The Experts below are selected from a list of 276 Experts worldwide ranked by ideXlab platform
Peter H Janssen - One of the best experts on this subject based on the ideXlab platform.
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laboratory cultivation of widespread and previously uncultured Soil Bacteria
Applied and Environmental Microbiology, 2003Co-Authors: Shayne J Joseph, Philip Hugenholtz, Parveen Sangwan, Catherine A Osborne, Peter H JanssenAbstract:Most Soil Bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. We cultured a collection of 350 isolates from Soil by using simple solid media in petri dishes. These isolates were assigned to 60 family-level groupings in nine Bacterial phyla on the basis of a comparative analysis of their 16S rRNA genes. Ninety-three (27%) of the isolates belonged to 20 as-yet-unnamed family-level groupings, many from poorly studied Bacterial classes and phyla. They included members of subdivisions 1, 2, 3, and 4 of the phylum AcidoBacteria, subdivision 3 of the phylum Verrucomicrobia, subdivision 1 of the phylum Gemmatimonadetes, and subclasses Acidimicrobidae and Rubrobacteridae of the phylum ActinoBacteria. In addition, members of 10 new family-level groupings of subclass Actinobacteridae of the phylum ActinoBacteria and classes AlphaproteoBacteria, BetaproteoBacteria, and GammaproteoBacteria of the phylum ProteoBacteria were obtained. The high degree of phylogenetic novelty and the number of isolates affiliated with so-called unculturable groups show that simple cultivation methods can still be developed further to obtain laboratory cultures of many phylogenetically novel Soil Bacteria.
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cultivation of globally distributed Soil Bacteria from phylogenetic lineages previously only detected in cultivation independent surveys
Environmental Microbiology, 2002Co-Authors: Michelle Sait, Philip Hugenholtz, Peter H JanssenAbstract:Summary The culturability of microorganisms in a 10 cm core of an Australian pasture Soil was investigated using a minimal agar medium with xylan as the growth sub- strate. Culturability decreased with increasing depth, from a maximum of 19% of the total microscopically countable cells in the 0-2 cm section to 2.4% in the 8-10 cm section. Seventy-one isolates from the core were identified by comparative 16S rRNA gene sequence analysis. Many of these isolates belong to groups of globally distributed Soil Bacteria, including well-characterized families of the classes Alphapro- teoBacteria and BetaproteoBacteria , and of the sub- class Actinobacteridae . Other isolates belong to groups with few or no cultivated representatives: 10 isolates in two subdivisions of the phylum Acido- Bacteria , five isolates in a new order and nine isolates in a new family of the class AlphaproteoBacteria , two isolates in a new order of the class Gammaproteobac- teria , three isolates in two new families of the sub- class Actinobacteridae , and two isolates in the subclass Rubrobacteridae . These new isolates repre- sent the first laboratory cultures able to be assigned to some of these groups and greatly increase the number of cultivated strains known for others. This demonstrates that a minimal change in cultivation strategy (using a polymeric growth substrate and longer incubation times) can result in the isolation of globally distributed but previously uncultured phylo- genetically novel Soil Bacteria.
Jo Handelsman - One of the best experts on this subject based on the ideXlab platform.
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uncultured Soil Bacteria are a reservoir of new antibiotic resistance genes
Environmental Microbiology, 2004Co-Authors: Christian S Riesenfeld, Robert M Goodman, Jo HandelsmanAbstract:Antibiotic resistance genes are typically isolated by cloning from cultured Bacteria or by polymerase chain reaction (PCR) amplification from environmental samples. These methods do not access the potential reservoir of undiscovered antibiotic resistance genes harboured by Soil Bacteria because most Soil Bacteria are not cultured readily, and PCR detection of antibiotic resistance genes depends on primers that are based on known genes. To explore this reservoir, we isolated DNA directly from Soil samples, cloned the DNA and selected for clones that expressed antibiotic resistance in Escherichia coli. We constructed four libraries that collectively contain 4.1 gigabases of cloned Soil DNA. From these and two previously reported libraries, we identified nine clones expressing resistance to aminoglycoside antibiotics and one expressing tetracycline resistance. Based on the predicted amino acid sequences of the resistance genes, the resistance mechanisms include efflux of tetracycline and inactivation of aminoglycoside antibiotics by phosphorylation and acetylation. With one exception, all the sequences are considerably different from previously reported sequences. The results indicate that Soil Bacteria are a reservoir of antibiotic resistance genes with greater genetic diversity than previously accounted for, and that the diversity can be surveyed by a culture-independent method.
Timothy M Lapara - One of the best experts on this subject based on the ideXlab platform.
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the effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among Soil Bacteria
The ISME Journal, 2007Co-Authors: Sudeshna Ghosh, Timothy M LaparaAbstract:The effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among Soil Bacteria
Michael R Gillings - One of the best experts on this subject based on the ideXlab platform.
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microcolony cultivation on a Soil substrate membrane system selects for previously uncultured Soil Bacteria
Applied and Environmental Microbiology, 2005Co-Authors: Belinda C. Ferrari, Svend Jorgen Binnerup, Michael R GillingsAbstract:Traditional microbiological methods of cultivation recover less than 1% of the total Bacterial species, and the culturable portion of Bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing Bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of Bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for Soil Bacteria that mimics natural conditions. Our Soil slurry membrane system combines a polycarbonate membrane as a growth support and Soil extract as the substrate. The result is abundant growth of uncharacterized Bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of Soil Bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used.
Christian S Riesenfeld - One of the best experts on this subject based on the ideXlab platform.
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uncultured Soil Bacteria are a reservoir of new antibiotic resistance genes
Environmental Microbiology, 2004Co-Authors: Christian S Riesenfeld, Robert M Goodman, Jo HandelsmanAbstract:Antibiotic resistance genes are typically isolated by cloning from cultured Bacteria or by polymerase chain reaction (PCR) amplification from environmental samples. These methods do not access the potential reservoir of undiscovered antibiotic resistance genes harboured by Soil Bacteria because most Soil Bacteria are not cultured readily, and PCR detection of antibiotic resistance genes depends on primers that are based on known genes. To explore this reservoir, we isolated DNA directly from Soil samples, cloned the DNA and selected for clones that expressed antibiotic resistance in Escherichia coli. We constructed four libraries that collectively contain 4.1 gigabases of cloned Soil DNA. From these and two previously reported libraries, we identified nine clones expressing resistance to aminoglycoside antibiotics and one expressing tetracycline resistance. Based on the predicted amino acid sequences of the resistance genes, the resistance mechanisms include efflux of tetracycline and inactivation of aminoglycoside antibiotics by phosphorylation and acetylation. With one exception, all the sequences are considerably different from previously reported sequences. The results indicate that Soil Bacteria are a reservoir of antibiotic resistance genes with greater genetic diversity than previously accounted for, and that the diversity can be surveyed by a culture-independent method.
