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Frontiers in Microbiology 2019Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium sp. XY-2, which could...
Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of sp. XY-2 and other spp. revealed that sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six (48) genes and two specificgenes and in sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to , and some unidentified sources. As a new species, sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.
PubMed: 30761094
DOI: 10.3389/fmicb.2019.00033 -
Journal of Applied Microbiology Oct 2007To isolate and characterize an oxalate-degrading Pandoraea sp. OXJ-11.
AIMS
To isolate and characterize an oxalate-degrading Pandoraea sp. OXJ-11.
METHODS AND RESULTS
A new bacterium Pandoraea sp. OXJ-11 was isolated from soil samples, which can grow in the medium with oxalate as the sole carbon and energy source. The isolate OXJ-11 is Gram-negative straight rod. It occurs singly and is motile by means of a double polar flagellum. Catalase is positive and nitrate is not reduced. It grows aerobically and the optimum growth temperature and the optimum pH are at 30 degrees C and pH 6.0, respectively. The polyphasic taxonomic data along with 16S rRNA sequence comparison demonstrate that the isolate OXJ-11 should belong to the genus Pandoraea and represent a new member in this family.
CONCLUSIONS
Oxalate could be degraded and the oxalate-degrading enzyme activity was detected when the isolate OXJ-11 grew in the medium with oxalate as carbon source.
SIGNIFICANCE AND IMPACT OF THE STUDY
Oxalate-degrading Pandoraea sp. OXJ-11 would be beneficial to the potential application in the control of sclerotinia stem rot in economically important plants caused by fungus Sclerotinia sclerotiorum, and in making plants resistant to the white mold disease by oxalate-degrading enzyme transgene.
Topics: Biomass; Burkholderia; Culture Media; Hydrogen-Ion Concentration; Oxalates; Phenotype; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Soil Microbiology; Temperature
PubMed: 17897211
DOI: 10.1111/j.1365-2672.2007.03363.x -
Journal of Clinical Microbiology May 2001CDC weak oxidizer group 2 (WO-2) consists of nine phenotypically similar human clinical isolates received by the Centers for Disease Control and Prevention between 1989...
CDC weak oxidizer group 2 (WO-2) consists of nine phenotypically similar human clinical isolates received by the Centers for Disease Control and Prevention between 1989 and 1998. Four of the isolates were from blood, three were from sputum, and one each was from bronchial fluid and maxillary sinus. All are aerobic nonfermentative, motile gram-negative rods with one to eight polar flagella per cell. All grew at 25 and 35 degrees C and were positive for catalase, urease (usually delayed 3 to 7 days), citrate, alkalinization of litmus milk, oxidization of glycerol (weakly), and growth on MacConkey agar and in nutrient broth without NaCl. All except one strain were oxidase positive with the Kovács method, and all except one isolate weakly oxidized D-glucose. All were negative for oxidation of D-xylose, D-mannitol, lactose, sucrose, maltose, and 20 other carbohydrates, esculin hydrolysis, indole production, arginine dihydrolase, and lysine and ornithine decarboxylase. Only two of nine isolates reduced nitrate. Broth microdilution susceptibilities were determined for all strains against 13 antimicrobial agents. Most of the strains were resistant to ampicillin, extended-spectrum cephalosporins, and aminoglycosides, including gentamicin, tobramycin, and amikacin, but they varied in their susceptibility to fluoroquinolones. High-performance liquid chromatographic and mass spectrometric analyses of the WO-2 group identified ubiquinone-8 as the major quinone component. The percent G+C of the WO-2 strains ranged from 65.2 to 70.7% (thermal denaturation method). All shared a common cellular fatty acid (CFA) profile, which was characterized by relatively large amounts (7 to 22%) of 16:1omega7c, 16:0, 17:0cyc, 18:1omega7c, and 19:0cyc(11-12); small amounts (1 to 3%) of 12:0 and 14:0; and eight hydroxy acids, 2-OH-12:0 (4%), 2-OH-14:0 (trace), 3-OH-14:0 (12%), 2-OH-16:1 (1%), 2-OH-16:0 (3%), 3-OH-16:0 (4%), 2-OH-18:1 (2%), and 2-OH-19:0cyc (3%). This profile is similar to the CFA profile of Pandoraea, a recently described genus associated with respiratory infections in cystic fibrosis patients (T. Coenye et al., Int. J. Syst. Evol. Microbiol., 50:887-899, 2000). Sequencing of the 16S rRNA gene (1,300 bp) for all nine strains indicated a high level (> or =98.8%) of homogeneity with Pandoraea spp. type strains. DNA-DNA hybridization analysis (hydroxyapatite method; 70 degrees C) confirmed the identity of WO-2 with the genus Pandoraea and assigned three strains to Pandoraea apista and three to Pandoraea pnomenusa, and identified three additional new genomospecies containing one strain each (ATCC BAA-108, ATCC BAA-109, ATCC BAA-110). This study also shows that Pandoraea isolates may be encountered in blood cultures from patients without cystic fibrosis.
