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

Cole, James R.; Chai, Benli; Farris, Ryan J.; Wang, Qiong; Kulam, S. A.; McGarrell, Donna M.; Tiedje, James M.

doi:10.1093/nar/gki038

Cited by 1,263 publications

(917 citation statements)

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“…msu.edu/) (Cole et al 2005). Sequence similarity analysis was performed using MatGAT 2.0 (Campanella et al 2003), with 99% minimum similarity as the threshold for any pair of sequences in a phylotype.…”

Section: Analysis Of Sequencesmentioning

confidence: 99%

Characterization of bacterial community in the stomach of yellow catfish (Pelteobagrus fulvidraco)

Tian

Wang

et al. 2012

World J Microbiol Biotechnol

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In this study, the traditional culture-based technique and the 16S rDNA sequencing method were used to investigate the characterization of bacterial community in the stomach contents and mucus of yellow catfish (Pelteobagrus fulvidraco). The culture-based technique disclosed that the average bacterial numbers in the gastric contents and mucus were 5.79 9 10 7 cfu/g (cfu: colony forming unit) and 1.89 9 10 5 cfu/g, respectively. Several different bacteria were obtained from gastric contents, including species from genera Bradyrhizobium, Phyllobacterium, Plesiomonas, Hafnia, Edwardsiella, Pseudomonas, and Bacillus. However, only two species were isolated from the gastric mucus, including species from genera Plesiomonas and Aeromonas. Forty-five phylotypes were observed from the 65 positive clones from the stomach contents (library SC); nineteen phylotypes were detected from the 45 clones from the stomach mucus (library SM). Further analyses revealed that the fish stomach harbored characteristic microbiota, where Firmicutes was dominant, followed by Proteobacteria and Bacteroidetes and Fusobacteria. This characterization of bacterial community is markedly different from that of the fish intestine, where Proteobacteria is predominant, followed by Fusobacteria and Firmicutes. Chloroflexi (1.5%) was only found in the library SC, while Actinobacteria (4.4%) was only found in the library SM, suggesting that microbiota of GI contents was quite different from that of GI mucus. In addition, several species of bacteria found in the stomach may be potentially opportunistic pathogens, indicating that fish digestive tract is a reservoir for many nosocomial pathogens.

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Section: Analysis Of Sequencesmentioning

confidence: 99%

Characterization of bacterial community in the stomach of yellow catfish (Pelteobagrus fulvidraco)

Tian

Wang

et al. 2012

World J Microbiol Biotechnol

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“…The partial sequences that were generated were assembled using BioEdit v5.0.1 (Hall, 1999) and the consensus sequence of 1627 nucleotides was corrected manually for errors. The most closely related sequences in the GenBank (version 152) and the Ribosomal Database Project II (release 9.37) identified using BLAST (Altschul et al, 1997) and the Sequence Match program (Cole et al, 2005) were extracted, aligned and manually adjusted according to the 16S rRNA secondary structure using BioEdit. Nucleotide ambiguities were omitted and evolutionary distances were calculated by using the Jukes and Cantor option (Jukes & Cantor, 1969) in TREECON (Van de Peer et al, 1997).…”

mentioning

confidence: 99%

Thermotalea metallivorans gen. nov., sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia aquifer

