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International Journal of Systematic and... Jan 2018A Gram-stain-positive, endospore-forming, rod-shaped, aerobic bacterium, designated LPB0068, was isolated from a Pacific oyster (Crassostrea gigas) in Korea. This...
A Gram-stain-positive, endospore-forming, rod-shaped, aerobic bacterium, designated LPB0068, was isolated from a Pacific oyster (Crassostrea gigas) in Korea. This isolate was found to share the highest 16S rRNA gene sequence similarity with Paenibacillus macquariensis subsp. macquariensis DSM 2 (98.1 %) and Paenibacillus macquariensis subsp. defensor JCM 14954 (98.0 %). To establish the genomic relatedness of this isolate to its phylogenetic neighbours, its genome sequence and those of Paenibacillus antarcticus CECT 5836, P. macquariensis subsp. macquariensis DSM 2, P. macquariensis subsp. defensor JCM 14954, and Paenibacillus glacialis DSM 22343 were determined. The low average nucleotide identity and digital DNA-DNA hybridization values exhibited by LPB0068 in relation to the other strains in this analysis revealed that it is distinct from other Paenibacillus species. The genome of strain LPB0068 consists of one chromosome and three circular plasmids, and had a DNA G+C content of 40.0 mol%. The major respiratory quinone was menaquinone-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified glycolipid, and two unidentified polar lipids. The major cellular fatty acids were anteiso-C15 : 0, C14 : 0, and C16 : 0. Based on genomic, phylogenetic, and phenotypic characteristics, this strain was clearly distinguished from other Paenibacillus species with validly published names and should therefore be classified as a novel species of the genus. The name Paenibacillus crassostreae sp. nov. is proposed, the type strain of which is LPB0068 (=KACC 18694=JCM 31183).
Topics: Animals; Bacterial Typing Techniques; Base Composition; Crassostrea; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Nucleic Acid Hybridization; Paenibacillus; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Vitamin K 2
PubMed: 29068277
DOI: 10.1099/ijsem.0.002444 -
Microbiology Spectrum Jun 2023Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units....
Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units. Complete degradation of xylan requires an arsenal of xylanolytic enzymes that can remove the substitutions and mediate internal hydrolysis of the xylan backbone. Here, we describe the xylan degradation potential and underlying enzyme machinery of the strain, sp. LS1. The strain LS1 was able to utilize both beechwood and corncob xylan as the sole source of carbon, with the former being the preferred substrate. Genome analysis revealed an extensive xylan-active CAZyme repertoire capable of mediating efficient degradation of the complex polymer. In addition to this, a putative xylooligosaccharide ABC transporter and homologues of the enzymes involved in the xylose isomerase pathway were identified. Further, we have validated the expression of selected xylan-active CAZymes, transporters, and metabolic enzymes during growth of the LS1 on xylan substrates using qRT-PCR. The genome comparison and genomic index (average nucleotide identity [ANI] and digital DNA-DNA hybridization) values revealed that strain LS1 is a novel species of the genus . Lastly, comparative genome analysis of 238 genomes revealed the prevalence of xylan-active CAZymes over cellulose across the genus. Taken together, our results indicate that sp. LS1 is an efficient degrader of xylan polymers, with potential implications in the production of biofuels and other beneficial by-products from lignocellulosic biomass. Xylan is the most abundant hemicellulose in the lignocellulosic (plant) biomass that requires cooperative deconstruction by an arsenal of different xylanolytic enzymes to produce xylose and xylooligosaccharides. Microbial (particularly, bacterial) candidates that encode such enzymes are an asset to the biorefineries to mediate efficient and eco-friendly deconstruction of xylan to generate products of value. Although xylan degradation by a few spp. is reported, a complete genus-wide understanding of the said trait is unavailable till date. Through comparative genome analysis, we showed the prevalence of xylan-active CAZymes across spp., therefore making them an attractive option towards efficient xylan degradation. Additionally, we deciphered the xylan degradation potential of the strain sp. LS1 through genome analysis, expression profiling, and biochemical studies. The ability of sp. LS1 to degrade different xylan types obtained from different plant species, emphasizes its potential implication in lignocellulosic biorefineries.
Topics: Cellulose; Xylans; Paenibacillus; Xylose; DNA
PubMed: 37071006
DOI: 10.1128/spectrum.05028-22 -
International Journal of Molecular... Feb 2021Application of diazotrophs (N-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph...