Topics: Aged; Anti-Bacterial Agents; Bacterial Typing Techniques; Betaproteobacteria; Child, Preschool; Fatty Acids; Female; Genes, rRNA; Gram-Negative Bacterial Infections; Humans; Male; Microbial Sensitivity Tests; Middle Aged; Molecular Sequence Data; Oxidation-Reduction; Phenotype; Quinones; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 11325997
DOI: 10.1128/JCM.39.5.1819-1826.2001 -
Frontiers in Microbiology 2016To date, information on plasmid analysis in spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from spp. namely DSM...
To date, information on plasmid analysis in spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from spp. namely DSM 23572 (pPF72-1, pPF72-2), DSM 23570 (pPO70-1, pPO70-2, pPO70-3, pPO70-4), NS15 (pPV15) and DSM 16535 (pPA35) were studied for the first time in this study. The information on plasmid sequences in spp. is useful as the sequences did not match any known plasmid sequence deposited in public databases. Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. Some plasmids were also void of genes and intriguingly, gene was also not discovered in these plasmids. This further leads to the hypothesis of host-plasmid interaction. Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. Toxin-antitoxin systems MazEF, VapBC, RelBE, YgiT-MqsR, HigBA, and ParDE were identified across the plasmids and their presence would improve plasmid maintenance. Conjugation genes were identified portraying the conjugation ability amongst plasmids. Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. The observed features in the plasmids shed light on the spp. as opportunistic pathogens.
PubMed: 27790203
DOI: 10.3389/fmicb.2016.01606 -
Frontiers in Microbiology 2019The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called acyl-homoserine lactones (AHLs), which are synthesized by an...
The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called acyl-homoserine lactones (AHLs), which are synthesized by an enzyme AHL synthase (LuxI) and detected by a transcriptional regulator (LuxR) that are usually located in close proximity. However, many recent studies have also evidenced the presence of LuxR solos that are LuxR-related proteins in Proteobacteria that are devoid of a cognate LuxI AHL synthase. species are opportunistic pathogens frequently isolated from sputum specimens of cystic fibrosis (CF) patients. We have previously shown that strains possess QS activity. In this study, we examined the presence of QS activity in all type strains of species and acquired their complete genome sequences for holistic bioinformatics analyses of QS-related genes. Only four out of nine type strains (, , and ) showed QS activity, and C8-HSL was the only AHL detected. A total of 10 canonical s with adjacent s were predicted by bioinformatics from the complete genomes of aforementioned species and publicly available genomes. No orphan was identified in any of the genomes. However, genes for two LuxR solos (LuxR2 and LuxR3 solos) were identified in all genomes (except two draft genomes with one LuxR solo gene), and was the only species that harbored no QS-related activity and genes. Except the canonical LuxR genes, LuxIs and LuxR solos of species were distantly related to the other well-characterized QS genes based on phylogenetic clustering. LuxR2 and LuxR3 solos might represent two novel evolutionary branches of LuxR system as they were found exclusively only in the genus. As a few solos were located in close proximity with prophage sequence regions in the genomes, we thus postulated that these solos could be transmitted into genus by transduction process mediated by bacteriophage. The bioinformatics approach developed in this study forms the basis for further characterization of closely related species. Overall, our findings improve the current understanding of QS in species, which is a potential pharmacological target in battling infections in CF patients.
