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Wunderlin, Tina
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Wunderlin, Tina
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Voici les éléments 1 - 10 sur 11
- PublicationMétadonnées seulementGenome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent(2015)
; ; ;Junier, Thomas; ;Johnson, Shannon ;McMurry, Kim ;Gleasner, Cheryl D. ;Lo, Chien-Chi ;Li, Po-E ;Vuyisich, Momchilo ;Chain, Patrick S.Bacillus alveayuensis strain 24KAM51 was isolated from a marine hydrothermal vent in Milos, Greece. Its genome depicts interesting features of halotolerance and resistance to heavy metals. - PublicationMétadonnées seulementEndospore-forming bacteria as new proxies to assess impact of eutrophication in Lake Geneva (Switzerland?France)(2014)
; ;Corella, Juan Pablo ;Junier, Thomas; ;Loizeau, Jean-Luc ;Girardclos, Stéphanie - PublicationMétadonnées seulementPhysical Isolation of Endospores from Environmental Samples by Targeted Lysis of Vegetative Cells(2016)
; ;Junier, Thomas; ; Endospore formation is a survival strategy found among some bacteria from the phylum Firmicutes. During endospore formation, these bacteria enter a morpho-physiological resting state that enhances survival under adverse environmental conditions. Even though endospore-forming Firmicutes are one of the most frequently enriched and isolated bacterial groups in culturing studies, they are often absent from diversity studies based on molecular methods. The resistance of the spore core is considered one of the factors limiting the recovery of DNA from endospores. We developed a method that takes advantage of the higher resistance of endospores to separate them from other cells in a complex microbial community using physical, enzymatic and chemical lysis methods. The endospore-only preparation thus obtained can be used for re-culturing or to perform downstream analysis such as tailored DNA extraction optimized for endospores and subsequent DNA sequencing. This method, applied to sediment samples, has allowed the enrichment of endospores and after sequencing, has revealed a large diversity of endospore-formers in freshwater lake sediments. We expect that the application of this method to other samples will yield a similar outcome. - PublicationMétadonnées seulementGenome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species(2015)
; ;Jaussi, Marion ;Junier, Thomas; ; ; ;Vieth-Hillebrand, Andrea ;Vetter, Alexandra ;Regenspurg, Simona ;Johnson, Shannon ;McMurry, Kim ;Gleasner, Cheryl D. ;Lo, Chien-Chi ;Li, Po-E ;Vuyisich, Momchilo ;Chain, Patrick S.Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium isolated from filter deposits in a geothermal site. This novel species has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species, and it possesses genes that support its phenotypic metabolic characterization and suggest an intriguing link to metals. - PublicationMétadonnées seulementGenome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir(2015)
; ;Jaussi, Marion ;Junier, Thomas; ; ;Regenspurg, Simona ;Li, Po-E ;Lo, Chien-Chi ;Johnson, Shannon ;McMurry, Kim ;Gleasner, Cheryl D. ;Vuyisich, Momchilo ;Chain, Patrick S.The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera. - PublicationMétadonnées seulementQuantification of endospore-forming Firmicutes by quantitative PCR with the functional gene spo0A(2013)
; ; ; ;Junier, Thomas ;Sauvain, Loic; - PublicationMétadonnées seulementBacterial communities in trace metal contaminated lake sediments are dominated by endospore-forming bacteria(2014)
; ; ;Junier, Thomas ;Masson, Matthieu; ;Kohler-Milleret, Roxane ;Diez, Elena Gascon ;Loizeau, Jean-Luc ;Tercier-Waeber, Mary-Lou - PublicationMétadonnées seulementUnder-detection of endospore-forming Firmicutes in metagenomic data(2015)
; ;Junier, Thomas; ;Lo, Chien-Chi ;Li, Po-E ;Chain, Patrick S.Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches. - PublicationMétadonnées seulement
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