP search revealed 913 (34.0%) protein-coding genes that are present in strain YY7918 but absent in E. lenta VPI0255T. The genome of strain YY7918 is 509 kb shorter than that of E. lenta VPI0255T (circular; 3,632,260 bp) (3).
The predicted CDSs were submitted to the Kyoto Encyclopedia of Genes and Genomes Automatic Annotation Server (http://www.genome.jp/tools/kaas/) (2) and the virulence factor database (VFDB) (http://www.mgc.ac.cn/VFs/) (7). We could assign 975 CDSs (36%) to known functions, 108 (4%) as conserved hypothetical genes, and 1,597 (60%) as novel hypothetical genes. As expected, strain YY7918 possesses an incomplete carbohydrate metabolic pathway in KEGG, indicating that the strain is nonsaccharolytic. By contrast, this organism posseses genes for arginine deiminase (arcA), ornithine carbamoyltransferase (argF or agI), and carbamate kinase (arcC), suggesting that the strain utilizes arginine as an important energy source, similarly to E. lenta (5). The VFDB result indicates that the strain expresses genes for streptomycin adenyltransferase (aadE) and erythromycin resistance methylase (ermB). This organism also carries antibiotic ABC transport systems, such as permease (yadH) and ATP-binding protein (yadG) genes. These results correspond with our previous report that the strain is resistant to erythromycin. However, the strain is sensitive to aminoglycoside antibiotics despite possessing aadE (7). Excluding these elements, other known virulence factors were not present.
This organism also has a notable gene cluster (EGYY_15730 to EGYY_15760). Recently, Shimada et al. reported a gene that might encode NADP(H)-dependent daidzein reductase (L-DZNR; DDBJ accession no. AB558141) from Lactococcus strain 20-92 (4). The EGYY_15730 gene has 99.6% homology with both the nucleoside and protein sequences of L-DZNR. This suggests that EGYY_15730 retains L-DZNR activity. Because EGYY_15750 and EGYY_15760 construct a cluster with EGYY_15730, these genes are expected to be related to equol production from dihydrodaidzein. We will report the characterization of these gene products in the near future.
Nucleotide sequence accession number.
The sequence data of the Eggerthella sp. strain YY7918 genome have been deposited in GenBank/DDBJ/EMBL under accession number AP012211.
Acknowledgments
We thank K. Furuya, C. Shindo, H. Inaba, E. Iioka, and Y. Hattori for technical support.
This research was supported by a Grant-in-Aid for Scientific Research on Priority Areas ‘Comprehensive Genomics’ (M.H.), the global COE project ‘Genome Information Big Bang’ (M.H. and K.O.), and a Grant-in Aid for Scientific Research (C), 20510189 (T.S.), from the Ministry of Education, Culture, Sports, Science and Technology of Japan and the Iijima Memorial Foundation for the Promotion of Food Science and Technology, 2011 (T.S.).
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