PubMed: 31447806
DOI: 10.3389/fmicb.2019.01758 -
Frontiers in Microbiology 2017Several environmental bacteria are considered as opportunistic pathogens in cystic fibrosis (CF) and are able to persistently colonize the CF respiratory tract (CFRT)....
Several environmental bacteria are considered as opportunistic pathogens in cystic fibrosis (CF) and are able to persistently colonize the CF respiratory tract (CFRT). Beside and complex, spp. are defined as pathogenic. During chronic colonization, adaptive evolution and diversified population have been demonstrated, notably for . However, the persistence of in the CFRT remains largely unexplored. We studied genomic and phenotypic traits of isolates successively recovered from the airways of a single CF patient and relate the results to qualitative and quantitative evolution of other cultivable pathogens and to patient clinical status. A total of 31 isolates recovered from 18 sputum samples over a 7-year period in a single CF patient were studied. Genome dynamics was assessed by pulsed-field gel electrophoresis, ERIC-PCR fingerprinting and 16S rRNA gene PCR-temporal temperature gel electrophoresis. Phenotypic features included antimicrobial susceptibility, motility, biofilm production, and virulence in model. Variability was observed for all the characteristics studied leading to highly diversified patterns (24 patterns) for the 31 clonally related isolates. Some of these modifications, mainly genomic events were concomitantly observed with CFRT microbiota composition shifts and with severe exacerbations. The diversity of population studied, observed for isolates recovered from successive samples but also within a sample suggested that existence of a diversified population may represent a patho-adaptive strategy for host persistence in the heterogeneous and fluctuating CFRT environment.
PubMed: 29056926
DOI: 10.3389/fmicb.2017.01892 -
ACS Omega Dec 2017The present study investigates polyhydroxyalkanoate (PHA) production from lignin and its derivatives by a previously reported lignin-degrading bacterial strain sp....
The present study investigates polyhydroxyalkanoate (PHA) production from lignin and its derivatives by a previously reported lignin-degrading bacterial strain sp. ISTKB. PHA production was screened by fluorescence microscopy and flow cytometry using a Nile red stain. PHA and biomass accumulation, while screening, was found to be maximum on 4-hydroxybenzoic acid followed by -coumaric acid, vanillic acid, 2,6-dimethoxyphenol, and kraft lignin after 96 h. Monomer composition was analyzed by gas chromatography-mass spectrometry (GC-MS) and was followed by Fourier transform infrared and H NMR analysis, indicating PHA to be a copolymer of P(hydroxybutyrate--hydroxyvalerate). Genomic analysis of sp. ISTKB also complemented the results of GC-MS and NMR, and the relevant genes responsible for the synthesis of small chain length PHA were discovered in the genome. Process parameters were optimized by response surface methodology for enhanced production of PHA and biomass on 4-hydroxybenzoate. Optimization results showed 30 and 66% increase in the biomass and PHA production, respectively. The results obtained were promising and indicated that if lignin is depolymerized into low-molecular-weight intermediates, then it can easily be utilized and converted into value-added products like PHA by microbes.
PubMed: 30023602
DOI: 10.1021/acsomega.7b01615 -
Toxics May 2023As a kind of ubiquitous emerging pollutant, microplastics (MPs) are persistent in the environment and have a large impact on the ecosystem. Fortunately, some...
As a kind of ubiquitous emerging pollutant, microplastics (MPs) are persistent in the environment and have a large impact on the ecosystem. Fortunately, some microorganisms in the natural environment can degrade these persistent MPs without creating secondary pollution. In this study, 11 different MPs were selected as carbon sources to screen the microorganisms for degradable MPs and explore the possible mechanism of degradation. After repeated domestication, a relatively stable microbial community was obtained after approximately 30 days later. At this time, the biomass of the medium ranged from 88 to 699 mg/L. The growth of bacteria with different MPs ranged from 0.030 to 0.090 optical density (OD) 600 of the first generation to 0.009-0.081 OD 600 of the third generation. The weight loss method was used to determine the biodegradation ratios of different MPs. The mass losses of polyhydroxybutyrate (PHB), polyethylene (PE), and polyhydroxyalkanoate (PHA) were relatively large, at 13.4%, 13.0%, and 12.7%, respectively; these figures for polyvinyl chloride (PVC) and polystyrene (PS) were relatively slight, 8.90% and 9.10%, respectively. The degradation half-life (t) of 11 kinds of MPs ranges from 67 to 116 days. Among the mixed strains, sp., sp., and sp. grew well. The possible degradation mechanism is that such microbial aggregates can adhere to the surface of MPs and form complex biofilms, secrete extracellular and intracellular enzymes, etc., break the hydrolyzable chemical bonds or ends of molecular chains by attacking the plastic molecular chains, and produce monomers, dimers, and other oligomers, leading to the reduction of the molecular weight of the plastic itself.
