MicrobiologyOpen最新文献

{"title":"Assessing the in Planta Efficacy of Oxathiapiprolin as a Potential Treatment for Kauri Dieback Disease.","authors":"Hannah F Robinson, Jade T T Palmer, Monica L Gerth","doi":"10.1002/mbo3.70066","DOIUrl":"10.1002/mbo3.70066","url":null,"abstract":"<p><p>Phytophthora agathidicida, a plant pathogenic oomycete, causes fatal dieback disease in New Zealand kauri trees (Agathis australis). Currently, few treatments exist to prevent or cure this infection. Previous research has demonstrated the potent in vitro inhibition of multiple lifecycle stages of P. agathidicida by the oomycide oxathiapiprolin. In this study, we have evaluated the efficacy of oxathiapiprolin in planta as either a protective or curative treatment. Kauri seedlings (1-2 years old) were treated with 10 or 50 mg of oxathiapiprolin, in the form of Zorvec Enicade, per seedling as a soil drench either before (7 days) or after (15 days) inoculation with P. agathidicida NZFS 3770 to test for protective and curative activities, respectively. Results showed that oxathiapiprolin treatments successfully protected the kauri seedlings from disease, with the higher dose (50 mg) demonstrating greater efficacy. However, the treatments did not cure kauri seedlings already infected with P. agathidicida, likely because the infection was already well-established by the time of treatment. This study demonstrates that, while oxathiapiprolin shows protective effects against P. agathidicida infection in kauri seedlings, its lack of curative properties significantly limits its potential as a practical tool for managing kauri dieback disease.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":"e70066"},"PeriodicalIF":4.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Examine the Impact of Self-Medicated Antibiotics on Gut Bacterial Diversity From COVID-19 Patients in Gopalganj, Bangladesh","authors":"Rabeya Khanam,&nbsp;Md. Yamun Hasan,&nbsp;Abdul Malek,&nbsp;Sazzad Hossain Sagor,&nbsp;Chandan Sikder,&nbsp;Md. Sahabuddin","doi":"10.1002/mbo3.70063","DOIUrl":"10.1002/mbo3.70063","url":null,"abstract":"<p>The COVID-19 pandemic has claimed millions of lives globally and continues to pose a threat to public health. It has influenced the self-medication (SM) of antibiotics during the pandemic due to coronaphobia, similar symptoms to flu, cold, respiratory illnesses, insufficiency of reverse transcription polymerase chain reaction (PCR) test, and easy access to the drug, and so forth. Self-medication with antibiotics (SMA) raises the resistance profile of gut bacteria to antibiotics. This cross-sectional study evaluated the connection between antibiotic consumption and the antibiotic-resistant patterns of gut bacteria isolated from 29 COVID-19 patients in Gopalganj, Bangladesh. Standard microbiological tests and molecular methods such as PCR and <i>16S rRNA</i> sequencing were performed for bacterial identification. The disk diffusion method was used for antibiotic susceptibility testing. A total of 48 bacterial isolates, including <i>Escherichia coli</i> (<i>n</i> = 24), <i>Klebsiella pneumoniae</i> (<i>n</i> = 7), <i>Pseudomonas aeruginosa</i> (<i>n</i> = 7), <i>Salmonella</i> spp. (<i>n</i> = 4), <i>Shigella flexneri</i> (<i>n</i> = 3), <i>Providencia alcalifaciens</i> (<i>n</i> = 1), <i>Proteus vulgaris</i> (<i>n</i> = 1), and <i>Yersinia enterocolitica</i> (<i>n</i> = 1), were identified. The prevalence of SM and multidrug resistance patterns was 65.5% and 89.58%, respectively. Self-medicated COVID-19 patients reported higher antibiotic resistance than patients who consumed prescribed antibiotics regularly. This study demonstrated that, in addition to SMA, other factors such as diet, water, sanitation, and so on can contribute to the development of antibiotic-resistant bacteria. A healthy lifestyle and awareness while using antibiotics can limit our gut microbes from becoming antimicrobial-resistant.