Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota.

Lactobacillus species are common inhabitants of the 'healthy' female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus, L. gasseri, L. iners, L. jensenii, and L. paragasseri. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.

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

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.

Draft genome sequences of three Lactobacillus crispatus strains, isolated from the female urinary tract.

Lactobacillus crispatus is a frequent member of the female urogenital microbiota. Here, we present the draft genome assemblies of three L. crispatus strains: UMB4356, UMB5661, and UMB6244. All strains were isolated from voided urine samples from females with type 2 diabetes.

Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements.

The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.

Draft genomes of Lactobacillus jensenii UMB0908, UMB1545, and UMB5777 from the urinary tract.

Lactobacillus jensenii is a member of the female urogenital microbiome. Previous research has identified strains of L. jensenii that are capable of inhibiting or killing uropathogens, including E. coli. Here, we present the draft genomes of three L. jensenii strains collected from urine samples.

Draft genome sequences of Lactobacillus paragasseri strains isolated from the female urinary tract.

Lactobacillus species are often associated with a healthy environment in the female urogenital tract. Here, we present the draft genome assemblies for three L. paragasseri strains isolated from voided urine samples from females with type II diabetes; two of the strains were collected from the same individual 3 months apart.

Draft genome sequences of five Lactobacillus gasseri strains isolated from voided urine samples.

Lactobacillus gasseri is a member of the gut, oral, and female urogenital microbiota. Here, we present the draft genome assemblies of L. gasseri UMB1549, UMB1579, UMB1644, UMB3348, and UMB5890, which were isolated from voided urine samples from females with Type 2 diabetes.

Draft genome sequences of Lactobacillus mulieris strains isolated from the female urinary tract.

Lactobacillus mulieris is a frequent member of the healthy female urogenital tract. Here, we present the draft genomes of two L. mulieris strains isolated from urine samples: UMB0446 and UMB3420. The draft genomes presented here further expand our understanding of the female urinary microbiome.

Genomic insights into Lactobacillus gasseri and Lactobacillus paragasseri.

Background: Antimicrobial and antifungal species are essential members of the healthy human microbiota. Several different species of lactobacilli that naturally inhabit the human body have been explored for their probiotic capabilities including strains of the species Lactobacillus gasseri. However, L. gasseri (identified by 16S rRNA gene sequencing) has been associated with urogenital symptoms. Recently a new sister taxon of L. gasseri was described: L. paragasseri. L. paragasseri is also posited to have probiotic qualities. Methods: Here, we present a genomic investigation of all (n = 79) publicly available genome assemblies for both species. These strains include isolates from the vaginal tract, gastrointestinal tract, urinary tract, oral cavity, wounds, and lungs. Results: The two species cannot be distinguished from short-read sequencing of the 16S rRNA as the full-length gene sequences differ only by two nucleotides. Based upon average nucleotide identity (ANI), we identified 20 strains deposited as L. gasseri that are in fact representatives of L. paragasseri. Investigation of the genic content of the strains of these two species suggests recent divergence and/or frequent gene exchange between the two species. The genomes frequently harbored intact prophage sequences, including prophages identified in strains of both species. To further explore the antimicrobial potential associated with both species, genome assemblies were examined for biosynthetic gene clusters. Gassericin T and S were identified in 46 of the genome assemblies, with all L. paragasseri strains including one or both bacteriocins. This suggests that the properties once ascribed to L. gasseri may better represent the L. paragasseri species.