PubMed: 37235247
DOI: 10.3390/toxics11050432 -
Cancer Research and Treatment Jan 2024Triple-negative breast cancer (TNBC) is a breast cancer subtype that has poor prognosis and exhibits a unique tumor microenvironment. Analysis of the tumor microbiome...
PURPOSE
Triple-negative breast cancer (TNBC) is a breast cancer subtype that has poor prognosis and exhibits a unique tumor microenvironment. Analysis of the tumor microbiome has indicated a relationship between the tumor microenvironment and treatment response. Therefore, we attempted to reveal the role of the tumor microbiome in patients with TNBC receiving neoadjuvant chemotherapy.
MATERIALS AND METHODS
We collected TNBC patient RNA-sequencing samples from the Gene Expression Omnibus and extracted microbiome count data. Differential and relative abundance were estimated with linear discriminant analysis effect size. We calculated the immune cell fraction with CIBERSORTx and conducted survival analysis using the Cancer Genome Atlas patient data. Correlations between the microbiome and immune cell compositions were analyzed and a prediction model was constructed to estimate drug response.
RESULTS
Among the pathological complete response group (pCR), the beta diversity varied considerably; consequently, 20 genera and 24 species were observed to express a significant differential and relative abundance. Pandoraea pulmonicola and Brucella melitensis were found to be important features in determining drug response. In correlation analysis, Geosporobacter ferrireducens, Streptococcus sanguinis, and resting natural killer cells were the most correlated factors in the pCR, whereas Nitrosospira briensis, Plantactinospora sp. BC1, and regulatory T cells were key features in the residual disease group.
CONCLUSION
Our study demonstrated that the microbiome analysis of tumor tissue can predict chemotherapy response of patients with TNBC. Further, the immunological tumor microenvironment may be impacted by the tumor microbiome, thereby affecting the corresponding survival and treatment response.
Topics: Humans; Triple Negative Breast Neoplasms; Neoadjuvant Therapy; Tumor Microenvironment; Antineoplastic Combined Chemotherapy Protocols; Prognosis
PubMed: 37499695
DOI: 10.4143/crt.2023.330 -
Microorganisms Jan 2023It is claimed that one g of soil holds ten billion bacteria representing thousands of distinct species. These bacteria play key roles in the regulation of terrestrial...
It is claimed that one g of soil holds ten billion bacteria representing thousands of distinct species. These bacteria play key roles in the regulation of terrestrial carbon dynamics, nutrient cycles, and plant productivity. Despite the overwhelming diversity of bacteria, most bacterial species remain largely unknown. Here, we used an oligotrophic medium to isolate novel soil bacteria for positive interaction with soybean. Strictly 22 species of bacteria from the soybean rhizosphere were selected. These isolates encompass ten genera (, , , , , , , , , and ) and have potential as novel species. Furthermore, the novel bacterial species exhibited plant growth-promoting traits in vitro and enhanced soybean growth under drought stress in a greenhouse experiment. We also reported the draft genome sequences of sp. strain SOY2 and sp. strain SOY23. Along with our analysis of 169 publicly available genomes for the genera reported here, we demonstrated that these bacteria have a repertoire of genes encoding plant growth-promoting proteins and secondary metabolite biosynthetic gene clusters that directly affect plant growth. Taken together, our findings allow the identification novel soil bacteria, paving the way for their application in crop production.
PubMed: 36838264
DOI: 10.3390/microorganisms11020300