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Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. Expand
Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations
Fluorescent oligonucleotide hybridization probes were used to label bacterial cells for analysis by flow cytometry and the intensity of fluorescence was increased additively by the combined use of two or three fluorescent probes complementary to different regions of the same 16S rRNA. Expand
A marine microbial consortium apparently mediating anaerobic oxidation of methane
A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments. Strong geochemical evidence for net methane consumption in anoxic sediments is based onExpand
Phylogenetic Oligodeoxynucleotide Probes for the Major Subclasses of Proteobacteria: Problems and Solutions
Based on comparative analyses of 16S and 23S ribosomal RNA sequences, sites specific for the alpha-, beta-, and gamma-subclasses of Proteobacteria are located and will be useful for determinative studies and for the in situ monitoring of population distribution and dynamics in microbial communities. Expand
Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology
Fluorescent-dye-conjugated oligonucleotides were used to classify 14 Fibrobacter strains by fluorescence microscopy and the direct detection of F. intestinalis in mouse cecum samples demonstrated the application of this technique to the characterization of complex natural samples. Expand
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
This article proposes rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggests a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and Archaea. Expand
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains.
The signing authors together with the journal Systematic and Applied Microbiology (SAM) have started an ambitious project to reconstruct a single 16S rRNA tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria. Expand
The species concept for prokaryotes.
The validity of the concept in use is discussed, which is believed to be more pragmatic in comparison with those concepts described for eukaryotes. Expand
The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set.
Two supplementary versions of probe EUB338 are designed and evaluated for in situ detection of most of those phyla not detected with this probe, which should allow a more accurate quantification of members of the domain Bacteria in future molecular ecological studies. Expand
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota
Methodology is described to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. Expand