Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8

Chhe, Chinda; Uke, Ayaka; Baramee, Sirilak; Ungkulpasvich, Umbhorn; Tachaapaikoon, Chakrit; Pason, Patthra; Waeonukul, Rattiya; Kosugi, Akihiko

doi:10.1016/j.dib.2021.106784

Cited by 6 publications

(8 citation statements)

References 10 publications

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“…P. cisolokensis LC2-13A and X. composti K-13 are closely related to the thermophilic, facultatively anaerobic, xylanolytic bacterium Paenibacillus sp. strain DA-C8 (Accession number: BMAQ00000000.1), as was previously reported [5] . Strain DA-C8 shows strong xylan degradation ability under anaerobic growth conditions.…”

Section: Data Descriptionmentioning

confidence: 87%

Draft genome sequence data of Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13

et al. 2021

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To discover more efficient degradation processes of lignocellulosic biomass, it is still important to analyze genomic and enzymatic data from bacteria that have strong xylanolytic ability. Here, we present the draft genome sequences of the xylanolytic bacteria Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13 that are closest to Paenibacillus sp. strain DA-C8, which has strong xylan degradation ability under anaerobic growth conditions. Whole-genome sequencing on the Ion GeneStudio S5 System yielded 277 contigs with total size 5,305,208 bp and G+C content 52.3 mol% for strain LC2-13A and 115 contigs with total size 4,652,266 bp and G+C content of 56.2 mol% for strain K-13. The LC2-13A genome had 5,744 protein-coding sequences (CDSs), 57 tRNAs, and 4 clustered regularly interspaced short palindromic repeats (CRISPRs), and the K-13 genome had 4,388 CDSs, 1 rRNA gene, 45 tRNAs, and 5 CRISPRs. The CDSs of LC2-13A and K-13 encoded the following carbohydrate-active enzymes: 98 and 67 glycoside hydrolases, 31 and 29 glycosyl transferases, 23 and 17 carbohydrate esterases, and 13 and 37 carbohydrate-binding modules, respectively. The whole-genome sequences of LC2-13A and K-13 have been deposited in DDBJ/ENA/GenBank under accession numbers BOVK00000000 and BOVJ00000000. The versions described in this paper are version 1.

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Section: Data Descriptionmentioning

confidence: 87%

Draft genome sequence data of Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13

et al. 2021

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“…Among these species, only P. cisolokensis LC2-13A T [19], P. xylanilyticus XIL14 T [5] and X. composti K13 T [7] reportedly use xylan. Moreover, among these four strains, only DA-C8 T uses xylan in anaerobic growth [25].…”

Section: S Rrna Gene Phylogenymentioning

confidence: 99%

“…The assembled genome sequence of strain DA-C8 T included 3 110 565 bp with a G+C content of 52.3 mol%, and was composed of 69 contigs with an N50 of 108 510 bp. The whole-genome sequence was deposited in GenBank under accession number BMAQ00000000 [25]. The closely related strain P. cisolokensis LC2-13A T was nearly identical in its G+C content (56.6 mol%), but its genome was approximately 1.7 times (5 305 208 bp) that of strain DA-C8 T [26].…”

Section: Genome Featuresmentioning

confidence: 99%

“…composti K13 T [7] reportedly use xylan. Moreover, among these four strains, only DA-C8 T uses xylan in anaerobic growth [25].…”

Section: S Rrna Gene Phylogenymentioning

confidence: 99%

“…Whole-genome sequencing of strain DA-C8 T was carried out using the Ion GeneStudio S5 system [25]. CLC Genomics Workbench 20.0.1 (CLC Bio, Qiagen) was used for de novo assembly of the genome.…”

Section: Genome Featuresmentioning

confidence: 99%

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Insulambacter thermoxylanivorax sp. nov., a thermophilic xylanolytic bacterium isolated from compost

Chhe

Uke

Baramee

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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We isolated and analysed a Gram-negative, facultatively thermophilic, xylan-degrading bacterium that we designated as strain DA-C8T. The strain was isolated from compost from Ishigaki Island, Japan, by enrichment culturing using beech wood xylan as the sole carbon source. The strain showed high xylan degradation ability under anaerobic growth conditions. The isolate grew at 37–60 °C (optimum, 55 °C) and pH 4.0–11.0 (optimum, pH 9.0). As well as xylan, strain DA-C8T could use polysaccharides such as arabinoxylan and galactan as carbon sources. Comparison of 16S rRNA gene sequences indicated that strain DA-C8T was most closely related to Paenibacillus cisolokensis LC2-13AT (93.9 %) and Paenibacillus chitinolyticus HSCC596 (93.5 %). In phylogenetic analysis, strain DA-C8T belonged to the same lineage as Xylanibacillus composti K13T (92.5 %), but there was less statistical support for branching (70 %). Digital DNA–DNA hybridization, average nucleotide identity values and average amino acid sequence identity between strain DA-C8T and P. cisolokensis LC2-13AT were 21.8, 68.3 and 58.2 %, respectively. Those between strain DA-C8T and X. composti K13 were 23.7, 67.7 and 57.6 %, respectively. The whole-genome DNA G+C content of strain DA-C8T was 52.3 mol%. The major cellular fatty acids were C16 : 0 (42.9 %), anteiso-C15 : 0 (20.0 %) and anteiso-C17 : 0 (16.7 %), the major quinone was menaquinone 7, and the major polar lipids were unidentified glycolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, a novel genus is proposed—Insulambacter gen. nov.—for the novel species Insulambacter thermoxylanivorax sp. nov. The type strain is DA-C8T (=JCM 34211T=DSM 111723T).

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Cultivation Techniques and Molecular Methods of Identification of Thermophilic, Anaerobic Bacteria

Scully,

Orlygsson

2023

Grand Challenges in Biology and Biotechnology

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Draft genome sequence data of the facultative, thermophilic, xylanolytic bacterium Paenibacillus sp. strain DA-C8

Cited by 6 publications

References 10 publications

Draft genome sequence data of Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13

Draft genome sequence data of Paenibacillus cisolokensis strain LC2-13A and Xylanibacillus composti strain K-13

Insulambacter thermoxylanivorax sp. nov., a thermophilic xylanolytic bacterium isolated from compost

Cultivation Techniques and Molecular Methods of Identification of Thermophilic, Anaerobic Bacteria

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