Fems Microbiology Letters最新文献_第10页

Analysis of the life cycle of Helicobacter pylori bacteriophage KHP40 belonging to the genus Schmidvirus. 幽门螺杆菌噬菌体 KHP40（属于施米德病毒属）的生命周期分析。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae082

Masahiro Iwamoto, Michiko Takahashi, Hiromichi Maeda, Hiroaki Takeuchi, Jumpei Uchiyama, Takako Ujihara, Keizo Nagasaki, Kazuhiro Hanazaki, Satoru Seo, Naoya Kitamura, Tetsuya Yamamoto, Shigenobu Matsuzaki

{"title":"Analysis of the life cycle of Helicobacter pylori bacteriophage KHP40 belonging to the genus Schmidvirus.","authors":"Masahiro Iwamoto, Michiko Takahashi, Hiromichi Maeda, Hiroaki Takeuchi, Jumpei Uchiyama, Takako Ujihara, Keizo Nagasaki, Kazuhiro Hanazaki, Satoru Seo, Naoya Kitamura, Tetsuya Yamamoto, Shigenobu Matsuzaki","doi":"10.1093/femsle/fnae082","DOIUrl":"10.1093/femsle/fnae082","url":null,"abstract":"Bacteriophage (phage) KHP40 was previously isolated from the supernatant of a culture of Helicobacter pylori KMT83 cells. In this study, we analysed the infection characteristics of KHP40, phage release pattern from KMT83 cells, and state of KHP40 DNA in KMT83 cells. The findings revealed that KHP40 phage showed varied adsorption efficiencies for different strains, long latent periods, and small burst sizes. Additionally, KHP40 activity was maintained at pH 2.5-12. KHP40 phages were released during the vegetative growth phase of the KMT83 cells. PCR analysis demonstrated that KHP40 DNA was stably maintained in KMT83 clones. Next-generation sequencing analysis revealed the presence of two distinct types of circular double-stranded DNA in H. pylori KMT83 cells. One was an H. pylori-specific DNA consisting of 1 578 403 bp, and the other was a 26 412-bp sequence that represented the episomal form of phage KHP40 DNA. Furthermore, defective KHP40-lysogenic DNA was detected in the H. pylori-specific DNA, the deleted portion of which appeared to have been transferred to another location in the bacterial genome. These findings indicate that KHP40 DNA exists in both episomal and defectively lysogenized states in KMT83 cells, and active phages are produced from KHP40-episomal DNA.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The pangenome analysis of the environmental source Salmonella enterica highlights a diverse accessory genome and a distinct serotype clustering. 对环境源肠炎沙门氏菌的庞基因组分析突出显示了多样化的附属基因组和独特的血清型聚类。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae090

José Roberto Aguirre-Sánchez, Cristóbal Chaidez, Nohelia Castro-Del Campo

{"title":"The pangenome analysis of the environmental source Salmonella enterica highlights a diverse accessory genome and a distinct serotype clustering.","authors":"José Roberto Aguirre-Sánchez, Cristóbal Chaidez, Nohelia Castro-Del Campo","doi":"10.1093/femsle/fnae090","DOIUrl":"10.1093/femsle/fnae090","url":null,"abstract":"Salmonella remains the leading cause of foodborne infections globally. Environmental reservoirs, particularly aquatic bodies, serve as conduits for the fecal-oral transmission of this pathogen. While the gastrointestinal tract is traditionally considered the primary habitat of Salmonella, mounting evidence suggests the bacterium's capacity for survival in external environments. The application of advanced technological platforms, such as next-generation sequencing, facilitates a comprehensive analysis of Salmonella's genomic features. This study aims to characterize the genomic composition of Salmonella isolates from river water, contributing to a potential paradigm shift and advancing public health protection. A total of 25 river water samples were collected and processed, followed by microbiological isolation of Salmonella strains, which were then sequenced. Genomic characterization revealed adaptive mechanisms, including gene duplication. Furthermore, an open pangenome, predisposed to incorporating foreign genetic material, was identified. Notably, antibiotic resistance genes were found to be part of the core genome, challenging previous reports that placed them in the accessory genome.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Knockout of adenylosuccinate synthase purA increases susceptibility to colistin in Escherichia coli. 敲除腺苷琥珀酸合成酶 purA 会增加大肠杆菌对可乐定的敏感性。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae007

