Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T

Bosma, Elleke Fenna; Koehorst, Jasper J.; Hijum, Sacha A. F. T. van; Renckens, Bernadet; Vriesendorp, Bastienne; Weijer, Antonius H. P. van de; Schaap, Peter J.; Vos, Willem M. de; Oost, John van der; Kranenburg, Richard van

doi:10.1186/s40793-016-0172-8

Cited by 16 publications

(15 citation statements)

References 45 publications

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“…Since B . smithii is known to be able to utilize a range of carbohydrates that can be derived from lignocellulosic feedstocks 19 , utilization of carbohydrates was examined for the thermophiles isolated in this study and a B . smithii type strain DSM 4216, the genome of which has been completely sequenced.…”

Section: Resultsmentioning

confidence: 99%

Isolation of levoglucosan-utilizing thermophilic bacteria

Iwazaki

Hirai

Hamaguchi

et al. 2018

Sci Rep

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We previously developed an industrial production process for novel water-soluble indigestible polysaccharides (resistant glucan mixture, RGM). During the process, an anhydrosugar—levoglucosan —is formed as a by-product and needs to be removed to manufacture a complete non-calorie product. Here, we attempted to isolate thermophilic bacteria that utilize levoglucosan as a sole carbon source, to establish a removing process for levoglucosan at higher temperature. Approximately 800 natural samples were used to isolate levoglucosan-utilizing microorganisms. Interestingly, levoglucosan-utilizing microorganisms—most of which were filamentous fungi or yeasts—could be isolated from almost all samples at 25°C. We isolated three thermophilic bacteria that grew well on levoglucosan medium at 60°C. Two of them and the other were identified as Bacillus smithii and Parageobacillus thermoglucosidasius, respectively, by 16S rDNA sequence analysis. Using B. smithii S-2701M, which showed best growth on levoglucosan, glucose and levoglucosan in 5% (wt/vol) RGM were completely diminished at 50°C for 144 h. These bacteria are known to have a biotechnological potential, given that they can ferment a range of carbon sources. This is the first report in the utilization of levoglucosan by these thermophiles, suggesting that our results expand their biotechnological potential for the unutilized carbon resources.

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Section: Resultsmentioning

confidence: 99%

Isolation of levoglucosan-utilizing thermophilic bacteria

Iwazaki

Hirai

Hamaguchi

et al. 2018

Sci Rep

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“…This species is most closely related to Bacillus coagulans , which is also a facultatively thermophilic species. The complete genome of B. smithii type strain ( B. smithii DSM 4216 T ) is available (Bosma et al., ).…”

Section: Assessmentmentioning

confidence: 99%

Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA†

Ricci¹,

Allende²,

Bolton³

et al. 2017

EFS2

223

135

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EFSA is requested to assess the safety of a broad range of biological agents in the context of notification for market authorisation as sources of food and feed additives, food enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic preassessment to support safety risk assessments performed by EFSA's scientific Panels. The safety of unambiguously defined biological agents (at the highest taxonomic unit appropriate for the purpose for which an application is intended), and the completeness of the body of knowledge are assessed. Identified safety concerns for a taxonomic unit are, where possible and reasonable in number, reflected as 'qualifications' in connection with a recommendation for a QPS status. The list of QPS recommended biological agents was reviewed and updated in the current opinion and therefore becomes the valid list. The 2016 update reviews previously assessed microorganisms including bacteria, yeasts and viruses used for plant protection purposes following an Extensive Literature Search strategy. The taxonomic units related to the new notifications received since the 2013 QPS opinion, were periodically evaluated for a QPS status and the results published as Statements of the BIOHAZ Panel. Carnobacterium divergens, Lactobacillus diolivorans, Microbacterium imperiale, Pasteuria nishizawae, Pediococcus parvulus, Bacillus flexus, Bacillus smithii, Xanthomonas campestris and Candida cylindracea were recommended for the QPS list. All taxonomic units previously recommended for the 2013 QPS list had their status reconfirmed as well their qualifications with the exception of Pasteuria nishizawae for which the qualification was removed. The exclusion of filamentous fungi and enterococci from the QPS evaluations was reconsidered but monitoring will be maintained and the status will be re-evaluated in the next QPS Opinion update. Evaluation of bacteriophages should remain as a case-by-case procedure and should not be considered for QPS status. Acknowledgements: The BIOHAZ Panel wishes to thank the EFSA staff member: Mirena Ivanova for the support provided to this scientific output.

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“…The complete genome sequence of DX4 was sequenced using Illumina HiSeq2000 for the initial sequencing and assembly, followed by PacBio sequencing to fully close the genome sequence [ 18 , 19 ]. The Illumina platform generated 1,864,026 reads totaling 561,071,826 bp, and the data were assembled into 9 scaffolds by using SOAP denovo V2.3 [ 20 ].…”

Section: Genome Sequencing Informationmentioning

confidence: 99%

The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4

Chang¹,

Zhang²,

Chen³

et al. 2017

Stand in Genomic Sci

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Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequenced and served as basis for analysis its metabolic mechanism. It is the first genome of crude oil degrading strain in Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4 has cold shock proteins, abundant response regulators for cell motility, and enzymes involved in energy conversion and fatty acid metabolism. The genomic characteristics could provide information for further study of oil-degrading microbes for recovery of crude oil polluted environment.

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Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T

Cited by 16 publications

References 45 publications

Isolation of levoglucosan-utilizing thermophilic bacteria

Isolation of levoglucosan-utilizing thermophilic bacteria

Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA†

The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4

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