Journal of medical microbiology最新文献

{"title":"Dissecting rifampicin heteroresistance in <i>Mycobacterium tuberculosis</i>: integrating whole-genome sequencing with phenotypic and clonal validation.","authors":"Katherine Vallejos-Sanchez, Diego A Taquiri-Díaz, Omar A Romero-Rodriguez, A Paula Vargas-Ruiz, Jorge Coronel, Arturo Torres, Jose L Perez-Martinez, Adiana Ochoa-Ortiz, Robert H Gilman, Louis Grandjean, Martin Cohen-Gonsaud, Mirko Zimic, Patricia Sheen","doi":"10.1099/jmm.0.002048","DOIUrl":"10.1099/jmm.0.002048","url":null,"abstract":"<p><p><b>Introduction.</b> This study underscores the critical role of identifying heteroresistant infections of <i>Mycobacterium tuberculosis</i> (Mtb) in enhancing the diagnostics of tuberculosis (TB). These conditions complicate diagnostics and treatment, underlining the need for advanced techniques to detect and characterize resistant populations effectively.<b>Hypothesis/Gap statement.</b> Current diagnostics may fail to identify heteroresistance and mixed infections, limiting the understanding of their impact on treatment outcomes.<b>Aim.</b> This pilot study aimed to phenotypically and genotypically characterize rifampicin-heteroresistant clinical isolates and assess their genetic diversity and resistance patterns.<b>Methodology.</b> A retrospective analysis of 2,917 Mtb genomes from Peru (1999-2020) was conducted using MTBseq and TB-Profiler. Techniques included indirect microscopic observation drug susceptibility, MIC determination via tetrazolium microplate assay, agar proportion method and sequencing. From each clinical isolate, three colonies were isolated from both rifampicin-supplemented (1 µg mL^-1) and drug-free media for subsequent phenotypic and genotypic characterization, including <i>rpoB</i> sequencing.<b>Results.</b> Of the 2,917 genomes analysed, 14.6% were classified as mixed infections, 3.8% exhibited heteroresistance to at least 1 drug between 21 antibiotics analysed and 0.79% were rifampicin-heteroresistant. Colonies from rifampicin-supplemented media displayed high resistance (MIC >1 µg mL^-1) with mutations such as S450L in the RpoB protein. In contrast, those from drug-free media exhibited sensitivity to rifampicin (MIC <1 µg ml^-1), harbouring other RpoB mutations including D435Y, L452P and L430P. Notably, some colonies retained WT RpoB sequences, suggesting a diversity of subpopulations within isolates.<b>Conclusion.</b> Whole-genome sequencing and phenotypic analysis confirmed the coexistence of rifampicin-susceptible and rifampicin-resistant Mtb populations within single clinical isolates. Subculturing in drug-free media favoured the selection of sensitive strains, emphasizing the critical need for advanced diagnostic tools to accurately detect and characterize heteroresistant and mixed infections. These findings pave the way for more targeted treatment strategies to combat antimicrobial resistance in TB.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12310241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic value of nanopore-based metagenomic third-generation sequencing in the diagnosis of <i>Pneumocystis jirovecii</i> infection in patients with lung cancer.","authors":"Yuyan Luo, Wei Cheng, Lei Ma, Tiantian Wang, Weirong Shi","doi":"10.1099/jmm.0.002031","DOIUrl":"10.1099/jmm.0.002031","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Pneumocystis jirovecii</i> pneumonia (PJP, formerly known as <i>Pneumocystis carinii</i> pneumonia), an opportunistic fungal infection caused by the fungus <i>P. jirovecii</i>, is a severe pulmonary infection that primarily affects immunocompromised patients, including those with lung cancer. Traditional diagnostic methods for PJP, such as Grocott-Gomori's methenamine silver staining and real-time PCR, have limitations, including low positivity and high missed diagnosis rates.<b>Gap Statement.</b> Despite the critical need for accurate and sensitive diagnostic tools for PJP, especially in immunocompromised populations, existing methods fall short in providing the necessary reliability and efficiency.<b>Aim.