Global Meta-analysis of Urine Microbiome: Colonization of Polycyclic Aromatic Hydrocarbon–degrading Bacteria Among Bladder Cancer Patients

Bukavina, Laura; Isali, Ilaha; Ginwala, Rashida; Sindhani, Mohit; Calaway, Adam; Magee, Diana; Miron, Benjamin; Correa, Andres; Kutikov, Alexander; Zibelman, Matthew R.; Ghannoum, Mahmoud A.; Retuerto, Mauricio; Ponsky, Lee; Markt, Sarah C.; Uzzo, Robert; Abbosh, Philip

doi:10.1016/j.euo.2023.02.004

Cited by 16 publications

(5 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In 2019, Liu et al. (2019) identified high expression of Ralstonia in BCa tissues, and meanwhile, the presence of Ralstonia in BCa was similarly highlighted in a recent study by Bukavina et al. (2023) Sphingomonas is widely present in the environment and has an environmental restorative role ( Asaf et al., 2020 ).…”

Section: Discussionmentioning

confidence: 86%

The bladder microbiome of NMIBC and MIBC patients revealed by 2bRAD-M

Sun

Xia

Zhong

et al. 2023

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

BackgroundBladder cancer (BCa) is the most common malignancy of the urinary tract which can be divided into non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC), and their microbial differences are not fully understood. This study was conducted by performing 2bRAD sequencing for Microbiome (2bRAD-M) on NMIBC and MIBC tissue samples to investigate the microbiota differences between NMIBC and MIBC individuals.MethodsA total of 22 patients with BCa, including 7 NMIBC and 15 MIBC, were recruited. Tumor tissues were surgically removed as samples and DNA was extracted. Type IIB restriction endonucleases were used to enzymatically cleave the microbial genome for each microbe’s tag and map it to species-specific 2bRAD markers to enable qualitative and quantitative studies of microbes between MIBC and NMIBC tissues.ResultsA total of 527 species were detected. The microbial diversity of NMIBC tissues was significantly higher than that of MIBC tissues. Microbial composition of the two tumor tissues was similar, where Ralstonia_sp000620465 was the most dominant species. 4 species (Acinetobacter_guillouiae, Anoxybacillus_A_rupiensis, Brevibacillus_agri and Staphylococcus_lugdunensis) were enriched in NMIBC, while Ralstonia_mannitolilytica, Ralstonia_pickettii, and Ralstonia_sp000620465 were overrepresented in MIBC. 252 discriminatory character taxa were also revealed by linear discriminant analysis effect sizea (LEfSe). Species importance point plots identified Ralstonia_sp000620465, Cutibacterium_acnes and Ralstonia_pickettii as the three most important species between the two groups. Meanwhile, functional annotation analysis showed 3011 different COGs and 344 related signaling pathways between MIBC and NMIBC microbiome.ConclusionThis first 2bRAD-M microbiome study on MIBC and NMIBC tissues revealed significant differences in the microbial environment between the two groups, which implies a potential association between tumor microbial dysbiosis and BCa, and provides a possible target and basis for subsequent studies on the mechanisms of BCa development and progression.

show abstract

Section: Discussionmentioning

confidence: 86%

The bladder microbiome of NMIBC and MIBC patients revealed by 2bRAD-M

Sun

Xia

Zhong

et al. 2023

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Compared with catheterized urines, BCa washouts showed specific increases of some taxa, such as Burkholderiaceae , whereas midstream urine was enriched with Streptococcus . In the same way, Bukavina et al [17] demonstrated that catheterized urine samples showed lower genera variability combined with a lower contamination than voided urine samples. Thus, to explore the urobiome, many scientists prefer the use of urine samples from a urethral catheter [21] .…”

Section: Discussionmentioning

confidence: 83%

“…Owing to the absence of standardized urine sample collection, common investigation procedures, and assessment of intra- and interindividual variability [16] , it is not surprising to find conflicting data in urobiome studies. In fact, a recent global meta-analysis of urine microbiome reported that the type of urine collection methodology biased the genera abundance because of skin, vaginal, and urethral contamination in the first-morning (FM) catch samples [17] .…”

