Frontiers in Microbiology最新文献

{"title":"Microbiomic insights into the unique effects of vaginal microbiota on preterm birth in Chinese pregnant women.","authors":"Jun Zhang, Zhimin Xu, Mengjun Zhang, Jiaoning Fang, Yijing Zheng, Caihong Jiang, Mian Pan","doi":"10.3389/fmicb.2025.1560528","DOIUrl":"10.3389/fmicb.2025.1560528","url":null,"abstract":"<p><p>Preterm birth is a major cause of perinatal morbidity and mortality. The disruption of vaginal microbiota in pregnant women is the most significant risk factor for preterm delivery. In this study, 65 pregnant women were enrolled, of which 29 were women with term births and 36 were women with preterm births, and were then categorized based on gestational age at delivery. The results showed that the <i>α</i>-diversity (ACE, Chao1, Simpson, and Shannon indices) of the vaginal microbiota in the term birth group (TG) was significantly higher than that in the preterm birth group (PG). The relative abundance of beneficial bacteria (e.g., <i>Lactobacillus</i>) was significantly reduced in the PG compared to the TG, while the relative abundance of harmful bacteria (e.g., <i>Gardnerella</i>, <i>Atopobium</i>, <i>Ralstonia</i>, and <i>Sneathia</i>) was significantly increased. A prediction model for gestational age at delivery was established based on key microbial phylotypes, and this model was further verified using clinical samples. Statistical analysis revealed that the prediction model utilizing <i>Methyloversatilis</i>, <i>Atopobium</i>, <i>Ralstonia</i>, <i>Sneathia</i>, <i>Brevundimonas</i>, <i>Gardnerella</i>, <i>Acinetobacter</i>, and <i>Peptostreptococcus</i> had higher accuracy. These results suggest that certain bacteria could serve as prospective predictors for preterm birth and provide a theoretical basis for the treatment of preterm birth.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1560528"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum: Molecular surveillance and antimicrobial susceptibility profile of bacterial contamination in pastries of Iranian confectioneries: a public health concern.","authors":"Shiva Hosseini, Tahereh Motallebirad, Mohammad Reza Mohammadi, Mehdi Safarabadi, Zeynab Beheshti, Mohammad Ali Orouji, Omid Mardanshah, Davood Azadi","doi":"10.3389/fmicb.2025.1573099","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1573099","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fmicb.2024.1494623.].</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1573099"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Ruminococcus bromii</i>-generated acetate alleviated <i>Clonorchis sinensis</i>-induced liver fibrosis in mice.","authors":"Chun Li, Changsheng Cheng, Liping Jiang, Xin Zhong, Guoyang Huang, Gang Mo, Deping Cao, Xiaohong Peng","doi":"10.3389/fmicb.2025.1532599","DOIUrl":"10.3389/fmicb.2025.1532599","url":null,"abstract":"<p><strong>Introduction: </strong>Infection with <i>Clonorchis sinensis</i> (<i>C. sinensis</i>) has the potential to induce liver fibrosis and significantly alter the gut microbiota. However, it remains unclear how these changes in the gut microbiota, through the gut-liver axis, influence the progression of liver fibrosis. Furthermore, it is uncertain whether targeting the gut microbiota, based on the concept of the gut-liver axis, could be a potential therapeutic strategy for alleviating liver fibrosis.</p><p><strong>Methods: </strong>The gut microbiota alterations in <i>C. sinensis</i>-infected mice at multiple time points were analyzed through 16S rDNA high-throughput sequencing. <i>Ruminococcus bromii (R.bromii)</i> therapeutic effect on <i>C. sinensis</i> infected mice was evaluated. Metabolic changes following produced by <i>R. bromii</i> were analyzed using short-chain fatty acids (SCFAs) metabolomics. Additionally, <i>R. bromii</i> conditioned medium (R.b CM) or its metabolites were co-cultured with two hepatic stellate cell lines (LX2 and JS1) <i>in vitro</i> to assess their anti-fibrotic effects. Finally, RNA sequencing was employed to investigate the specific mechanism by which acetate inhibits hepatic stellate cells (HSCs) activation.