Relevant bibliographies by topics / Eubacterial isolates

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters

Academic literature on the topic 'Eubacterial isolates'

Author: Grafiati
Published: 18 May 2024

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Journal articles on the topic "Eubacterial isolates"

1

Sahm, Kerstin, Christian Knoblauch, and Rudolf Amann. "Phylogenetic Affiliation and Quantification of Psychrophilic Sulfate-Reducing Isolates in Marine Arctic Sediments." Applied and Environmental Microbiology 65, no. 9 (September 1, 1999): 3976–81. http://dx.doi.org/10.1128/aem.65.9.3976-3981.1999.

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ABSTRACT Thirteen psychrophilic sulfate-reducing isolates from two permanently cold fjords of the Arctic island Spitsbergen (Hornsund and Storfjord) were phylogenetically analyzed. They all belonged to the δ subclass of Proteobacteria and were widely distributed within this group, indicating that psychrophily is a polyphyletic property. A new 16S rRNA-directed oligonucleotide probe was designed against the largest coherent cluster of these isolates. The new probe, as well as a set of available probes, was applied in rRNA slot blot hybridization to investigate the composition of the sulfate-reducing bacterial community in the sediments. rRNA related to the new cluster of incompletely oxidizing, psychrophilic isolates made up 1.4 to 20.9% of eubacterial rRNA at Storfjord and 0.6 to 3.5% of eubacterial rRNA at Hornsund. This group was the second-most-abundant group of sulfate reducers at these sites. Denaturing gradient gel electrophoresis and hybridization analysis showed bands identical to those produced by our isolates. The data indicate that the psychrophilic isolates are quantitatively important in Svalbard sediments.
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Teigell-Perez, Gonzalez-Martin, Valladares, Smith, and Griffin. "Virus-Like Particle Production in Atmospheric Eubacteria Isolates." Atmosphere 10, no. 7 (July 19, 2019): 417. http://dx.doi.org/10.3390/atmos10070417.

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Culturable eubacterial isolates were collected at various altitudes in Earth’s atmosphere, including ~1.5 m above ground in Tallahassee, FL, USA; ~10.0 m above sea level over the mid-Atlantic ridge (~15° N); ~ 20 km above ground over the continental United States; ~20 km above sea level over the Pacific Ocean near southern California; and from the atmosphere of Carlsbad Cavern, Carlsbad Cavern National Park, NM, USA. Isolates were screened for the presence of inducible virus-like particles (VLP) through the use of mitomycin C and epifluorescent direct counts. We determined that 92.7% of the isolates carried inducible VLP counts in exposed versus non-exposed culture controls and that the relationship was statistically significant. Further statistical analyses revealed that the number of isolates that demonstrated VLP production did not vary among collection sites. These data demonstrate a high prevalence of VLP generation in isolates collected in the lower atmosphere and at extreme altitudes. They also show that species of eubacteria that are resistant to the rigors of atmospheric transport play a significant role in long-range atmospheric inter- and intra-continental dispersion of VLP and that long-range atmospheric transport of VLP may enhance rates of evolution at the microbial scale in receiving environments.
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Ventura, Marco, Roberto Reniero, and Ralf Zink. "Specific Identification and Targeted Characterization ofBifidobacterium lactis from Different Environmental Isolates by a Combined Multiplex-PCR Approach." Applied and Environmental Microbiology 67, no. 6 (June 1, 2001): 2760–65. http://dx.doi.org/10.1128/aem.67.6.2760-2765.2001.

