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International Journal of Systematic and... Nov 2023A novel bacterial strain, designated as PHS-Z3, was isolated from a marine sponge belonging to the genus on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3...
A novel bacterial strain, designated as PHS-Z3, was isolated from a marine sponge belonging to the genus on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3 were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3 showed 97.9 %, 96.7 %, and 96.2 % identities to C/2, DT7-4 and RC11, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3 formed an independent cluster with C/2. The total genome of PHS-Z3 was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3 and other type strains of species of the genus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3 and those of members of the genus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C and C. The major polar lipids of PHS-Z3 consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3 was diamino heptanoic acid (-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain PHS-Z3 (=MCCC 1K07848=KCTC 43443).
Topics: Animals; Theonella; Phylogeny; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Paenibacillus; Amino Acids
PubMed: 37910170
DOI: 10.1099/ijsem.0.006122 -
Journal of Microbiology and... Jun 2023The genus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock,...
The genus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4 (KCTC 43402 = GDMCC 1.3498), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4. 16S rRNA sequence analysis showed that strain SS4 most closely resembled DSM 29850 (98.22%), JJ-59 (98.19%), and KCTC 13870 (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4 belongs to the genus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4 was determined to belong to the genus . Comparing DSM 29850 with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4 can be classified as a species and is a novel member of the genus .
Topics: Fatty Acids; Soil; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Soil Microbiology; Base Composition; Paenibacillus; Republic of Korea
PubMed: 37072682
DOI: 10.4014/jmb.2211.11033 -
Archives of Microbiology Aug 2022An isolate, designated MBLB2552, was isolated from the gut of the honey bees (Apis mellifera L.) and identified as a member of the genus Paenibacillus based on the...
An isolate, designated MBLB2552, was isolated from the gut of the honey bees (Apis mellifera L.) and identified as a member of the genus Paenibacillus based on the sequences of the 16S rRNA gene sequences. The most closely related species to strain MBLB2552 were Paenibacillus timonensis 2301032, Paenibacillus barengoltzii NBRC 101215, and Paenibacillus macerans IAM 12467, with similarity values of 98.1, 97.21 and 97.0%, respectively, based on 16S rRNA gene sequences. The genome size and G + C content of MBLB2552 were 5.2 Mb and 52.4%, respectively. The Ortho average nucleotide identity (OrthoANI) and in silico DNA-DNA hybridization (isDDH) values between strain MBLB2552 and the type strains of the closest species were below the species delineation threshold. Comparative genomic analysis showed that most core POGs of strain MBLB2552 and other related taxa were related to translation, ribosomal structure and biogenesis (J) and carbohydrate metabolism in the COG category and KEGG pathways, respectively. Strain MBLB2552 was Gram stain-positive, spore-forming, rod-shaped, facultative anaerobic, motile, and grew at 20‒45 °C in 0‒2% (w/v) NaCl at pH 6.0‒9.0. The major polar lipids identified were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, unidentified polar lipids, and an unidentified glycolipid. We propose that strain MBLB2552 represents the type strain of the genus Paenibacillus and its name Paenibacillus mellifer sp. nov. is proposed. The type of strain was MBLB2552 (= JCM 35371 = KCTC 43386).
Topics: Animals; Bacterial Typing Techniques; Bees; DNA, Bacterial; Fatty Acids; Paenibacillus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35974114
DOI: 10.1007/s00203-022-03178-0 -
Archives of Microbiology Jul 2022A gram-stain-negative, endo-spore forming, facultatively anaerobic, motile, rod-shaped bacterial strain SM69, isolated from soil samples of Rohtak, Haryana, India was...
A gram-stain-negative, endo-spore forming, facultatively anaerobic, motile, rod-shaped bacterial strain SM69, isolated from soil samples of Rohtak, Haryana, India was characterized using polyphasic approach. White colonies were 2-3 mm, in diameter and growth occurred between 20 and 55 °C, pH 6.0-10.0 with 0-2.0% (w/v) NaCl. Based on 16S rRNA gene sequence similarity the strain is placed in the genus Paenibacillus as it is closely related to 'Paenibacillus tyrfis MSt1' (99.7%) and P. elgii SD17 (99.6%). The cell wall peptidoglycan contained meso-diaminopimelic acid. The dominant fatty acids included anteiso-C (50%), C (12%) and anteiso-C (10%). Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The size of the draft genome was 7,848,017 bp, with 53.1% G+C content. dDDH (51.6%) and ANI (93.5%) of strain SM69 with its close relatives indicates that it represents a novel species, for which the name Paenibacillus oleatilyticus sp. nov. (Type strain SM69 = MCC 3064 = JCM 33981 = KACC 21649) is proposed.