</b> This study aims to evaluate the efficacy of nanopore-based metagenomic third-generation sequencing in diagnosing <i>P. jirovecii</i> infection in lung cancer patients, hypothesizing that this approach may offer superior sensitivity and specificity.<b>Methodology.</b> A prospective observational study was conducted on 118 lung cancer patients with suspected pulmonary <i>P. jirovecii</i> infection at the Sixth Hospital of Nantong City, China, from January 2021 to December 2023. The identification of pathogens in bronchoalveolar lavage fluid samples was performed using both metagenomics and traditional tests.<b>Results.</b> Metagenomics showed a significantly higher detection rate of <i>P. jirovecii</i> (33.0%) compared to methenamine silver staining (4.2%) and real-time PCR (30.5%). The sensitivity, specificity and accuracy of metagenomics detection were all 100%, which is markedly superior to traditional methods. Furthermore, metagenomics also identified mixed infections with other pathogens, such as <i>Cytomegalovirus</i> and Epstein-Barr virus.<b>Conclusion.</b> Metagenomics technology demonstrates high sensitivity and specificity in diagnosing <i>P. jirovecii</i> infection, including mixed infections with other pathogens, in lung cancer patients. It provides a clear direction for clinical treatment and is a powerful tool for diagnosing PJP, contributing to improved diagnostic efficiency and accuracy, reducing misdiagnosis and missed diagnosis rates and improving clinical outcomes in these patients.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical evaluation of two commercial PCR kits for the detection of nonviral sexually transmitted infections.","authors":"Alexandre Gaudin, Nadège Hénin, Marie Gardette, Cécile Bébéar, Sabine Pereyre","doi":"10.1099/jmm.0.002037","DOIUrl":"10.1099/jmm.0.002037","url":null,"abstract":"<p><p><b>Introduction.</b> Sexually transmitted infections (STIs) are a worldwide health issue with a high number of asymptomatic cases and the possibility of multiple infections.<b>Gap statement.</b> New multiplex real-time PCR kits targeting pathogens involved in nonviral STIs are regularly launched, but only some of them have been evaluated in comparative studies.<b>Aim.</b> This study evaluated the clinical performance of two multiplex real-time PCR commercial kits for the detection of <i>Chlamydia trachomatis</i>, <i>Neisseria gonorrhoeae</i>, <i>Mycoplasma genitalium</i> and <i>Trichomonas vaginalis</i>: the Bosphore STD Urethritis Mini Bundle Kit (BK; Anatolia Geneworks) and the Viasure Sexually Transmitted Disease Real-Time PCR Detection Kit (VK; CerTest BIOTEC).<b>Methodology.</b> A total of 240 clinical specimens were evaluated. The results were compared with those of the Cobas CT/NG and TV/MG kits (Roche Diagnostics), used as reference methods.<b>Results.</b> Positive agreement ranged between 83.3% and 87.8% for the detection of <i>C. trachomatis</i>, <i>N. gonorrhoeae</i> and <i>T. vaginalis</i> using validated specimen types. For <i>M. genitalium</i> detection, positive agreement was 83.0% for the BK and 68.1% for the VK, which missed 31.9% of <i>M. genitalium</i>-positive specimens. Negative agreement ranged between 98.4% and 100% across the targeted micro-organisms. Both kits were easy to use and compatible with several DNA extraction and PCR thermal cyclers. The VK also detected the genital commensal bacteria <i>Ureaplasma</i> spp. and <i>Mycoplasma hominis</i>, which should not be targeted in STI detection kits.<b>Conclusion.</b> Both kits are convenient methods and showed good performance for the detection of nonviral STIs, but users should be aware of a lower sensitivity of the VK for the detection of <i>M. genitalium</i>.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12231094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patients in hospital with confirmed bacterial airway infection are significantly more likely to have a respiratory virus co-infection.","authors":"Yunas Panikkaveettil Hamza, Mohamed Ali Ben Hadj Kacem, Naema Hassan Al Molawi, Hadi Mohamad Yassine, Hebah Atef Mohammad AlKhatib, Fatiha Benslimane, Hanan Ibrahim Kh B Al-Remaihi, Reham Awni El Kahlout, Basema Ibrahim Ahmed El Kahlout, Hajar Al Khalili, Makiyeh Ahmed Al Khalili, Sanjay H Doiphode, Emad Bashier Ibrahim Elmagboul, Javed Akhter, Einas A/Aziz Eid Al Kuwari, Peter V Coyle","doi":"10.1099/jmm.0.001996","DOIUrl":"10.1099/jmm.0.001996","url":null,"abstract":"<p><p><b>Introduction.