Tomonori Kano, Kazuya Ishikawa, Kazuyuki Furuta, Chikara Kaito

{"title":"Knockout of adenylosuccinate synthase purA increases susceptibility to colistin in Escherichia coli.","authors":"Tomonori Kano, Kazuya Ishikawa, Kazuyuki Furuta, Chikara Kaito","doi":"10.1093/femsle/fnae007","DOIUrl":"10.1093/femsle/fnae007","url":null,"abstract":"Colistin is a cationic cyclic antimicrobial peptide used as a last resort against multidrug-resistant gram-negative bacteria. To understand the factors involved in colistin susceptibility, we screened colistin-sensitive mutants from an E. coli gene-knockout library (Keio collection). The knockout of purA, whose product catalyzes the synthesis of adenylosuccinate from IMP in the de novo purine synthesis pathway, resulted in increased sensitivity to colistin. Adenylosuccinate is subsequently converted to AMP, which is phosphorylated to produce ADP, a substrate for ATP synthesis. The amount of ATP was lower in the purA-knockout mutant than that in the wild-type strain. ATP synthesis is coupled with proton transfer, and it contributes to the membrane potential. Using the membrane potential probe, 3,3'-diethyloxacarbocyanine iodide [DiOC2(3)], we found that the membrane was hyperpolarized in the purA-knockout mutant compared to that in the wild-type strain. Treatment with the proton uncoupler, carbonyl cyanide m-chlorophenyl hydrazone (CCCP), abolished the hyperpolarization and colistin sensitivity in the mutant. The purA-knockout mutant exhibited increased sensitivity to aminoglycosides, kanamycin, and gentamicin; their uptake requires a membrane potential. Therefore, the knockout of purA, an adenylosuccinate synthase, decreases ATP synthesis concurrently with membrane hyperpolarization, resulting in increased sensitivity to colistin.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10876104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139671609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data. 测序读数的合并与连接：从扩增子数据全面分析微生物组的生物信息学工作流程。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae009

Meganathan P Ramakodi

{"title":"Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.","authors":"Meganathan P Ramakodi","doi":"10.1093/femsle/fnae009","DOIUrl":"10.1093/femsle/fnae009","url":null,"abstract":"A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139671610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Essential oils from Cuminum cyminum and Laurus nobilis and their principal constituents: evaluation of antifungal and antimycotoxigenic potential in Aspergillus species. 孜然和月桂的精油及其主要成分：对曲霉菌抗真菌和抗霉菌毒素潜力的评估。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae081

Gabriela Aguiar Campolina, Maria das Graças Cardoso, Carolina Salles Freire, Alex Rodrigues Silva Caetano, Anna Beatriz de Souza Campos, Vanuzia Rodrigues Fernandes Ferreira, Eduardo Alves, David Lee Nelson, Luis Roberto Batista

{"title":"Essential oils from Cuminum cyminum and Laurus nobilis and their principal constituents: evaluation of antifungal and antimycotoxigenic potential in Aspergillus species.","authors":"Gabriela Aguiar Campolina, Maria das Graças Cardoso, Carolina Salles Freire, Alex Rodrigues Silva Caetano, Anna Beatriz de Souza Campos, Vanuzia Rodrigues Fernandes Ferreira, Eduardo Alves, David Lee Nelson, Luis Roberto Batista","doi":"10.1093/femsle/fnae081","DOIUrl":"10.1093/femsle/fnae081","url":null,"abstract":"The antifungal and antimycotoxigenic activities of the essential oils (EO) from Cuminum cyminum and Laurus nobilis, and their respective principal compounds, cuminaldehyde and 1,8-cineole, were evaluated against fungi of the genus Aspergillus: A. carbonarius, A. niger, A. ochraceus, and A. westerdijkiae. The antifungal activity was determined by the contact method and the mycelial growth of the fungi was evaluated. Scanning electron microscopic (SEM) images were obtained to suggest modes of action of the compounds analysed. The antimycotoxigenic activity was determined by high-performance liquid chromatograph. Aspergillus carbonarius was completely inhibited by cumin EO (500 µl l-1), by laurel EO and by cuminaldehyde (5000 µl l-1). The cumin EO (500 µl l-1) completely inhibited the growth of A. niger. All the samples inhibited the mycelial growth of A. ochraceus, especially cumin EO and cuminaldehyde (250 µl l-1). Aspergillus westerdijkiae was completely inhibited by cumin EO and cuminaldehyde (1000 µl l-1), by laurel EO and 1,8-cineole (10 000 µl l-1). A decrease in the production of ochratoxin A (OTA) was observed post-treatment, except in A. ochraceus, only inhibited by laurel EO. SEM images showed morphological changes in fungal structures and spore inhibition post-treatment. The results confirmed the antifungal and antimycotoxigenic effect of EO and their principal constituents on fungi evaluated.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacteria involved in the sulfur cycle in tarballs collected from the Alabama Gulf Coast. 从阿拉巴马州海湾沿岸收集的焦油球中参与硫循环的细菌。

