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  • 1
    In: Journal of Endodontics, Elsevier BV, Vol. 46, No. 12 ( 2020-12), p. 1876-1883
    Materialart: Online-Ressource
    ISSN: 0099-2399
    Sprache: Englisch
    Verlag: Elsevier BV
    Publikationsdatum: 2020
    ZDB Id: 2083582-6
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 2
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 11, No. 2 ( 2023-04-13)
    Kurzfassung: This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated. Next, 39 primer pairs were used to search for matches in the genomes and obtain amplicons. For each primer, we calculated the number of gene amplicons, variants, genomes, and species detected and the percentage of coverage at the species level with no MAs (SC-NMA). The results showed that 94.09% of oral bacteria and 52.59% of oral archaea had more than one intragenomic 16S rRNA gene. From 1.29% to 46.70% of bacterial species and from 4.65% to 38.89% of archaea detected by the primers had MAs. The best primers were the following (SC-NMA; region; position for Escherichia coli [GenBank version no. J01859.1 ]): KP_F048-OP_R030 for bacteria (93.55%; V3 to V7; 342 to 1079), KP_F018-KP_R063 for archaea (89.63%; V3 to V9; undefined to 1506), and OP_F114-OP_R121 for both domains (92.52%; V3 to V9; 340 to 1405). In addition to 16S rRNA gene redundancy, the presence of MAs must be controlled to ensure an accurate interpretation of microbial diversity data. The SC-NMA is a more useful parameter than the conventional coverage percentage for selecting the best primer pairs. The pairs used the most in the oral microbiome literature were not among the best performers. IMPORTANCE Hundreds of publications have studied the oral microbiome through 16S rRNA gene sequencing. However, none have assessed the number of 16S rRNA genes in the genomes of oral microbes, or how the use of primer pairs targeting different regions affects the detection of MAs from different taxa. Here, we found that almost all oral bacteria and more than half of oral archaea have more than one intragenomic 16S rRNA gene. The performance of the primer pairs in not detecting MAs increases as the length of the amplicon augments. As none of those most employed in the oral literature were among the best performers, we selected a series of primers to detect bacteria and/or archaea based on their percentage of species detected without MAs. The intragenomic 16S rRNA gene redundancy and the presence of MAs between distinct taxa need to be considered to ensure an accurate interpretation of microbial diversity data.
    Materialart: Online-Ressource
    ISSN: 2165-0497
    Sprache: Englisch
    Verlag: American Society for Microbiology
    Publikationsdatum: 2023
    ZDB Id: 2807133-5
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 3
    Online-Ressource
    Online-Ressource
    Elsevier BV ; 2017
    In:  EBioMedicine Vol. 25 ( 2017-11), p. 14-15
    In: EBioMedicine, Elsevier BV, Vol. 25 ( 2017-11), p. 14-15
    Materialart: Online-Ressource
    ISSN: 2352-3964
    Sprache: Englisch
    Verlag: Elsevier BV
    Publikationsdatum: 2017
    ZDB Id: 2799017-5
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 4
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 10, No. 4 ( 2022-08-31)
    Kurzfassung: The tumor microbiome is believed to have a profound impact on tumor progression owing to its local colonization in the tumor microenvironment (TME). Using the Cancer Microbiome Atlas (TCMA), a database of curated, decontaminated microbial profiles for 3,689 oropharyngeal, esophageal, gastrointestinal, and colorectal tissue samples from 1,772 patients, we conducted a comprehensive multi-omics analysis to reveal microbial signatures among various cancers and the potential mechanisms involved in tumor progression of head and neck squamous cell carcinoma (HNSC). We found that compared with other cancer types, the tumor-resident microbiome of HNSC accounted for the highest bacterial abundance and strongest association with host TME signatures. Fusobacterium was found to be enriched in HNSC tissues, which was associated with an increased inflammatory effect and inferior prognosis. Moreover, we revealed that the microbiota-associated inflammatory TME was attributed to the competing endogenouse RNA (ceRNA) network and chromatin accessibility. IMPORTANCE Studies on revealing the composition and potential mechanisms of the tumor microbiome are still at an initial stage. We uncovered the potential contribution of the tumor-resident microbiota on the immunosuppressive microenvironment in HNSC, which will provide a new perspective for tumor microbiome research and yield valuable insights into the clinical management of HNSC.
