Frontiers in Microbiology最新文献

{"title":"Corrigendum: A mechanistic model of macromolecular allocation, elemental stoichiometry, and growth rate in phytoplankton.","authors":"Keisuke Inomura, Anne Willem Omta, David Talmy, Jason Bragg, Curtis Deutsch, Michael J Follows","doi":"10.3389/fmicb.2024.1486795","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1486795","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fmicb.2020.00086.].</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11529468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568258","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":"Different characteristics of the soil in marmot habitats might be one of the factors that influcting <i>Yersinia pestis</i> prevalent in which than pikas.","authors":"Wenlong Zhao, Shixiong Li, Yuechen Sun, Jingpeng Liu, Yixin Ma, Rui Qi","doi":"10.3389/fmicb.2024.1489125","DOIUrl":"10.3389/fmicb.2024.1489125","url":null,"abstract":"<p><strong>Introduction: </strong>Marmots are recognized as host animals for plague caused by <i>Yersinia pestis</i> infection. It is unclear that why plague prevalent in marmot rather than other rodents like pikas in the same habitats. This study aims to analyze the differences of the soil characteristics around marmots and pikas burrows to explore the soils factors impacting on different epidemic intensities of <i>Yersinia pestis</i> in these two rodents.</p><p><strong>Methods: </strong>Soil samples were collected from within and around marmot and pika burrows, as well as from the nearby areas not inhabited by them and Chinese baseline soil properties as control groups, in the Qilian Mountains of Gansu Province, China. The physicochemical properties and the bacterial 16S rRNA were measured to analyze the characteristics of soils from different groups. Subsequently, the data were analyzed using R studio.</p><p><strong>Results: </strong>The analysis revealed that marmot habitats exhibited distinct soil characteristics, including lower organic matter and alkaline hydrolyzed nitrogen, but higher electrical conductivity and total soluble salts. And soil in marmot areas tended to have higher concentrations of nickel, chromium, and iron, also lower levels of zinc and selenium. Additionally, the alpha diversity of soil microorganisms in marmot habitats was significantly low. Simultaneously, redundancy analysis was conducted, which showed that the low alpha diversity of marmot-soil was influenced by its physicochemical properties. The alpha diversity of the soil was positively correlated with EC, TSS, Na, and Cr, etc., while it was negatively correlated with AHN, OM, Se, Zn, and Fe, etc.</p><p><strong>Conclusion: </strong>These characteristics in marmot habitats, including low levels of organic matter, alkaline hydrolyzed nitrogen, zinc, selenium, and bacterial alpha diversity, as well as high levels of electrical conductivity, total soluble salts, iron, and nickel, played a crucial role in the spread of plague. It was discovered that the unique characteristics of marmot-soils provided essential elements necessary for the survival of <i>Yersinia pestis</i>, including high levels of Fe and Ca, or facilitated the spread of plague. Thus, the transmission of the plague was facilitated.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11528156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568284","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: Genomic profiling of methicillin-sensitive <i>Staphylococcus aureus</i> (MSSA) isolates in Kuwait hospitals.","authors":"Samar S Boswihi, Wadha A Alfouzan, Edet E Udo","doi":"10.3389/fmicb.2024.1507158","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1507158","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fmicb.2024.1361217.].</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11528211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568262","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":"A comprehensive review of integrated management strategies for damping-off disease in chili.","authors":"Chen Delai, Ghulam Muhae-Ud-Din, Rimsha Abid, Tian Tian, Ruirui Liu, Yan Xiong, Shirong Ma, Abazar Ghorbani","doi":"10.3389/fmicb.2024.1479957","DOIUrl":"10.3389/fmicb.2024.1479957","url":null,"abstract":"<p><p>Damping-off disease in chili (<i>Capsicum annum</i> L.) cultivation is a significant global issue, severely affecting seeds, seedlings, and young plants, regardless of the location of cultivation, whether in greenhouses or open fields. Despite chili being a widely popular vegetable used in various cuisines globally, farmers face challenges in meeting the growing demand due to the extensive damage caused by this disease, ranging from 20 to 85%. The shelf life and quality of mature pods are also severely affected. Damping-off disease is mainly caused by soil-borne fungus from the <i>Pythium</i> species, with additional contributions from <i>Phytophthora</i>, <i>Fusarium</i>, and <i>Rhizoctonia</i> species. These pathogens' adaptability to diverse environmental conditions and resistance to synthetic fungicides make controlling damping-off on a commercial scale challenging. However, integrated disease management has shown promising results as a remedial approach. In this review, we discuss the current state of chili diseases, the nature of the pathogens causing damping-off, the epidemiology of the disease, and various control mechanisms. In this review, we broadly discuss the current state of chili diseases, the nature of the pathogens causing damping-off, the epidemiology of the disease, and various control mechanisms. Furthermore, we highlight the importance and efficacy of integrated disease management techniques, along with future prospects in unexplored areas, such as host-pathogen interaction and sustainable disease control measures. The information in this review aims to assist chili growers in understanding the epidemiology and management of damping-off in chili cultivation.