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145192024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Characterization of Pan-Drug Resistant Klebsiella pneumoniae KPNW Isolated From UTI Patient in Bangladesh","authors":"Md. Wahid Murad,&nbsp;G. M. Shah Poran,&nbsp;Kalpana Baidya,&nbsp;Nazmul Ahsan","doi":"10.1002/mbo3.70064","DOIUrl":"10.1002/mbo3.70064","url":null,"abstract":"<p><i>Klebsiella pneumoniae</i> is a Gram-negative opportunistic bacterial pathogen and a common cause of urinary tract infections (UTIs). In Bangladesh, a rapid increase in antibiotic resistance in <i>K. pneumoniae</i>, with a concerning prevalence of pan-drug resistant (PDR) isolates, is severely limiting treatment options and posing a threat to public health. <i>K. pneumoniae</i> isolate KPNW was found in a clinical urine sample of a UTI patient from Dhaka, Bangladesh. In the disc diffusion test, KPNW showed resistance to 28 antibiotics across multiple classes, including carbapenems and colistin. Whole genome sequencing, assembly, and annotation yielded a 5.48 Mb genome encoding 5554 genes. Four plasmid replicons—lncFIB(K), lncFII(K), lncN2, and lncX3—were identified, all having known associations with antimicrobial resistance (AMR). KPNW belongs to multilocus sequence typing sequence type ST15 and capsular type KL112 and O1v2. We detected 42 AMR genes, including extended-spectrum β-lactamases, carbapenemase <i>bla</i>_NDM-1, and other families of AMR determinants, which altogether confer resistance to all clinically relevant antibiotics. We also identified 58 virulence determinants, including types 1 and 3 fimbrial proteins, enterobactin, and type VI secretion system proteins. However, major hypervirulence determinants were absent. Heavy metal resistance operons for arsenic, copper, and silver resistance were also detected. KPNW harbors multiple mobile genetic elements, some adjacent to AMR and virulence genes, indicating its capacity for horizontal gene acquisition and evolution as PDR, virulent, and heavy metal resistant. The findings of this study will have implications in public health and help better understand future trends of infections, plan effective treatment strategies, and surveillance.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145192059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insertion of Fluorescent Proteins Near the Plug Domain of MotB Generates Functional Stator Complexes","authors":"Jyoti P. Gurung,&nbsp;Pietro Ridone,&nbsp;Anaïs Biquet-Bisquert,&nbsp;Gary Bryant,&nbsp;Francesco Pedaci,&nbsp;Ashley L. Nord,&nbsp;Matthew A. B. Baker","doi":"10.1002/mbo3.70056","DOIUrl":"https://doi.org/10.1002/mbo3.70056","url":null,"abstract":"<p>Many bacteria swim by the rotation of the bacterial flagellar motor (BFM). The BFM is powered by proton translocation across the inner membrane through the heteroheptameric MotA₅MotB₂ protein complex. Two periplasmic domains of MotB are critical in activating BFM rotation: (1) the peptidoglycan (PG) binding domain that anchors MotB in the PG layer and (2) the plug domain that modulates the proton flow. Existing cytoplasmic fluorescent probes have been shown to negatively affect motor rotation and switching. Here, we inserted a fluorescent probe in the periplasm near the plug of MotB to circumvent issues with cytoplasmic probes and for possible use in observing the mechanism of plug-based regulation of proton flow. We inserted green fluorescent protein and improved light-oxygen-voltage (LOV), a fluorescent version of the LOV domain, in four periplasmic locations in MotB. Insertions near the plug retained motility but showed limited fluorescence for both fluorophores. Additional short, flexible glycine–serine linkers improved motility but did not improve brightness. Further optimization is necessary to improve the fluorescence of these periplasmic probes.