</p><p><strong>Results: </strong>The abundance of <i>R. bromii</i> increased during the inflammatory stage of <i>C. sinensis</i> infection and decreased significantly during the fibrosis stage. Oral gavage of <i>R. bromii</i> significantly inhibited <i>C. sinensis</i>-induced liver fibrosis while restoring the intestinal barrier. The activation of HSCs was significantly inhibited <i>in vitro</i> upon incubation with <i>R.b</i> CM. Acetate was identified as a key metabolite generated from <i>R. bromii</i> in <i>R.b</i> CM, and acetate attenuated <i>C. sinensis</i>-induced liver fibrosis <i>in vitro</i> and in vivo. Mechanistically, acetate inhibited the activation of HSCs by activating the PI3K/AKT signaling pathway to prevent the progression of liver fibrosis in mice infected with <i>C. sinensis</i>.</p><p><strong>Discussion: </strong><i>R. bromii</i> exerted a protective effect on hepatic fibrosis by delivering acetate via the gut-liver axis to active the PI3K/AKT signaling pathway in HSCs. Furthermore, <i>R. bromii</i> can be used as a probiotic therapy to alleviate hepatic fibrosis.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1532599"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 sequences in <i>mgrB</i> and mutations in two-component system genes confer high polymyxin resistance to carbapenem-resistant <i>Enterobacter cloacae</i> complex strains.","authors":"Jiming Wu, Jisheng Zhang, Jianmin Wang, Jin Wang, Xushan Liang, Chunli Wei, Wenzhang Long, Yang Yang, Yuhui Chen, Mingjing Liao, Youtao Liang, Kaixin Yu, Xiaoli Zhang","doi":"10.3389/fmicb.2025.1553148","DOIUrl":"10.3389/fmicb.2025.1553148","url":null,"abstract":"<p><p>Due to the complexity of identifying the <i>Enterobacter cloacae</i> complex (ECC) at the species level, little is known about the distribution of carbapenem-resistant ECC (CRECC). Plasmid-mediated <i>mcr</i> family genes are significant contributors to polymyxin resistance. The emergence of the <i>mcr-9</i> gene has further complicated the landscape of polymyxin resistance in CRECC. Our study aimed to ascertain the prevalence of CRECC and the <i>mcr-9</i> gene, and to elucidate the mechanisms underlying high-level resistance to polymyxin B (PB). In this study, we collected 212 non-replicating ECC strains, identifying 38 CRECC strains (17.9%, 38/212) and <i>Enterobacter hormaechei</i> (71.1%, 27/38) as the predominant endemic strains. Among these, 10 CRECC strains (36.3%, 10/38) were found to harbor the <i>mcr-9</i> gene. Interestingly, the presence of <i>mcr-9</i> did not significantly impact PB resistance or impose a fitness cost. While overexpression of <i>mcr-9</i> can enhance PB resistance within a certain range and may incur fitness costs, it does not result in high-level PB resistance. The PB resistance of 17 CRECC strains was notably increased (from 16 to 128 mg/L), accompanied by mutations in the <i>phoP</i>/<i>Q</i> and <i>mgrB</i> genes. Notably, two novel insertion sequences, IS<i>5D</i> and IS<i>1X2</i>, were discovered within the <i>mgrB</i> gene. The inactivation of <i>mgrB</i> results in the loss of its negative regulatory effect on the two-component system. Protein structure predictions indicated that mutations in <i>phoQ</i> primarily affect the phosphatase (HAMP) and histidine kinase domains. This research significantly expands our comprehension of the complexities of PB resistance, highlighting the multifactorial nature of antibiotic resistance mechanisms.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1553148"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of long-term continuous cropping on microbial community structure and function in tobacco rhizosphere soil.","authors":"Bingye Yang, Changchun Feng, Hong Jiang, Yulan Chen, Mengjiao Ding, Huaxin Dai, Zhen Zhai, Mengmeng Yang, Taibo Liang, Yanling Zhang","doi":"10.3389/fmicb.2025.1496385","DOIUrl":"10.3389/fmicb.2025.1496385","url":null,"abstract":"<p><p>As is well known, continuous cropping can lead to a decrease in crop yield and quality. Despite this, continuous cropping remains prevalent in practical agricultural production, particularly in the case of tobacco cultivation, owing to its high economic value. The samples for this study were collected from a flue-cured tobacco planting base located in Huili County, Liangshan Yi Autonomous Prefecture, Sichuan Province, China. After years of continuous planting, the yield of tobacco in this base has significantly decreased. In order to explain the microecological causes of this phenomenon, we collected non-continuous cropping, continuous cropping for 5 years, and continuous cropping for 10 years of tobacco rhizosphere soil, and analyzed the effects of long-term continuous cropping on nutrients, enzyme activities, microbial community structure, and function of tobacco rhizosphere soil. The results showed that with