Draft genome assembly of Lactobacillus johnsonii UMB3423 from a voided urine sample

ABSTRACT While the urogenital microbiota of asymptomatic females is often dominated by species of Lactobacillus, Lactobacillus johnsonii is not a common member. It is more frequently found in the gastrointestinal tract. Here, we present the draft genome sequence of L. johnsonii UMB3423, which was isolated from a voided urine sample.

L actobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are frequent dominant members of the asymptomatic ("healthy") female urogenital microbiota (1)(2)(3).The species Lactobacillus johnsonii also has been identified in voided urine (4) and vaginal samples (5,6).L. johnsonii, however, is more frequently found in the human gastrointestinal (GI) tract [see review reference (7)], and strains have been explored for their use as a probiotic for GI and vaginal health (8,9).Continuing our group's efforts to characterize bacterial species of the female urinary tract (10), we sequenced a strain of L. johnsonii isolated from a voided urine sample from a female with type 2 diabetes.
Strain UMB3423 was isolated from the urine sample using the enhanced quantitative urine culture method (11), which isolates bacteria from urine samples using a variety of culture conditions and volumes of sample, as part of a prior Institutional Review Board (IRB)-approved study (LUC # 204197) in 2016 (12).The strain was identified as L. johnsonii by MALDI-TOF, performed as described previously (13), and stored at −80°C in the Loyola Urinary Education and Research Collaborative (LUEREC) collection.We obtained the freezer stock of this isolate from this collection and streaked it onto a deMan-Rogosa-Sharpe (MRS) agar plate and incubated at 35°C with 5% CO 2 for 48 hours.MRS medium with 1 mL/L of Tween 80 (Sigma-Aldrich) was inoculated with a single colony from the plate and incubated for 48 hours at 35°C with 5% CO 2 .DNA was extracted using the DNeasy blood and tissue kit (Qiagen) following the manufacturer's protocol for Gram-positive bacteria.
DNA was sent to SeqCenter (Pittsburgh, PA USA) where libraries were prepared using the Illumina DNA Prep kit and custom IDT 10 bp unique dual indices with a target insert size of 320 bp.The library was sequenced on the Illumina NovaSeq 6000 platform, producing 2,220,089 pairs of reads (2 × 151 bp).Raw reads were trimmed using BBDuk (BBMap suite, v39.01; https://sourceforge.net/projects/bbmap/) and assembled using SPAdes v3.15.5 with the --only-assembler parameter (14).Genome coverage was calculated using BBMap's BBWrap script.The genome assembly was annotated upon submission to NCBI by the Prokaryotic Genome Annotation Pipeline v6.6 (15).Genome comparisons were conducted via BV-BRC (16,17) and the Type Strain Genome Server (18,19).Default parameters were used for all software tools unless otherwise noted.
The L. johnsonii UMB3423 assembly includes 2,066,246 bp in 37 contigs with a GC content of 34.2% (genome coverage = 290.615×;N 50 = 113,600 bp).Upon submission of the assembly to NCBI, the average nucleotide identity (ANI) was computed, producing a score of 94.83%, slightly below the 95% threshold commonly used to distinguish between species (20).This prompted us to further investigate L. johnsonii UMB3423 and other genomes for the species (see Table 1).Currently only 5-including UMB3423 -of the nearly 1,000 publicly available L. johnsonii genomes are from female urogeni tal samples.While both ANI and digital DNA-DNA hybridization (dDDH) suggest that UMB3423 is genetically different from other L. johnsonii strains, further sequencing of strains from the female urogenital tract is needed.

TABLE 1
Results of comparisons of the L. johnsonii UMB3423 genome sequence to publicly available assemblies