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ABSTRACT The species Bifidobacterium lactis, with its main representative strain Bb12 (DSM 10140), is a yoghurt isolate used as a probiotic strain and is commercially applied in different types of yoghurts and infant formulas. In order to ensure the genetic identity and safety of this bacterial isolate, species- and strain-specific molecular tools for genetic fingerprinting must be available to identify isolated bifidobacteria or lactic acid bacteria from, e.g., various clinical environments of relevance in medical microbiology. Two opposing rRNA gene-targeted primers have been developed for specific detection of this microorganism by PCR. The specificity of this approach was evaluated and verified with DNA samples isolated from single and mixed cultures of bifidobacteria and lactobacilli (48 isolates, including the type strains of 29Bifidobacterium and 9 Lactobacillusspecies). Furthermore, we performed a Multiplex-PCR using oligonucleotide primers targeting a specific region of the 16S rRNA gene for the genus Bifidobacterium and a conserved eubacterial 16S rDNA sequence. The specificity and sensitivity of this detection with a pure culture of B. lactis were, respectively, 100 bacteria/ml after 25 cycles of PCR and 1 to 10 bacteria/ml after a 50-cycle nested-PCR approach.
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Karahan, Z. Ceren, Ipek Mumcuoglu, Haluk Guriz, Deniz Tamer, Neriman Balaban, Derya Aysev, and Nejat Akar. "PCR evaluation of false-positive signals from two automated blood-culture systems." Journal of Medical Microbiology 55, no. 1 (January 1, 2006): 53–57. http://dx.doi.org/10.1099/jmm.0.46196-0.

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Rapid detection of micro-organisms from blood is one of the most critical functions of a diagnostic microbiology laboratory. Automated blood-culture systems reduce the time needed to detect positive cultures, and reduce specimen handling. The false-positive rate of such systems is 1–10 %. In this study, the presence of pathogens in ‘false-positive’ bottles obtained from BACTEC 9050 (Becton Dickinson) and BacT/Alert (Biomérieux) systems was investigated by eubacterial and fungal PCR. A total of 169 subculture-negative aerobic blood-culture bottles (104 BacT/Alert and 65 BACTEC) were evaluated. Both fungal and eubacterial PCRs were negative for all BACTEC bottles. Fungal PCR was also negative for the BacT/Alert system, but 10 bottles (9·6 %) gave positive results by eubacterial PCR. Sequence analysis of the positive PCR amplicons indicated the presence of the following bacteria (number of isolates in parentheses): Pasteurella multocida (1), Staphylococcus epidermidis (2), Staphylococcus hominis (1), Micrococcus sp. (1), Streptococcus pneumoniae (1), Corynebacterium spp. (2), Brachibacterium sp. (1) and Arthrobacter/Rothia sp. (1). Antibiotic usage by the patients may be responsible for the inability of the laboratory to grow these bacteria on subcultures. For patients with more than one false-positive bottle, molecular methods can be used to evaluate the microbial DNA in these bottles. False positives from the BACTEC system may be due to elevated patient leukocyte counts or the high sensitivity of the system to background increases in CO2 concentration.
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Wood, Jacqueline, Karen P. Scott, Gorazd Avguštin, C. James Newbold, and Harry J. Flint. "Estimation of the Relative Abundance of DifferentBacteroides and Prevotella Ribotypes in Gut Samples by Restriction Enzyme Profiling of PCR-Amplified 16S rRNA Gene Sequences." Applied and Environmental Microbiology 64, no. 10 (October 1, 1998): 3683–89. http://dx.doi.org/10.1128/aem.64.10.3683-3689.1998.

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ABSTRACT We describe an approach for determining the genetic composition ofBacteroides and Prevotellapopulations in gut contents based on selective amplification of 16S rRNA gene sequences (rDNA) followed by cleavage of the amplified material with restriction enzymes. The relative contributions of different ribotypes to total Bacteroides andPrevotella 16S rDNA are estimated after end labelling of one of the PCR primers, and the contribution ofBacteroides and Prevotellasequences to total eubacterial 16S rDNA is estimated by measuring the binding of oligonucleotide probes to amplified DNA.Bacteroides and Prevotella 16S rDNA accounted for between 12 and 62% of total eubacterial 16S rDNA in samples of ruminal contents from six sheep and a cow. Ribotypes 4, 5, 6, and 7, which include most cultivated rumen Prevotellastrains, together accounted for between 20 and 86% of the total amplified Bacteroides andPrevotella rDNA in these samples. The most abundantBacteroides or Prevotella ribotype in four animals, however, was ribotype 8, for which there is only one known cultured isolate, while ribotypes 1 and 2, which include many colonic Bacteroides spp., were the most abundant in two animals. This indicates that some abundantBacteroides and Prevotella groups in the rumen are underrepresented among cultured rumenPrevotella isolates. The approach described here provides a rapid, convenient, and widely applicable method for comparing the genotypic composition of bacterial populations in gut samples.
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Pryde, Susan E., Anthony J. Richardson, Colin S. Stewart, and Harry J. Flint. "Molecular Analysis of the Microbial Diversity Present in the Colonic Wall, Colonic Lumen, and Cecal Lumen of a Pig." Applied and Environmental Microbiology 65, no. 12 (December 1, 1999): 5372–77. http://dx.doi.org/10.1128/aem.65.12.5372-5377.1999.

