The RDP (Ribosomal Database Project) continues

Maidak, B.; Cole, James R.; Lilburn, Timothy; Saxman, Paul; Stredwick, Jason M.; Li, Bing; Olsen, Gary J.; Pramanik, Sakti; Schmidt, Thomas M.; Tiedje, James M.

doi:10.1093/nar/28.1.173

Cited by 528 publications

(328 citation statements)

References 5 publications

Supporting

Mentioning

326

Contrasting

Unclassified

Order By: Relevance

“…The sequences were aligned to the Ribosomal Database Project (RDP) small subunit rRNA alignment version 7.1 (26), running locally in the ARB sequence environment (4). The RDP 7.1 alignment comprises 7,008 entries of mostly full-length or partial sequences for the Bacteria domain.…”

Section: Methodsmentioning

confidence: 99%

Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited

Leser

Amenuvor

Jensen

et al. 2002

Appl Environ Microbiol

761

615

View full text Add to dashboard Cite

The phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16S ribosomal DNA (rDNA) sequence analysis. Samples were collected from a total of 24 pigs representing a variety of diets, ages, and herd health status. A library comprising 4,270 cloned 16S rDNA sequences obtained directly by PCR from 52 samples of either the ileum, the cecum, or the colon was constructed. In total, 375 phylotypes were identified using a 97% similarity criterion. Three hundred nine of the phylotypes (83%) had a <97% sequence similarity to any sequences in the database and may represent yet-uncharacterized bacterial genera or species. The phylotypes were affiliated with 13 major phylogenetic lineages. Three hundred four phylotypes (81%) belonged to the low-G؉C gram-positive division, and 42 phylotypes (11.2%) were affiliated with the Bacteroides and Prevotella group. Four clusters of phylotypes branching off deeply within the low-G؉C grampositive bacteria and one in the Mycoplasma without any cultured representatives were found. The coverage of all the samples was 97.2%. The relative abundance of the clones approximated a lognormal distribution; however, the phylotypes detected and their abundance varied between two libraries from the same sample. The results document that the intestinal microbial community is very complex and that the majority of the bacterial species colonizing the gastrointestinal tract in pigs have not been characterized.The microbial ecology of gastrointestinal tract ecosystems is not well understood due to the inadequacy of classical, culturedependent microbiological methods. Two decades ago, substantial efforts were put into characterizing the intestinal microbiota of pigs by using microbiological methods based on culturing and phenotypic analysis of the isolates (1,28,36,37,39,40). These studies showed that the majority of the culturable bacteria are gram-positive, strict anaerobic streptococci, lactobacilli, eubacteria, clostridia, and peptostreptococci, while the gram-negative part of the microbiota is dominated by Bacteroides. Because culture-based methods are very time-consuming, thereby limiting the number of samples that can be processed, no information on the population dynamics or community responses to perturbations was obtained.Detailed information of the microbial community composition in natural systems can be gained from the phylogenetic analysis of 16S ribosomal DNA (rDNA) sequences obtained directly from samples by PCR amplification, cloning, and sequencing, although this procedure may be biased as well (9,35,46,49,50). 16S rDNA cloning and sequencing has been applied to analyze the intestinal bacterial community in humans (45, 56) and in a pig (33) and compared to culture-based methods. The results showed that the microbial community is complex and that the bacterial diversity cannot be comprehended by culturing. However, these studies were limited, as only a single individual was sampled, the number of clones analyzed was small relative to the expected di...

show abstract

Section: Methodsmentioning

confidence: 99%

Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited

Leser

Amenuvor

Jensen

et al. 2002

Appl Environ Microbiol

761

615

View full text Add to dashboard Cite

show abstract

“…Phylogenetic analysis-Preliminary analyses using BLAST searches (Altschul et al 1990) of genbank and sequence match in the ribosomal database project (RDP; Maidak et al 2000)] showed that the organisms most closely related to strain BLI-41 are members of the genus Vibrio. Aligned sequences of representative Vibrios and relatives were downloaded from RDP, and additional sequences from Genbank were added to the alignment and aligned by eye using Sequencher (Gene Codes).…”

Section: Identification Of a Natural Desferrioxamine Siderophore Prodmentioning

confidence: 99%

Identification of a natural desferrioxamine siderophore produced by a marine bacterium

Martinez

Haygood

Butler

2001

Limnology & Oceanography

View full text Add to dashboard Cite

Desferrioxamine B (DFOB, a terrestrial bacterial siderophore) has been used in experiments on waters from iron‐replete areas of the oceans to manipulate the levels of iron available to the biota. Addition of DFOB complexes the available iron (III) and has been suggested to render this complexed iron unavailable to marine microorganisms. We have identified a marine bacterium belonging to the genus Vibrio that produces the siderophore desferrioxamine G. Desferrioxamine G, another known terrestrial siderophore, is very similar in structure to DFOB, differing only by the substitution of a terminal methyl group by a propionic acid moiety. These results could affect the interpretation of DFOB iron‐removal experiments and further suggest that addition of DFOB might not impose iron stress uniformly across the biological community.

show abstract

“…The resulting 16S rDNA sequence was compared with RDP (Maidak et al, 2000) and EMBL (Baker et al, 2000) database sequences to find the most closely related species. For phylogenetic analysis we used 18 data sets of sulfate-reducing bacteria and Escherichia coli as the prokaryotic outgroup.…”

Section: Methodsmentioning

confidence: 99%

In vitro and in vivo sulfate reduction in the gut contents of the termite Mastotermes darwiniensis and the rose-chafer Pachnoda marginata

Dröge

Limper

Emtiazi

et al. 2005

J. Gen. Appl. Microbiol.

View full text Add to dashboard Cite

The RDP (Ribosomal Database Project) continues

Cited by 528 publications

References 5 publications

Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited

Culture-Independent Analysis of Gut Bacteria: the Pig Gastrointestinal Tract Microbiota Revisited

Identification of a natural desferrioxamine siderophore produced by a marine bacterium

In vitro and in vivo sulfate reduction in the gut contents of the termite Mastotermes darwiniensis and the rose-chafer Pachnoda marginata

Contact Info

Product

Resources

About