Data on draft genome sequence of Bacillus sp. strain MHSD28, a bacterial endophyte isolated from Dicoma anomala

Makuwa, Sephokoane Cindy; Serepa-Dlamini, Mahloro Hope

doi:10.1016/j.dib.2019.104524

Cited by 9 publications

(5 citation statements)

References 22 publications

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“…steigerwaltii DSM 16691, and 97.71% with E. hormaechei subsp. oharae, both above the species boundary value (ANI > 95-96%), confirming the results obtained by TYGS analysis [25,27]. In turn, the OrthoANI value of LU1 strain with Enterobacter cloacae subsp.…”

Section: Phylogenomic Classification Of Enterobacter Sp Lu1supporting

confidence: 86%

“…steigerwaltii, which confirmed previous API-based identification [1]. A low δ value of 0.137 was observed, which corresponds to high average branch support for generated tree and high phylogenetic accuracy [25]. The digital DNA-DNA hybridization (dDDH) of LU1 strain with two best Basic Local Alignment Search Tool (BLAST) hits, namely, E. hormaechei subsp.…”

Section: Phylogenomic Classification Of Enterobacter Sp Lu1supporting

confidence: 79%

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A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

Szczerba

Dudziak

Krawczyk

et al. 2020

IJMS

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Enterobacter sp. LU1, a wild-type bacterium originating from goat rumen, proved to be a potential succinic acid producer in previous studies. Here, the first complete genome of this strain was obtained and analyzed from a biotechnological perspective. A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. A total of 4425 genes, including 4283 protein-coding genes, 25 ribosomal RNA (rRNA)-, 84 transfer RNA (tRNA)-, and 5 non-coding RNA (ncRNA)-encoding genes and 49 pseudogenes, were predicted. It has been shown that genes involved in transport and metabolism of carbohydrates and amino acids and the transcription process constitute the major group of genes, according to the Clusters of Orthologous Groups of proteins (COGs) database. The genetic ability of the LU1 strain to metabolize a wide range of industrially relevant carbon sources has been confirmed. The genome exploration indicated that Enterobacter sp. LU1 possesses all genes that encode the enzymes involved in the glycerol metabolism pathway. It has also been shown that succinate can be produced as an end product of fermentation via the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. The transport system involved in succinate excretion into the growth medium and the genes involved in the response to osmotic and oxidative stress have also been recognized. Furthermore, three intact prophage regions ~70.3 kb, ~20.9 kb, and ~49.8 kb in length, 45 genomic islands (GIs), and two clustered regularly interspaced short palindromic repeats (CRISPR) were recognized in the genome. Sequencing and genome analysis of Enterobacter sp. LU1 confirms many earlier results based on physiological experiments and provides insight into their genetic background. All of these findings illustrate that the LU1 strain has great potential to be an efficient platform for bio-based succinate production.

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Section: Phylogenomic Classification Of Enterobacter Sp Lu1supporting

confidence: 86%

Section: Phylogenomic Classification Of Enterobacter Sp Lu1supporting

confidence: 79%

A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

Szczerba

Dudziak

Krawczyk

et al. 2020

IJMS

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“…For genome comparison, reference genome sequences belonging to Bacillus were obtained from the NCBI database and compared using the Type Strain Genome Server (TYGS) ( Makuwa and Serepa-Dlamini, 2019 ). Genome BLAST Distance Phylogeny (GBDP) distances derived from genome sequences were processed by FastME 2.1.6.1 ( Lefort et al 2015 ) to construct the phylogenetic tree.…”

Section: Methodsmentioning

confidence: 99%

Evaluation and Genome Mining of Bacillus stercoris Isolate B.PNR1 as Potential Agent for Fusarium Wilt Control and Growth Promotion of Tomato

