rrndb: the Ribosomal RNA Operon Copy Number Database
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TLDR
This work has created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms in an attempt to understand the evolutionary implications of rRNA operon redundancy.Abstract:
The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu.read more
Citations
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The oxazolidinones: past, present, and future
TL;DR: The oxazolidinones share a relatively low frequency of resistance largely due to the requirement of mutations in 23S ribosomal RNA genes, however, maintaining potency against strains carrying the mobile cfr gene poses a challenge for the oxzolidinone class, as well as other 50S Ribosome inhibitors that target the peptidyl transferase center.
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Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification.
TL;DR: Three sets of primer pair together with probe previously designed for targeting different classes of bacterial extracellular peptidases were tested for their suitability for TaqMan-PCR based quantification of proteolytic bacteria.
Journal ArticleDOI
Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau
TL;DR: The effects of salinity and mineralogy on microbial community composition was studied by using a 900-cm sediment core collected from a stable, inland hypersaline lake, Lake Chaka, on the Tibetan Plateau, north-western China, using an integrated approach combining mineralogy and geochemistry, molecular microbiology, cultivation and lipid biomarker analyses.
Journal ArticleDOI
The human vaginal bacterial biota and bacterial vaginosis.
TL;DR: The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates as mentioned in this paper, and changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease and acquisition of HIV infection.
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Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities
TL;DR: The results suggest that stochastic events in early colonization, coupled with dispersal limitation, generated alternate trajectories of bacterial community assembly within the context of deterministic selection for community membership.
References
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Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
Journal ArticleDOI
Prokaryotes: The unseen majority
TL;DR: The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4-6 x 10(30) cells and 350-550 Pg of C (1 Pg = 10(15) g), respectively, which is 60-100% of the estimated total carbon in plants.
Journal ArticleDOI
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
TL;DR: Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragments lengths or "ribotypes."
Journal ArticleDOI
Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
Gerard Muyzer,Kornelia Smalla +1 more
TL;DR: The potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.
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