the continuous cropping, the majority nutrients (except for phosphorus and manganese) in rhizosphere soil decreased significantly, and the rhizosphere microbial community structure changed significantly. Correlation network analysis results showed that changes in the rhizosphere microbial community of tobacco were closely related to soil urease, active organic carbon, and available iron content. The results of functional analysis based on microorganisms and genes showed that the rhizosphere microbiota may change the content of soil nutrients through iron_respiration, sulfur_respiration, and Carbon fixation in prokaryotes pathways. The results of the correlation network analysis and the functional analysis mutually confirmed each other, both emphasizing the important role of soil carbon and iron in shaping the structure of the tobacco rhizosphere microbial community. Based on the results of this study, we propose to improve the microbial community structure of tobacco rhizosphere soil by increasing the levels of readily oxidizable organic carbon, available iron, and soil urease activity in the future, so as to alleviate the negative impact of continuous cropping on crop yield. The results of this study provide theoretical support for modifying the rhizosphere microbial environment through nutrient regulation, thereby enhancing plant growth in the context of continuous tobacco cropping.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1496385"},"PeriodicalIF":4.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Repeated biocide treatments cause changes to the microbiome of a food industry floor drain biofilm model.","authors":"Martin Laage Kragh, Nanna Hulbæk Scheel, Pimlapas Leekitcharoenphon, Lisbeth Truelstrup Hansen","doi":"10.3389/fmicb.2025.1542193","DOIUrl":"10.3389/fmicb.2025.1542193","url":null,"abstract":"<p><p>There is a concern about the development of microbial tolerance and resistance to biocides due to their repeated use within the food industry. This study aimed to develop a floor drain biofilm model and test whether repeated biocide treatment would result in increased tolerance to biocides. Culturomics and shotgun metagenomic analysis of 14 drains and 214 bacterial isolates from three industrial food production environments revealed microbiomes with great diversity and complexity, but with the dominance of a few highly abundant taxa, including <i>Pseudomonas</i>. A representative drain biofilm was created (3 days, 15°C) using 31 whole genome sequenced bacterial isolates from 24 genera. The biofilm model represented 47-58% and 76-81% of the microbial abundance observed in the metagenome and viable microbiota, respectively. The biofilm model was exposed on days 3 and 6 to water or different industrial concentrations of benzalkonium chloride (BC), peracetic acid (PAA), or sodium hypochlorite (SH). Analysis of the viable survivors using MALDI-TOF MS and the regrowing biofilms using 16S rRNA amplicon sequencing showed how the diversity of the biofilm decreased but without any change in biocide tolerance as seen in log reductions (CFU/cm²). The use of different biocides did, however, exert significantly different selective pressures on the microbiomes as <i>Citrobacter</i>, <i>Acinetobacter</i>, <i>Aeromonas</i>, and <i>Pseudomonas</i> dominated the biofilm after treatments with SH or PAA, while <i>Serratia</i> and <i>Moraxella</i> dominated after treatments with BC. The dominance of <i>Serratia marcescens</i> could be explained by the carriage of a BC efflux pump (<i>oqxB</i>) and the highest (20 mg/L BC) minimum inhibitory concentration (MIC) result of the drain isolates. In contrast, despite carrying a BC efflux pump (<i>qacH</i>), <i>Listeria monocytogenes</i> ST121 did not show increased survival or presence in the biofilm after BC treatments. Only the highest tested concentration of PAA was able to completely eradicate <i>L. monocytogenes</i>. The developed biofilm model and the repeated biocide treatments enabled a better understanding of how biocides affect the biofilm microbiome. Future research should involve testing biocide rotation strategies to control biofilm regrowth and inactivation of persistent foodborne pathogens in floor drains.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1542193"},"PeriodicalIF":4.