Ogg

Patel

2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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A strictly anaerobic, thermophilic bacterium, designated strain B2-1 T , was isolated from microbial mats colonizing a runoff channel formed by free-flowing thermal water from a Great Artesian Basin, Australia, bore well (registered number 17263). The cells of strain B2-1 T were slightly curved rods (3.0-3.5¾0.6-0.7 mm) which stained Gram-negative. The strain grew optimally in tryptone-yeast extract-glucose medium at 50 6C (temperature growth range 30-55 6C) and a pH of 8 (pH growth range 6.5-9). Strain B2-1 T grew poorly on yeast extract (0.2 %) and/or tryptone (0.2 %), which were obligately required for growth on other energy sources, including a range of other carbohydrates and organic acids, but not amino acids. The end-products of glucose fermentation were ethanol and acetate. In the presence of 0.2 % yeast extract, iron(III), manganese(IV) and elemental sulfur were reduced but sulfate, thiosulfate, sulfite, nitrate and nitrite were not reduced. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin, sodium azide and by NaCl concentrations greater than 4 % (w/v). The DNA G+C content was 48±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain B2-1 T was a member of the family Clostridiaceae, class Clostridia, phylum Firmicutes and was most closely related to Geosporobacter subterraneus DSM 17957 T (89.9 % similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain B2-1 T is considered to represent a novel species of a new genus, for which the name Thermotalea metallivorans gen. nov., sp. nov. is proposed. The type strain is B2-1 T (5KCTC 5625 T 5JCM 15105 T 5DSM 21119 T ).The Great Artesian Basin (GAB) underlies approximately 22 % of the arid and subarid regions of the Australian continent, an area of over 1.7610 6 km 2 , with a water storage capacity of 8.7610 12 m 3 , and is considered to be the world's largest geothermal subsurface aquifer (Habermahl, 1980). The GAB was formed between 100 and 250 million years ago and contains groundwaters which are estimated to be 2 million years old. It is composed of alternating layers of water-bearing permeable sandstone aquifers and non-water-bearing impermeable shale and includes two regions that contain the largest onshore oil and gas reserves in Australia. These geological formations have an immense influence on the chemical composition of GAB groundwaters, which can be bicarbonate-, chloride-, sulfate-or iron-rich. The GAB subsurface waters flow from the recharge areas at the edge of the basin to the discharge areas in central Australia as mound springs at an estimated rate of 1-5 m year 21 and are heated by the Earth's magma due to the aquifer's great depth. The GAB is tapped by more than 5000 free-flowing bores which provide vital water to outback communities where it is used for agricultural, industrial and domestic purposes. These bores can be found up to 3000 m deep, with source temperatures ranging from 30 to 100 u C d...

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“…Several available tools allow to identify rRNA sequences, some we presented previously (BIBI, RDP classifier); others can detect chimera, such as the Robison-Cox et al method [13], Check chimera [4], mglobalCHI package [14], Bellerophon [15], PhyID/CD, CCODE (Chimera and Cross-Over DEtection) [16], Mallard [17] or Pintail [18]. However these methods give various results.…”

Section: An Application Adapted To 16s Ribosomal Rna Sequence Databasmentioning

confidence: 99%

“…Several tools exist to make sequence identification and most of them are domain specific or data specific. For instance, some applications allow bacterial identification as BIBI (Bioinformatic Bacterial Identification) [1], PhyID/CD [2] or MicroSeq (Microbial identification System), others are specialized for the medical domain as RIDOM (Ribosomal Differenciation Of Medical Organisms) [3] or for the identification of Ribosomal RNA sequences as the RDP classifier (Ribosomal Database Project) [4], or TaxI [5] based on DNA barcodes.…”

Section: Introductionmentioning

confidence: 99%

Automatic identification of large collections of protein-coding or rRNA sequences

Arigon¹,

Perrière²,

Gouy³

2008

Biochimie

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Abstract:The number of available genomic sequences is growing very fast, due to the development of massive sequencing techniques. Sequence identification is needed and contributes to the assessment of gene and species evolutionary relationships. Automated bioinformatics tools are thus necessary to carry out these identification operations in an accurate and fast way. We developed HoSeqI (Homologous Sequence Identification), a software environment allowing this kind of automated sequence identification using homologous gene family databases. HoSeqI is accessible through a Web interface (http://pbil.univ-lyon1.fr/software/HoSeqI/) allowing to identify one or several sequences and to visualize resulting alignments and phylogenetic trees. We also implemented another application, MultiHoSeqI, to quickly add a large set of sequences to a family database in order to identify them, to update the database, or to help automatic genome annotation. Lately, we developed an application, ChiSeqI (Chimeric Sequence Identification), to automate the processes of identification of bacterial 16S ribosomal RNA sequences and of detection of chimeric sequences.

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

Cited by 1,263 publications

References 5 publications

Characterization of bacterial community in the stomach of yellow catfish (Pelteobagrus fulvidraco)

Characterization of bacterial community in the stomach of yellow catfish (Pelteobagrus fulvidraco)

Thermotalea metallivorans gen. nov., sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia aquifer

Automatic identification of large collections of protein-coding or rRNA sequences

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