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Current Microbiology Nov 2019Chlorobenzenes are ubiquitously distributed, highly persistent, and toxic environmental contaminants. Pandoraea pnomenusa MCB032 was isolated as a new dominant...
Chlorobenzenes are ubiquitously distributed, highly persistent, and toxic environmental contaminants. Pandoraea pnomenusa MCB032 was isolated as a new dominant chlorobenzene-utilizing strain from a functionally stable bioreactor during the treatment of chlorobenzenes when strain Burkholderia sp. JS150 disappeared. In study, we report the complete genome sequence of strain MCB032 which consists of a circular chromosome and three plasmids, which are ~ 6 Mb in length with 5450 open reading frames-12 encoding rRNAs and 77 encoding tRNAs. We further identified 17 putative genes encoding the enzymes involved in the methyl-accepting chemotaxis proteins in sensing chemical gradients during chemotaxis. The annotated complete genome sequence of this strain will provide genetic insights into the degradation of chlorinated aromatic compounds. The information will empower the elucidation of chlorobenzene affinity hierarchy and species succession in the bioreactor.
Topics: Biodegradation, Environmental; Burkholderiaceae; Chlorobenzenes; Genome, Bacterial; Plasmids; Whole Genome Sequencing
PubMed: 31432211
DOI: 10.1007/s00284-019-01760-2 -
International Journal of Systematic and... Mar 2019Pandoraea species have been isolated from diverse environmental samples and are emerging important respiratory pathogens, particularly in people with cystic fibrosis...
Pandoraea species have been isolated from diverse environmental samples and are emerging important respiratory pathogens, particularly in people with cystic fibrosis (CF). In the present study, two bacterial isolates initially recovered from consecutive sputum samples collected from a CF patient and identified as Pandoraea pnomenusa underwent a polyphasic taxonomic analysis. The isolates were found to be Gram-negative, facultative anaerobic motile bacilli and subsequently designated as strains 6399 (=LMG29626=DSM103228) and 7641 (=LMG29627=DSM103229), respectively. Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that 6399 and 7641 formed a distinct phylogenetic lineage within the genus Pandoraea. Genome sequence comparison analysis indicated that strains 6399 and 7641 are clonal and share 100 % similarity, however, similarity to other type strains (ANIb 73.2-88.8 %, ANIm 83.5-89.9 % and OrthoANI 83.2-89.3 %) indicates that 6399 and 7641 do not belong to any of the reported type species. The major cellular fatty acids of 6399 were C16 : 0 (32.1 %) C17 : 0cyclo (18.7 %) and C18 : 1ω7c (14.5 %), while Q-8 was the only respiratory quinone detected. The major polar lipids identified were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of 6399 was 62.9 (mol%). Strain 6399 can be differentiated from other members of Pandoraea by the absence of C19 : 0ω8c cyclo and by the presence of C17 : 0ω8c cyclo. Together our data show that the bacterial strains 6399 and 7641 represent a novel species of the genus Pandoraea, for which the name Pandoraea fibrosis sp. nov. is proposed (type strain 6399).
Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; Cystic Fibrosis; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Humans; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sputum; Tasmania; Ubiquinone
PubMed: 30676309
DOI: 10.1099/ijsem.0.003147 -
Bioinformatics (Oxford, England) Sep 2018Long-reads, point-of-care and polymerase chain reaction-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the...
MOTIVATION
Long-reads, point-of-care and polymerase chain reaction-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the end-to-end mapping between the raw electrical current signal sequence and the reference expected signal sequence serves as the key building block to signal labeling, and the following signal visualization, variant identification and methylation detection. One of the classic algorithms to solve the signal mapping problem is the dynamic time warping (DTW). However, the ultra-long nanopore sequencing and an order of magnitude difference in the sampling speed complexify the scenario and make the classical DTW infeasible to solve the problem.
RESULTS
Here, we propose a novel multi-level DTW algorithm, continuous wavelet DTW (cwDTW), based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can gain remarkable acceleration with tiny loss of the alignment accuracy. On the real nanopore datasets, cwDTW can finish an alignment task in few seconds, which is about 3000 times faster than the original DTW. By successfully applying cwDTW on the tasks of signal labeling and ultra-long sequence comparison, we further demonstrate the power and applicability of cwDTW.
