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Draft Genome Assemblies of 4 Lactobacillus jensenii and 3 Lactobacillus mulieris Strains from the Urinary Tract.

ABSTRACT: Lactobacilli are dominant members of the healthy female bladder microbiota. Here, we report the draft genome sequences of 4 Lactobacillus jensenii and 3 Lactobacillus mulieris strains isolated from catheterized urine samples.

SUBMITTER: Ene A

PROVIDER: S-EPMC9119073 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Draft Genome Assemblies of 4 Lactobacillus jensenii and 3 Lactobacillus mulieris Strains from the Urinary Tract.

Ene Adriana A Putonti Catherine C

Microbiology resource announcements 20220407 5

Lactobacilli are dominant members of the healthy female bladder microbiota. Here, we report the draft genome sequences of 4 Lactobacillus jensenii and 3 <i>Lactobacillus mulieris</i> strains isolated from catheterized urine samples. ...[more]

PMID: 35389247

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Project description:Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available strains and nine new strains sequenced here. Genomic analyses conducted include phylogenetics of the core genome as well as biosynthetic gene cluster analysis and metabolic pathway analyses. Urinary strains of both species were assayed for their ability to utilize four simple carbohydrates. We found that L. jensenii strains can efficiently catabolize maltose, trehalose, and glucose, but not ribose, and L. mulieris strains can utilize maltose and glucose, but not trehalose and ribose. Metabolic pathway analysis clearly shows the lack of treB within L. mulieris strains, indicative of its inability to catabolize external sources of trehalose. While genotypic and phenotypic observations provide insight into the differences between these two species, we did not find any association with urinary symptom status. Through this genomic and phenotypic investigation, we identify markers that can be leveraged to clearly distinguish these two species in investigations of the female urogenital microbiota. IMPORTANCE We have expanded upon our prior genomic analysis of L. jensenii and L. mulieris strains, including nine new genome sequences. Our bioinformatic analysis finds that L. jensenii and L. mulieris cannot be distinguished by short-read 16S rRNA gene sequencing alone. Thus, to discriminate between these two species, future studies of the female urogenital microbiome should employ metagenomic sequencing and/or sequence species-specific genes, such as those identified here. Our bioinformatic examination also confirmed our prior observations of differences between the two species related to genes associated with carbohydrate utilization, which we tested here. We found that the transport and utilization of trehalose are key distinguishing traits of L. jensenii, which is further supported by our metabolic pathway analysis. In contrast with other urinary Lactobacillus species, we did not find strong evidence for either species, nor particular genotypes, to be associated with lower urinary tract symptoms (or the lack thereof).

Project description:Lactobacilli are dominant members of the "healthy" female urogenital microbiota. One of these species, Lactobacillus jensenii, is routinely identified in the urinary microbiota of women both with and without urinary tract symptoms. In March 2020, the new bacterial species Lactobacillus mulieris was introduced, and phylogenetic and average nucleotide identity analysis identified eight L. jensenii strains that should be classified as members of the L. mulieris species. This prompted our phylogenomic study of all publicly available L. jensenii and L. mulieris genome sequences. While there is little variation in the 16S rRNA gene sequences, the core genome shows a clear distinction between genomes of the two species. We find eight additional strains of the species L. mulieris among these genomes. Furthermore, one strain, currently classified as L. mulieris UMB7784, is distinct from both L. jensenii and L. mulieris strains. As part of our comparative genomic study, we also investigated the genetic content that distinguishes these two species. Unique to the L. jensenii genomes are several genes related to catabolism of disaccharides. In contrast, L. mulieris genomes encode several cell surface and secreted proteins that are not found within the L. jensenii genomes. These L. jensenii-specific and L. mulieris-specific loci provide insight into phenotypic differences of these two species.IMPORTANCELactobacillus species play a key role in the health of the urinary tract. For instance, Lactobacillus crispatus and L. jensenii have been found to inhibit uropathogenic Escherichia coli growth. While L. crispatus is typically found only within the microbiota of women without lower urinary tract symptoms (LUTS), L. jensenii has been found in the microbiota of women both with and without LUTS. With the recent introduction of the new species Lactobacillus mulieris, several strains of L. jensenii were reclassified as L. mulieris based upon gene marker and average nucleotide identity. We took a phylogenomic and comparative genomic approach to ascertain the genetic determinants of these two species. Looking at a larger data set, we identified additional L. mulieris strains, including one distinct from other members of the species-L. mulieris UMB7784. Furthermore, we identified unique loci in each species that may have clinical implications.

Dataset Information

Draft Genome Assemblies of 4 Lactobacillus jensenii and 3 Lactobacillus mulieris Strains from the Urinary Tract.

Publications

Draft Genome Assemblies of 4 Lactobacillus jensenii and 3 Lactobacillus mulieris Strains from the Urinary Tract.

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