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International Journal of Systematic and... Jun 2012A Gram-positive, rod-shaped, xylanolytic, spore-forming bacterium, strain GTH-3(T), was isolated from a tidal flat adjacent to Ganghwa Island, Republic of Korea, and was...
A Gram-positive, rod-shaped, xylanolytic, spore-forming bacterium, strain GTH-3(T), was isolated from a tidal flat adjacent to Ganghwa Island, Republic of Korea, and was characterized to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain GTH-3(T) was shown to belong to the family Paenibacillaceae, being most closely related to the type strains of Paenibacillus ginsengisoli (94.9 %), Paenibacillus anaericanus (94.8 %), Paenibacillus urinalis (94.4 %), Paenibacillus cookii (94.2 %), Paenibacillus alvei (94.1 %) and Paenibacillus chibensis (94.0 %). The G+C content of the genomic DNA of strain GTH-3(T) was 45.9±0.2 mol% (mean±sd). The major menaquinone was MK-7. The major fatty acids were anteiso-C(15:0) and iso-C(16:0). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain GTH-3(T) to the genus Paenibacillus. The results of physiological and biochemical tests allowed strain GTH-3(T) to be distinguished genotypically and phenotypically from recognized species of the genus Paenibacillus. Strain GTH-3(T) is therefore considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sediminis sp. nov. is proposed. The type strain is GTH-3(T) ( = DSM 23491(T) = LMG 25635(T)).
Topics: DNA, Bacterial; Geologic Sediments; Molecular Sequence Data; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Xylans
PubMed: 21784963
DOI: 10.1099/ijs.0.032102-0 -
Food and Chemical Toxicology : An... May 2017Paenibacillus alvei, a naturally occurring soil microorganism, may be used in the control and/or elimination of human/animal pathogens present on/within produce...
Paenibacillus alvei, a naturally occurring soil microorganism, may be used in the control and/or elimination of human/animal pathogens present on/within produce commodities associated with human consumption. The safety of oral exposure to P. alvei in male, nulliparous females, the pregnant dam and developing fetus was assessed. Adult male and female rats received a single oral dose (gavage) of P. alvei and tissues were collected at post exposure days 0, 3 and 14. To evaluate the effect of the test organism on fetal development, sperm positive female rats received the test organism every 3 days thereafter throughout gestation. As human exposure would be no more than 1 × 10 CFU/ml the following dose levels were evaluated in both study phases: 0 CFU/ml tryptic soy broth (negative control); 1 × 10 CFU/ml; 1 × 10 CFU/ml or 1 × 10 CFU/ml. Neither sex specific dose-related toxic effects (feed or fluid consumption, body weight gain, and histopathology) nor developmental/reproductive effects including the number of implantations, fetal viability, fetal weight, fetal length and effects on ossification centers were observed. The test organism did not cross the placenta and was not found in the amniotic fluid.
Topics: Administration, Oral; Amniotic Fluid; Animals; Biological Control Agents; Body Weight; Drinking; Eating; Female; Male; Organ Size; Paenibacillus; Pregnancy; Rats, Sprague-Dawley; Toxicity Tests
PubMed: 28288930
DOI: 10.1016/j.fct.2017.03.009 -
Applied and Environmental Microbiology Jul 2014Recently, tomatoes have been implicated as a primary vehicle in food-borne outbreaks of Salmonella enterica serovar Newport and other Salmonella serovars. Long-term...