</b> Respiratory viruses are seen as cofactors in bacterial airway infection, often leading to bacterial pneumonia. This study addressed their role in hospitalized patients with bacterial infection confirmed by culture, 16S real-time PCR (16S RT-PCR) and 16S rRNA sequencing (16S Sequencing). The potential for using 16S RT-PCR and 16S Sequencing as diagnostic tools was also addressed.<b>Gap Statement.</b> The significance of virus infections on the lung microbiome and on bacterial superinfection in hospitalized patients needs additional evidence from real-world studies.<b>Aim.</b> The primary objective was to assess the impact of respiratory viruses on bacterial airway infection, with the secondary objective to see if 16S Sequencing had potential as a faster diagnostic tool that could augment culture.<b>Methodology.</b> A total of 83 lower airway samples - 36 bronchoalveolar lavage fluids, 39 bronchial washes, 5 sputa and 3 endotracheal aspirates - were tested for respiratory virus and bacterial co-infection. Bacteria were tested by (a) culture, (b) 16S RT-PCR and (c) 16S Sequencing. The performance of culture-independent assays against culture was assessed, and the impact of confirmed viral infections on the airway bacterial load was determined.<b>Results.</b> Virus infections reflected those co-circulating in the community and were significantly associated with culture and 16S Sequencing-confirmed bacterial infections [1-tailed mid P exact test (χ²: <i>P</i>=0.04; <i>P</i>=0.05)]. There was substantive agreement of culture and 16S RT-PCR and 16S Sequencing: kappa score: 0.66 (CI: 0.50-0.82); diagnostic accuracy 83.13% (73.32-90.46%). Virus infections were highly associated with increased bacterial load by 16S RT-PCR [2-tailed χ² (χ²: 2.4 <i>P</i>=0.003)]. Altered microbial diversity by 16S Sequencing was seen for samples stratified by culture but not by virus detection.<b>Conclusion.</b> Acute respiratory viral infections were significantly associated with bacterial airway infections confirmed by culture and 16S Sequencing. Airway dysbiosis was seen with bacterial-confirmed but not viral-confirmed infections, even though the latter were highly associated with increased bacterial loads using 16S RT-PCR. This suggests that virus infections induce changes in lung bacteria missed by culture and sequencing. The study supported a potential role for 16S Sequencing and 16S RT-PCR alongside culture.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12251083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144612769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Ebola virus - going beyond the bleeding edge.","authors":"Saadiya K Umar, Mathew A Diggle","doi":"10.1099/jmm.0.001998","DOIUrl":"10.1099/jmm.0.001998","url":null,"abstract":"<p><p>The Ebola virus (EBV) genus is responsible for severe viral haemorrhagic illness caused by a group of viruses belonging to the Filoviridae family. Five species have been identified as causative agents for Ebola virus disease (EVD). The EBV (Zaire) strain is the most predominant organism involved in recorded EVD outbreaks and has been reported as the most virulent. EVD was first identified in the Democratic Republic of Congo in 1976 and has occurred in sporadic outbreaks over the last few decades with the most recent episode in Uganda over the period September 2022-January 2023. EVD is zoonotic in nature with bats as reservoir host and humans become infected via a spillover event from contact with infected animals. EVD is transmitted through contact with infected bodily fluids. It is considered fatal with a high mortality and high infectivity rate. Treatment is generally supportive with the availability of intravenous fluids and medicines. Research into vaccine development is ongoing. EVD is a particular public health concern given the potential for global spread during an outbreak.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The bibliometric analysis of documents concerning the relationship between the microbiota and urological malignancies.","authors":"Uygar Bağcı, Özlem Ulusan Bağcı","doi":"10.1099/jmm.0.002041","DOIUrl":"10.1099/jmm.0.002041","url":null,"abstract":"<p><p><b>Introduction.