The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is [email protected]

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task

Micro-Mar: a database for dynamic representation of marine microbial biodiversity

BACKGROUND: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes. DESCRIPTION: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information. CONCLUSION: The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at

Bacterial diversity detected in osteoradionecrosis

Direct microscopy, culture based studies and DNA-DNA hybridization have previously demonstrated an association between microorganisms and osteoradionecrosis. The purpose of our study was to use culture independent molecular techniques to detect bacteria in necrotic bone lesions of the mandible after radiotherapy. Bacterial DNA was extracted from six deep medullary specimens from resected mandibles, including one sample of a relapse. 16S rRNA genes were PCR amplified, cloned, transformed into Escherichia coli and sequenced to determine species identity and closest relatives. From the analysis of 438 clones, 59 predominant species were detected, of which 27% have not been cultivated. The predominant species detected from radionecrotic mandibles were Campylobacter gracilis, Streptococcus intermedius, Peptostreptocooccus sp. oral clone FG014, Uncultured bacterium clone RL178, Fusobacterium nucleatum, and Prevotella spp.. The analysis demonstrated intersubject variability of the bacteria present in osteoradionecrosis. In contrast to the diverse bacterial profile detected in primary infection, only a few members of the oral indigenous flora were identified from a case of relapse. Detection of all members of the complex bacterial flora associated with osteoradionecrosis seems to be necessary to better understand the pathogenesis and to improve the therapeutic approach of the infection

The bacterial pedome associated with foot pathologies in sheep::a case study

Hoof lameness is considered to be a major health issue in sheep, and can impact on both animal welfare and production of livestock. However the causes, although generally assumed to have a microbiological basis, are poorly understood. The work presented here investigated the pedome (the bacterial community of the foot) of sheep which were seen to have one of the following conditions: foot rot; a toe granuloma; Ovine Interdigital Dermatitis (OID) / scald. These were compared relative to samples collected from the healthy feet of the same animals. Samples were collected from commercial lambs from two flocks of sheep (one Beulahs, one Suffolks) at times of routine husbandry work. All animals in the flocks and those which showed signs of lameness (7 per flock) were used for sample collection. Interdigital scrapes were collected from lame feet, together with controls (i.e. non-lame feet) from the same animals. Of the lame feet, 3 were classified as having foot rot, 10 had OID / scald and 1 had a toe granuloma. DNA was isolated from the interdigital scrapes and analysed by next generation sequencing following amplification of DNA by PCR. All foot rot samples showed unusual microbial communities: one having an elevated abundance of Fusobacterium spp.; another with an elevated level of a Corynebacterium sp.; and the third an increased level of a number of unidentified sequences. One of the OID samples also had a high abundance of Fusobacterium spp., and another had a similar pattern of unknown organisms to that seen in the example of the foot rot case. The toe granuloma case showed an elevated level of a Mycoplasma sp. Therefore the organisms described here are different from those previously identified in a similar investigation into this topic. However the other eight OID samples had patterns similar to those in controls. This suggests microbial communities associated with ovine foot rot are complex, and that there are bacteria associated with the condition which remain unknown

Untangling the Genetic Basis of Fibrolytic Specialization by Lachnospiraceae and Ruminococcaceae in Diverse Gut Communities

The Lachnospiraceae and Ruminococcaceae are two of the most abundant families from the order Clostridiales found in the mammalian gut environment, and have been associated with the maintenance of gut health. While they are both diverse groups, they share a common role as active plant degraders. By comparing the genomes of the Lachnospiraceae and Ruminococcaceae with the Clostridiaceae, a more commonly free-living group, we identify key carbohydrate-active enzymes, sugar transport mechanisms, and metabolic pathways that distinguish these two commensal groups as specialists for the degradation of complex plant material

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website ()

REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a widespread technique for rapidly fingerprinting microbial communities. Users of T-RFLP frequently overlook the resolving power of well-chosen restriction endonucleases and often fail to report how they chose their enzymes. REPK (Restriction Endonuclease Picker) assists in the rational choice of restriction endonucleases for T-RFLP by finding sets of four restriction endonucleases that together uniquely differentiate user-designated sequence groups. With REPK, users can provide their own sequences (of any gene, not just 16S rRNA), specify the taxonomic rank of interest and choose from a number of filtering options to further narrow down the enzyme selection. Bug tracking is provided, and the source code is open and accessible under the GNU Public License v.2, at http://code.google.com/p/repk. The web server is available without access restrictions at http://rocaplab.ocean.washington.edu/tools/repk

miRAS: a data processing system for miRNA expression profiling study

<p>Abstract</p> <p>Background</p> <p>The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studies try to discover new miRNAs and reveal the miRNA expression profile in cancer using a SAGE-based total RNA clone method. However, the data processing of this method is labor-intensive with several different biological databases and more than ten data processing steps involved.</p> <p>Results</p> <p>With miRAS, miRNAs and possible miRNA candidates contained in the submitted sequencing data were obtained together with their expression profile. The functions of known and predicted miRNAs were then analyzed by miRNA target prediction followed by target gene annotations. Finally, to extract the biological significance of the miRNAs in the samples, further annotations of the known miRNA and target genes were performed by collecting the public expression datasets of miRNA and target genes in normal and cancer tissues.</p> <p>Conclusion</p> <p>We introduce a web-based analysis platform called miRNA Analysis System (miRAS), for processing and analyzing of the sequence data obtained from the total RNA clone method. The system was built on generalizing the study of a liver cancer cell line total RNA sequencing project. miRAS is freely available on the web.</p

Evaluation of the microbiome of decaying alder nodules by next generation sequencing

This work investigated the microbial content of decaying nodules from alders. The 16S rDNA composition of the microbiome of six senescent alder nodules was investigated by 454 sequencing. All nodules still had some Frankia sequences present, but in each case it was only detected at minor levels, with other organisms predominating. Although organisms from three different phyla (Bacteroidetes, Proteobacteria and Actinobacteria) constituted almost all (98% or more) of all sequences, Bacteroidetes were most abundant in four nodules with Proteobacteria being most abundant in the other two. In addition a few families were represented at a level of 10% or more of the total sequences: Sphingobacteriaceae (all 6 nodules); Chitinophagaceae (5 of 6); non-Frankia Actinomycetales (2 of 6); Caulobacteraceae (2 of 6); Flavobacteriaceae (2 of 6); Oxalobacteraceae (1 of 6); and Xanthomoadaceae (1 of 6). Analysis at the genus level showed a diverse range of organisms, with members of the genus Pedobacter being found at an abundant level within most nodules