Journal ArticleDOI
Genetic diversity in Sargasso Sea bacterioplankton.
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TLDR
The phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton indicate the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community.Abstract:
BACTERIOPLANKTON are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities. Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques. Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species1–3. We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction4. The analysis indicates the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community. A second cluster of lineages related to the oxygenic phototrophs—cyanobacteria, prochlorophytes and chloroplasts—was also observed. However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats. The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors.read more
Citations
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Analyses of Intestinal Microbiota: Culture versus Sequencing.
TL;DR: In this review, differences and pitfalls in current experimental protocols are summarized, including all steps from nucleic acid extraction to bioinformatical analysis which may produce variation that outweighs subtle biological differences.
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Flow sorting of marine bacterioplankton after fluorescence in situ hybridization.
TL;DR: An approach to sort cells from coastal North Sea bacterioplankton by flow cytometry after in situ hybridization with rRNA-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats.
Journal ArticleDOI
Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA‐targeted oligonucleotide probes
TL;DR: The microbial community structure of the gastrointestinal tracts of various domestic animals (bovine, ovine, caprine, and swine) was evaluated using oligonucleotide probes targeting the small subunit (SSU) ribosomal RNA (rRNA) of major microbial groups.
Journal ArticleDOI
Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments
TL;DR: The technique appears to be promising as a rapid method for microbial biodiversity fingerprinting, useful to compare several environments and detect major shifts in species composition of the microbial population.
Journal ArticleDOI
Application of 16S rRNA gene PCR to study bowel flora of preterm infants with and without necrotizing enterocolitis.
TL;DR: In the present study uncultured bacteria detected by PCR-DGGE were no more frequent in fecal samples from infants with NEC than in samples from infant without NEC, although these findings do not exclude the possibility of unrecognized bacteria associated with the mucosa of the small intestine of infant with NEC.
References
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DNA sequencing with chain-terminating inhibitors
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
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Randall Keichi Saiki,David H. Gelfand,Susanne Stoffel,Stephen J. Scharf,Russell Higuchi,Glenn Thomas Horn,Kary B. Mullis,Henry A. Erlich +7 more
TL;DR: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction, which significantly improves the specificity, yield, sensitivity, and length of products that can be amplified.
Journal ArticleDOI
Site-directed mutagenesis by overlap extension using the polymerase chain reaction.
TL;DR: In this paper, complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate two DNA fragments having overlapping ends, and these fragments are combined in a subsequent 'fusion' reaction in which the overlapping ends anneal, allowing the 3' overlap of each strand to serve as a primer for the three' extension of the complementary strand.
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