</b> The microbiota, which has a major impact on both health and illness, has recently become one of the most popular research topics.<b>Hypothesis/Gap statement.</b> To the best of our knowledge, no research has undertaken a bibliometric analysis of publications examining the connection between microbiome and urological cancer to date. In this respect, it is thought that our study will contribute to the literature.<b>Aim.</b> The purpose of this study is to raise awareness of the topic by performing a bibliometric analysis of the publications examining the connection between the microbiota and the most common urological cancers, including bladder, prostate, and kidney cancers.<b>Methodology.</b> All publications about prostate, renal and bladder cancers and microbiota indexed in Web of Science between 2000 and 2024 were included in the study.<b>Results.</b> A total of 310 publications were obtained. Before 2018, there were only three or fewer publications annually; however, following 2018, the number of publications increased rapidly, reaching a peak of 77 in 2024. The USA led with 98 (31.61%) documents, followed by China (60, 19.35%) and Italy (31, 10%). With 19 publications, Hirotsugu Uemura is the most contributing author, followed by Norio Nonomura with 17. Prostate cancer accounted for 45.48% of the publications, bladder cancer for 36.77% and kidney malignancies for 17.64%.<b>Conclusion.</b> Despite the fact that microbiota has been known for 80 years, research on the connection between microbiota and cancer accelerated after the completion of the Human Microbiome Project. The number of studies examining the connection between urological cancer and microbiota peaked in 2024 and is probably going to rise. More research is required on this topic, since the correlation between microbiota and especially prostate and bladder malignancies raises the possibility that variations in microbiota may be utilized in diagnosis, treatment and prognosis.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12222730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-antifungal medications administered during fungal infections drive drug tolerance and resistance in <i>Candida albicans</i>.","authors":"Mariella Obermeier, M Alejandra Esparza-Mora, Olivia Heese, Nir Cohen, Sreejith Jayasree Varma, Pinkus Tober-Lau, Johannes Hartl, Florian Kurth, Judith Berman, Markus Ralser","doi":"10.1099/jmm.0.002046","DOIUrl":"10.1099/jmm.0.002046","url":null,"abstract":"<p><p><b>Introduction.</b> Fungal infections are increasingly concerning, particularly in immunocompromised patients. These patients often suffer from comorbidities and receive multiple, non-antifungal medications.<b>Gap Statement.</b> The effects of these co-administered medications on fungal cells - and their potential to influence antifungal drug efficacy - are poorly understood.<b>Aim.</b> This study investigates non-antifungal medications commonly administered in parallel to antifungals and evaluates their impact on fungal susceptibility.<b>Methodology.</b> We systematically reviewed clinical guidelines to identify non-antifungal medications frequently co-prescribed with antifungals. Focusing on <i>Candida albicans</i>, the most prevalent fungal pathogen, we examined whether the presence of these drugs influences antifungal responses of <i>C. albicans</i>. First, we tested the selected compounds together with antifungals in combination assays. Interactions were then characterized using checkerboard assays, and the impact on antifungal resistance and tolerance was evaluated through disc diffusion assays. To further explore these effects <i>in vivo</i>, the influence of selected antagonistic interactions on treatment efficacy was assessed using a <i>Galleria mellonella</i> model of disseminated candidiasis.<b>Results.