Polynucleotide Probes That Target a Hypervariable Region of 16S rRNA Genes To Identify Bacterial Isolates Corresponding to Bands of Community Fingerprints

Heuer, Holger; Hartung, Kathrin; Wieland, Gabriele; Krämer, Ina; Smalla, Kornelia

doi:10.1128/aem.65.3.1045-1049.1999

Cited by 147 publications

(49 citation statements)

References 35 publications

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“…For the amplification of bacterial 16S rRNA gene sequences, DNA was amplified with the primer pair 341f/985r (Muyzer et al, 1993;Heuer et al, 1999). For DGGE analysis, 200-bp fragments spanning the hypervariable V3 region of the 16S rRNA gene, were amplified with a nested PCR using the eubacterial-specific primer 341f-GC with a 40-bp GC clamp added to its 5′ end (Muyzer et al, 1993) and the universal consensus primer 518r (Neefs et al, 1990).…”

Section: Pcr Amplification Of Extracted Dnamentioning

confidence: 99%

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air

Piñar

Piombino‐Mascali

Maixner

et al. 2013

FEMS Microbiology Ecology

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The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and – as a result of salt emanating from the walls – on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors.

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Section: Pcr Amplification Of Extracted Dnamentioning

confidence: 99%

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air

Piñar

Piombino‐Mascali

Maixner

et al. 2013

FEMS Microbiology Ecology

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“…Purified DNA was amplified with primers 341f-gc/518r (Muyzer et al 1993) and 968f-gc/1378r (Heuer et al 1999) spanning the V3 region and V6-V9 region of the 16S ribosomal DNA, respectively. The 40-nucleotide GC-rich sequence at the 5¢-end of the forward primers (341f and 968f) was attached to improve the detection of sequence variations of amplified DNA fragments by subsequent DGGE (Muyzer et al 1993).…”

Section: Analysis Of Enrichment Cultures By Pcr-dggementioning

confidence: 99%

Lactic acid bacteria associated with wine grapes from several Australian vineyards

2006

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Aims: The detection and isolation of lactic acid bacteria by enrichment methods from wine grapes cultivated in vineyards located in New South Wales, Australia. Methods and Results: Enrichment cultures in de Man, Rogosa and Sharpe (MRS) broth, MRS + ethanol (5%), MRS broth supplemented with 15% (v/v) tomato juice (MRST), pH 5·5 and 3·5 and autoenrichment in grape juice homogenate were used to detect lactic acid bacteria on wine grapes. Bacteria were isolated from enrichment cultures by plating onto MRS and MRST agar and identified by 16S rDNA sequence analysis and phenotypical methods. A molecular method, PCR‐denaturing gradient gel electrophoresis (DGGE) was also used to examine the bacteria that developed in enrichment cultures. Species of Lactobacillus, Enterococcus, Lactococcus and Weissella were detected in enrichments by plating and PCR‐DGGE. Other bacteria (Sporolactobacillus, Asaia, Bacillus ssp.) were also found in some enrichment cultures. The principal malolactic bacterium, Oenococcus oeni, was not isolated. Conclusions: The incidence and populations of lactic acid bacteria on wine grapes were very low. Damaged grape berries showed a greater presence of these bacteria than undamaged berries. The diversity of bacterial species isolated from the grapes was greater than those previously reported and represented both lactic acid bacteria and nonlactic acid bacteria. Some of these bacteria (i.e. Lactobacillus lindneri, Lactobacillus kunkeei) could be detrimental to wine production. Oenococcus oeni was not found on grapes, but its recovery could be obscured by overgrowth from other species. Significance and Impact of the Study: Lactic acid bacteria are significant in wine production because they conduct the malolactic fermentation and cause stuck or sluggish alcoholic fermentation and wine spoilage. This study investigates wine grapes as a potential source of these bacteria.

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“…PCR-based detection of BHR plasmids and generation of probes was done as described by Go « tz et al [5]. The ampli¢cation of 16S rDNA fragments from isolates or from community DNA was done as described previously [26].…”

Section: Pcr-based Detection Of Gm R Genes and Broad Host Range Plasmidsmentioning

confidence: 99%

Gentamicin resistance genes in environmental bacteria: prevalence and transfer

Heuer¹

2002

FEMS Microbiology Ecology

111

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A comprehensive multiphasic survey of the prevalence and transfer of gentamicin resistance (Gm r ) genes in different non-clinical environments has been performed. We were interested to find out whether Gm r genes described from clinical isolates can be detected in different environmental habitats and whether hot spots can be identified. Furthermore, this study aimed to evaluate the impact of selective pressure on the abundance and mobility of resistance genes. The study included samples from soils, rhizospheres, piggery manure, faeces from cattle, laying and broiler chickens, municipal and hospital sewage water, and coastal water. Six clusters of genes coding for Gmmodifying enzymes (aac(3)-I, aac(3)-II/VI, aac(3)-III/IV, aac(6P)-II/Ib, ant(2Q)-I, aph(2Q)-I) were identified based on a database comparison and primer systems for each gene cluster were developed. Gm-resistant bacteria isolated from the different environments had a different taxonomic composition. In only 34 of 207 isolates, mainly originating from sewage, faeces and coastal water polluted with wastewater, were known Gm r genes corresponding to five of the six clusters detected. The strains belonged to genera in which the genes had previously been detected (Enterobacteriaceae, Pseudomonas, Acinetobacter) but also to phylogenetically distant bacteria, such as members of the CFB group, K-and L-Proteobacteria. Gm r genes located on mobile genetic elements (MGE) could be captured in exogenous isolations into recipients belonging to K-, L-and Q-Proteobacteria from all environments except for soil. A high proportion of the MGE, conferring Gm resistance isolated from sewage, were identified as IncPL plasmids. Molecular detection of Gm r genes, and broad host range plasmidspecific sequences (IncP-1, IncN, IncW and IncQ) in environmental DNA indicated a habitat-specific dissemination. A high abundance and diversity of Gm r genes could be shown for samples from faeces (broilers, layers, cattle), from sewage, from seawater, collected close to a wastewater outflow, and from piggery manure. In the latter samples all six clusters of Gm r genes could be detected. The different kinds of selective pressure studied here seemed to enhance the abundance of MGE, while an effect on Gm r genes was not obvious.

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Polynucleotide Probes That Target a Hypervariable Region of 16S rRNA Genes To Identify Bacterial Isolates Corresponding to Bands of Community Fingerprints

Cited by 147 publications

References 35 publications

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air

Lactic acid bacteria associated with wine grapes from several Australian vineyards

Gentamicin resistance genes in environmental bacteria: prevalence and transfer

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