UNDERSTANDING THE CHALLENGES IN THE STUDY AND EVALUATION OF UROBIOMES Urobiome, also known as the urinary microbiome, is the term used to describe the microbial population that resides in the urinary tract. The last 10 years have seen them come into the limelight because of advancements in diagnostic technologies. Men and women differ in their urobiomes, and it also vary depending on their age.1 It was found that several Lactobacillus species are present in the urobiome of healthy women; some of these species may prevent the growth of Escherichia coli in the urinary tract. The other most common genera found in women are Gardnerella, Sneathia, Staphylococci, and Enterobacteriaceae. While Lactobacillus spp. have been identified in the microbiome of the male urethra, their presence in the microbiome of the male bladder is less certain. The most common organisms comprising the male urobiome are Sneathia, Veillonella, Corynebacterium, Prevotella, Gardnerella, and Streptococcus.2 In urobiome research, two complementary assays, such as enhanced urine culture techniques (EUCT) and next-generation sequencing (NGS) of 16S ribosomal RNA (rRNA), are commonly employed. Current research on urobiomes has dispelled the myth that urine is sterile, thus making it possible to conduct research on other sterile body sites. One of the EUCT procedures, the expanded quantitative urine culture (EQUC), strengthened the evidence that the bacteria discovered by the NGS are still alive. Over the last few years, EQUC has been used in clinical laboratories as it can identify a variety of bacteria and fungi that the conventional urine culture would miss, by using a vast amount of urine samples subjected to various culture conditions. It is only recommended when traditional urine cultures are negative, and there are unexplained clinical complaints. The urobiome is a novel field with scant literature. On the other hand, urobiome research studies may significantly influence our comprehension of the etiology of urogenital illnesses and may even open up new avenues of inquiry. As a result, the upcoming years will present ideal conditions for additional study into the diagnosis, management, and preventive measures of urological disorders.3 The fundamental strategy for microbiome sampling is selecting noninvasive samples with minimal to no cross-contamination. Urine is a good material for urobiome investigations because it is easy to collect and has few compounds that can interfere with the amplification process. Finding proof of microbial contamination of the lower genitalia is not impossible, though. However, urine frequently contains large levels of salt, which prolongs the viability of organisms and nucleic acids. Midstream urine is a convenient sample to discover intra-bladder urobiome communications, such as those associated with interstitial cystitis, bladder pain syndrome, UTIs, and bladder cancer. This contrasts with the methods of transurethral catheterization and suprapubic aspiration for collecting urine samples. These methods are more invasive, but they are less likely to be contaminated by bacteria from the genitalia and rectal tract.4 The genitourinary system is frequently traversed by kidney stones, which can contaminate specimens with bacteria. For patients with renal calculi, surgical procedures such as nephrolithotomy may provide more accurate and enhanced urobiome analysis. If researchers wish to look into the connection between bacterial composition and stone disease, they must take into account the original site of the clinical material. Despite the operating rooms being clean, they are not totally sterile. It is also very helpful to discuss the precise composition of the material and the methods of removal with the surgeon in order to rule out contamination. The extracorporeal shock wave lithotripsy (ESWL) is a non-invasive technique used to extract tiny stone pieces, and percutaneous nephrolithotomy is a minimally invasive procedure to remove large and complex renal calculi. The analysis of postoperative urine samples could hypothetically indicate the composition of urobiomes from that particular anatomical site where the procedure was performed. However, it might be challenging to distinguish it from uropathogens that cause UTIs. Since ESWL may potentially loosen biofilms at the bladder, thereby releasing bacteria, it is therefore important to fully comprehend where the stone sample is located.5 Although genetic studies have already been used to differentiate between the gut, vaginal, and urine microbiomes, EUCTs may be useful in assessing the condition of the microbiota.6 Gene libraries like Kyoto Encyclopedia of Genes and Genomes could validate the ontology of a greater number of confirmed genes (KEGG). It was found that there were multiple specific genes linked to sulfamethoxazole/trimethoprim (SXT/TMT) resistance in the urobiomes of kidney transplant recipients who had frequent SXT/TMT prophylaxis.7 Despite several important findings on the urobiome assembly in recent years, generalization remains challenging. Variations in the course of bladder cancer appear to be very visible and likely to have an impact on prognosis. All of the eukaryotic species (protozoa and fungi) that comprise the urobiome, however, have not yet been studied. This is primarily due to the difficulty of extracting DNA and doing further analysis. The additional disadvantages include the absence of standard techniques for DNA isolation and sample collection, which have a significant impact on the approach’s results and make it difficult to compare results between different research sites. While metagenomics has made it possible to study microbiomes in sterile body areas, its inability to distinguish between living and dead organisms is by far its biggest drawback. Thus, there is much opportunity for future research on the urobiome.
Khan et al. (Wed,) studied this question.