Application of diazotrophs (N-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, gene and ITS (Inter Transcribed Spacer) region. BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of , and in all three compartments, in the rhizosphere and in the root and shoot were significantly increased, while the abundances of and were greatly reduced. was significantly correlated with plant dry weight, nitrogenase, N-fixing rate, P solubilization and other properties of the soil and plant.
Topics: Bacteria; DNA Barcoding, Taxonomic; Fungi; Microbiota; Mycobiome; Nitrogen Fixation; Paenibacillus; Plant Roots; Rhizosphere; Soil Microbiology; Zea mays
PubMed: 33540521
DOI: 10.3390/ijms22031460 -
Emerging Infectious Diseases Jul 2021Paenibacillus thiaminolyticus is a nonvirulent organism found in human and ruminant microbiota. However, P. thiaminolyticus can act as an opportunistic pathogen in...
Paenibacillus thiaminolyticus is a nonvirulent organism found in human and ruminant microbiota. However, P. thiaminolyticus can act as an opportunistic pathogen in humans. We describe a case of abdominal wall hematoma secondarily infected by P. thiaminolyticus. Our findings emphasize the risk for unusual Paenibacillus infections in otherwise healthy persons.
Topics: Humans; Paenibacillus; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Switzerland; Wound Infection
PubMed: 34152975
DOI: 10.3201/eid2707.203348 -
Archives of Microbiology Jan 2022Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2 and UniB3, were isolated from digestive syrup containing fungal diastase...
Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2 and UniB3, were isolated from digestive syrup containing fungal diastase (10 mg/ml), pepsin (2 mg/ml) and sugar base containing polyethylene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2 has the highest sequence similarity with Paenibacillus humicus NBRC 102415 (98.3%) and strain UniB3 showed the highest sequence similarity with Niallia circulans DSM 11 (98.9%). The DNA G + C content of UniB2 was 63.7 mol %. The dDDH and ANI values between the strain UniB2 and its phylogenetically close relative were < 38.3% and < 89.5%, respectively. The major fatty acids of the strain UniB2 were C (13.9%), C anteiso (39.7%), C anteiso (15.5%). The DNA G + C content of UniB3 was 35.6 mol %. The dDDH and ANI values between the strain UniB3 and its close relatives were < 29.1% and 84.6%, respectively. The major fatty acids of strain UniB3 were C (13.5%), C anteiso (40.1%) and C anteiso (16.0%). Major polar lipids for both strains were Diphosphatidylglycerol and phosphatidylethanolamine. Both strains showed unique carbon utilization and assimilation pattern that differentiated them from their phylogenetically related neighbours. These phenotypic, genotypic and chemotaxonomic characters indicated the strains UniB2 and UniB3 represent two novel species for which the names Paenibacillus albicereus sp. nov. (Type strain UniB2 = MCC 3997 = KCTC 43095 = JCM34513) and Niallia alba sp. nov. (Type strain UniB3 = MCC 3998 = KCTC 43235 = JCM 34492) are proposed.
Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2
PubMed: 34997867
DOI: 10.1007/s00203-021-02749-x -
International Journal of Food... Jun 2020Spoilage microorganisms can occur at many points throughout food production systems. Bacillus spp. and Paenibacillus spp. are important aerobic spoilage bacteria in...
Spoilage microorganisms can occur at many points throughout food production systems. Bacillus spp. and Paenibacillus spp. are important aerobic spoilage bacteria in various sectors of the food industry. In this study, we developed a rapid detection and quantification technique for Bacillus group-specific and the genus Paenibacillus by using multiplex quantitative PCR (mqPCR). The 1st was the Bacillus cereus group containing B. cereus and B. weihenstephanensis; the 2nd was the B. subtilis group containing B. subtilis, B. licheniformis, B. safensis, and B. pumilus; the 3rd was the B. simplex group containing B. megaterium and B. simplex; and the 4th was the genus Paenibacillus. Depending on the assays, the detection limit was 10 copy numbers. In addition, mqPCR assays were validated by spiking potato salad and milk samples with four strains; B. weihenstephanensis, B. licheniformis, B. megaterium, and P. lautus. The detection dynamic range for potato salad was 10 CFU/mL-10 CFU/mL with B. weihenstephanensis and B. licheniformis, and 10 CFU/mL-10 CFU/mL with B. megaterium and P. lautus, while, for milk, all strains were 10 CFU/mL-10 CFU/mL. We also stored these food matrices spiked with four bacterial suspensions (approximately 10 CFU/mL) at various temperatures. Results showed that B. weihenstephanensis and B. licheniformis were able to grow in potato salad, whereas, the populations of B. weihenstephanensis, B. licheniformis, and P. lautus increased in milk. Consequently, the mqPCR assays developed here in facilitated the differentiation, quantification, and confirmation of the presence of the psychrophilic and psychrotolerant Bacillus group and Paenibacillus spp.