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary characterization and pathogenicity of the highly virulent human-porcine reassortant G9P[23] porcine rotavirus HB05 strain in several Chinese provinces.","authors":"Xi Li, Jingjing Wang, Yuankui Zhang, Yarong Zhao, Yanli Shi","doi":"10.3389/fmicb.2025.1539905","DOIUrl":"10.3389/fmicb.2025.1539905","url":null,"abstract":"<p><p>Rotavirus A (RVA), a member of the <i>Sedoreoviridae</i> family, is significant intestinal pathogen that cause diarrhea in both piglets and humans. During of an outbreak that struck nursing piglets with diarrhea, a human-porcine reassortment rotavirus, named as RVA/Pig-wt/China/HB05/2023/G9P[23] (hereafter referred to as HB05), was identified. This specific strain was found to be prevalent in pig farms in several regions, including Hebei, Liaoning, Sichuan, Zhejiang and Henan, and caused significant economic losses from March to August 2023. To further explore the evolutionary diversity of HB05, a comprehensive analysis of all gene segments was conducted. The genome constellation was identified as G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. Nucleotide sequence identity and phylogenetic analyses indicated that the NSP3 gene of HB05 is most closely related to the corresponding genes of Human strains, with the highest homology at 95.45% identity. The other genes (VP1-VP4, VP6-VP7, NSP1-NSP2, NSP4-NSP5) exhibited the closest relationship to porcine strains, with the highest homology ranging from 94.79 to 98.89% similarity. Therefore, it is likely that HB05 originated from genetic reassortment between porcine and human rotaviruses. The pathogenicity study performed on 3-day-old piglets revealed that severe diarrhea manifested 8 h post-infection after oral inoculation with the PoRV HB05 strain at a dose of 2 × 10^5.5 TCID50/mL per piglet. To our knowledge, this marks the first report of a prevalent and highly virulent human-porcine reassortment G9P[23] rotavirus A (RVA) strain identified in mainland China. This finding provides valuable insights into the evolutionary traits of the G9P[23] strain and suggests a possible risk of cross-species transmission.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1539905"},"PeriodicalIF":4.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probiotics and muscle health: the impact of <i>Lactobacillus</i> on sarcopenia through the gut-muscle axis.","authors":"Jingjun Zhu, Fei Peng, Huixin Yang, Jing Luo, Li Zhang, Xiaolong Chen, Huazhi Liao, Hao Lei, Shuai Liu, Tingqian Yang, Guanghua Luo, Guodong Chen, Heng Zhao","doi":"10.3389/fmicb.2025.1559119","DOIUrl":"10.3389/fmicb.2025.1559119","url":null,"abstract":"<p><p>Sarcopenia refers to the decline in skeletal muscle mass and function. Due to its increased mortality rate and severe disability, the clinical importance of sarcopenia is becoming increasingly prominent. Although the exact cause of sarcopenia is not fully understood, the gut microbiota (GM) plays a crucial role in the pathogenesis of sarcopenia, and increasing evidence suggests that gut dysbiosis may be associated with disease development. In the past few decades, the use of probiotics has surged, few studies have explored their impact on sarcopenia prevention and treatment. <i>Lactobacillus</i> probiotics are commonly used for gut health and immune support, but their mechanism in sarcopenia via the gut-muscle axis remains uncertain. This review highlights the treatment challenges, GM's role in sarcopenia, and the potential of <i>Lactobacillus</i> as an adjunct therapy. In addition, we also discuss the possible mechanisms by which <i>Lactobacillus</i> affect muscle function, such as alleviating inflammatory states, clearing excessive reactive oxygen species (ROS), improving skeletal muscle metabolism, enhancing intestinal barrier function and modulating the gut microbiota and its metabolites. These mechanisms may collectively contribute to the preservation of muscle mass and function, offering a promising avenue for advancing microbial therapies for sarcopenia.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1559119"},"PeriodicalIF":4.