Topics: Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Paenibacillus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil; Soil Microbiology
PubMed: 35869333
DOI: 10.1007/s00203-022-03116-0 -
Bioscience, Biotechnology, and... May 2021Chitin and its derivatives have valuable potential applications in various fields that include medicine, agriculture, and food industries. Paenibacillus sp. str. FPU-7... (Review)
Review
Chitin and its derivatives have valuable potential applications in various fields that include medicine, agriculture, and food industries. Paenibacillus sp. str. FPU-7 is one of the most potent chitin-degrading bacteria identified. This review introduces the chitin degradation system of P. str. FPU-7. In addition to extracellular chitinases, P. str. FPU-7 uses a unique multimodular chitinase (ChiW) to hydrolyze chitin to oligosaccharides on the cell surface. Chitin oligosaccharides are converted to N-acetyl-d-glucosamine by β-N-acetylhexosaminidase (PsNagA) in the cytosol. The functions and structures of ChiW and PsNagA are also summarized. The genome sequence of P. str. FPU-7 provides opportunities to acquire novel enzymes. Genome mining has identified a novel alginate lyase, PsAly. The functions and structure of PsAly are reviewed. These findings will inform further improvement of the sustainable conversion of polysaccharides to functional materials.
Topics: Chitin; Chitinases; Hydrolysis; Paenibacillus
PubMed: 33792636
DOI: 10.1093/bbb/zbab058 -
Archives of Microbiology Feb 2022Microbial-based products are a promising alternative to agrochemicals in sustainable agriculture. However, little is known about their impact on human health even if...
Microbial-based products are a promising alternative to agrochemicals in sustainable agriculture. However, little is known about their impact on human health even if some of them, i.e., Bacillus and Paenibacillus species, have been increasingly implicated in different human diseases. In this study, 18 bacteria were isolated from 2 commercial biostimulants, and they were genotypically and phenotypically characterized to highlight specific virulence properties. Some isolated bacteria were identified as belonging to the genus Bacillus by BLAST and RDP analyses, a genus in-depth studied for plant growth-promoting ability. Moreover, 16S rRNA phylogenetic analysis showed that seven isolates grouped with Bacillus species while two and four clustered, respectively, with Neobacillus and Peribacillus. Unusually, bacterial strains belonging to Franconibacter and Stenotrophomonas were isolated from biostimulants. Although Bacillus species are generally considered nonpathogenic, most of the species have shown to swim, swarm, and produced biofilms, that can be related to bacterial virulence. The evaluation of toxins encoding genes revealed that five isolates had the potential ability to produce the enterotoxin T. In conclusion, the pathogenic potential of microorganisms included in commercial products should be deeply verified, in our opinion. The approach proposed in this study could help in this crucial step.
Topics: Bacillus; Humans; Paenibacillus; Phylogeny; Plant Development; RNA, Ribosomal, 16S
PubMed: 35119529
DOI: 10.1007/s00203-022-02769-1 -
International Journal of Systematic and... Oct 2022A Gram-positive, rod-shaped, motile, spore-forming bacterium, designated strain IB182496, was isolated from coastal sand of the South China Sea. The strain grew...
A Gram-positive, rod-shaped, motile, spore-forming bacterium, designated strain IB182496, was isolated from coastal sand of the South China Sea. The strain grew optimally at pH 7.0-9.0, 20-30 °C, and with NaCl 3.0-5.0 %. The predominant menaquinone was MK-7 and the major cellular fatty acids were anteiso-C, iso-C and C. The polar lipids in the cell wall included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and one unidentified lipid. The comparison of 16S rRNA gene sequences indicated that strain IB182496 was most closely related to '' SMB1 and SA-7-6 with similarities of 95.7 and 95.5 %, respectively. The whole-genome average nucleotide identity values between strain IB182496 and the two reference strains were 70.8 and 70.5%, and the digital DNA-DNA hybridization values were 18.7 and 18.0 %, respectively. Genomic analyses showed that strain IB182496 presented a genome of 6.22 Mbp with chromosomal G+C content of 60.3 %, and a total of 5261 genes were predicted. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain IB182496 should be considered as representing a novel species of the genus , for which we propose the name sp. nov. with the type strain IB182496 (=MCCC 1K04627=JCM 34216).