</b> From 119 medications used to manage 40 conditions linked to a high risk of fungal infections, we identified 34 compounds that altered the effectiveness of the antifungals fluconazole (FLC) and/or anidulafungin. Most of these compounds reduced or antagonized antifungal efficacy, often due to increased resistance or tolerance. Validation in a <i>G. mellonella</i> infection model confirmed that compounds antagonistic to FLC, including loperamide, estradiol and levothyroxine, interfere with antifungal treatment efficacy in this <i>in vivo</i> model.<b>Conclusion.</b> Our findings highlight that medications frequently used by patients at risk for fungal infections can inadvertently increase fungal pathogen drug tolerance or resistance. We suggest that drugs targeting non-fungal conditions yet affecting fungal pathogens might represent an underestimated factor contributing to rising antifungal resistance and tolerance.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144736418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Marginal notes, June 2025. Artificial Stupidity.","authors":"Timothy J J Inglis","doi":"10.1099/jmm.0.002049","DOIUrl":"10.1099/jmm.0.002049","url":null,"abstract":"","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144710402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum: Species-level quantification of <i>Faecalibacterium</i> spp. in faeces of healthy Japanese adults.","authors":"Masahiro Hirasaki, Ren Kadowaki, Adeline Ang, Gaku Harata, Kenji Miyazawa, Shintaro Maeno, Miguel Gueimonde, Akihito Endo","doi":"10.1099/jmm.0.002043","DOIUrl":"10.1099/jmm.0.002043","url":null,"abstract":"","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meta-analysis of gut microbiome reveals patterns of dysbiosis in colorectal cancer patients.","authors":"Ranxin Yan, Rui Zheng, Yucheng Han, Ge Song, Ban Huo, Han Sun","doi":"10.1099/jmm.0.002042","DOIUrl":"10.1099/jmm.0.002042","url":null,"abstract":"<p><p><b>Introduction.</b> Colorectal cancer (CRC) is a malignant tumour in which dysbiosis of the gut microbiome is a contributing factor in the development of cancer. However, the species composition and species-specific changes in the gut microbiome related to CRC still require comprehensive investigation.<b>Hypothesis.</b> There is a significant difference in gut microbiome between CRC patients and healthy individuals.<b>Aim.</b> The microbiome-based association test methods are used for the association between the microbiome and host phenotypes, and linear discriminant analysis effect size (LEfSe) analysis is employed to search for microbial biomarkers associated with CRC.<b>Methodology.</b> We conducted a meta-analysis of microbiome data from multiple cohorts, totalling 1,462 samples and 320 genus-level features. Considering the data obtained under different experimental conditions, we removed the batch effect using conditional quantile regression. Then, we employed the common analysis processes and methods of microbiome data, including microbial diversity analysis, microbiome-based association test analysis and microbial differential abundance analysis.<b>Results.</b> The experimental results showed that there were significant differences in <i>α</i>-diversity between the CRC group and the healthy group, as well as in the overall microbial community (PERMANOVA <i>P</i>-value less than 0.05). LEfSe analysis also demonstrated the genus-level features enriched in the gut of CRC patients and the genus-level features enriched in the gut of healthy individuals. Notably, the batch effect-corrected data exhibit more significant performance than the raw data.<b>Conclusion.</b> Gut microbiome composition is a significant factor associated with the development of CRC. <i>Enterobacter</i> and <i>Fusobacterium</i> enriched in the gut of CRC patients may be CRC-related microbial biomarkers, while <i>Bacteroides</i> and <i>Faecalibacterium</i> enriched in the gut of healthy individuals are core genera of the healthy gut. In addition, batch effects in microbiome data caused by differences in sample handling may lead to false discoveries, especially large-scale microbiome data. These findings could deepen the understanding of the role played by gut microbes in CRC and are expected to provide recommendations for the diagnosis of cancer and the development of new microbial therapies.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12309989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}