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142557519","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":"CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome.","authors":"Sara Pita, Pernille Neve Myers, Joachim Johansen, Jakob Russel, Mads Cort Nielsen, Aron C Eklund, Henrik Bjørn Nielsen","doi":"10.3389/fmicb.2024.1425489","DOIUrl":"10.3389/fmicb.2024.1425489","url":null,"abstract":"<p><strong>Introduction: </strong>Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites.</p><p><strong>Methods: </strong>CHAMP uses a reference database derived from 30,382 human microbiome samples, covering 6,567 prokaryotic and 244 eukaryotic species, as well as 64,003 viruses. We benchmarked CHAMP against established profiling tools (MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta) using a diverse set of <i>in silico</i> metagenomes and DNA mock communities.</p><p><strong>Results: </strong>CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. The false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than other tools at low sequencing depths, highlighting its application for low biomass samples.</p><p><strong>Discussion: </strong>Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. CHAMP profiling is offered as a service by Clinical Microbiomics A/S and is available for a fee at https://cosmosidhub.com.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142557520","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":"Distinct lower respiratory tract microbiota profiles linked to airway mucus hypersecretion in children with <i>Mycoplasma pneumoniae</i> pneumonia.","authors":"Xiwen Wei, Wan Wang, Hang Cheng, Yin Huang, Qixian Zhou, Xiaopeng Yuan","doi":"10.3389/fmicb.2024.1491506","DOIUrl":"10.3389/fmicb.2024.1491506","url":null,"abstract":"<p><strong>Background: </strong>Airway mucus hypersecretion (AMH) can occur in children with acute respiratory diseases, but its underlying mechanisms and relationship with the lower respiratory tract microbiota (LRTM) are not yet fully understood. This study investigates the characteristics of LRTM in children with <i>Mycoplasma pneumoniae</i> pneumonia (MPP) and its impact on AMH.</p><p><strong>Methods: </strong>We collected bronchoalveolar lavage fluid and related clinical indicators from 202 children with MPP. 16S rRNA gene amplicon sequencing was used for detection and identification. Microbial diversity and characteristic genera were compared, and their abundance was analyzed for correlations with clinical factors.</p><p><strong>Results: </strong>As the disease course (days from onset to bronchoscopy, grouped into T1, T2, T3) extended, α-diversity of the LRTM gradually increased, particularly in the T3 hypersecretion group. Moreover, significant differences were observed in the incidence of AMH, co-infection rates, peripheral white blood cell (WBC) count, and C-reactive protein levels. In AMH, <i>Mycoplasmoides</i> and <i>Veillonella</i> abundance and peripheral neutrophils were risk factors for increased secretions. In addition, in the T3 co-infection group, <i>Streptococcus</i> and <i>Prevotella</i> increased, replacing <i>Stenotrophomonas</i> as the dominant genus, possibly due to β-lactam antibiotic use. <i>Prevotella</i> abundance was strongly correlated with WBC.</p><p><strong>Conclusion: </strong>The composition and structure of LRTM in children with MPP played a crucial role in AMH and disease progression.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142557522","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":"Editorial: Studying plant virus-host interactions: elucidating the natural resistance mechanism.","authors":"R Vinoth Kumar, Prabu Gnanasekaran","doi":"10.3389/fmicb.2024.1500580","DOIUrl":"10.3389/fmicb.2024.1500580","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11528540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568344","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":"Enhanced cold tolerance mechanisms in <i>Euglena gracilis</i>: comparative analysis of pre-adaptation and direct low-temperature exposure.","authors":"Shuai Yuan, Wen Fu, Ming Du, Rao Yao, Dan Zhang, Chao Li, Zixi Chen, Jiangxin Wang","doi":"10.3389/fmicb.2024.1465351","DOIUrl":"10.3389/fmicb.2024.1465351","url":null,"abstract":"<p><strong>Introduction: </strong>Microalgae, known for their adaptability to extreme environments, are important for basic research and industrial applications. <i>Euglena</i>, unique for its lack of a cell wall, has garnered attention due to its versatility and the presence of bioactive compounds. Despite its potential, few studies have focused on <i>Euglena</i>'s cold adaptation mechanisms.</p><p><strong>Methods: </strong>This study investigates the cold adaptation mechanisms of <i>Euglena gracilis</i>, a microalga found in highly diverse environmental habitats, by comparing its growth, photosynthetic performance, and physiological and biochemical responses under two low-temperature cultivation modes: pre-adaptation to 16°C followed by exposure to 4°C (PreC) and direct exposure to 4°C (DirC).