Topics: RNA, Ribosomal, 16S; Phylogeny; Phosphatidylethanolamines; Base Composition; Sodium Chloride; Vitamin K 2; Sand; Cardiolipins; DNA, Bacterial; Bacterial Typing Techniques; Fatty Acids; Sequence Analysis, DNA; Paenibacillus; Phospholipids; Nucleotides
PubMed: 36268856
DOI: 10.1099/ijsem.0.005568 -
Food Microbiology Feb 2023The objective of the present study was to compare the growth of food-pathogens Listeria monocytogenes, Salmonella enterica, food spoilage Bacillus subtilis, an...
The objective of the present study was to compare the growth of food-pathogens Listeria monocytogenes, Salmonella enterica, food spoilage Bacillus subtilis, an industrial milk product isolate, and spore-forming Paenibacillus in commercially available ultrahigh temperature processed (UHT) bovine milk and non-dairy, plant-based beverages (coconut, almond, cashew) stored at chilled and ambient temperatures (4 °C, 8 °C or 20 °C). Beverage samples were inoculated with a strain cocktail or individual strains of either Listeria or Salmonella, or Paenibacillus or Bacillus, respectively (approximately 1 × 10 CFU/mL). The findings indicate that the bacterial strains used in the study were capable of proliferating in plant-based beverages at higher rates than in bovine milk at 8 °C and 20 °C for Listeria and 20 °C for Salmonella and Paenibacillus, respectively. Bacillus subtilis grew equally fast in bovine milk and plant-based almond drink at 20 °C. No statistically significant difference (p > 0.05) in growth rates between different types of tested beverages was observed at 4 °C and at 8 °C for Listeria and Salmonella cocktails, respectively. These data suggest that plant-based beverages may present a significant risk for listeriosis and salmonellosis and post-opening recommendations should be carefully considered.
Topics: Animals; Milk; Paenibacillus; Bacillus; Listeria; Food Microbiology; Colony Count, Microbial; Spores, Bacterial; Salmonella; Listeria monocytogenes
PubMed: 36309444
DOI: 10.1016/j.fm.2022.104143 -
Journal of Natural Products Mar 2020Social insects establish complex interactions with microorganisms, some of which play defensive roles in colony protection. The important role of pollinators such as the...
Social insects establish complex interactions with microorganisms, some of which play defensive roles in colony protection. The important role of pollinators such as the stingless bee in nature encouraged us to pursue efforts to study its associated microbiota. Here we describe the discovery of two novel cyclic hexadepsipeptides, meliponamycin A () and meliponamycin B (), from sp. ICBG1318 isolated from nurse bees. Their structures were established by interpretation of NMR and MS data, and the absolute configuration of the constituent amino acids was determined by the advanced Marfey's method. Compounds and showed strong activity against the entomopathogen and human pathogens and .
Topics: Animals; Anti-Infective Agents; Bees; Leishmania infantum; Microbiota; Molecular Structure; Paenibacillus larvae; Staphylococcus aureus; Streptomyces
PubMed: 32073851
DOI: 10.1021/acs.jnatprod.9b01011 -
International Journal of Systematic and... Apr 2023A Gram-positive, facultatively anaerobic, agar-hydrolytic and rod-shaped bacterium with peritrichous flagellation, designated strain SCIV0701, was isolated from soya...
A Gram-positive, facultatively anaerobic, agar-hydrolytic and rod-shaped bacterium with peritrichous flagellation, designated strain SCIV0701, was isolated from soya bean rhizosphere soil collected from Bazhong, Sichuan Province, PR China and characterized by using polyphasic taxonomy. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCIV0701 belonged to the genus , and showed highest similarity to MX2-3 (97.59 %), M4BSY-1 (97.45 %) and NB5 (97.45 %). The average nucleotide identity values and DNA-DNA hybridization scores between strain SCIV0701 and MX2-3, M4BSY-1 and NB5 were lower than recommended thresholds of 95% and 70 %, respectively, for species delineation. Menaquinone-7 was the predominant respiratory quinone. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified phospholipids and one unidentified aminophospholipid. The major fatty acids were anteiso-C, C and iso-C. Physiological and biochemical features differentiated strain SCIV0701 from the closely related species. Based on the results of polyphasic taxonomic analysis, strain SCIV0701 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SCIV0701 (=GDMCC 1.2482=JCM 34672).
Topics: Fatty Acids; Phylogeny; Rhizosphere; RNA, Ribosomal, 16S; Base Composition; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Paenibacillus
PubMed: 37017632
DOI: 10.1099/ijsem.0.005761