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symbiotic bacteria associated with different species of <i>Curculio</i> (Coleoptera: Curculionidae) and their host plants.","authors":"Yingshan Liu, Yue Ying, Yan Li, Wei Zhang, Jinping Shu","doi":"10.3389/fmicb.2025.1531847","DOIUrl":"10.3389/fmicb.2025.1531847","url":null,"abstract":"<p><p>Bacteria often play important roles in the host adaptation of phytophagous insects. Beetles of the genus <i>Curculio</i> (Coleoptera: Curculionidae) include pest species that bore into the seeds of trees in the family Fagaceae and damage the cotyledons. At present, there are few studies of the taxonomic diversity and functional effects of symbiotic bacteria involved in changes in host ranges and host adaptation of <i>Curculio</i>. Here, we used 16S rRNA gene Illumina and metagenomic sequencing to compare the composition and functions of the bacterial communities of three species of host plants and several <i>Curculio</i> species combinations: <i>Curculio bimaculatus</i> feeding on <i>Castanopsis sclerophylla</i>, <i>C. bimaculatus</i> feeding on <i>Castanopsis tibetana</i>, and <i>Curculio davidi</i> feeding on <i>Ca. tibetana</i>. The host plants influenced the diversity of symbiotic bacteria, while the <i>Curculio</i> species influenced the community structure of the symbiotic bacteria. Functional predictions showed that symbiotic bacteria contributed to the metabolism of the hosts. However, consistent with the variation in bacteria, the major metabolism-related bacterial genera varied among the treatment groups. Comparisons of metabolic enzymes based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed differences in the enzymes involved in insect development and detoxification of plant secondary compounds among the three groups, and the patterns were influenced by the dominance of the <i>Curculio</i> species on the host plants. This study provides valuable insights into the possible role of symbiotic bacteria in <i>Curculio</i> as host insects.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1531847"},"PeriodicalIF":4.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.","authors":"Sohail Naushad, Ruimin Gao, Marc-Olivier Duceppe, Andree Ann Dupras, Sarah J Reiling, Harriet Merks, Brent Dixon, Dele Ogunremi","doi":"10.3389/fmicb.2025.1566579","DOIUrl":"10.3389/fmicb.2025.1566579","url":null,"abstract":"<p><strong>Introduction: </strong>Infections with protozoan parasites associated with the consumption of fresh produce is an on-going issue in developed countries but mitigating the risk is hampered by the lack of adequate methods for their detection and identification.</p><p><strong>Materials and methods: </strong>We developed a metagenomic next-generation sequencing (mNGS) assay using a MinION sequencer for the identification of parasites in intentionally contaminated lettuce to achieve a more accurate and rapid method than the traditional molecular and microscopy methods commonly used for regulatory purposes. Lettuce (25 g) was spiked with varying numbers of <i>Cryptosporidium parvum</i> oocysts, and microbes washed from the surface of the lettuce were lysed using the OmniLyse device. DNA was then extracted by acetate precipitation, followed by whole genome amplification. The amplified DNA was sequenced by nanopore technology and validated with the Ion Gene Studio S5, and the generated fastq files raw reads were uploaded to the CosmosID webserver for the bioinformatic identification of microbes in the metagenome. To demonstrate the ability of the procedure to distinguish other common food and waterborne protozoan parasites, lettuce was also spiked with <i>C. hominis, C. muris, Giardia duodenalis</i> and <i>Toxoplasma gondii</i> individually or together.</p><p><strong>Results: </strong>The efficient lysis of oocysts and cysts was a prerequisite for the sensitive detection of parasite DNA and was rapidly achieved within 3 min. Amplification of extracted DNA led to the generation of 0.16-8.25 μg of DNA (median = 4.10 μg), sufficient to perform mNGS. Nanopore sequencing followed by bioinformatic analysis led to the consistent identification of as few as 100 oocysts of <i>C. parvum</i> in 25 g of fresh lettuce. Similar results were obtained using the Ion S5 sequencing platform. The assay proved useful for the simultaneous detection of <i>C. parvum, C. hominis, C. muris, G. duodenalis</i> and <i>T. gondii</i>.</p><p><strong>Discussion: </strong>Our metagenomic procedure led to the identification of <i>C. parvum</i> present on lettuce at low numbers and successfully identified and differentiated other protozoa either of the same genus or of different genera. This novel mNGS assay has the potential for application as a single universal test for the detection of foodborne parasites, and the subtyping of parasites for foodborne outbreak investigations and surveillance studies.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1566579"},"PeriodicalIF":4.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}