Search results for "Pyrosequencing"
showing 8 items of 58 documents
High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation
2014
Abstract We compared pyrosequencing technology with the PCR-ITS-RFLP analysis of yeast isolates and denaturing gradient gel electrophoresis (DGGE). These methods gave divergent findings for the yeast population. DGGE was unsuitable for the quantification of biodiversity and its use for species detection was limited by the initial abundance of each species. The isolates identified by PCR-ITS-RFLP were not fully representative of the true population. For population dynamics, high-throughput sequencing technology yielded results differing in some respects from those obtained with other approaches. This study demonstrates that 454 pyrosequencing of amplicons is more relevant than other methods …
The Largest Subunit of RNA Polymerase II as a New Marker Gene to Study Assemblages of Arbuscular Mycorrhizal Fungi in the Field
2014
Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an…
Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets.
2014
The routine use of chemotherapy to control bacterial diseases in aquatic populations has resulted in the development and spread of antibiotic resistance. The inclusion of immunostimulants in fish diets (functional diets) is one of the main strategies to solve this threat. This study aimed to analyse the intestinal microbiota of cultured European sea bass (Dicentrarchus labrax) fed two functional diets applying pyrosequencing of PCR-amplified 16S rRNA gene. Quality-filtered reads were assigned to family and genus taxonomic levels using the Ribosomal Database Project classifier. The autochthonous intestinal microbiota of sea bass consisted of two dominant bacterial genera: Dysgonomonas (Bacte…
Impact of environmental factors on grapevine physiology and responsiveness to elicitor-induced resistance against Plasmopara viticola
2012
Denitrifying microbial communities along a boreal stream with varying land-use
2019
Streams have an important role in regulating nitrogen (N) transportation from terrestrial ecosystems to downstream waters. Here, we examined how catchment land-use affects potential denitrification rates and the function and composition of denitrifier communities in boreal stream sediments, using stable isotope incubations and qPCR and 454-pyrosequencing targeted on nirS, nirK and nosZ genes. Although land-use influenced the water chemistry as higher nitrite + nitrate (NO x − ) concentration at the agriculture-affected sampling point, sediment organic matter content was found to be the key factor in regulating potential denitrification rates. However, the abundance as well as the diversity …
The Administration of Escherichia coli Nissle 1917 Ameliorates Development of DSS-Induced Colitis in Mice
2018
The beneficial effects of probiotics on immune-based pathologies such as inflammatory bowel disease (IBD) have been well reported. However, their exact mechanisms have not been fully elucidated. Few studies have focused on the impact of probiotics on the composition of the colonic microbiota. The aim of the present study was to correlate the intestinal anti-inflammatory activity of the probiotic Escherichia coli Nissle 1917 (EcN) in the dextran sodium sulfate (DSS) model of mouse colitis with the changes induced in colonic microbiota populations. EcN prevented the DSSinduced colonic damage, as evidenced by lower disease activity index (DAI) values and colonic weight/length ratio, when compa…
Isolation and characterization of microsatellite markers in the portunid crab Liocarcinus depurator using FIASCO and 454 next-generation sequencing
2012
The portunid crab Liocarcinus depurator is the dominant decapod crustacean present on mud bottoms of the continental shelf of the Mediterranean Sea. In order to better describe its genetic structure, a total of 11 microsatellites were isolated and tested in 28 L. depurator individuals from the Mediterranean locality of Tarragona. Initially, microsatellite isolation was carried out using the FIASCO methodology, but only 2 useful primer pairs could be designed. Given the low yield obtained, an alternative method based on 454 next-generation sequencing was assayed, which provided excellent results and from which another 9 primer pairs gave positive genotyping. All loci tested were polymorphic,…