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ABSTRACT Random clones of 16S ribosomal DNA gene sequences were isolated after PCR amplification with eubacterial primers from total genomic DNA recovered from samples of the colonic lumen, colonic wall, and cecal lumen from a pig. Sequences were also obtained for cultures isolated anaerobically from the same colonic-wall sample. Phylogenetic analysis showed that many sequences were related to those ofLactobacillus or Streptococcus spp. or fell into clusters IX, XIVa, and XI of gram-positive bacteria. In addition, 59% of randomly cloned sequences showed less than 95% similarity to database entries or sequences from cultivated organisms. Cultivation bias is also suggested by the fact that the majority of isolates (54%) recovered from the colon wall by culturing were related toLactobacillus and Streptococcus, whereas this group accounted for only one-third of the sequence variation for the same sample from random cloning. The remaining cultured isolates were mainly Selenomonas related. A higher proportion ofLactobacillus reuteri-related sequences than ofLactobacillus acidophilus- and Lactobacillus amylovorus-related sequences were present in the colonic-wall sample. Since the majority of bacterial ribosomal sequences recovered from the colon wall are less than 95% related to known organisms, the roles of many of the predominant wall-associated bacteria remain to be defined.
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Peters, Sabine, Stefanie Koschinsky, Frank Schwieger, and Christoph C. Tebbe. "Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes." Applied and Environmental Microbiology 66, no. 3 (March 1, 2000): 930–36. http://dx.doi.org/10.1128/aem.66.3.930-936.2000.

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ABSTRACT A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4–V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8–V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA molecules by exonuclease digestion and were subsequently electrophoretically separated by their single-strand-conformation polymorphism (SSCP). Genetic profiles obtained by this technique showed a succession and increasing diversity of microbial populations with all primers. A total of 19 single products were isolated from the profiles by PCR reamplification and cloning. DNA sequencing of these molecular isolates showed similarities in the range of 92.3 to 100% to known gram-positive bacteria with a low or high G+C DNA content and to the SSU rDNA of γ-Proteobacteria. The amplified 18S rRNA gene sequences were related to the respective gene regions of Candida krusei and Candida tropicalis. Specific molecular isolates could be attributed to different composting stages. The diversity of cultivated bacteria isolated from samples taken at the end of the composting process was low. A total of 290 isolates were related to only 6 different species. Two or three of these species were also detectable in the SSCP community profiles. Our study indicates that community SSCP profiles can be highly useful for the monitoring of bacterial diversity and community successions in a biotechnologically relevant process.
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Navrátilová, Lucie, Magdalena Chromá, Vojtěch Hanulík, and Vladislav Raclavský. "Possibilities in Identification of Genomic Species of Burkholderia cepacia Complex by PCR and RFLP." Polish Journal of Microbiology 62, no. 4 (2013): 373–76. http://dx.doi.org/10.33073/pjm-2013-051.

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The strains belonging to Burkholderia cepacia complex are important opportunistic pathogens in immunocompromised patients and cause serious diseases. It is possible to obtain isolates from soil, water, plants and human samples. Taxonomy of this group is difficult. Burkholderia cepacia complex consists of seventeen genomic species and the genetic scheme is based on recA gene. Commonly, first five genomovars occurre in humans, mostly genomovars II and III, subdivision IIIA. Within this study we tested identification of first five genomovars by PCR with following melting analysis and RFLP. The experiments were targeted on eubacterial 16S rDNA and specific gene recA, which allowed identification of all five genomovars. RecA gene appeared as more suitable than 16S rDNA, which enabled direct identification of only genomovars II and V; genomovars I, III and IV were similar within 16S rDNA sequence.
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9

Kukkurainen, S., A. Leino, S. Vähämiko, H. R. Kärkkäinen, K. Ahanen, S. Sorvari, R. Rugienius, and O. Toldi. "Occurrence and Location of Endophytic Bacteria in Garden and Wild Strawberry." HortScience 40, no. 2 (April 2005): 348–52. http://dx.doi.org/10.21273/hortsci.40.2.348.