AVAILABILITY AND IMPLEMENTATION
Our program is available at https://github.com/realbigws/cwDTW.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Algorithms; Humans; Nanopores; Sequence Analysis; Time Factors
PubMed: 30423085
DOI: 10.1093/bioinformatics/bty555 -
Chemosphere Oct 2018The present study delineated the dehydrogenation mechanism of cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) and cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl...
The present study delineated the dehydrogenation mechanism of cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) and cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl (2,3-DD-4,4'-DBPH) by Pandoraea pnomenusa strain B-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) in atomistic detail. The enzymatic process was investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Five different snapshots were extracted and calculated, which revealed that the Boltzmann-weighted average barriers of 2,3-DDBPH and 2,3-DD-4,4'-DBPH dehydrogenation processes are 10.7 and 11.5 kcal mol, respectively. The established dehydrogenation mechanism provides new insight into the degradation processes of other chlorinated 2,3-DDBPH. In addition to Asn115, Ser142, and Lys149, the importance of Ile 89, Asn143, Pro184, Met 187, Thr189, and Lue 191 during the dehydrogenation process of 2,3-DDBPH and 2,3-DD-4,4'-DBPH were also highlighted to search for promising mutation targets for improving the catalytic efficiency of BphB.
Topics: Burkholderiaceae; Catalysis; Oxidoreductases Acting on CH-CH Group Donors; Quantum Theory; Substrate Specificity
PubMed: 29860146
DOI: 10.1016/j.chemosphere.2018.05.063 -
Journal of Invertebrate Pathology Nov 2017Wireworms (Coleoptera: Elateridae) are serious agricultural pests, with soil-dwelling larvae attacking subterranean tissues of crop plants and their fruit when in...
Wireworms (Coleoptera: Elateridae) are serious agricultural pests, with soil-dwelling larvae attacking subterranean tissues of crop plants and their fruit when in contact with the soil surface. Researchers collect wireworms for laboratory experiments to study their behaviour and test pest control agents but frequently lose them to Metarhizium Petch (Ascomycota: Hypocreales: Clavicipitaceae) infection. We found latent M. brunneum infection in 13-100% of live, asymptomatic Agriotes obscurus and A. lineatus wireworms acquired from agricultural fields and in wireworms maintained indoors, indicating its enzootic presence. M. brunneum DNA in the wireworms maintained indoors sometimes exceeded 250pg/ug total DNA (0.025% of whole-sample DNA mass). Expressed as copies of M. brunneum DNA/g, unadulterated soil levels of M. brunneum ranged from 4037 in agricultural field soil to 721,538 in soil harbouring a wireworm collection indoors, with the prevalence of latently-infected live wireworm specimens being directly related to soil levels. M. brunneum levels in live wireworms, when regressed against relative levels of 394 bacteria species in the microbiome, were proportionally related to only four: Pantoea agglomerans, Pandoraea pnomenusa, Nocardia pseudovaccinii, and Mycobacterium frederiksbergense. All four of these bacteria have previously been reported to express antimicrobial mechanisms. Consistent with occurrences of disease immunity reported for other pathogen-insect pairs, symbiotic bacteria may be suppressing M. brunneum-induced wireworm mortality. This would help explain why wireworms commonly succumb to infection after being brought into sterilized conditions, as well as the sometimes limited efficacy of M. brunneum when using it as a pest control agent in the field.
Topics: Agriculture; Animals; Coleoptera; Larva; Metarhizium; Mycoses; Pest Control, Biological
PubMed: 28919016
DOI: 10.1016/j.jip.2017.09.012 -
Journal of Environmental Science and... Jul 2017This study employed the use of 16S rRNA gene sequence analysis to identify three of four native bacterial strains isolated from crude oil-contaminated site in Poza Rica,...
This study employed the use of 16S rRNA gene sequence analysis to identify three of four native bacterial strains isolated from crude oil-contaminated site in Poza Rica, Veracruz, Mexico. The identified bacteria were Ochrobactrum intermedium, Pandoraea pnomenusa and Ochrobactrum sp., but SA2-09 strain was not identified. The ability of the isolates to degrade polycyclic aromatic hydrocarbons (PAHs) was evaluated at 31.61 and 54.52 mg/kg PAHs in soil, when used as crude oil in soil microcosm during 80 days of incubation at 30°C. The results demonstrated that O. intermedium biodegraded many PAHs, including the high molecular weight (HMW) PAHs fluoranthene (100% equivalent 0.24 mg/kg), benzo [b] fluoranthene (81.8% equal 0.18 mg/kg), Benzo[a]pyrene (87.0%, 0.20 mg/kg) and Benzo[g,h,i]perylene (52.7%, 0.39 mg/kg). P. pnomenusa had a degradation profile of HMW PAHs, which was similar to O. intermedium, while Ochrobactrum sp. and the strain SA-09 exhibited lower degradation rates of HMW.
