Complete Genome Sequence of Coprobacter fastidiosus JCM 33896^T

ABSTRACT

We generated a complete genome sequence of Coprobacter fastidiosus JCM 33896^T by nanopore sequencing. The genome consists of a single circular chromosome of 3,444,538 bp with a G+C content of 38.4%. Annotation predicted 15 rRNA genes, 67 tRNA genes and 2,662 protein-coding sequences.

ANNOUNCEMENT

Coprobacter fastidiosus is an obligatory anaerobic Gram-negative bacterium that was originally isolated from feces of a healthy infant (1) and represents the first of two validly described species within the genus Coprobacter (2). Members of the species are frequently detected in human feces and have been associated with a range of health conditions; for example, C. fastidiosus, as well as Coprobacter secundus, was found to be less abundant in patients with chronic obstructive pulmonary disease (3), and the abundance of members of Coprobacter has been associated with ulcerative colitis (4). In another study, the abundance of Coprobacter was increased in feces of patients with neurosyphilis (5), suggesting a potential association with neuropsychiatric disorders. In this work, we generated a complete genome sequence of the authentic type strain of C. fastidiosus (JCM 33896^T = DSM 26242^T = VKM B-2743^T) by Oxford Nanopore Technologies (ONT) sequencing.

Cells were obtained from the Japan Collection of Microorganisms (JCM) and cultured in peptone-yeast extract-glucose (PYG) medium under an atmosphere of N₂:CO₂ (80:20, vol/vol) at 37°C. Genomic DNA was extracted using the MagAttract high-molecular-weight (HMW) DNA kit (Qiagen). Libraries for sequencing were constructed with ONT’s Native Barcoding kit 24 (SQK-NBD114.24), and sequenced on an R10.4.1 flow cell with a GridION device, with default settings (translocation speed of 400 basepairs/s and sampling rate of 4 kHz). All bioinformatics tools were run with default parameters, unless stated otherwise. Basecalling was performed using Dorado v0.2.1 (https://github.com/nanoporetech/dorado) with model dna_r10.4.1_e8.2_400bps_sup@v4.0.0. Duplex Tools v0.3.1 (https://github.com/nanoporetech/duplex-tools), four iterations with option -allow_multiple_splits, was used to identify and split the chimeric and/or concatenated reads. Guppy’s guppy_barcoder command (v6.4.6) with concurrent barcode trimming (options -enable_trim_barcodes -barcode_kits SQK-NBD114-24) was then used for demultiplexing libraries. After removal of reads with a length of <1,000 bases and an average quality score of <12 using NanoFilt v2.8.0 (6), a set of high-quality reads was obtained using Filtlong v0.2.0 (https://github.com/rrwick/Filtlong), with option -mean_q_weight 10. This resulted in a total of 172,610 reads (516,695,412 bases with an estimated genome coverage of 150×) with an N₅₀ of 3,501 bases. The genome was assembled using Flye v2.9.1 (7), followed by polishing by Medaka v1.7.3 (https://github.com/nanoporetech/medaka) with model r1041_e82_400bps_sup_v4.0.0. Completeness (99.6%) and contamination (0.0%) of the genome were confirmed using CheckM v1.1.3, lineage_wf (8). The genome was annotated with the DDBJ Fast Annotation and Submission Tool v1.2.18 (9).

The genome of C. fastidiosus JCM 33896^T consists of a single circular chromosome with a length of 3,444,538 bp. It has a G+C content of 38.4% and was predicted to contain 5 complete rRNA operons and 67 tRNA genes and to encode 2,662 proteins. The availability of a complete genome of C. fastidiosus JCM 33896^T will contribute to improving our understanding of this bacterium in the human gut.

Data availability.

This genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number AP028032. Sequencing reads are available in the DDBJ Sequence Read Archive under accession number DRR457763.