IF 2.1 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae003

Joo-Han Gwak, Sung-Keun Rhee, Joong-Wook Park

引用次数: 0

Metabolic reprogramming in the food-borne pathogen Listeria monocytogenes as a critical defence against acid stress. 食源性病原体单核细胞增生李斯特菌的代谢重编程是抵御酸胁迫的关键。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae060

Jialun Wu, Chuhan Wang, Conor O'Byrne

{"title":"Metabolic reprogramming in the food-borne pathogen Listeria monocytogenes as a critical defence against acid stress.","authors":"Jialun Wu, Chuhan Wang, Conor O'Byrne","doi":"10.1093/femsle/fnae060","DOIUrl":"10.1093/femsle/fnae060","url":null,"abstract":"The ability to sense and respond effectively to acidic stress is important for microorganisms to survive and proliferate in fluctuating environments. As specific metabolic activities can serve to buffer the cytoplasmic pH, microorganisms rewire their metabolism to favour these reactions and thereby mitigate acid stress. The orally acquired pathogen Listeria monocytogenes exploits alternative metabolic activities to overcome the acidic stress encountered in the human stomach or food products. In this minireview, we discuss the metabolic processes in L. monocytogenes that mitigate acid stress, with an emphasis on the proton-depleting reactions, including glutamate decarboxylation, arginine/agmatine deimination, and fermentative acetoin production. We also summarize the recent findings on regulatory mechanisms that control the expression of genes that are responsible for these metabolic activities, including the general stress response regulator SigB, arginine repressor ArgR, and the recently discovered RofA-like transcriptional regulatory GadR. We further discuss the importance of this metabolic reprogramming in the context of food products and within the host. Finally, we highlight some outstanding challenges in the field, including an understanding of acid-sensing mechanisms, the role of intraspecies heterogeneity in acid resistance, and how a fundamental understanding of acid stress response can be exploited for food formulation to improve food safety and reduce food waste.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The influence of cigR gene on the pathogenicity of Salmonella paratyphi A in vitro and in vivo. cigR 基因对副伤寒甲型沙门氏菌体外和体内致病性的影响。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae067

Junlei Yin, Lijun Wang, Ronghua Shen, Jinjiao He, Shaozu Li, Huajian Wang, Zhao Cheng

{"title":"The influence of cigR gene on the pathogenicity of Salmonella paratyphi A in vitro and in vivo.","authors":"Junlei Yin, Lijun Wang, Ronghua Shen, Jinjiao He, Shaozu Li, Huajian Wang, Zhao Cheng","doi":"10.1093/femsle/fnae067","DOIUrl":"10.1093/femsle/fnae067","url":null,"abstract":"Salmonella Paratyphi A is the causative agent of paratyphoid fever A which is a serious threat to human health in many countries. The cigR gene located in Salmonella pathogenicity island 3 is a type III secretion system 2 effector gene. However, the influence of cigR gene on the pathogenicity of Salmonella Paratyphi A remains unclear. Here, a cigR gene deletion mutant of Salmonella Paratyphi A was constructed and its pathogenic changes were also evaluated. It was found that both the growth and biochemical features have not changed after the loss of cigR, but the absence of cigR significantly enhanced the replication and/or survival ability in phorbol-12-myristate-13-acetate (PMA)-differentiated human macrophage THP-1 cells and in mouse; the proliferative activity and apoptosis of PMA-differentiated THP-1 cell were significantly decreased and increased, respectively, after the lack of cigR gene; and the mutant showed increased virulence to a mouse infection model by decreased half-lethal dose (LD50) value and enhanced the proliferation ratio of bacteria in vivo. These results demonstrated that CigR is an anti-virulence factor and plays an important role in the pathogenicity of Salmonella Paratyphi A.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In memoriam: Prof Yuri Alexandrovich Trotsenko (1941-2021). 悼念尤里-亚历山德罗维奇-特罗岑科教授（1941-2021）。

IF 2.1 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae024

Rich Boden

引用次数: 0

Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China. 元基因组学揭示了中国两种常见鼠兔（Ochotona curzoniae和Ochotona daurica）肠道微生物组组成和功能的差异。

IF 2.2 4区生物学

Fems Microbiology Letters Pub Date : 2024-01-09 DOI: 10.1093/femsle/fnae092

Xueqian Hu, Jie Bi, Qiaoling Yu, Huan Li

{"title":"Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China.","authors":"Xueqian Hu, Jie Bi, Qiaoling Yu, Huan Li","doi":"10.1093/femsle/fnae092","DOIUrl":"10.1093/femsle/fnae092","url":null,"abstract":"Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.","PeriodicalId":12214,"journal":{"name":"Fems Microbiology Letters","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0