Pengproh,

Thanyasiriwat,

Sangdee

et al. 2023

Plant Pathol J

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Recently, strategies for controlling Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol agents. In this study, an analysis of the biocontrol and plant growth promoting (PGP) attributes of 11 isolates of loamy soil Bacillus spp. has been conducted. Among them, the isolates B.PNR1 and B.PNR2 inhibited the mycelial growth of Fol by inducing abnormal fungal cell wall structures and cell wall collapse. Moreover, broad-spectrum activity against four other plant pathogenic fungi, F. oxysporum f. sp. cubense race 1 (Foc), Sclerotium rolfsii, Colletotrichum musae, and C. gloeosporioides were noted for these isolates. These two Bacillus isolates produced indole acetic acid, phosphate solubilization enzymes, and amylolytic and cellulolytic enzymes. In the pot experiment, the culture filtrate from B.PNR1 showed greater inhibition of the fungal pathogens and significantly promoted the growth of tomato plants more than those of the other treatments. Isolate B.PNR1, the best biocontrol and PGP, was identified as Bacillus stercoris by its 16S rRNA gene sequence and whole genome sequencing analysis (WGS). The WGS, through genome mining, confirmed that the B.PNR1 genome contained genes/gene cluster of a nonribosomal peptide synthetase/polyketide synthase, such as fengycin, surfactin, bacillaene, subtilosin A, bacilysin, and bacillibactin, which are involved in antagonistic and PGP activities. Therefore, our finding demonstrates the effectiveness of B. stercoris strain B.PNR1 as an antagonist and for plant growth promotion, highlighting the use of this microorganism as a biocontrol agent against the Fusarium wilt pathogen and PGP abilities in tomatoes.

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“…The draft genome of strain MHSD28 T was sequenced and annotated [33]. The genome of strain MSHD28 T was 5571729 bp with a DNA G+C content of 35.2 mol% [33], which is within the range of genomic DNA G+C contents of B. cereus group species (32–43 %) [34].…”

Section: Full-textmentioning

confidence: 99%

“…Strain MHSD28 T has significant industrial value due to its capacity for synthesizing secondary metabolites with antimicrobial, antioxidant, anti-inflammatory and antitumor properties [13]. Furthermore, strain MHSD28 T has genes that facilitate an endophytic lifestyle and promote plant growth [33].…”

mentioning

confidence: 99%

Bacillus dicomae sp. nov., a new member of the Bacillus cereus group isolated from medicinal plant Dicoma anomala

Makuwa,

Motadi,

Choene

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-positive, endospore-forming endophytic bacterial strain designated MHSD28T was isolated from surface-sterilized leaves of Dicoma anomala collected from Eisleben, Botlokwa, Limpopo Province, South Africa. The phenotypic and phylogenetic characteristics of strain MHSD28T were consistent with those of members within the Bacillus cereus group. Comparative analysis between this strain and its relatives confirmed that it belongs to this group and forms a monophyletic branch. The digital DNA–DNA hybridization values between strain MHSD28T and its relatives were lower than the 70 % threshold for species delineation. To further determine its phylogenetic position, multi-locus sequence analysis (MLSA) based on five concatenated housekeeping gene (gyrB, atpD, DnaK, rpoB and rpoD) sequences, phenotypic analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) biotyper identification, fatty acid and polar lipid profile analyses were carried out. Phenotypic characterization, MLSA, whole genome sequence based analyses and MALDI-TOF results placed strain MHSD28T within the B. cereus group. The major fatty acids were iso-C15 : 0 and summed feature 3 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The respiratory quinone was menaquinone-7. The cell-wall peptidoglycan structure included meso-diaminopimelic acid. Considering the above results, strain MHSD28T represents a novel species of the B. cereus group, for which the name Bacillus dicomae sp. nov. is proposed. The type strain is MHSD28T (=BD 2262T=LMG 32287T=CECT 30671T).

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Data on draft genome sequence of Bacillus sp. strain MHSD28, a bacterial endophyte isolated from Dicoma anomala

Cited by 9 publications

References 22 publications

A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

Evaluation and Genome Mining of Bacillus stercoris Isolate B.PNR1 as Potential Agent for Fusarium Wilt Control and Growth Promotion of Tomato

Bacillus dicomae sp. nov., a new member of the Bacillus cereus group isolated from medicinal plant Dicoma anomala

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