Topics: Animals; Bacillus; Food Microbiology; Limit of Detection; Milk; Multiplex Polymerase Chain Reaction; Paenibacillus; Real-Time Polymerase Chain Reaction; Salads
PubMed: 32203753
DOI: 10.1016/j.ijfoodmicro.2020.108573 -
International Journal of Systematic and... Nov 2015A novel bacterium, designated DCY95T, was isolated from ginseng-cultivated soil in Quang Nam province, Vietnam. On the basis of 16S rRNA and gyrB gene sequence analysis,...
A novel bacterium, designated DCY95T, was isolated from ginseng-cultivated soil in Quang Nam province, Vietnam. On the basis of 16S rRNA and gyrB gene sequence analysis, this isolate was assigned to the genus Paenibacillus and found to be closely related to Paenibacillus sacheonensis SY01T (97.1 % 16S rRNA gene sequence similarity) and Paenibacillus taihuensis THMBG22T (96.4 %). The partial gyrB gene of DCY95T possessed 69.6-83.9 % sequence identity to those of other members of the genus Paenibacillus. Strain DCY95T was Gram-reaction-negative, catalase-negative, oxidase-positive, strictly aerobic, rod-shaped and motile by means of peritrichous flagella. Ellipsoidal free spores or subterminal endospores were produced in sporangia. MK-7 was the diagnostic menaquinone. The cell-wall peptidoglycan contained meso-diamonopimelic acid as the diamino acid. Whole-cell sugars comprised ribose, mannose and glucose. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, and two unidentified phospholipids. The genomic DNA G+C content was 60.7 ± 0.9 mol%. Phenotypic and chemotaxonomic results placed strain DCY95T within the genus Paenibacillus. However, DNA-DNA relatedness values between strain DCY95T and P. sacheonensis KACC 14895T or P. taihuensis NBRC 108766T were lower than 36 %. The low DNA relatedness data in combination with phylogenetic and (GTG)5-PCR analyses, as well as biochemical tests, indicated that strain DCY95T could not be assigned to any recognized species. In conclusion, the results in this study support the classification of strain DCY95T as a representative of a novel species within the genus Paenibacillus, for which the name Paenibacillus panaciterrae is proposed. The type strain is DCY95T ( = KCTC 33581T = DSM 29477T).
Topics: Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Paenibacillus; Panax; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vietnam; Vitamin K 2
PubMed: 26294902
DOI: 10.1099/ijsem.0.000540 -
Applied Microbiology and Biotechnology Sep 2020Lytic polysaccharide monooxygenases (LPMOs) play an important role in the degradation of complex polysaccharides in lignocellulosic biomass. In the present study, we...
Lytic polysaccharide monooxygenases (LPMOs) play an important role in the degradation of complex polysaccharides in lignocellulosic biomass. In the present study, we characterized a modular LPMO (PcAA10A), consisting of a family 10 auxiliary activity of LPMO (AA10) catalytic domain, and non-catalytic domains including a family 5 carbohydrate-binding module, two fibronectin type-3 domains, and a family 3 carbohydrate-binding module from Paenibacillus curdlanolyticus B-6, which was expressed in a recombinant Escherichia coli. Comparison of activities between full-length PcAA10A and the catalytic domain polypeptide (PcAA10A_CD) indicates that the non-catalytic domains are important for the deconstruction of crystalline cellulose and complex polysaccharides contained in untreated lignocellulosic biomass. Interestingly, PcAA10A_CD acted not only on cellulose and chitin, but also on xylan, mannan, and xylan and cellulose contained in lignocellulosic biomass, which has not been reported for the AA10 family. Mutation of the key residues, Trp51 located at subsite - 2 and Phe171 located at subsite +2, in the substrate-binding site of PcAA10A_CD revealed that these residues are substantially involved in broad substrate specificity toward cellulose, xylan, and mannan, albeit with a low effect toward chitin. Furthermore, PcAA10A had a boosting effect on untreated corn hull degradation by P. curdlanolyticus B-6 endo-xylanase Xyn10D and Clostridium thermocellum endo-glucanase Cel9A. These results suggest that PcAA10A is a unique LPMO capable of cleaving and enhancing lignocellulosic biomass degradation, making it a good candidate for biotechnological applications. KEY POINTS: • PcAA10A is a novel modular LPMO family 10 from Paenibacillus curdlanolyticus. • PcAA10A showed broad substrate specificity on β-1,4 glycosidic linkage substrates. • Non-catalytic domains are important for degrading complex polysaccharides. • PcAA10A is a unique LPMO capable of enhancing lignocellulosic biomass degradation.