    Materialart: Online-Ressource
    ISSN: 2165-0497
    Sprache: Englisch
    Verlag: American Society for Microbiology
    Publikationsdatum: 2022
    ZDB Id: 2807133-5
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 5
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 10, No. 5 ( 2022-10-26)
    Kurzfassung: Biofilm production is responsible for persistent food contamination by Listeria monocytogenes , threatening food safety and public health. Human infection and food contamination with L. monocytogenes are caused primarily by serotypes 1/2a, 1/2b, and 4b. However, the association of biofilm production with phylogenic lineage and serotype has not yet been fully understood. In this study, we measured the levels of biofilm production in 98 clinical strains of L. monocytogenes at 37°C, 25°C, and 4°C. The phylogenetic clusters grouped by core genome multilocus sequence typing (cgMLST) exhibited association between biofilm production and phylogenetic lineage and serotype. Whereas clusters 1 and 3 consisting of serotype 4b strains exhibited weak biofilm production, clusters 2 (serotype 1/2b) and 4 (serotype 1/2a) were composed of strong biofilm formers. Particularly, cluster 2 (serotype 1/2b) strains exhibited the highest levels of biofilm production at 37°C, and the levels of biofilm production of cluster 4 (serotype 1/2a) strains were significantly elevated at all tested temperatures. Pan-genome analysis identified 22 genes unique to strong biofilm producers, most of which are related to the synthesis and modification of teichoic acids. Notably, a knockout mutation of the rml genes related to the modification of wall teichoic acids with l- rhamnose, which is specific to serogroup 1/2, significantly reduced the level of biofilm production by preventing biofilm maturation. Here, the results of our study show that biofilm production in L. monocytogenes is related to phylogeny and serotype and that the modification of wall teichoic acids with l- rhamnose is responsible for serotype-specific strong biofilm formation in L. monocytogenes . IMPORTANCE Biofilm formation on the surface of foods or food-processing facilities by L. monocytogenes is a serious food safety concern. Here, our data demonstrate that the level of biofilm production differs among serotypes 1/2a, 1/2b, and 4b depending on the temperature. Furthermore, sugar decoration of bacterial cell walls with l- rhamnose is responsible for strong biofilm production in serotypes 1/2a and 1/2b, commonly isolated from foods and listeriosis cases. The findings in this study improve our understanding of the association of biofilm production with phylogenetic lineage and serotype in L. monocytogenes .
    Materialart: Online-Ressource
    ISSN: 2165-0497
    Sprache: Englisch
    Verlag: American Society for Microbiology
    Publikationsdatum: 2022
    ZDB Id: 2807133-5
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 6
    Online-Ressource
    Online-Ressource
    Bio-Protocol, LLC ; 2017
    In:  BIO-PROTOCOL Vol. 7, No. 11 ( 2017)
    In: BIO-PROTOCOL, Bio-Protocol, LLC, Vol. 7, No. 11 ( 2017)
    Materialart: Online-Ressource
    ISSN: 2331-8325
    Sprache: Englisch
    Verlag: Bio-Protocol, LLC
    Publikationsdatum: 2017
    ZDB Id: 2833269-6
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 7
    In: Glycobiology, Oxford University Press (OUP), Vol. 33, No. 3 ( 2023-04-19), p. 245-259
    Kurzfassung: Streptococcus mutans is a key pathogen associated with dental caries and is often implicated in infective endocarditis. This organism forms robust biofilms on tooth surfaces and can use collagen-binding proteins (CBPs) to efficiently colonize collagenous substrates, including dentin and heart valves. One of the best characterized CBPs of S. mutans is Cnm, which contributes to adhesion and invasion of oral epithelial and heart endothelial cells. These virulence properties were subsequently linked to post-translational modification (PTM) of the Cnm threonine-rich repeat region by the Pgf glycosylation machinery, which consists of 4 enzymes: PgfS, PgfM1, PgfE, and PgfM2. Inactivation of the S. mutans pgf genes leads to decreased collagen binding, reduced invasion of human coronary artery endothelial cells, and attenuated virulence in the Galleria mellonella invertebrate model. The present study aimed to better understand Cnm glycosylation and characterize the predicted 4-epimerase, PgfE. Using a truncated Cnm variant containing only 2 threonine-rich repeats, mass spectrometric analysis revealed extensive glycosylation with HexNAc2. Compositional analysis, complemented with lectin blotting, identified the HexNAc2 moieties as GlcNAc and GalNAc. Comparison of PgfE with the other S. mutans 4-epimerase GalE through structural modeling, nuclear magnetic resonance, and capillary electrophoresis demonstrated that GalE is a UDP-Glc-4-epimerase, while PgfE is a GlcNAc-4-epimerase. While PgfE exclusively participates in protein O-glycosylation, we found that GalE affects galactose metabolism and cell division. This study further emphasizes the importance of O-linked protein glycosylation and carbohydrate metabolism in S. mutans and identifies the PTM modifications of the key CBP, Cnm.
