Complete genome sequences of Blautia hydrogenotrophica DSM 10507T isolated from human feces and Blautia coccoides DSM 935T isolated from mouse feces

TL;DR

This paper presents the complete genome sequences of two Blautia species isolated from human and mouse feces.

Contribution

The study provides closed genome sequences for Blautia hydrogenotrophica and Blautia coccoides, including chromosome and plasmid details.

Findings

The genome of Blautia hydrogenotrophica includes a 3.59 Mb chromosome and a 7.18 kb plasmid.

Blautia coccoides has a single chromosome of 6.10 Mb.

Abstract

We report on the closed genome sequences of the acetogen Blautia hydrogenotrophica S5a33T (DSM 10507T) and of Blautia coccoides CLC-1T (DSM 935T). The B. hydrogenotrophica S5a33T genome harbors a chromosome (3,590,609 bp) and a plasmid (7,176 bp). The B. coccoides CLC-1T genome consists of a single chromosome (6,097,890 bp).

Tables

TABLE 1. Sequencing statistics and genome features of B. hydrogenotrophica DSM 10507T and B. coccoides DSM 935T

Feature	B. hydrogenotrophica DSM 10,507T	B. coccoides DSM 935T
Chromosome size (bp)	3,590,609	6,097,890
Number of Illumina reads (250 bp)	804,958	646,392
Number of Nanopore reads/mean length (bp)	80,177/4,543	55,589/7,066
Chromosome mean coverage (Illumina/Nanopore)	103/96	56/63
Plasmid size (bp)	7,176	–
Plasmid mean coverage (Illumina/Nanopore)	2,894/1,418	–
GC content (%)	45	46
Genes	3,465	5,466
CDS	3,387	5,391
Functional proteins	1,869	2,803
Hypothetical proteins	1,518	2,588
rRNAs (5S, 16S, 23S)	8 (4, 4, 4)	10 (5, 5, 5)
tRNAs	69	64
tmRNAs	1	1
CheckM2:
Completeness score (%)	98.25	100
Contamination score (%)	0.47	3.88

Full text

ANNOUNCEMENT

The strains Blautia hydrogenotrophica S5a33^T^ (DSM 10507^T^), Blautia schinkii B^T^ (DSM 10518^T^), Blautia producta U-1 (DSM 3507), and Blautia coccoides GA-1 were described to grow autotrophically with H_2_ + CO_2_ using the Wood-Ljungdahl pathway (1–4). However, with the exception of B. producta, high-quality type strain genomes were not available for acetogenic bacteria of the genus Blautia. Here, we report complete genome sequences of the type strains B. hydrogenotrophica S5a33^T^ (DSM 10507^T^, formerly Ruminococcus hydrogenotrophicus) isolated from human feces and B. coccoides CLC-1^T^ (DSM 935^T^, formerly Clostridium coccoides) isolated from mouse feces (1, 5). Both strains were cultivated in 10 mL of DSM 311c medium as listed by the German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany) under anaerobic conditions. Cells were inoculated from lyophilized stock cultures from the DSMZ in an anaerobic chamber and incubated in Hungate tubes at 35°C for 12 h without shaking. Cells were harvested by centrifugation at 18,000 × g for 5 min. Illumina and Nanopore sequencing were performed with separately grown cell cultures. DNA was isolated by using the Master-Pure Complete DNA and RNA purification kit (Epicentre, Madison, WI, USA) following the instructions for cell samples. Illumina sequencing was performed by preparation of Illumina sequencing libraries using the Nextera XT DNA sample preparation kit and a MiSeq system with v3 chemistry (2 × 300  bp, 600 cycles) following the instructions of the manufacturer (Illumina, San Diego, CA, USA). Long-read sequencing was performed by preparation of Nanopore sequencing libraries with 1.5 µg high-molecular-weight DNA using the ligation sequencing kit 1D (SQK-LSK109) and the native barcode expansion kit (EXP-NBD114) as recommended by the manufacturer (Oxford Nanopore Technologies, Oxford, UK). Nanopore sequencing was conducted for 72 h with the MinION device Mk1B, a SpotON flow cell R9.4.1, and the MinKNOW software (v21.06.13) following the instructions of the manufacturer (Oxford Nanopore Technologies). Default parameters were used for all software unless otherwise specified. Demultiplexing and base calling of Nanopore sequencing data were performed with the Guppy software in HAC mode (v.5.0.16). Long-read de novo genome assemblies were obtained by following the described Trycycler workflow and parameters for bacterial genome assemblies by Wick et al. (6). The following programs were used for genome assemblies: fastp (v0.23.2), trimmomatic (v0.39; LEADING: 3, TRAILING: 3, SLIDINGWINDOW:4:15, MINLEN:50), Porechop (v0.2.4), Filtlong (v0.2.1), Trycycler (v0.5.3), Flye (v2.9.1), Canu (v2.2), and Raven (v1.8.1) (7–12). Flye, Canu, and Raven assemblies were combined to a single consensus sequence with Trycycler, and the consensus sequence was polished with long-read data using Medaka (v1.5.0) and finally polished with Illumina sequences using Polypolish (v0.5.0) (13), resulting in a circular chromosome in both cases. Genome annotations were performed with Prokka (v1.14.6) and quality assessment of the final genome assemblies was conducted with CheckM2 (v1.0.2) (14, 15). Details of sequencing and genome statistics of B. hydrogenotrophica and B. coccoides obtained in both cases are summarized in Table 1.