Topics: Biodegradation, Environmental; Burkholderia; Mexico; Ochrobactrum; Petroleum; Phylogeny; Polycyclic Aromatic Hydrocarbons; RNA, Ribosomal, 16S; Soil Pollutants
PubMed: 28463567
DOI: 10.1080/10934529.2017.1316170 -
International Journal of Systematic and... Sep 2016A Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21T, was isolated from forest soil of Jeju Island in Korea. Cells...
A Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21T, was isolated from forest soil of Jeju Island in Korea. Cells were motile rods with a single polar flagellum, showing catalase- and oxidase-positive reactions. Growth was observed at 10-40 °C (optimum, 30 °C), pH 4.0-10.0 (optimum, pH 7.0-7.5) and with 0-4.0 % (w/v) NaCl (optimum, 0-2 %). Only ubiquinone-8 was detected as the isoprenoid quinone, and C16 : 0, C17 : 0 cyclo, C19 : 1ω8c cyclo and summed feature 2 (comprising C12 : 0 aldehyde and/or unknown) were found to be the major fatty acids. Phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. Putrescine and 2-hydroxyputrescine were the predominant polyamines. The DNA G+C content was 61.0 mol%. Phylogenetic analyses based on 16S rRNA and DNA gyrase B gene sequences revealed that strain SE-S21T formed a phyletic lineage within the genus Pandoraea. Strain SE-S21T was most closely related to Pandoraea faecigallinarum KOxT and Pandoraea pnomenusa CCUG 38742T with 98.8 % and 98.7 % 16S rRNA gene sequence similarities, respectively. However, the DNA-DNA relatedness values between strain SE-S21T and the type strains of P. faecigallinarum and P. pnomenusa were 26.6±5.7 % and 20.5±3.7 %, respectively. On the basis of phenotypic, chemotaxonomic and molecular features, strain SE-S21T clearly represents a novel species of the genus Pandoraea, for which the name Pandoraea terrae sp. nov. is proposed. The type strain is SE-S21T (=KACC 18127T=JCM 30137T). An emended description of the genus Pandoraea is also proposed.
Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Forests; Islands; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone
PubMed: 27267599
DOI: 10.1099/ijsem.0.001229 -
Frontiers in Microbiology 2016Pandoraea species are considered as emerging pathogens in people with cystic fibrosis (CF). The contribution of these organisms to disease progression in CF patients is...
Pandoraea species are considered as emerging pathogens in people with cystic fibrosis (CF). The contribution of these organisms to disease progression in CF patients is not fully understood owing in large measure to the scant reports in clinical and research literature describing their colonization of CF patients and their associated virulence determinants. In an effort to increase awareness and evidence for Pandoraea spp. infection in people with CF, and to stimulate research aimed at unraveling the pathogenic properties of Pandoraea, we report a case of a 26-year-old Australian (Tasmanian) man with CF who was chronically infected with Pandoraea pnomenusa for at least one year prior to his death from respiratory failure. In addition, we describe for the first time evidence suggesting that this bacterium is a facultative anaerobe and report on the availability of a whole genome sequence for this organism. To the best of our knowledge, this report represents only the second clinical case study of P. pnomenusa infection in the world, and the first in an Australian CF patient.
PubMed: 27242717
DOI: 10.3389/fmicb.2016.00692 -
Medicina Clinica Aug 2016
Topics: Bacteremia; Burkholderiaceae; Catheter-Related Infections; Cross Infection; Gram-Negative Bacterial Infections; Humans; Infant; Male; Precursor Cell Lymphoblastic Leukemia-Lymphoma
PubMed: 27236613
DOI: 10.1016/j.medcli.2016.04.009 -
Frontiers in Microbiology 2016
PubMed: 26903988
DOI: 10.3389/fmicb.2016.00109