Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates

Wolfe, Alan J.; Du, Jingjie; Khemmani, Mark; Halverson, Thomas; Ene, Adriana; Limeira, Roberto; Tinawi, Lana; Hochstedler-Kramer, Baylie R.; Noronha, Melline Fontes; Putonti, Catherine

doi:10.1101/2023.05.23.541916

Cited by 3 publications

(2 citation statements)

References 106 publications

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“…Aerobic subgroup of these taxa (like Corynebacterium , Staphylococcus and Streptococcus are also present in a recent genome collection of bladder-specific isolates and thus thier metabolic potential might be assessed. (36) Other taxa like Peptoniphilus are more elusive due to their anaerobic growth. The fact that Lactobacillus does not feature among the top OTUs in our dataset may be explained by the postmenopausal status of the study female participants (37); indeed, Lactobacillus was detected in both paired samples in only 40% of women.…”

Section: Discussionmentioning

confidence: 99%

Short- and mid-term temporal variability of the human urinary microbiota: an observational cohort study

Tláskal,

Hrbáček,

Hanáček

et al. 2024

Preprint

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Understanding the temporal variability of the microbiome is critical for translating associations of the microbiome with health and disease into clinical practice. The aim of this study is to assess the extent of temporal variability of the human urinary microbiota.A pair of catheterized or mid-stream urine samples were collected from study participants at 3–40 month interval. DNA was extracted and the bacterial V4 hypervariable region of the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The alpha and beta diversity of paired samples was analyzed using Chao1 and Shannon indices and PERMANOVA.A total of 63 participants (43 men and 20 women with a mean age of 63.0 and 57.1 years, respectively) were included in the final analysis. An average of 152±128 bacterial operational taxonomic units (OTUs) were identified in each urine sample from the entire cohort. There was an average of 41±32 overlapping OTUs in each sample pair, accounting for 66.3±29.4% of the relative abundance. There was a clear correlation between the number of overlapping OTUs and the relative abundance covered. The difference in Chao1 index between paired samples was statistically significant; the difference in Shannon index was not. Beta diversity did not differ significantly within the paired samples. Neither age nor sex of the participants influenced the variation in community composition. With a longer time interval between the collections, the relative abundance covered by the overlapping OTUs changed significantly but not the number of OTUs.The abundance of bacterial taxa present in both collections fluctuated, but the proportion of these taxa in the community was about two-thirds of the total bacterial community. No significant intraindividual differences in beta diversity were observed between the two urine samples.

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Section: Discussionmentioning

confidence: 99%

Short- and mid-term temporal variability of the human urinary microbiota: an observational cohort study

Tláskal,

Hrbáček,

Hanáček

et al. 2024

Preprint

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“…gov/ biopr oject/? term= PRJNA 316969) [120]. The 1134 bladder-specific isolated bacterial genomes and 387 gut-specific isolated E. coli genomes used in the study are also available in figshare (https:// figsh are.…”

Section: Supplementary Informationmentioning

confidence: 99%

Cataloging the phylogenetic diversity of human bladder bacterial isolates

Du,

Khemmani,

Halverson

et al. 2024

Genome Biol

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Background Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. Results To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. Conclusions This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.

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Tarnished gold—the “standard” urine culture: reassessing the characteristics of a criterion standard for detecting urinary microbes

et al. 2023

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Diagnosis and treatment of urinary tract infections (UTIs) remains stagnant. The presumption that a patient either has a UTI or does not (binary choice) is inappropriately simplistic. Laboratory diagnostic tests have not advanced for decades. The goal of UTI treatment has not been rigorously defined and may increase the prescription of potentially harmful, inappropriate antibiotics. Despite the high incidence of UTI diagnoses, the high cost of UTI treatment, and increasing concerns associated with antimicrobial resistance, the development of novel and more accurate UTI tests has not been considered a priority, in part due to the general perception that current UTI care is already sufficient. In this review, we discuss the importance of improving UTI diagnostic testing to improve treatment outcomes. We discuss the problems associated with UTI diagnosis. Urinary microbes are alive and exist in both healthy and symptomatic individuals—urine is not sterile. We specifically outline the limitations of standard urine culture methods used by clinical microbiology laboratories, explaining clearly why such methods cannot be considered to be the “gold standard,” as standard culture methods underreport most of the urinary tract microbes, including some acknowledged and many emerging uropathogens. We do not recommend abandonment of this test, as no universally accepted substitute yet exists. However, we strongly encourage the development of new and improved diagnostic tests that can both improve outcomes and preserve antibiotic stewardship.

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Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates

Cited by 3 publications

References 106 publications

Short- and mid-term temporal variability of the human urinary microbiota: an observational cohort study

Short- and mid-term temporal variability of the human urinary microbiota: an observational cohort study

Cataloging the phylogenetic diversity of human bladder bacterial isolates

Tarnished gold—the “standard” urine culture: reassessing the characteristics of a criterion standard for detecting urinary microbes

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