</p><p><strong>Results and discussion: </strong>In this study, the PreC group exhibited superior growth rates, higher photosynthetic efficiency, and more excellent antioxidant activity compared to the DirC group. These advantages were attributed to higher levels of protective compounds, enhanced membrane stability, and increased unsaturated fatty acid content. The PreC group's ability to maintain higher cell vitality under cold stress conditions underscores the significance of pre-adaptation in enhancing cold tolerance. The findings from this research provide valuable insights into the mechanisms underlying cold adaptation in <i>E. gracilis</i>, emphasizing the benefits of pre-adaptation. These insights are crucial for optimizing the cultivation of algal species under cold stress conditions, which is essential for both biotechnological applications and ecological studies. This study not only advances our understanding of <i>Euglena</i>'s adaptive responses to low temperatures but also contributes to the broader field of algal research and its industrial exploitation.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142557523","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":"Metabolic adaptations of <i>Shewanella eurypsychrophilus</i> YLB-09 for survival in the high-pressure environment of the deep sea.","authors":"Xu Qiu, Xixiang Tang","doi":"10.3389/fmicb.2024.1467153","DOIUrl":"10.3389/fmicb.2024.1467153","url":null,"abstract":"<p><p>Elucidation of the adaptation mechanisms and survival strategies of deep-sea microorganisms to extreme environments could provide a theoretical basis for the industrial development of extreme enzymes. There is currently a lack of understanding of the metabolic adaptation mechanisms of deep-sea microorganisms to high-pressure environments. The objective of this study was to investigate the metabolic regulatory mechanisms enabling a strain of the deep-sea bacterium <i>Shewanella eurypsychrophilus</i> to thrive under high-pressure conditions. To achieve this, we used nuclear magnetic resonance-based metabolomic and RNA sequencing-based transcriptomic analyses of <i>S. eurypsychrophilus</i> strain YLB-09, which was previously isolated by our research group and shown to be capable of tolerating high pressure levels and low temperatures. We found that high-pressure conditions had pronounced impacts on the metabolic pattern of YLB-09, as evidenced by alterations in energy, amino acid, and glycerolipid metabolism, among other processes. YLB-09 adapted to the high-pressure conditions of the deep sea by switching from aerobic intracellular energy metabolism to trimethylamine N-oxide respiration, altering the amino acid profile, and regulating the composition and the fluidity of cell membrane. The findings of our study demonstrate the capacity of microorganisms to alter their metabolism in response to elevated pressure, thereby establishing a foundation for a more profound understanding of the survival mechanisms of life in high-pressure environments.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11527400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142557536","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":"Evaluation of the relationships between physico-chemical parameters and the abundance of <i>Vibrio</i> spp. in blue crabs (<i>Callinectes sapidus</i>) and seawater from the Maryland Coastal Bays.","authors":"Jasmine Smalls, John Jacobs, Howard Townsend, Paulinus Chigbu, Salina Parveen","doi":"10.3389/fmicb.2024.1459077","DOIUrl":"10.3389/fmicb.2024.1459077","url":null,"abstract":"<p><strong>Introduction: </strong>Fluctuations in water quality characteristics influence the productivity of blue crabs (<i>Callinectes sapidus</i>), and the risk of human exposure to pathogenic <i>Vibrio</i> species. Thus, this study assessed the prevalence of total and pathogenic/clinical markers of <i>Vibrio parahaemolyticus</i> and <i>Vibrio vulnificus</i> in blue crabs and seawater from the Maryland Coastal Bays (MCBs) and the correlation between <i>Vibrio</i> levels and physicochemical parameters.</p><p><strong>Methods: </strong>Three to five crabs and 1 L of seawater were collected monthly for 3 years (May 2018 to December 2020) from six sites within the MCBs. Hemolymph and crab tissue were extracted and pooled for each site. Extracted hemolymph, crab tissue, and seawater were analyzed for <i>V. parahaemolyticus</i> and <i>V. vulnificus</i> using the Most Probable Number (MPN) and real-time PCR methods. A one-way Analysis of Variance (ANOVA), correlations, and linear models were used to analyze the data. Akaike Information Criterion (AICc) was evaluated to determine the model that provides the best fit to the data relating to <i>Vibrio</i> concentrations and environmental factors.</p><p><strong>Results: </strong>Results suggested that environmental factors could influence the growth of <i>Vibrio</i> spp. Both <i>V. parahaemolyticus</i> and <i>V. vulnificus</i> were more prevalent during the warmer months than colder months. <i>Vibrio</i> was more prevalent in crab samples compared to seawater. <i>Vibrio vulnificus</i> concentrations in seawater and hemolymph were positively correlated with temperature (<i>p</i> = 0.0143 seawater) and pH (<i>p</i> = 0.006 hemolymph). A negative correlation was observed between the concentration of <i>V. vulnificus</i> in whole crab (tissue) and dissolved oxygen level (<i>p</i> = 0.0256). The concentration of <i>V. parahaemolyticus</i> in seawater was positively correlated with temperature (<i>p</i> = 0.009) and negatively correlated with dissolved oxygen (<i>p</i> = 0.012).</p><p><strong>Discussion: </strong>These results provide current information on the spatial and temporal distributions of <i>Vibrio</i> spp. in the MCBs that are useful for implementing more efficient processing and handling procedures of seafood products.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544750","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}