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.70056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145057748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Human Polyomavirus BK Genome Analysis in BKPyV Induced Rodent Cell Lines","authors":"Setsuko Shioda,&nbsp;Fumio Kasai,&nbsp;Midori Ozawa,&nbsp;Azusa Ohtani,&nbsp;Masashi Iemura,&nbsp;Ken Watanabe,&nbsp;Arihiro Kohara","doi":"10.1002/mbo3.70061","DOIUrl":"10.1002/mbo3.70061","url":null,"abstract":"<p>In this study, we analyzed the BK polyomavirus (BKPyV) genome derived from three rodent cell lines established from experimentally induced tumors by injecting BKPyV into newborn rodents. Three cell lines (Vn-324, In-1024, and Vn1919) were recently deposited in the JCRB Cell Bank (Japanese Collection of Research Bioresource Cell Bank). Vn-324 was established from a hamster choroid plexus papilloma induced by BKPyV Gardner strain wild-type 501 (<i>wt-501</i>). This cell line was reported to be negative for the large T-antigen using indirect immunofluorescence. In this study, we examined the large T-antigen expression using the reverse-transcriptase-polymerase chain reaction (RT-PCR). In-1024 cells were established from hamster insulinoma. The strain of BKPyV from which were induced has not been reported. Vn1919 was established from a mouse ependymoma induced by the plaque morphology mutant 522 (<i>pm-522</i>). The noncoding control region (NCCR) of BKPyV derived from Vn-324 genomic DNA and <i>wt</i>-501 had the same structure, whereas the NCCR of BKPyV derived Vn1919 genomic DNA and <i>pm-522</i> had the same structure. But the NCCR derived In-1024 was unique. We revealed that BKPyV derived from In-1024 genomic DNA had a large deletion in the viral proteins 1, 2, and 3 (VP1,(VP1, VP2, and VP3) coding region. This variant may be a proliferation-defective mutant, which was expanded in human embryonic kidney cells with other mutants. These findings provide insights into the role of NCCR mutations in viral oncogenesis.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.70061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibacterial and Antibiofilm Activity of Closantel Against Staphylococcus epidermidis","authors":"Wu Pingyun,&nbsp;Wu Yuan,&nbsp;Wu Ruolan,&nbsp;Wan Xueting,&nbsp;Yang Qi,&nbsp;She Pengfei","doi":"10.1002/mbo3.70062","DOIUrl":"https://doi.org/10.1002/mbo3.70062","url":null,"abstract":"<p><i>Staphylococcus epidermidis</i> is recognized as the major cause of implanted indwelling medical device-related infections. The ability of <i>S. epidermidis</i> to form biofilms largely increases its resistance to conventional antibiotics, which is the major cause of treatment failure. Therefore, there is a pressing need to discover novel antimicrobials against <i>S. epidermidis</i> biofilms. In this study, Closantel (Clos), an antiparasitic drug, was repurposed to be effective against <i>S. epidermidis</i> planktonic cells with the minimal inhibitory concentration values of 0.25–0.5 μg/mL. Clos exhibited potent biofilm inhibition at ≥ 0.5 μg/mL and achieved effective eradication at ≥ 1 μg/mL. Notably, Clos induced lower resistance in <i>S. epidermidis</i> compared to Rifampicin. Mechanism study indicated that Clos exerted the bactericidal activity mainly through inducing bacterial cell membrane depolarization and further disruption. And the antibiofilm activity of Clos could be partially due to the inhibition of initial adhesion and extracellular polysaccharides production. In addition, CCK-8 assay showed that Clos at 16 μg/mL had limited cytotoxicity in A2780, HaCaT and 293 T cells. In conclusion, this study demonstrates that Clos, a molecule targeting bacterial cell membranes, exhibits strong antimicrobial and antibiofilm effects in vitro against <i>S. epidermidis</i>. Although, side effects were reported in mammals, developing Clos derivatives could be still an effective therapeutic strategy to treat <i>S. epidermidis</i>-related infections.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.70062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic Characterization of Pectinase-Producing Alkaliphilic Microbial Isolates From Lake Bogoria, Baringo County, Kenya","authors":"Kevin Raymond Oluoch,&nbsp;Edward Kirwa Muge,&nbsp;Maxwell Omondi Onyango,&nbsp;Francis Jakim Mulaa","doi":"10.1002/mbo3.70058","DOIUrl":"https://doi.org/10.1002/mbo3.70058","url":null,"abstract":"<p>Alkaline pectinases are in demand in industrial processes that require the degradation of plant pectins at high pH, for example, removal of pectin stains from fabrics, cutlery, and porcelain; treatment of pectic wastewater; fermentation of coffee, tea, and cocoa; manufacture of poultry and animal feeds, and processing of textiles, and so forth. The present study aimed to (a) screen four alkaliphilic