Recently, tomatoes have been implicated as a primary vehicle in food-borne outbreaks of Salmonella enterica serovar Newport and other Salmonella serovars. Long-term intervention measures to reduce Salmonella prevalence on tomatoes remain elusive for growing and postharvest environments. A naturally occurring bacterium identified by 16S rRNA gene sequencing as Paenibacillus alvei was isolated epiphytically from plants native to the Virginia Eastern Shore tomato-growing region. After initial antimicrobial activity screening against Salmonella and 10 other bacterial pathogens associated with the human food supply, strain TS-15 was further used to challenge an attenuated strain of S. Newport on inoculated fruits, leaves, and blossoms of tomato plants in an insect-screened high tunnel with a split-plot design. Survival of Salmonella after inoculation was measured for groups with and those without the antagonist at days 0, 1, 2, and 3 and either day 5 for blossoms or day 6 for fruits and leaves. Strain TS-15 exhibited broad-range antimicrobial activity against both major food-borne pathogens and major bacterial phytopathogens of tomato. After P. alvei strain TS-15 was applied onto the fruits, leaves, and blossoms of tomato plants, the concentration of S. Newport declined significantly (P ≤ 0.05) compared with controls. Astonishingly, >90% of the plants had no detectable levels of Salmonella by day 5 for blossoms. The naturally occurring antagonist strain TS-15 is highly effective in reducing the carriage of Salmonella Newport on whole tomato plants. The application of P. alvei strain TS-15 is a promising approach for reducing the risk of Salmonella contamination during tomato production.
Topics: Antibiosis; DNA, Bacterial; DNA, Ribosomal; Food Microbiology; Fruit; Solanum lycopersicum; Microbial Viability; Paenibacillus; Pest Control, Biological; Plant Leaves; RNA, Ribosomal, 16S; Salmonella enterica; Sequence Analysis, DNA; Virginia
PubMed: 24747888
DOI: 10.1128/AEM.00835-14 -
Current Research in Microbial Sciences Dec 2021Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that... (Review)
Review
Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by a human pathogen, and , a bee secondary invader, respectively. Both proteases seem to be involved in mediating bacterial adhesion by cleaving cell surface anchor proteins on the bacterium itself. By using basic alignment and phylogenetic profiling analysis, this work shows that the complete family of proteins that contain a PPEP domain includes proteins from more than 130 species spread over 9 genera. These analyses also suggest that the PPEP domain spread through horizontal gene transfer events between species within the Firmicutes' classes Bacilli and Clostridia. Bacterial species containing PPEP homologs are found in diverse habitats, varying from human pathogens and gut microbiota to free-living bacteria, which were isolated from various environments, including extreme conditions such as hot springs, desert soil and salt lakes. The phylogenetic tree reveals the relationships between family members and suggests that smaller subgroups could share cleavage specificity, substrates and functional similarity. Except for PPEP-1 and PPEP-2, no cleavage specificity, specific physiological target, or function has been assigned for any of the other PPEP-family members. Some PPEP proteins have acquired additional domains that recognize and bind noncovalently to various elements of the bacterial peptidoglycan cell-wall, anchoring these PPEPs. Secreted or anchored to the cell-wall surface PPEP proteins seem to perform various functions.
PubMed: 34841315
DOI: 10.1016/j.crmicr.2021.100024 -
Genomics Data Dec 2017Here we report the draft genome sequence of an endophytic strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was...
Here we report the draft genome sequence of an endophytic strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family with the highest similarity to SD (99%). Whole genome comparison of SUK123 with related species using average nucleotide identity (ANI) analysis revealed a similarity of 98% to Mst1, 94% to B69, 91% to A2, 68% to SC2 and 69% to DMS29. The draft genome was deposited at the European Nucleotide Archive (PRJEB21373).
PubMed: 28856101
DOI: 10.1016/j.gdata.2017.08.005 -
International Journal of Systematic and... Nov 2005A polyphasic approach was used to characterize a bacterium, GPTSA 11(T), isolated from a warm spring located in a reserve forest in Assam, India. The cells are...