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The occurrence of bacteria in different tissues was studied using field-grown strawberries, in vitro-grown strawberries, wild strawberries, and aseptically germinated strawberry seedlings. Strawberry has a number of endophytic bacteria in its the internal tissue, most of which appear to be nonpathogenic. In the in vitro-grown strawberries, all identified isolates were in the genus Pantoea. In field-grown garden and wild strawberries the most common genera were Pantoea and Pseudomonas. Location of eubacterial inhabitants within strawberry tissue sections was studied by in situ hybridization. Bacteria were detected in flower stalks, leaf stalks, leaves, stolons, berries and aseptically germinated seedlings. The existence of bacteria in seeds and seedlings suggests that bacteria are able to move up to the generative tissue and, ultimately, to the next generation, forming a symbiosis-like chain of plant-bacteria coexistence.
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Babb, Kelly, Tomasz Bykowski, Sean P. Riley, M. Clarke Miller, Edward DeMoll, and Brian Stevenson. "Borrelia burgdorferi EbfC, a Novel, Chromosomally Encoded Protein, Binds Specific DNA Sequences Adjacent to erp Loci on the Spirochete's Resident cp32 Prophages." Journal of Bacteriology 188, no. 12 (June 15, 2006): 4331–39. http://dx.doi.org/10.1128/jb.00005-06.

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ABSTRACT All examined isolates of the Lyme disease spirochete, Borrelia burgdorferi, naturally maintain numerous variants of a prophage family as circular cp32 episomes. Each cp32 carries a locus encoding one or two different Erp outer membrane, surface-exposed lipoproteins. Many of the Erp proteins bind a host complement regulator, factor H, which is hypothesized to protect the spirochete from complement-mediated killing. We now describe the isolation and characterization of a novel, chromosomally encoded protein, EbfC, that binds specific DNA sequences located immediately 5′ of all erp loci. This is one of the first site-specific DNA-binding proteins to be identified in any spirochete. The location of the ebfC gene on the B. burgdorferi chromosome suggests that the cp32 prophages have evolved to use this bacterial host protein for their own benefit and that EbfC probably plays additional roles in the bacterium. A wide range of other bacteria encode homologs of EbfC, none of which have been well characterized, so demonstration that B. burgdorferi EbfC is a site-specific DNA-binding protein has broad implications across the eubacterial kingdom.
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Dissertations / Theses on the topic "Eubacterial isolates"

1

Ranjan, Vivek Kumar. "Search for molecular diversity of metallo-B-lactamase genes in eubacterial isolates of Karala and Mahananda rivers of West Bengal." Thesis, University of North Bengal, 2021. http://ir.nbu.ac.in/handle/123456789/4663.

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Book chapters on the topic "Eubacterial isolates"

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Prado, A., M. S. da Costa, J. Laynez, and V. M. C. Madeira. "Physical Properties of Membrane Lipids Isolated from a Thermophilic Eubacterium (Thermus sp.)." In Advances in Experimental Medicine and Biology, 47–58. New York, NY: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4684-7908-9_5.

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Kubota, H., and K. Willison. "CCTη,." In Guidebook to Molecular Chaperones and Protein-Folding Catalysts, 224. Oxford University PressOxford, 1997. http://dx.doi.org/10.1093/oso/9780198599494.003.0085.

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Abstract Mouse Cctq cDNA (GenBank accession number Z31399) was isolated by random selection from a testis cDNA library (Kubota et al., 1994). The mouse CCT protein is 544 amino acids in length, it shares approximately 30% identity with the other subunits of CCT, 40% with the archaebacterial chaperonin TF55 (Kubota et al., 1994). The CCT17 protein also shows weak similarity to the eubacterial chaperonin GroEL, intraorganellar chaperonins Hsp60, rubisco subunit-binding protein (Kim et al., 1994; Kubota et al., 1994, 1995a).
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Davis, J. E., L. P. Jones, and J. E. Zajic. "Heterotrophic Eubacteria Isolated from Cultures of the Cyanobacterium, Spirulina Maxima." In 1990, 99–104. De Gruyter, 1990. http://dx.doi.org/10.1515/9783112581964-025.

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