Journal of Microbiology

Review

Metabolite-mediated mechanisms linking the urinary microbiome to bladder cancer: Thu Anh Trần, Ho Young Lee, Hae Woong Choi; J. Microbiol. 2025;63(11):e2509001. Published online November 30, 2025; DOI: https://doi.org/10.71150/jm.2509001

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Abstract PDF: Bladder cancer is the most common malignancy of the urinary tract and is a major health burden globally. Recent advances in microbiome research have revealed that the urinary tract harbors a resident microbial community, overturning the long-held belief in its sterility. Increasing evidence suggests that microbial dysbiosis and microbially derived metabolites contribute to bladder cancer carcinogenesis, progression, and therapeutic responses. Distinct microbial signatures have been observed in bladder cancer patients, with notable differences across disease stages and between primary and recurrent cases. Mechanistic studies have demonstrated that microbe-associated metabolites and toxins can drive DNA damage, chronic inflammation, extracellular matrix remodeling, and epithelial–mesenchymal transition. In addition, biofilm formation allows bacteria to evade immune responses and promotes persistent inflammation, creating a tumor-permissive niche. Beyond pathogenesis, microbial activity also influences therapeutic outcomes; for instance, some microbial pathways can inactivate frontline chemotherapy, while others generate metabolites with anti-tumor properties. Collectively, these patterns define a microbiota–metabolite–immunity axis, presenting opportunities for precision oncology. Targeting microbial pathways, profiling urinary microbiota, and harnessing beneficial metabolites offer promising advancements in biomarker discovery, prognostic refinement, and the development of novel therapeutic strategies for bladder cancer.

Protocol

Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates: Yeong-Jun Park, Jae Kyu Lim, Yeon-Ju Lee, Kae Kyoung Kwon; J. Microbiol. 2025;63(9):e2507003. Published online September 30, 2025; DOI: https://doi.org/10.71150/jm.2507003

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Abstract PDF: Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts’ immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.

Full articles

Microbial signatures in oral sites of patients with primary Sjögren’s syndrome: Association with salivary gland hypofunction: Sarah Kamounah, Arjun Sarathi, Christiane Elisabeth Sørensen, Manimozhiyan Arumugam, Anne Marie Lynge Pedersen; J. Microbiol. 2025;63(6):e2501030. Published online June 30, 2025; DOI: https://doi.org/10.71150/jm.2501030

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Abstract PDF Supplementary Material: This study aimed to determine if the microbiota in four different oral sites and the oral health status differ between patients with primary Sjögren’s syndrome (pSS), non-pSS sicca symptoms, and healthy controls. All participants underwent an interview and clinical oral examination. Stimulated whole saliva (SWS), supragingival plaque (SGP), buccal mucosa tissue (BLM), and tongue scrape (TGS) samples from 23 pSS patients, 36 patients with sicca symptoms, not fulfilling the classification criteria for pSS (non-pSS sicca), and 21 age-matched healthy controls (HC) were analyzed using V3–V4 16S rRNA gene amplicon sequencing, and determination of amplicon sequence variants (ASVs). PSS and non-pSS sicca patients did not differ with respect to oral health status, saliva flow rates, abundance of predominant genera, relative abundance on genus level or bacterial diversity in any of the oral sites. Both patient groups differed significantly from the healthy control group in the abundance of 61 ASVs across all sites. The alpha-diversity was lower in SGP from non-pSS sicca patients (p = 0.019), and in TGS from pSS patients (p = 0.04). The proportion of variation in the beta-diversity across all four sites could be explained by the diagnosis (pSS, non-pSS sicca, and HC). However, subgrouping of patients according to their stimulated salivary flow rates (SWS > 0.7 ml/min versus SWS ≤ 0.7 ml/min), revealed significantly different abundance of three ASVs in SWS, 11 in SGP, and six in TGS. Our findings suggest that hyposalivation rather than pSS itself modifies the microbial composition in oral site-specific patterns leading to oral diseases.

Microbiome therapeutic PMC72 through reverse translational research in gout: Mohammed Solayman Hossain, Hoonhee Seo, Kyung-Ann Lee, Asad ul-Haq, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Hanieh Tajdozian, Fatemeh Ghorbanian, Youjin Yoon, Indrajeet Barman, Md Sarower Hossen Shuvo, Hyun-Sook Kim, Ho-Yeon Song; J. Microbiol. 2025;63(5):e2501002. Published online May 27, 2025; DOI: https://doi.org/10.71150/jm.2501002

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Abstract PDF Supplementary Material

Gout is an inflammatory arthritis resulting from the deposition of monosodium urate crystals. Urate-lowering therapies for gout have limitations, including side effects and limited efficacy, highlighting the need for novel therapeutic approaches to improve patient outcomes. In this context, our research team conducted a microbiome analysis of fecal samples from healthy individuals and gout patients, identifying Bifidobacterium as a key biomarker. Subsequently, we isolated and identified this strain, B. longum PMC72, and demonstrated its efficacy in a gout mouse model. In potassium oxonate (PO)-induced hyperuricemia mice, PMC72 significantly alleviated nausea, gait disturbances, ankle inflammation, and improved renal health. These effects were associated with marked reductions in oxidative stress markers, including serum uric acid, blood urea nitrogen, hepatic xanthine oxidase, and malondialdehyde (MDA) levels in serum, liver, and joint samples, as well as the downregulation of inflammation and uric acid transport-related gene expression in kidney samples. These benefits were comparable to those treated with Febuxostat, a standard urate-lowering therapy for gout. Furthermore, gut microbiome analysis revealed that PMC72 restored dysbiosis induced by hyperuricemia, contrasting with the reduced microbial diversity observed with febuxostat alone, and showed a complete recovery to eubiosis when combined with Febuxostat. These findings position PMC72 as a promising microbial therapeutic candidate for gout management, demonstrating significant development potential and serving as a benchmark for reverse translational microbiome-based therapeutic research.

Citations

Citations to this article as recorded by

Characterization of Gut Microbiota of Honey Bees in Korea
Md Sarower Hossen Shuvo, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Indrajeet Barman, Mohammed Solayman Hossain, Yoonkyoung Jeong, Hwasik Jeong, Sangrim Kim, Hoonhee Seo, Ho-Yeon Song
Polish Journal of Microbiology.2025;[Epub] CrossRef
Quantitative assessment of microbial dynamics in livestock manure and municipal wastewater treatment plants
Geon Choi, Hokyung Song, Tatsuya Unno
Applied Biological Chemistry.2025;[Epub] CrossRef

Research Article

Synbiotic combination of fructooligosaccharides and probiotics ameliorates the metabolic dysfunction-associated steatotic liver disease: Sang Yoon Lee, Su-Been Lee, Goo-Hyun Kwon, Seol Hee Song, Jeong Ha Park, Min Ju Kim, Jung A Eom, Kyeong Jin Lee, Sang Jun Yoon, Hyunjoon Park, Sung-Min Won, Jin-Ju Jeong, Ki-Kwang Oh, Young Lim Ham, Gwang Ho Baik, Dong Joon Kim, Satya Priya Sharma, Ki Tae Suk; J. Microbiol. 2025;63(2):e2411002. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411002

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