Complete genome sequence of Parabacteroides distasonis strain GP102, isolated from the cecum of a morbid pregnant laboratory guinea pig (Cavia porcellus)

ABSTRACT

Parabacteroides distasonis is an anaerobic bacterium with ambivalent health effects. P. distasonis strain GP102 was isolated from the cecum content of a morbid pregnant laboratory guinea pig (Cavia porcellus). The genome consists of one circular 5.39-Mbp chromosome with a G + C content of 44.79%.

ANNOUNCEMENT

Parabacteroides distasonis (formerly Bacteroides distasonis), a member of the genus Parabacteroides, is a Gram-negative, rod-shaped, obligatory anaerobic bacterium (1). P. distasonis, first isolated from human feces in 1933, is a commensal bacterium in the gastrointestinal tract of humans and animals (2, 3). P. distasonis has been known for its ambivalent roles, pathogenic and probiotic, in humans and animals (2, 4). Some recent reports indicate that P. distasonis plays protective roles against certain disease such as multiple sclerosis, diabetes, cancer, and Crohn’s disease while it also plays pathogenic roles including antimicrobial resistance and clinical development (2, 4). This genome report provides additional genetic information about the bacterium.

Under the health monitoring program, a sick pregnant guinea pig was submitted for microbiological evaluation in April 2023 at a research center with multiple-species laboratory animal facilities in Jefferson, Arkansas, under Protocol S0006 approved by the NCTR Institutional Animal Care and Use Committee. The cecum content was directly streaked on Campylobacter Selective Agar containing 10-mg vancomycin, 50-mg cefoperazone, 5-mg trimethoprim, and 2,500 IU polymyxin B per liter (Remel, San Diego, CA) and cultured in anaerobic condition (80% N₂, 10% CO₂, 10% N₂) at 35°C for 4 days. Small colonies (1–2 mm) were selected and subcultured under anaerobic conditions 35°C for 2 days. The bacterium was identified as P. distasonis using matrix-assisted laser desorption/ionization-time of flight Biotyper (Bruker, Billerica, MA).

Genomic DNA was isolated from a colony on a plate using the Blood & Tissue Kit (Qiagen, Redwood City, CA), and the same DNA was used for Illumina short-read and Nanopore long-read sequencing with no shearing or size selection. The quality and quantity of DNA were determined using Nanodrop and Qubit (Fisher Scientific, Waltham, MA). Default parameters were used for all software unless otherwise noted. A short-read genomic library was constructed using the Nextera XT library prep kit and sequenced using the MiSeq v3 reagent kit (2 × 300 bp) on MiSeq (Illumina, San Diego, CA). For long reads, a genomic library was constructed using the ligation sequencing kit SQK-LAK114 and sequenced on Nanopore MinIon FLO-MIN1114 R10, and data acquisition and basecalling were done in the FAST mode using MinKNOW22.12.5 (Guppy6.4.6) on MinION Mk1C (Oxford Nanopore, Oxford, UK). Raw short reads were quality checked and trimmed using Fastq Utilities (CutAdapt v2.2 with Python v3.7.9) in BV-BRC^3.33.16 (5), and raw long reads were quality checked and trimmed with Porechop v0.2.1 and Galore v0.6.7 in Galaxy (6). Illumina short reads (n = 1,487,056) and Nanopore long reads (n = 35,990; N₅₀ = 3,369 bp) were assembled in one circular contig with 193× depth using Unicycler v0.4.8 (default normal bridging mode, rotation) in BV-BRC^3.33.16 (5). The genome of P. distasonis GP102 is 5,387,833 bp in length with a G + C content of 44.79%. The GP102 genome, annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP v4.11), has 4,730 coding genes, 122 pseudo genes, 84 tRNAs, 21 rRNAs, and 1 CRISPR array (7). The closest reference genome is P. distasonis ATCC8503 with an average nucleotide identity of 81.7% (8). The genome of P. distasonis strain GP102 is annotated to contain katE and oxyR that confer aerotolerance of the species (2).

DATA AVAILABILITY

The whole-genome sequence has been deposited at DDBJ/ENA/GenBank under the accession number CP132899. The raw reads have been deposited in the Sequence Read Archive (SRA) under the accession numbers SRR25757805 and SRR25757806.