Complete Genome Sequence of Adlercreutzia equolifaciens subsp. celatus DSM 18785

Adlercreutzia equolifaciens subsp. celatus DSM 18785 was isolated from the cecal contents of a rat and is an obligately anaerobic equol-producing bacterium. Here, we report the finished and annotated genome sequence of this organism, which has a genome size of 2,929,991 bp and a G+C content of 63.2%.

ABSTRACT

Adlercreutzia equolifaciens subsp. celatus DSM 18785 was isolated from the cecal contents of a rat and is an obligately anaerobic equol-producing bacterium. Here, we report the finished and annotated genome sequence of this organism, which has a genome size of 2,929,991 bp and a G+C content of 63.2%.

ANNOUNCEMENT

Adlercreutzia equolifaciens subsp. celatus DSM 18785 (Asaccharobacter celatus DSM 18785) is a Gram-positive, non-spore-forming, and obligately anaerobic bacterium which has been isolated from the cecal contents of a rat in Japan (1). Strain DSM 18785 produces equol from the soy isoflavone daidzein, which is an agonist of the female hormone estrogen (1). The estrogen-like action of soy isoflavones and their metabolites has long been thought to have health benefits. Equol is one of the metabolites of soy isoflavones converted by gut microbes. Recently, it has been the focus of research due to its physiological action (2, 3).

In this study, strain DSM 18785 was obtained from the Japan Collection of Microorganisms (JCM), RIKEN BRC, which participates in the National BioResource Project of the MEXT, Japan. A single colony was cultured overnight at 37°C and grown in Gifu anaerobic medium (GAM) broth (Nissui) supplemented with 0.5% arginine (adjusted to a pH of 7 by 1 N HCl) (4). Genomic DNA was extracted and purified using a Genomic-tip 20/G kit (Qiagen) according to the manufacturer’s protocol. A long-read sequencing library was prepared using a rapid barcoding sequencing kit (product number SQK-RBK004; Oxford Nanopore Technologies) and sequenced using a FLO-MIN106 flow cell on a GridION device (Oxford Nanopore Technologies). The reads were base called, demultiplexed, and adapter trimmed using GridION v.20.06.17 software with Guppy high-accuracy mode.

From a total of 728.4 Mb long reads (N₅₀, 13.4 kbp) sequenced, reads over 20 kbp (287 Mbp in total, for an estimated coverage of 100×) were used for assembly with Canu v.2.1.1 (5). The reads were not filtered by quality nor error corrected prior to assembly. The genome was assembled into a single contig and was circularized manually by deleting the overlapping end. The draft assembly was subsequently error corrected with one round of Pilon v.1.23 (6), polished using 59.9 million raw Illumina short reads obtained from Sequence Read Archive (SRA) data (accession number SRX5082739) (7) in the National Center for Biotechnology Information (NCBI) (8) mapped to the Canu assembly using the Burrows-Wheeler Aligner (BWA) v.0.7.11 (9). The genome completeness was assessed using the CheckM tool provided by the DDBJ Fast Annotation and Submission Tool (DFAST) (10, 11), resulting in 100% completeness with the Coriobacteriaceae taxon. The genes were annotated using DFAST, and the genome was rotated according to the location of the dnaA gene. The final genome size is 2,929,991 bp, with a G+C content of 63.2%, containing 2,466 putative coding sequences (CDSs), 9 rRNAs, and 51 tRNAs. Default parameters were used for all software unless otherwise specified.

As previous reported, the equol production genes daidzein reductase (dzr), dihydrodaidzein reductase (ddr), tetrahydrodaidzein reductase (tdr), and dihydrodaidzein racemase which present in A. equolifaciens subsp. equolifaciens DSM 19450^T (12) were also found in A. equolifaciens subsp. celatus DSM 18785 (13). The homologs of two giant genes, AEQU_0093 and AEQU_1251, encoding putative extracellular surface proteins in A. equolifaciens subsp. equolifaciens DSM 19450^T (14) were found in A. equolifaciens subsp. celatus DSM 18785 as well. However, the sizes of the open reading frames were smaller, 37,689 bp and 61,890 bp, respectively. The complete genome sequence reported in this study will enable comparative analysis with closely related species to elucidate the mechanisms allowing the production of equol.

Data availability.

The chromosome sequence reported here was deposited in the DDBJ under accession number AP024470, and the raw reads were deposited in the Sequence Read Archive (SRA) under BioProject accession number PRJNA698616.