    Materialart: Online-Ressource
    ISSN: 1460-2423
    Sprache: Englisch
    Verlag: Oxford University Press (OUP)
    Publikationsdatum: 2023
    ZDB Id: 1478140-2
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 8
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 200, No. 14 ( 2018-07-15)
    Kurzfassung: The Dps-like peroxide resistance protein (Dpr) is essential for H 2 O 2 stress tolerance and aerobic growth of the oral pathogen Streptococcus mutans . Dpr accumulates during oxidative stress, protecting the cell by sequestering iron ions and thereby preventing the generation of toxic hydroxyl radicals that result from the interaction of iron with H 2 O 2 . Previously, we reported that the SpxA1 and SpxA2 regulators positively regulate expression of dpr in S. mutans . Using an antibody raised against S. mutans Dpr, we confirmed at the protein level the central and cooperative nature of SpxA1 and SpxA2 regulation in Dpr production. During phenotypic characterization of the S. mutans Δ dpr strain, we observed the appearance of distinct colony variants, which sometimes lost the oxidative stress sensitivity typical of Δ dpr strains. Whole-genome sequencing of these phenotypically distinct Δ dpr isolates revealed that a putative iron transporter operon, smu995-smu998 , was a genomic hot spot with multiple single nucleotide polymorphisms identified within the different isolates. Deletion of smu995 or the entire smu995-smu998 operon in the Δ dpr background strain completely reversed the oxidative stress-sensitive phenotypes associated with dpr inactivation. Conversely, inactivation of genes encoding the ferrous iron transport system FeoABC did not alleviate phenotypes of the Δ dpr strain. Preliminary characterization of strains lacking smu995-smu998 , feoABC , and the iron/manganese transporter gene sloABC revealed the interactive nature of these three systems in iron transport but also indicated that there may be additional iron uptake systems in S. mutans . IMPORTANCE The dental caries-associated pathogen Streptococcus mutans routinely encounters oxidative stress within the human plaque biofilm. Previous studies revealed that the iron-binding protein Dpr confers protection toward oxidative stress by limiting free iron availability, which is associated with the generation of toxic hydroxyl radicals. Here, we report the identification of spontaneously occurring mutations within Δ dpr strains. Several of those mutations were mapped to the operon smu995-smu998 , revealing a previously uncharacterized system that appears to be important in iron acquisition. Disruption of the smu995-smu998 operon resulted in reversion of the stress-sensitive phenotype typical of a Δ dpr strain. Our data suggest that the Smu995-Smu998 system works along with other known metal transport systems of S. mutans , i.e., FeoABC and SloABC, to coordinate iron uptake.
