Biology subjects

Khemmani, M.

Publications and source records attributed to Khemmani, M..

3 recordsLinked to original sources

bioRxiv2026

A comparison of two culture and three sequencing methods for detection of the urobiome

Standard urine culture (SUC), the clinical reference method, is optimized for fast-growing aerobes and misses much of the urinary microbiota. Enhanced culture and sequencing methods have rarely been compared on the same specimens. We compared five methods (SUC, expanded quantitative urine culture [EQUC], short-read V4 16S rRNA gene sequencing, long-read near full-length 16S rRNA gene sequencing, and PCR-free long-read shotgun metagenomic sequencing) on parallel aliquots of urine from pregnant participants screened for asymptomatic bacteriuria. Of 98 cultured samples, 98 (100.0%) were EQUC-positive while 85 (86.7%) SUC-positive. EQUC detected 102 species, but SUC only detected 41. Short-read 16S rRNA gene sequencing, long-read 16S rRNA gene sequencing, and shotgun sequencing were positive for 188/188, 186/188 and 139/139 samples, detecting 195, 69 and 528 species, respectively. In the 79 samples positive by EQUC and all three sequencing methods, sequencing profiles resembled each other more than culture profiles, and SUC captured only a subset of taxa detected by every other method. Shotgun sequencing gave the broadest taxonomic coverage and was the only sequencing method to identify Escherichia coli to the species level. With EQUC, it outperformed both 16S sequencing methods in detecting Gardnerella vaginalis and distinguishing Lactobacillus species, and it resolved six Gardnerella species, three detected by no other method. Long-read 16S rRNA gene sequencing gave the most confident amplicon-based species assignments, whereas culture better recovered Corynebacterium and Staphylococcus species. No single method was best across all endpoints, but long-read shotgun metagenomics provided the broadest species-level view. Method choice should match the research or clinical question; outcome-based studies are needed to establish clinical utility.

bioinformatics↗

bioRxiv2025

Evidence for an indigenous female mouse urobiome

Mice have been used as a valuable model of understanding pathophysiological mechanisms of urinary tract infection for almost six decades. Mice offer many advantages including genetic manipulation to test the role of genes and mechanisms, the availability of germ-free mice, and similarities to humans in innate immune defenses and the strain-dependent presence of vesicoureteral reflux. However, like with humans, the mouse bladder urine above the urinary sphincter has generally been assumed to be sterile. Yet, given the presence of urobiomes in other mammals and the emerging role of the human urobiome in the defense of the urinary bladder and upper urinary tract, the existence of a mouse urobiome should be critically examined as indigenous microbiota may influence experimental results. To determine if an indigenous murine urobiome exists, we obtained expressed urine from two sets of female C57BL/6J mice during three different intervals using two different extraction and sequencing methods and analyzed them simultaneously by a single method. For one set, we also obtained urine by suprapubic aspiration, which we compared to the paired expressed urine samples. We conclude that an indigenous murine urobiome exists and that expressed urine contains post-urethral microbes.

microbiology↗

bioRxiv2023

Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates

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, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial 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 we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder E. coli isolates and 387 gut E. coli isolates supports the hypothesis that phylogroup distribution and functions of E. coli strains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.

microbiology↗