microbial isolates, previously obtained from samples collected around Lake Bogoria (soda lake), Baringo County, Kenya, for alkaline pectinases, and (b) characterize the pectinase-producers. The screening data revealed that all the isolates were pectinase producers, exhibiting catalytic activities that ranged from 1.4 to 1.6 pectinolytic indices (PI) (primary screening) and 0.04–0.15 U/mL (secondary screening). These isolates' colonies, which featured smooth textures and umbonate elevations, were moist, white, or cream. Their cells were motile, aerobic rods that were Gram-, catalase-, and oxidase-positive. In addition, they a) utilized inositol, sucrose, lactose, and glucose, and b) hydrolyzed starch, pullulan, casein, and gelatin. Furthermore, they grew optimally at pH 10.5, 45°C, and in the absence of NaCl but tolerated growth at higher temperatures (up to 55°C) and saline conditions [up to 12.5% (w/v) NaCl]. No growth was detected at neutral pH. Based on these phenotypic characteristics, the indigenous pectinase-producing microbial isolates from Lake Bogoria were identified as thermo-halo-tolerant obligate alkaliphiles that belonged to the species <i>Bacillus halodurans</i>. The alkaline pectinases that they produced can potentially find applications in the fore-mentioned local industrial processes, if harnessed.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.70058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145012840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Analysis for the Safety Assessment of a Potential Probiotic Strain Pediococcus pentosaceus BBS1 Isolated From Lao Fermented Bamboo Shoots (Nor Mai Som)","authors":"Viengvilaiphone Botthoulath,&nbsp;Ida F. Dalmacio,&nbsp;Francisco B. Elegado,&nbsp;Lawrence Yves Uy,&nbsp;Hsiang-Chun Lin","doi":"10.1002/mbo3.70048","DOIUrl":"https://doi.org/10.1002/mbo3.70048","url":null,"abstract":"<p>Currently, there is an increasing use of whole-genome sequencing (WGS) studies to investigate the molecular taxonomy, metabolic properties, enzyme capabilities, and bioactive substances of lactic acid bacteria (LAB) species. In this study, the genome of strain <i>Pediococcus pentosaceus</i> BBS1 was sequenced using the Illumina HiSeq. 2500 platform to determine its classification, annotate its main features, and evaluate its safety characteristics. Results showed an average nucleotide identity (ANI) value of 99.60% for <i>Pediococcus pentosaceus</i> BBS1. <i>P. pentosaceus</i> BBS1 genome was composed of a 1,840,613 bp circular chromosome with a GC content of 37.23%, which contained 1778 predicted protein-coding sequences (CDSs). Rapid Annotation using Subsystems Technology (RAST) linked to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that strain BBS1 possesses <span>l</span>-acetate dehydrogenase (<i><span>l</span>-LDH</i>; EC 1.1.1.27) and <span>d</span>-lactate dehydrogenase (<i><span>d</span>-LDH</i>; EC 1.1.1.28), which are the genes responsible for lactic acid production. Additionally, it was found to contain <i>linamarase</i>, or <i>β-glucosidases</i> (EC 3.2.1.21), a gene that functions for cyanide degradation. Significantly, the safety studies carried out using WGS confirmed the absence of virulence factors, biogenic amines, and antibiotic-resistance genes in BBS1. Our previous research conducted in this study have shown that BBS1 possesses probiotic features, including tolerance to the simulated artificial gastrointestinal tract, bacterial adhesion, antibacterial activity, and antioxidant function. The findings provided herein significantly enhanced the known information on BBS1, supporting its potential application in promoting health through food products.