Journal•ISSN: 0003-6072
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology
Springer Science+Business Media
About: Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology is an academic journal published by Springer Science+Business Media. The journal publishes majorly in the area(s): Yeast & Fermentation. It has an ISSN identifier of 0003-6072. Over the lifetime, 6652 publications have been published receiving 174013 citations.
Topics: Yeast, Fermentation, Population, Streptomyces, Strain (chemistry)
Papers published on a yearly basis
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TL;DR: The potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.
Abstract: Here, the state of the art of the application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology will be presented. Furthermore, the potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.
2,181 citations
TL;DR: Divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species.
Abstract: Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.
2,174 citations
TL;DR: ANI calculation can be greatly sped up by the OrthoANIu method without losing accuracy, and when genomes that are larger than 7 Mbp were analysed, the run-times of ANIm and Orthoaniu were shorter than that of ANIb by 53- and 22-fold, respectively.
Abstract: Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes. By comparing values to the ANIb that is considered a standard, OrthoANIb and OrthoANIu exhibited good correlation in the whole range of ANI values. ANIm showed poor correlation for ANI of <90%. ANIm and OrthoANIu runs faster than ANIb by an order of magnitude. When genomes that are larger than 7 Mbp were analysed, the run-times of ANIm and OrthoANIu were shorter than that of ANIb by 53- and 22-fold, respectively. In conclusion, ANI calculation can be greatly sped up by the OrthoANIu method without losing accuracy. A web-service that can be used to calculate OrthoANIu between a pair of genome sequences is available at http://www.ezbiocloud.net/tools/ani
. For large-scale calculation and integration in bioinformatics pipelines, a standalone JAVA program is available for download at http://www.ezbiocloud.net/tools/orthoaniu
.
1,977 citations
TL;DR: Results from well conducted clinical studies will expand and increase the acceptance of probiotics for the treatment and prevention of selected diseases.
Abstract: Food products fermented by lactic acid bacteria have long been used for their proposed health promoting properties. In recent years, selected probiotic strains have been thoroughly investigated for specific health effects. Properties like relief of lactose intolerance symptoms and shortening of rotavirus diarrhoea are now widely accepted for selected probiotics. Some areas, such as the treatment and prevention of atopy hold great promise. However, many proposed health effects still need additional investigation. In particular the potential benefits for the healthy consumer, the main market for probiotic products, requires more attention. Also, the potential use of probiotics outside the gastrointestinal tract deserves to be explored further. Results from well conducted clinical studies will expand and increase the acceptance of probiotics for the treatment and prevention of selected diseases.
981 citations
TL;DR: The progress to date in using PGPR in a variety of applications with different plants is summarized and discussed here.
Abstract: Free-living plant growth-promoting rhizobacteria (PGPR) can be used in a variety of ways when plant growth enhancements are required. The most intensively researched use of PGPR has been in agriculture and horticulture. Several PGPR formulations are currently available as commercial products for agricultural production. Recently developing areas of PGPR usage include forest regeneration and phytoremediation of contaminated soils. As the mechanisms of plant growth promotion by these bacteria are unravelled, the possibility of more efficient plant-bacteria pairings for novel and practical uses will follow. The progress to date in using PGPR in a variety of applications with different plants is summarized and discussed here.
958 citations