Section: Introductionmentioning

confidence: 99%

Microbiome Profiling in Bladder Cancer Patients Using the First-morning Urine Sample

Nardelli,

Aveta,

Pandolfo

et al. 2024

European Urology Open Science

View full text Add to dashboard Cite

“…In order to accomplish this, the initial steps such as sample collection and sample preparation are of uttermost importance. Sample collection for the urinary microbiome can be troublesome as the most common and only noninvasive method, midstream urine sampling, can become contaminated from surrounding areas of the urethra, skin and genital tract; and thus, create unreliable/contaminated taxonomic profiles and lead to term genitourinary/urogenital microbiota for microbial communities obtained from voided urine samples in females [ 26 , 27 , 28 , 29 ].…”

Section: Urogenital Microbiomementioning

confidence: 99%

“…It is worth noting that the composition of the urogenital microbiota varies between individuals and can be influenced by factors such as age, sex, diet and health status [ 8 , 9 ]. Changes in composition of endogenous urinary microbiota have been commonly associated with urinary tract infection, but it has also been correlated with kidney stones, incontinence, bladder cancer, prostate inflammation and cancer, among other things [ 29 , 37 , 38 ]. Since most of this insight comes from high-throughput DNA sequencing efforts, it is not actual microorganisms that are being observed, but instead it is their DNA fragments these conclusions have been drawn upon.…”

Section: Urogenital Microbiomementioning

confidence: 99%

Current Viewpoint on Female Urogenital Microbiome—The Cause or the Consequence?

et al. 2023

View full text Add to dashboard Cite

An increasing amount of evidence implies that native microbiota is a constituent part of a healthy urinary tract (UT), making it an ecosystem on its own. What is still not clear is whether the origin of the urinary microbial community is the indirect consequence of the more abundant gut microbiota or a more distinct separation exists between these two systems. Another area of uncertainty is the existence of a link between the shifts in UT microbial composition and both the onset and persistence of cystitis symptoms. Cystitis is one of the most common reasons for antimicrobial drugs prescriptions in primary and secondary care and an important contributor to the problem of antimicrobial resistance. Despite this fact, we still have trouble distinguishing whether the primary cause of the majority of cystitis cases is a single pathogen overgrowth or a systemic disorder affecting the entire urinary microbiota. There is an increasing trend in studies monitoring changes and dynamics of UT microbiota, but this field of research is still in its infancy. Using NGS and bioinformatics, it is possible to obtain microbiota taxonomic profiles directly from urine samples, which can provide a window into microbial diversity (or the lack of) underlying each patient’s cystitis symptoms. However, while microbiota refers to the living collection of microorganisms, an interchangeably used term microbiome referring to the genetic material of the microbiota is more often used in conjunction with sequencing data. It is this vast amount of sequences, which are truly “Big Data”, that allow us to create models that describe interactions between different species contributing to an UT ecosystem, when coupled with machine-learning techniques. Although in a simplified predator—prey form these multi-species interaction models have the potential to further validate or disprove current beliefs; whether it is the presence or the absence of particular key players in a UT microbial ecosystem, the exact cause or consequence of the otherwise unknown etiology in the majority of cystitis cases. These insights might prove to be vital in our ongoing struggle against pathogen resistance and offer us new and promising clinical markers.

show abstract

Global Meta-analysis of Urine Microbiome: Colonization of Polycyclic Aromatic Hydrocarbon–degrading Bacteria Among Bladder Cancer Patients

Cited by 16 publications

References 39 publications

The bladder microbiome of NMIBC and MIBC patients revealed by 2bRAD-M

The bladder microbiome of NMIBC and MIBC patients revealed by 2bRAD-M

Microbiome Profiling in Bladder Cancer Patients Using the First-morning Urine Sample

Current Viewpoint on Female Urogenital Microbiome—The Cause or the Consequence?

Contact Info

Product

Resources

About