    Materialart: Online-Ressource
    ISSN: 0021-9193 , 1098-5530
    Sprache: Englisch
    Verlag: American Society for Microbiology
    Publikationsdatum: 2018
    ZDB Id: 1481988-0
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 9
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 200, No. 23 ( 2018-12)
    Kurzfassung: Cnm is a surface-associated protein present in a subset of Streptococcus mutans strains that mediates binding to extracellular matrices, intracellular invasion, and virulence. Here, we showed that cnm transcription is controlled by the global regulators CovR and VicRKX. In silico analysis identified multiple putative CovR- and VicR-binding motifs in the regulatory region of cnm as well as in the downstream gene pgfS , which is associated with the posttranslational modification of Cnm. Electrophoretic mobility shift assays revealed that CovR and VicR specifically and independently bind to the cnm and pgfS promoter regions. Quantitative real-time PCR and Western blot analyses of Δ covR and Δ vicK strains as well as of a strain overexpressing vicRKX revealed that CovR functions as a positive regulator of cnm , whereas VicRKX acts as a negative regulator. In agreement with the role of VicRKX as a repressor, the Δ vicK strain showed enhanced binding to collagen and laminin and higher intracellular invasion rates. Overexpression of vicRKX was associated with decreased rates of intracellular invasion but did not affect collagen or lamin binding activities, suggesting that this system controls additional genes involved in binding to these extracellular matrix proteins. As expected, based on the role of CovR in cnm regulation, the Δ covR strain showed decreased intracellular invasion rates, but, unexpectedly collagen and laminin binding activities were increased in this mutant strain. Collectively, the results presented here expand the repertoire of virulence-related genes regulated by CovR and VicRKX to include the core gene pgfS and the noncore gene cnm . IMPORTANCE Streptococcus mutans is a major pathogen associated with dental caries and also implicated in systemic infections, in particular, infective endocarditis. The Cnm adhesin of S. mutans is an important virulence factor associated with systemic infections and caries severity. Despite its role in virulence, the regulatory mechanisms governing cnm expression are poorly understood. Here, we describe the identification of two independent regulatory systems controlling the transcription of cnm and the downstream pgfS-pgfM1-pgfE-pgfM2 operon. A better understanding of the mechanisms controlling expression of virulence factors like Cnm can facilitate the development of new strategies to treat bacterial infections.
    Materialart: Online-Ressource
    ISSN: 0021-9193 , 1098-5530
    Sprache: Englisch
    Verlag: American Society for Microbiology
    Publikationsdatum: 2018
    ZDB Id: 1481988-0
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 10
    Online-Ressource
    Online-Ressource
    American Society for Microbiology ; 2008
    In:  Journal of Bacteriology Vol. 190, No. 1 ( 2008-01), p. 28-36
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 190, No. 1 ( 2008-01), p. 28-36
    Kurzfassung: The production of (p)ppGpp by Streptococcus mutans UA159 is catalyzed by three gene products: RelA, RelP, and RelQ. Here, we investigate the role of the RelA (Rel) homologue of S. mutans in the stringent response and in the global control of gene expression. RelA of S. mutans was shown to synthesize pppGpp in vitro from GTP and ATP in the absence of added ribosomes, as well as in vivo in an Escherichia coli relA-spoT mutant. Mupirocin (MUP) was shown to induce high levels of (p)ppGpp production in S. mutans in a relA -dependent manner, with a concomitant reduction in GTP pools. Transcription profiling after MUP treatment of S. mutans revealed that 104 genes were upregulated and 130 were downregulated ( P ≤ 0.001); mainly, genes for macromolecular biosynthesis, translation, and energy metabolism were downregulated. When a derivative of UA159 carrying a complete deletion of the relA gene was treated with MUP, 72 genes were upregulated and 52 were downregulated ( P ≤ 0.001). The expression of 50 genes ( P ≤ 0.001) was commonly affected by MUP treatment in the two strains, suggesting that S. mutans can mount a relA -independent response to MUP. Consistent with the gene expression profiling, RelA was shown to play major roles in the regulation of phenotypic traits that are required for establishment, persistence, and virulence expression by this oral pathogen. Thus, RelA is the major (p)ppGpp synthase controlling the stringent response in S. mutans , and it coordinates the expression of genes and phenotypes that contribute to the pathogenic potential of the organism.
    Materialart: Online-Ressource
    ISSN: 0021-9193 , 1098-5530
    Sprache: Englisch
    Verlag: American Society for Microbiology
    Publikationsdatum: 2008
    ZDB Id: 1481988-0
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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