A polyphasic approach was used to characterize a bacterium, GPTSA 11(T), isolated from a warm spring located in a reserve forest in Assam, India. The cells are Gram-variable, strictly aerobic, sporulating motile rods. The major fatty acids of the strain are C(15 : 0) anteiso (48.42 %), C(16 : 0) iso (11.59 %), C(16 : 1)omega11c (6.16 %), C(15 : 0) iso (6.03 %), C(17 : 0) anteiso (5.68 %) and C(16 : 1)omega7c alcohol (5.01 %). The presence of the fatty acid C(16 : 1)omega7c alcohol distinguishes this strain from other closely related species of the genus Paenibacillus. The strain contains MK-7 as the diagnostic menaquinone. The G+C content of the genomic DNA is 41.2 mol%. Analysis of the 16S rRNA gene sequence (1466 nt) revealed the presence of signature sequences PAEN 515F (5'-GAGTAACTGCTCTCGGAATGACGGTACTTGAGAAGAAAGCCCC-3') and PAEN 862F (5'-TCGATACCCTTGGTGCCGAAGT-3'), which were found in the species of the genus Paenibacillus surveyed by Shida et al. [Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. (1997). Int J Syst Bacteriol 47, 289-298]. The sequence shows closest similarity (95.85 %) to that of Paenibacillus apiarius, followed by Paenibacillus alvei (94.34 %), Paenibacillus cineris (93.87 %), Paenibacillus favisporus (93.80 %), Paenibacillus chibensis (93.47 %) and Paenibacillus azoreducens (93.40 %). Biochemical, physiological, chemotaxonomic and phylogenetic analyses justify placement of the strain in the genus Paenibacillus but not within any existing species. It should, therefore, be considered as representing a novel species, for which the name Paenibacillus assamensis sp. nov. is proposed. The type strain is GPTSA 11T (=MTCC 6934T=JCM 13186T).
Topics: DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Gram-Positive Endospore-Forming Rods; Hot Springs; India; Molecular Sequence Data; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 16280530
DOI: 10.1099/ijs.0.63846-0 -
Advances in Microbiology Dec 2012Surface (S)-layer proteins are model systems for studying protein glycosylation in bacteria and simultaneously hold promises for the design of novel,...
Surface (S)-layer proteins are model systems for studying protein glycosylation in bacteria and simultaneously hold promises for the design of novel, glyco-functionalized modules for nanobiotechnology due to their 2D self-assembly capability. Understanding the mechanism governing S-layer glycan biosynthesis in the Gram-positive bacterium CCM 2051 is necessary for the tailored glyco-functionalization of its S-layer. Here, the putative oligosaccharyl:S-layer protein transferase WsfB from the S-layer glycosylation gene locus is characterized. The enzyme is proposed to catalyze the final step of the glycosylation pathway, transferring the elongated S-layer glycan onto distinct tyrosine -glycosylation sites. Genetic knock-out of WsfB is shown to abolish glycosylation of the S-layer protein SpaA but not that of other glycoproteins present in CCM 2051, confining its role to the S-layer glycosylation pathway. A transmembrane topology model of the 781-amino acid WsfB protein is inferred from activity measurements of green fluorescent protein and phosphatase A fused to defined truncations of WsfB. This model shows an overall number of 13 membrane spanning helices with the Wzy_C domain characteristic of -oligosaccharyl:protein transferases (-OTases) located in a central extra-cytoplasmic loop, which both compares well to the topology of OTases from Gram-negative bacteria. Mutations in the Wzy_C motif resulted in loss of WsfB function evidenced in reconstitution experiments in ΔWsfB cells. Attempts to use WsfB for transferring heterologous oligosaccharides to its native S-layer target protein in CWG702 and SL3749, which should provide lipid-linked oligosaccharide substrates mimicking to some extent those of the natural host, were not successful, possibly due to the stringent function of WsfB. Concluding, WsfB has all features of a bacterial -OTase, making it the most probable candidate for the oligosaccharyl:S-layer protein transferase of , and a promising candidate for the first -OTase reported in Gram-positives.
PubMed: 25893145
DOI: 10.4236/aim.2012.24069 -
Applied and Environmental Microbiology May 2009The gram-positive bacterium Paenibacillus alvei CCM 2051T is covered by an oblique surface layer (S-layer) composed of glycoprotein subunits. The S-layer O-glycan is a...