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.70048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145012841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Profiling Listeria monocytogenes in Hummus, Fresh Produce, and Food Processing Environments in the Western Cape, South Africa","authors":"Samantha Anne du Toit,&nbsp;Pieter A. Gouws,&nbsp;Diane Rip","doi":"10.1002/mbo3.70060","DOIUrl":"https://doi.org/10.1002/mbo3.70060","url":null,"abstract":"<p><i>Listeria monocytogenes</i> is pervasive in agricultural environments and difficult to eradicate from food-processing facilities. Consequently, various foods become contaminated, posing health risks to immunocompromised individuals. This surveillance study aimed to enhance the understanding of the genetic diversity, virulence, plasmid content, sanitizer tolerance, and antibiotic resistance of <i>L. monocytogenes</i> from ready-to-eat (RTE) hummus, fresh produce and food-processing environments in the Western Cape, South Africa (2018–2021). Sixty <i>L. monocytogenes</i> isolates were classified as lineage I or lineage II using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Lineage I was notably prevalent overall (57%; <i>n</i> = 34) and significantly associated with fresh produce (88%; <i>n</i> = 7) (<i>p</i> = 0.04). Whole-genome sequencing (WGS) and bioinformatic analysis characterized a subset of 20 <i>L. monocytogenes</i> isolates into seven sequence types (STs) (ST1, ST2, ST3, ST5, ST101, ST121, ST204), and three serotypes (1/2a, 1/2b, 4b). ST204 (38%; <i>n</i> = 3) was most prevalent in the food-processing environment, ST5 (50%; <i>n</i> = 3) in fresh produce, and ST5 (33%; <i>n</i> = 2), ST101 (33%; <i>n</i> = 2) and ST121 (33%; <i>n</i> = 2), in RTE hummus. However, no single serotype or ST was significantly overrepresented in any category (<i>p</i> &gt; 0.05). All isolates carried both <i>Listeria</i> pathogenicity island (LIPI)-1 and LIPI-2 gene clusters. Two isolates (ST1 and ST3) contained all genes comprising LIPI-3. Two ST5 isolates from RTE hummus contained the <i>tetM</i> gene. Isolates from different origins contained the <i>emr</i>C, <i>bcr</i>ABC or <i>qac</i>H genes conferring tolerance to benzalkonium chloride, a quaternary ammonium compound class of sanitizer. RTE hummus, fresh produce and the food-processing environment are susceptible to contamination by diverse and virulent <i>L. monocytogenes</i> strains.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.70060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145012322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Freezing of Vaginal Swabs Prior to DNA Purification Does Not Statistically Significantly Affect Microbiome Composition","authors":"Khaled Saoud Ali Ghathian,&nbsp;Julie Elm Heintz,&nbsp;Sarah Mollerup,&nbsp;Sarah Juel Paulsen,&nbsp;Karen Angeliki Krogfelt,&nbsp;Niels Frimodt-Møller,&nbsp;Katrine Hartung Hansen,&nbsp;Sofie Ingdam Halkjær,&nbsp;Anne Holm,&nbsp;Mette Pinholt,&nbsp;Andreas Munk Petersen","doi":"10.1002/mbo3.70053","DOIUrl":"https://doi.org/10.1002/mbo3.70053","url":null,"abstract":"<p>Vaginal microbiome profiles may be affected by storage conditions, especially after human DNA depletion, yet systematic evaluations are limited. To assess the short-term impact of storage temperature on vaginal microbiome composition following host DNA depletion. Vaginal swabs were stored at 5°C (48 h), −20°C (3 weeks), or −80°C (3 weeks). DNA was extracted using the MolYsis Complete5 kit and profiled with MetaPhlAn4. Alpha and beta diversity metrics and differential abundance tests (CLR-transformed, Kruskal–Wallis and Wilcoxon with FDR correction) were applied. Internal quality controls (IQCs) assessed reproducibility and storage bias. No significant differences were found in alpha diversity, relative abundances (Kruskal–Wallis <i>p</i> = 0.786), or global beta diversity (ANOSIM <i>R</i> = − 0.042, <i>p</i> = 0.937). PERMANOVA showed a trend (<i>F</i> = 3.51, <i>p</i> = 0.061), but ANCOM-BC2 found no differentially abundant taxa. IQCs revealed variation in low-abundance Gram-negative species after freezing. Vaginal microbiome composition remained largely stable under short-term freezing conditions (−20°C and −80°C), supporting their use in clinical and research workflows. Nonetheless, subtle shifts in low-abundance or fragile taxa may occur and should be interpreted with caution in studies emphasizing microbial fine structure or biomarker discovery.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"14 5","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.70053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144915013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}