Topics: Chitin; Mixed Function Oxygenases; Paenibacillus; Polysaccharides; Substrate Specificity
PubMed: 32651597
DOI: 10.1007/s00253-020-10758-x -
International Journal of Systematic and... Jan 2020A rod-shaped, Gram-stain-positive bacterial strain, MS74, was isolated from soil beside Itaewon road, Seoul, Republic of Korea. The strain could grow well on R2A,...
A rod-shaped, Gram-stain-positive bacterial strain, MS74, was isolated from soil beside Itaewon road, Seoul, Republic of Korea. The strain could grow well on R2A, nutrient agar and tryptone soya agar, but not in LB agar. MS74 tolerated 3.0 % NaCl (w/v), pH 9.0 and a temperature range from 10 to 35 °C (optimal temperature, 28 °C). From the comparison of 16S rRNA gene sequence, the strain is most closely related to CCUG 53270 CFH S0170, JCM 16352 and YN2 with similarity percentages of 96.6 %, 96.4 %, 95.9 % and 95.8 % respectively. Major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE). The major menaquinone was MK-7. The fatty acids profile mainly consisted of C anteiso, C iso, C iso, and C. The DNA G+C content of the isolated strain determined from the whole-genome sequence was 51 mol%. MS74 had an average nucleotide identity (ANI) value of 73.9 % and a digital DNA-DNA hybridization (dDDH) value of 20.6 % with most closely related strain, CCUG 53270. On the basis of phenotypic, chemotypic and genotypic evidence, the isolate was identified as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is MS74 (=KACC 19385 =DSM 105496).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Paenibacillus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 31661046
DOI: 10.1099/ijsem.0.003811 -
International Journal of Systematic and... Dec 2017A nitrogen-fixing bacterium, designated NF2-4-5, was isolated from a paddy soil in Anseong City, Korea. Cells of strain NF2-4-5 were Gram-staining-positive, motile rods...
A nitrogen-fixing bacterium, designated NF2-4-5, was isolated from a paddy soil in Anseong City, Korea. Cells of strain NF2-4-5 were Gram-staining-positive, motile rods and aerobic. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus and was closely related to Paenibacillus graminis RSA19 (98.7 %), Paenibacillus jilunlii Be17 (98.6 %), Paenibacillus salinicaeni LAM0A28 (98.6 %) and Paenibacillus riograndensis SBR5 (98.6 %). Growth of strain NF2-4-5 occurs at temperatures of 18-37 °C, at pH 6.0-8.5 and between 0.5% and 2 % NaCl (w/v). The only respiratory quinone was MK-7. The cell wall peptidoglycan of strain NF2-4-5 contained meso-diaminopimelic acid. The main cellular fatty acids were C16 : 0 and anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The DNA G+C content was 56.36 mol%. The DNA-DNA hybridization relatedness between strain NF2-4-5 and four reference strains, Paenibacillus graminis RSA19, Paenibacillus jilunlii Be17, Paenibacillus sonchi X19-5 and Paenibacillus riograndensis SBR5, was 22.0±0.3, 20.1±0.7, 18.3±0.3 and 12.6±0.5 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that the strain NF2-4-5 represents a novel species of the genus Paenibacillus, for which the name Paenibacillus azotifigens sp. nov. is proposed. The type strain is NF2-4-5 (=KACC 18967=LMG 29963).
Topics: Bacterial Typing Techniques; Cell Wall; DNA, Bacterial; DNA, Ribosomal; Diaminopimelic Acid; Fatty Acids; Nitrogen Fixation; Nucleic Acid Hybridization; Paenibacillus; Peptidoglycan; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 29039306
DOI: 10.1099/ijsem.0.002269