The gram-positive bacterium Paenibacillus alvei CCM 2051T is covered by an oblique surface layer (S-layer) composed of glycoprotein subunits. The S-layer O-glycan is a polymer of [-->3)-beta-D-Galp-(1[alpha-D-Glcp-(1-->6)]-->4)-beta-D-ManpNAc-(1-->] repeating units that is linked by an adaptor of -[GroA-2-->OPO2-->4-beta-D-ManpNAc-(1-->4)]-->3)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-beta-D-Galp-(1--> to specific tyrosine residues of the S-layer protein. For elucidation of the mechanism governing S-layer glycan biosynthesis, a gene knockout system using bacterial mobile group II intron-mediated gene disruption was developed. The system is further based on the sgsE S-layer gene promoter of Geobacillus stearothermophilus NRS 2004/3a and on the Geobacillus-Bacillus-Escherichia coli shuttle vector pNW33N. As a target gene, wsfP, encoding a putative UDP-Gal:phosphoryl-polyprenol Gal-1-phosphate transferase, representing the predicted initiation enzyme of S-layer glycan biosynthesis, was disrupted. S-layer protein glycosylation was completely abolished in the insertional P. alvei CCM 2051T wsfP mutant, according to sodium dodecyl sulfate-polyacrylamide gel electrophoresis evidence and carbohydrate analysis. Glycosylation was fully restored by plasmid-based expression of wsfP in the glycan-deficient P. alvei mutant, confirming that WsfP initiates S-layer protein glycosylation. This is the first report on the successful genetic manipulation of bacterial S-layer protein glycosylation in vivo, including transformation of and heterologous gene expression and gene disruption in the model organism P. alvei CCM 2051T.
Topics: Bacterial Proteins; Carbohydrates; Electrophoresis, Polyacrylamide Gel; Gene Knockout Techniques; Genetic Complementation Test; Genetic Vectors; Glycosyltransferases; Gram-Positive Bacteria; Membrane Glycoproteins; Models, Biological; Models, Molecular; Promoter Regions, Genetic
PubMed: 19304819
DOI: 10.1128/AEM.00087-09 -
Journal of Laboratory Physicians Jul 2013Paenibacilli, the Gram positive, aerobic spore bearing bacilli are found normally in the environment. Though these organisms were not known to cause human disease, until...
Paenibacilli, the Gram positive, aerobic spore bearing bacilli are found normally in the environment. Though these organisms were not known to cause human disease, until recently; few species of this genus have been reported to cause infections in humans. We report here, a case of urinary tract infection in a 60-year-old chronic kidney disease patient due to this rare bacterium. The patient presented with complains of fever, dysuria, and flank pain. Routine and microscopic examination of urine revealed no abnormality except plenty of pus cells and albumin (1+). Bacterial culture showed significant bacteruria and the isolated bacteria was identified to be Paenibacillus alvei based on standard biochemical reactions.
PubMed: 24701110
DOI: 10.4103/0974-2727.119872 -
International Journal of Systematic... Oct 1996Seventy-seven strains representing 10 species in the Paenibacillus polymyxa 16S rRNA group and 3 other species that exhibit phenetic relatedness to members of this...
A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae.
Seventy-seven strains representing 10 species in the Paenibacillus polymyxa 16S rRNA group and 3 other species that exhibit phenetic relatedness to members of this group, Bacillus lautus, "Bacillus longisporus," and Bacillus peoriae, were characterized genotypically and phenotypically by performing an amplified ribosomal DNA restriction analysis, a randomly amplified polymorphic DNA analysis, a fatty acid methyl ester analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, pyrolysis mass spectrometry, and API and other routine phenotypic tests. These analyses revealed distinct clusters representing Paenibacillus alvei, Paenibacillus amylolyticus, Paenibacillus azotofixans, Paenibacillus durum, Paenibacillus larvae subsp. larvae, Paenibacillus larvae subsp. pulvifaciens, B. lautus, Paenibacillus macerans, Paenibacillus macquariensis, B. peoriae, P. polymyxa, and Paenibacillus validus, which confirmed the distinctness of these species, but appreciable within-species heterogeneity was observed in P. alvei, B. lautus, P. macerans, P. polymyxa, and P. validus. The type strain of Paenibacillus pabuli did not cluster with other strains of this species, and in several analyses a relationship between strains of P. pabuli and "B. longisporus" was observed. As the analyses showed that B. lautus and B. peoriae are closely related to the genus Paenibacillus, these species are reclassified as members of this genus.
Topics: Bacillus; DNA, Ribosomal; Fatty Acids; RNA, Ribosomal, 16S
PubMed: 8863428
DOI: 10.1099/00207713-46-4-988