Complete Genome Sequence of Lactobacillus johnsonii MR1, Isolated from a BALB/c Mouse Cecum

ABSTRACT

Lactobacillus johnsonii strain MR1, which was isolated from the cecum of a BALB/cJ mouse in an airway allergy model, can decrease allergic airway inflammation in the model upon oral administration. Long-read sequencing of this isolate, which was performed using a MinION sequencer, yielded a single, closed genome of 1,953,837 bp, with a GC content of 34.67%.

ANNOUNCEMENT

Lactobacillus johnsonii, a lactic acid bacterium, is associated with a healthy gut microbiome. Classified as generally regarded as safe (GRAS) (1), this species has several health-promoting effects, including inhibition and exclusion of pathogens (2–4) and host immunomodulation (5, 6). L. johnsonii strain MR1, which was sequenced here, was isolated from the cecum of a BALB/cJ mouse (purchased from the Jackson Laboratory) in an airway allergy study performed at the University of Michigan, in which house-dust-mediated protection against disease was associated with significant enrichment of L. johnsonii in the cecum (7). Oral supplementation of mice with L. johnsonii MR1 during respiratory syncytial virus infection resulted in decreased airway inflammation and reduced allergic airway disease in both adults and neonates (5, 8). Here, we report the complete genome sequence of immunomodulatory L. johnsonii strain MR1.

L. johnsonii strain MR1 was initially isolated from the cecum of a mouse and identified as described by Fujimura et al. (7). A frozen stock of L. johnsonii strain MR1 was inoculated in de Man, Rogosa, and Sharpe (MRS) broth and grown overnight at 37°C under static aerobic conditions. High-molecular-weight (HMW) DNA for long-read sequencing was isolated from this overnight bacterial culture using the Nanobind HMW DNA extraction kit (Circulomics) with RNase treatment.

Sequencing libraries were prepared by using the ligation sequencing kit (SQK-LSK109) and selecting DNA fragments of all sizes with the short fragment buffer (SFB), according to the Oxford Nanopore Technologies library preparation protocol. The libraries were sequenced on an R9.4.1 flow cell for 3 h using a MinION sequencer (Oxford Nanopore Technologies). Base calling for the raw reads was performed using Guppy v4.3.4 in high-accuracy mode. A total of 86,118 reads, with an N₅₀ value of 5,730 bp, were obtained after base calling. The genome sequences were assembled de novo using Flye v2.8.1 (9) with default parameters. The assembly was further polished through two rounds with Racon v1.4.20 (10) using the default settings for all parameters except the scores for matching and mismatching bases (–match 8 –mismatch -6). A final round of polishing was performed with Medaka v1.2.3 (11) using default parameters. MR1 (genome coverage, 120×) was assembled into one circular contig with a length of 1.9 Mb. Circularization of the contig was confirmed through visualization of the assembled sequence in Bandage (12).

The MR1 genome has a GC content of 34.67%. Sequence annotation for the strain was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (13). The annotation predicted 1,879 genes, 1,776 coding sequences, and 103 RNA genes (including 79 tRNAs, 21 rRNAs, and 3 noncoding RNAs).

Data availability.

All data are available under BioProject accession number PRJNA791710 and BioSample accession number SAMN23978983. The genome was deposited under GenBank accession number CP091981.1. Nanopore base-called data were submitted to the SRA and are available under SRA accession number SRR18944281.